02/03Catalog

www.ogi.edu/catalog

OGI School ofScience & Engineering

TA B L E O F C O N T E N T S | O G I

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W E L C O M E T O T H E O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G

L E T T E R F R O M T H E D E A N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

H I S T O R I C A L B A C K G R O U N D A N D R E C E N T M E R G E R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

M I S S I O N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

E Q U A L O P P O R T U N I T Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

A B O U T T H I S C ATA L O G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

A C A D E M I C C A L E N D A R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

O V E R V I E W

A C A D E M I C D E P A R T M E N T S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

D E G R E E P R O G R A M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

C E R T I F I C AT E P R O G R A M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

S T U D E N T S N O T S E E K I N G D E G R E E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

C O L L A B O R AT I V E / J O I N T P R O G R A M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

A C C R E D I TAT I O N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

A D M I S S I O N S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

R E Q U I R E M E N T S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

P R O C E D U R E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

S T U D E N T V I S A S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

T U I T I O N / F I N A N C E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

A C A D E M I C P O L I C I E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

S C H O O L C A M P U S

G E O G R A P H I C S E T T I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

L I B R A R Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

C O M P U T E R FA C I L I T I E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 0

H O U S I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 0

S T U D E N T C O U N C I L . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 0

P E T S O N C A M P U S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 0

A C A D E M I C D E P A R T M E N T S / P R O G R A M S / R E S E A R C H / FA C U LT Y

B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1

B I O M E D I C A L E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3

C O M P U T E R S C I E N C E A N D E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 7

E L E C T R I C A L A N D C O M P U T E R E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 9

E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 9

M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 9

Photography by Jerome Hart, Anne Rybak, Viewfinders Stock Photography, and bbg Marketing.

O G I | L E T T E R F R O M T H E D E A N

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A L E T T E R F R O M T H E D E A N

This has been a remarkable year for the OGI School of Science & Engineering. July 1,2002, marked the first anniversary of the merger that made us the fourth school ofOregon Health & Science University, in addition to Dentistry, Medicine and Nursing. Themerger has been widely heralded in the local press, and we are excited at thepossibilities it has opened for interdisciplinary collaboration in such fields asbiomedical engineering, information technology, environmental science, andmanagement of biotechnology and health care enterprises. As a health and researchuniversity, OHSU is unique in having a school of engineering to further innovation inthese important areas. Our newest department, Biomedical Engineering, is one fruit ofthis merger. There will be many more to come.

At the same time, we are committed to the same high-quality graduate education andresearch in our traditional disciplines: biochemistry and molecular biology, computerscience and engineering, electrical and computer engineering, environmental scienceand engineering, and management in science and technology. The OGI School has beenthe region’s premier provider of high-technology graduate education since its inceptionin 1963. The school is home to world-class scientists and researchers, and our alumnigo on to careers in academia, government and industry.

We are also an important partner with the local high-tech industry. Many of our part-time students, for instance, are full-time employees of companies both large and small,and are looking to acquire expertise that will enhance their careers. Our full-timestudents establish valuable contacts within industry. And classroom interactions benefitfrom real-world experience.

OGI’s size has long been one of its attractions. We focus exclusively on graduateeducation, with about 170 full-time students and 380 part-time. Our faculty membersdevote close attention to each student. For Ph.D. students, our faculty/student ratio isan impressive 1.6 to 1.

Our research competes favorably with much larger schools, with about $18 million inresearch annually, funded mostly by the federal government. That translates roughly to$290,000 per year in research expenditures for each faculty member — a figure sometop-tier schools would envy. Students can thus be assured that the education theyreceive is grounded in leading-edge research in their discipline.

Classroom instruction and research interactions benefit from the diverse backgroundsof our faculty and students. We are a truly international community at OGI.

For all of these reasons, our alumni are well equipped for careers in a world whereflexible thinking and innovation are in demand, where technology grows more importantand more useful every day, where diversity is the norm, and where the ability to assessand solve problems is life’s most vital skill. Wherever they go, our graduates excel. Wemeasure our success by theirs.

AC A D E M I C C A L E N DA R | O G I

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*Management in Science and Technology Compressed and Distance Learning courses haveunique late registration deadlines. Please refer to OGI’s quarterly course schedule for thespecific MST registration information.

A C A D E M I C C A L E N D A R 2 0 0 2 | 2 0 0 3

FALL QUARTER 2002

August 12 Registration begins for Fall Quarter

September 9 Fall classes begin for Computational Finance

September 27 New student orientation

September 29 Last day to register without late fees

September 30 Fall Quarter instruction begins

November 11 Registration begins for Winter Quarter

November 28-29 Thanksgiving holiday (no classes, OGI offices closed)

December 9-13 Final exams

December 25 Christmas holiday (OGI offices closed)

WINTER QUARTER 2003

November 11 Registration begins for Winter Quarter

January 1 New Year’s holiday (OGI offices closed)

January 5 Last day to register without late fees

January 20 Martin Luther King Jr.’s Birthday

(no classes, OGI offices closed)

February 10 Registration begins for Spring Quarter

February 17 President’s Day (no classes, OGI offices closed)

March 18-21 Final exams (Monday, March 17, is a regular class day)

SPRING QUARTER 2003

February 10 Registration begins for Spring Quarter

March 30 Last day to register without late fees

March 31 Spring quarter instruction begins

May 5 Registration begins for Summer Quarter

May 26 Memorial Day holiday (no classes, OGI offices closed)

June 4 Commencement (Wednesday)

June 9-13 Final exams

SUMMER QUARTER 2003

May 5 Registration begins for Summer Quarter

June 22 Last day to register without late fees

June 23 Summer Quarter instruction begins

July 4 Independence Day holiday (no classes, OGI offices closed)

September 1 Labor Day holiday (OGI offices closed)

September 2-5 Final exams

O G I | O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G

OVERVIEW

A C A D E M I C D E P A R T M E N T S

The OGI School of Science & Engineeringhas five academic departments:Biochemistry and Molecular Biology (BMB),Computer Science and Engineering (CSE),Electrical and Computer Engineering (ECE),Environmental Science and Engineering(ESE) and Management in Science andTechnology (MST). The sixth department,Biomedical Engineering, is in development.Students benefit from cross-disciplinaryresearch and education as faculty memberstake part in research projects outside theirmain department. This encourages theexchange of ideas across related researchareas and provides fullest use of thewide range of instrumentation availableat the school.

D E G R E E P R O G R A M S

The OGI School of Science & Engineeringoffers M.S. and Ph.D. degrees inBiochemistry and Molecular Biology,Computer Science and Engineering,Electrical Engineering, and EnvironmentalScience and Engineering. We offer Master ofScience degrees in Management in Scienceand Technology and in ComputationalFinance, and a professional degree, OregonMaster of Software Engineering.

C E R T I F I C AT E P R O G R A M S

Various certificate programs are availablethrough the Computational Finance,Management in Science and Technology andthe Oregon Master of Software Engineeringacademic programs.

S T U D E N T S N O T S E E K I N G D E G R E E S

Any qualified student may take coursesat OGI, in a part-time capacity, withoutenrolling in a degree program. Studentsmay take a full-time course load for onlyone quarter while waiting for a decisionregarding admission to a degree program.Up to 21 credits taken at OGI beforematriculation (enrollment in a degreeprogram) may be accepted toward degreerequirements. Departmental regulationsmay be more restrictive.

C O L L A B O R AT I V E / J O I N T P R O G R A M S

Full-time matriculated students in the OGISchool’s Computer Science and Engineering

(CSE), Electrical and Computer Engineering(ECE) and Management in Science andTechnology (MST) departments may takecertain courses at Portland State Universityat no additional cost. Contact the Departmentof Graduate Education for details.

The OGI School also participates in theOregon Master of Software Engineering(OMSE) program, a joint program withPortland State University, Oregon StateUniversity and the University of Oregon.Students apply for this master’s degreethrough one of the participating schools.For more information visit www.omse.org.

ACCREDITATION

Oregon Health & Science University isaccredited by the Commission on Colleges ofthe Northwest Association of Schools andColleges, an institutional accrediting bodyrecognized by the Council for HigherEducation Accreditation and/or the U.S.Department of Education. The address is:Commission on Colleges, NWASC, 11130N.E. 33rd Place, Suite 120, Bellevue, WA98004.

ADMISSIONS

A D M I S S I O N S R E Q U I R E M E N T S

Individual academic departments havespecific requirements in addition to thoseshown below. These are found in thedepartment sections of the catalog.

• To enroll in any degree program at the OGISchool, an applicant must have completed therequirements for a bachelor’s degree or itsequivalent, although a student may beprovisionally admitted prior to that time.

• The GRE general test is required forM.S. applicants in Computational Finance(GMAT could be substituted); ComputerScience and Engineering; EnvironmentalScience and Engineering; and Oregon Masterof Software Engineering.

• The GRE general test is required for Ph.D.applicants in Biochemistry and MolecularBiology (subject test is also required);Computer Science and Engineering; Electricaland Computer Engineering and EnvironmentalScience and Engineering.

• Official transcripts from each college oruniversity attended are required.

• Three original letters of recommendation arerequired. The recommendation should attest to

the student’s ability to succeed in a graduateprogram and must be signed.

A D D I T I O N A L R E Q U I R E M E N T S F O R

I N T E R N AT I O N A L S T U D E N T S

To be considered for admission to the OGISchool for a full course of study,international students must also providedocuments to show that they meet thefollowing requirements.

• Evidence of adequate financial resources to payfor their OGI education and their cost of living.

• Written TOEFL scores are required of all MSand Ph.D. applicants whose native language isnot English. Students who have earned a degreein the United States are exempt from thisrequirement. The OGI School will accept boththe paper-based test and the computer-basedtest. Minimum required TOEFL scores vary bydepartment: BMB 550 paper/213 computer; CSE600 paper/250 computer; ECE 575 paper/233computer; ESE 600 paper/250 computer; MST625 paper/263 computer. The minimum desiredTOEFL score for admission is 575 paper/233computer, but a lower score may be offset byexcellent GRE scores. For more information onthe TOEFL please visit www.toefl.org.

A P P L I C AT I O N P R O C E D U R E S

For degree programs, the following items mustbe submitted:

• Completed OGI School of Science & Engineeringapplication form or Oregon Master of SoftwareEngineering (OMSE) degree program applicationform, if applicable.

• $65 nonrefundable application fee, whichis valid for one year and cannot be waivedor deferred.

• Official transcripts from each college oruniversity attended. The transcripts must arrivein a sealed envelope and may be mailed directlyto the Department of Graduate Education ordelivered by the student.

• Three letters of recommendation.

• Official GRE scores (if applicable, see above).

For certificate programs, the following items mustbe submitted:

• Completed OGI certificate programapplication form.

• $25 nonrefundable application fee, whichis valid for one year and cannot be waivedor deferred.

Printed application forms are available bycontacting the Department of GraduateEducation. You may also apply for admissiononline at www.ogi.edu/forms/application.

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O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G | O G I

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Completed applications, transcripts andother application materials should besent to:

Department of Graduate EducationOGI School of Science and Engineering20000 N.W. Walker RoadBeaverton, Oregon 97006-8921

Phone: 503 748-1027Toll-free: 800 685-2423Fax: 503 748-1285E-mail to: admissions@admin.ogi.eduwww.ogi.edu/grad_ed/

Applications may be submitted as early asone year before the proposed date ofenrollment. Applications received by March1 (February 15 for the EnvironmentalScience and Engineering department) willreceive priority review for admission andfinancial support.

S T U D E N T V I S A S

Information on student visas and otherimmigration services can be found on the Website for OGI’s Office of International Studentsand Scholars, www.ogi.edu/immigration.

TUIT ION AND FINANCES

T U I T I O N A N D F E E S

For the 2002-2003 academic year, tuitionfor full-time matriculated students (definedas nine or more credit hours per quarter) is$5,049 per quarter, with the exception ofComputational Finance as described below.Part-time tuition for regular OGI School ofScience & Engineering courses is $561 percredit hour or audit unit. Please note thatthere is no full-time tuition rate for non-matriculated students, except when anadmission decision is pending. Tuitionincludes OHSU’s activity fee, building fee,technology fee and incidental fee.

• Students matriculated in the ComputationalFinance degree program pay on a per-creditbasis of $561 for the first 48 credits duringthe 12-month program. Students may takeadditional courses above the 48 credits withinthe 12-month program time frame at noadditional cost, up to a total of 54 credits.

• ESE students pay tuition on an annual basis,which may be paid in full at the beginning of theyear or in quarterly installments.

• Courses in the Oregon Masters of SoftwareEngineering (OMSE) program are $495 per

credit hour. Full-time matriculated students mayregister for OMSE courses when paying full-timeOGI tuition.

• Deposits. Upon admission as a master’sstudent, Environmental Science and Engineeringrequires a deposit of $100 and ComputationalFinance requires a deposit of $500 to reserve aplace in their respective programs. Deposits willbe applied toward tuition and are nonrefundable.

H E A LT H I N S U R A N C E

Full-time students enrolled in an OGI degreeprogram are eligible for group studentmedical insurance through the school. OGIpays the entire premium for full-time Ph.D.students and two-thirds of the premium forfull-time master’s students. The currentmonthly premium is $149, effective throughJune 30, 2003. Insurance for family membersmay be purchased for an additional charge.

F I N A N C I A L A I D

Entering full-time Ph.D. students may beeligible for financial support through acombination of tuition scholarships, OGIfellowships, named fellowships and graduateresearch assistantships. Offers of supportare initiated by the individual academicdepartments. Part-time Ph.D. students maybe eligible for some of the above. Partial-tuition scholarships may be awarded byindividual academic departments to enteringfull-time M.S. students.

Subsidized and Unsubsidized FederalStafford Loans are available to students whohave been formally admitted to an M.S. orPh.D. program at the School of Science &Engineering. To be eligible for a loan,students must take at least five credits eachquarter, and must be U.S citizens or eligiblenoncitizens (e.g., permanent residents) Forapplication materials and additionalinformation, contact the Financial Aid Officeat OHSU at 503 494-7800 or 800 775-5460or finaid@ohsu.edu. Information aboutfinancial aid may also be found on OHSU’sWeb site, http://www.ohsu.edu/finaid/ or OGI’sWeb site, http://www.ogi.edu/ students/fin.html.The “Free Application for Student Aid”(FAFSA) forms may be found athttp://www.fafsa.ed.gov/. Hard copy formsare available from the OGI Department ofGraduate Education. Use Federal School Code004883 when completing the FAFSA form.

ACADEMIC POLICIESThe following is a summary of selected OGISchool of Science & Engineering academicpolicies. A more comprehensive listing can befound in the OGI School Student Handbook athttp://www.ogi.edu/students/studenthandbook.pdf.

A U D I T I N G A C O U R S E

OGI courses are offered for graded graduatecredit hours or ungraded audit units. Studentsmay register to audit a course on a space-available basis. Students taking a course forcredit have priority over students auditing acourse. Audits are recorded on the student’stranscript at the discretion of the instructor,based upon a reasonable expectation ofattendance and minimal participationdetermined by the instructor. Audits arecharged at the standard tuition rate. Auditunits do not count toward a student’s full-time status. Instructors have final discretionover allowing audits of their classes anddefining their academic expectations.

C O N F I D E N T I A L I T Y O F S T U D E N T R E C O R D S

With the passage of the Federal FamilyEducational Rights and Privacy Act (FERPA)of 1974, the OGI School adopted rules togovern the collection, use and disclosure ofstudent records with the goal of ensuringtheir privacy. Students have the right toinspect their educational records that aremaintained by OGI, the right to a hearing tochallenge the contents of those recordswhen they allege the records containmisleading or inaccurate information, andthe right to give their written consent beforetheir records are released to any person,agency or organization other than OGIofficials and certain authorized federal andstate authorities.

Directory Information. The OGI Schoolcan release certain public domain informa-tion, known as directory information, unlessa student files a written request in theGraduate Education Department. The schoollimits directory information to the student’sname, permanent and local home addresses,e-mail address, date(s) of attendance,degrees and awards received, number ofcredits earned and the fact of enrollment,including whether the student is enrolledfull- or part-time. The school does not makethis information available to vendors.

O G I | O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G

C O N T I N U O U S E N R O L L M E N T

A Ph.D. or master’s student who has begunwork on the dissertation or thesis mustregister and pay for at least one credit hourof research per quarter in order to maintainmatriculated status. If all requirements havenot been satisfied at the end of fourconsecutive academic quarters ofregistering for only one credit per quarter,or if an alternate plan of completion has notbeen approved by the department and theEducational Policy Committee, matriculatedstatus may be terminated. If the studentwishes to return to his/her program at alater date, it will be necessary to reapply foradmission. Continuous enrollment is notrequired of master’s students not pursuing athesis, nor of master’s or Ph.D. studentswho have not yet begun working on thethesis or dissertation. However, allmatriculated students are required toregister for classes or to indicate temporaryinactive status by filing a TemporaryInactive Status form with the Department ofGraduate Education.

C R E D I T L O A D P E R Q U A R T E R

Twelve credits per quarter is considereda normal course load for full-time students,although nine or more is considered full-time. Up to 18 credits plus four audit unitsmay be taken with the approval of thestudent’s academic department. Registeringfor more than 18 credits plus four auditunits requires Educational PolicyCommittee (EPC) permission and will incuran additional tuition cost. Students in theElectrical and Computer EngineeringDepartment are limited to 12 creditsper quarter, but may take up to16 with their advisor’s and home department’swritten approval.

G R A D I N G / S AT I S FA C T O R Y

A C A D E M I C P R O G R E S S

Most OGI School courses are graded with aletter grade. Research work may be gradedwith either a Pass/No Pass or letter gradeat the discretion of the faculty.

Transfer credits and Pass/No Pass gradesare not counted in students’ Grade PointAverages (GPA’s). The GPA is a weightedaverage of all eligible credits.

The following scale is employed at theOGI School:

A = 4.00 B = 3.00 C = 2.00

A- = 3.67 B- = 2.67 C- = 1.67

B+= 3.33 C+ = 2.33 F = 0.00

The grading system is defined as:

A = Excellent

B = Satisfactory

C = Below graduate standard

F = Failure

The following marks are also used:

AU = Audit, no credit

P = Satisfactory completion

NP = No credit, unsatisfactory

I = Incomplete

PI = Permanent Incomplete

W = Withdrawn (after the add/drop period)

Matriculated students must maintain acumulative GPA of 3.0. Failure to do so willresult in academic probation, and if the GPAis not improved, may lead to dismissal.

Incompletes. An Incomplete must be completedby the end of the quarter following that inwhich the Incomplete was awarded. In caseswhere the Incomplete is not completed, theinstructor has the choice of assigning agrade or converting the Incomplete into aPermanent Incomplete. The grade may be anF, if the course work was not completed, butinstructors have the option of assigninganother grade if they feel quality andquantity of work accomplished warrants it.If a student wants an extension of this one-quarter deadline, the student may petitionthe Educational Policy Committee (EPC)showing the instructor’s support of theextension (a separate letter, e-mail orsignature on the petition will suffice).Usually an extension will be granted, as longas the plan is specific, includes a date bywhich the grade will be assigned and issubmitted to the Graduate EducationManager in writing.

L E A V E O F A B S E N C E

In special circumstances, leaves of absencefrom a graduate program may be allowed. Astudent considering a leave should first

discuss the issue with his/her advisor oranother faculty member. If the departmentsupports the leave of absence, the studentthen submits a petition to the school’sEducational Policy Committee (EPC) forapproval. International students shouldconsult with OGI’s Manager of InternationalStudents and Scholars before considering aleave of absence.

M AT R I C U L AT E D V S . N O N - M AT R I C U L AT E D

A matriculated student is admitted andenrolled in a degree program. A non-matriculated student has not applied andbeen admitted to a degree program. Full-time matriculated students carry aminimum of nine credits per quarter. Auditunits do not count toward the nine-creditminimum. Academic departments mayrequire students to carry more than ninecredits per quarter as a condition ofeligibility for a stipend and/or tuitionscholarship. Part-time matriculatedstudents are admitted to a degree program,carry fewer than nine credits per quarterand pay tuition at the per-credit rate. Non-matriculated students typically carry fewerthan nine credits per quarter and paytuition at the per-credit rate.

M E A S L E S I M M U N I Z AT I O N P O L I C Y

Every full-time student who was born on orafter Jan. 1, 1957, must provide the OGISchool with evidence of having received asufficient measles vaccination. Students areexpected to submit a completedImmunization Form when they first registerfor classes at OGI. Students who do notprovide the needed evidence on this formwill not be allowed to register for classes forthe second or succeeding quarters followingtheir initial registration. The completeMeasles Immunization Policy andImmunization Form are available at theGraduate Education office.

O N - S I T E ( R E S I D E N C Y ) P H . D . R E Q U I R E M E N T S

The OGI School has a two-year on-site Ph.D.program requirement. Full-time Ph.D.students usually meet this requirement byan on-site dissertation project under theadvisement of an OGI faculty member. Part-time Ph.D. students can satisfy the firstyear of the on-site requirement byattendance in classes on the OGI campus.Because part-time Ph.D. students, by

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O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G | O G I

definition, are not on campus full time,the student’s academic department willdetermine residency requirements for thesecond year.

In exceptional circumstances (e.g.,dissertation topics requiring access tospecial facilities only available elsewhere),other arrangements may be proposed tothe student’s academic department forwritten approval.

There is no on-site program requirement forM.S. or certificate programs at OGI.

P R E - M AT R I C U L AT I O N C R E D I T S A P P L I E D

T O W A R D A D E G R E E

A maximum of 21 credits earned beforematriculation at OGI may be applied towarddegree requirements. This maximum mayinclude a combination of up to 12 (up to 18from Portland State University, theUniversity of Oregon and Oregon StateUniversity) transfer credits and creditstaken at OGI. Individual departmentalregulations may be more restrictive. Ifnecessary, a student may petition theEducational Policy Committee (EPC) for anexception to this policy.

R E G I S T R AT I O N

Any qualified student may take courses atthe School of Science & Engineering, in apart-time capacity, without enrolling in adegree program. Students may take a full-time course load for only one quarter, whilewaiting for a decision regarding admissionto a degree program.

Each quarter a student must register forcourses by submitting a registration form(may be found at http://www.ogi.edu/schedule/registrationform.pdf)to the Department of GraduateEducation or registering online athttp://www.ogi.edu/forms/regform.html.Each quarter a class schedule is publishedwith the specific courses being offered withthe dates, times and locations. To access acurrent class schedule online, visithttp://www.ogi.edu/schedule/. All studentsattending a course must be registered forthat course. A student will not earn a gradeor credits for the course if s/he is notregistered for that course.

Department Approvals. Full- and part-time matriculated students in Biochemistry

and Molecular Biology, ComputationalFinance, Electrical and ComputerEngineering and Environmental Science andEngineering, as well as full-timematriculated students in Computer Scienceand Engineering, must have departmentapproval for all registrations, adds, dropsand changes.

T I M E L I M I T S T O C O M P L E T E T H E D E G R E E

Ph.D.: Six years of full-time study or eightyears of part-time study.

M.S.: Three years of full-time study or fouryears of part-time study.

Petitions for extensions must be approvedby the department and submitted to theEducational Policy Committee for approval.

T R A N S C R I P T S

Your official transcript is a formal, writtenrecord of your OGI School of Science &Engineering educational experience. Allcourses you take at the OGI School andother OHSU schools are recorded on it, asare all grades and degrees you earn while atOGI/OHSU. If you have transferred creditsfrom another institution, they will berecorded on your transcript, as well.Requests for transcripts must be in writingwith a signature, submitted either by fax,mail or in person to the OHSU Registrar’soffice. Alternatively, you may submit thetranscript request form to the Departmentof Graduate Education on the OGI campus.Official transcripts are on special paper andhave the official OHSU seal. Officialtranscripts cost $8 per copy when ordered24 hours in advance. For same day serviceor a faxed official transcript the fee is$10. A request form for an official transcriptcan be found at http://www.ohsu.edu/academic/txreq.pdf.

T R A N S F E R C R E D I T

The OGI School of Science & Engineeringaccepts transfer credits from accreditedinstitutions that have not previously beenapplied toward another degree. Up to 12credits may be transferred to OGI (up to 18from Portland State University, University ofOregon and Oregon State University).Credits transferred to OGI must typicallycome from courses completed beforematriculation at OGI. The specific credits, ifany, which will be accepted as transfercredits into OGI and applied toward degree

requirements are determined solely by theacademic department. Transfer creditgrades are not calculated in the OGI gradepoint average. Credits graded on a Pass/NoPass basis may not be transferred.

THE CAMPUS

G E O G R A P H I C S E T T I N G

The greater-Portland metropolitan area hasa population of about 1 million, nearly halfthe population of Oregon. It provides diversecultural activities including art, music,entertainment and sports. Portland has anextensive park system, including the largestwilderness park within the limits of any cityin the United States. The OGI School ofScience & Engineering is located 12 mileswest of downtown Portland, an area knownas the Silicon Forest. OGI’s neighborsinclude Intel’s largest research anddevelopment facility, Tektronix, IBM,Hewlett-Packard, Mentor Graphics, Nike,Adidas and hundreds of other technology-based companies.

We are the newest school within OregonHealth & Science University (OHSU), joiningthe Schools of Medicine, Dentistry andNursing, located on the Marquam HillCampus in downtown Portland. The OGISchool is now part of OHSU’s West Campus,which also includes the NeurologicalSciences Institute, Oregon Regional PrimateResearch Center and the Vaccine and GeneTherapy Institute. The OGI School campusconsists of modern buildings, providingspacious laboratories, faculty andadministrative offices and a research library.

L I B R A R Y

The Samuel L. Diack Library’s collectionincludes more than 19,000 monographictitles and 350 current print and electronicjournal subscriptions. These support theteaching and research efforts at the OGISchool by providing texts, conferenceproceedings, reference materials, journalsand research monographs in the subjectareas of computer science, electricalengineering, environmental science,biochemistry, molecular biology andmanagement as related to science andtechnology. In addition, the OHSU Libraryholds more than 74,000 monographs and1,200 journal print subscriptions. Theseprint collections are available for use when

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visiting the libraries. Materials unavailableat the OGI School are obtained oninterlibrary loan for faculty, staff andstudents. An online catalog, acquisitions andcirculation system is in place. The library isa member of two consortia that provideaccess to other college and universitycollections. The Orbis consortium allows fordirect-request borrowing from 18institutions in Oregon and Washington,including the University of Oregon andOregon State University. The PORTALSconsortium includes libraries in thePortland metropolitan area, includingPortland State University and Reed College.

The OGI School Library’s publicworkstations not only provide for searchingthe catalog and the library’s databases butalso provide entry to Web resources forfaculty, staff and students. The librarianswill perform searches on the systems anddatabases that are not available directly tostudents. Library orientation is part of theintroduction to OGI for new students, andclasses on library research methods areoffered throughout the year.

Many of the electronic resources of OHSUMarquam Hill Library and the OGI Libraryare already available to all OHSU students,and integration is expected to be completeby 2003.

C O M P U T E R FA C I L I T I E S

The OGI School of Science & Engineering’scomputing environment gives members ofthe community access to a rich array oftechnologies and information resources.Many of these resources, includingnetworks and telecommunications, are theresponsibility of OHSU’s central InformationTechnology Group (ITG). In addition, manyOGI School departments and laboratoriesmaintain their own computing facilities.Most of the OGI School’s computers connectto a schoolwide local area network and tothe Internet, providing convenient access tothe World Wide Web. The local area networkis connected to the Internet through twohigh-speed data paths. In addition, it is alsoconnected to the Internet 2 (Internet2.edu)resources. The Internet 2 connection wasmade possible through an alliance of localacademic institutions.

H O U S I N G

While the OGI School has no on-campushousing, it is in the middle of a very largeresidential area. There are numerousapartment complexes, rental houses, bus andlight-rail lines and shopping areas nearby.The Office of Student Services in theGraduate Education Department maintains alist of local apartment buildings, available athttp://www.ogi.edu/students/housing.shtml.Additionally, the Student Council has a Website for current, new and prospective OGIstudents who are looking for housing informa-tion, roommates, etc. This service is found athttp://cslu.cse.ogi.edu/council/st_forum.html.

S T U D E N T C O U N C I L

The OGI Student Council serves as theliaison between the student body and thefaculty and administration, and strives toimprove the quality of life for students atthe OGI School. Student representativesmake themselves available to students intheir department to forward comments,ideas and concerns to the Student Counciland to promote involvement in student-bodyactivities. Representatives also disseminatepertinent information to other students intheir departments. As liaisons, members ofthe Student Council represent the studentbody and student interests on a wide varietyof OGI School task forces and committees,including the Faculty Senate, theEducational Policy Committee and theSafety Committee. Two Student Councilmembers are also representatives onOHSU’s All-Hill Council to represent OGI’sstudent body to the larger institution.

Additionally, the Student Council sponsorsand coordinates at least one major socialevent each quarter, open to everyone at theOGI School. These events have included acoffeehouse with live music performed bypeople from the school community, anannual International Food and Cultural Fair,the fall orientation lunch and barbecue, andnumerous educational forums. Periodicskiing and rafting trips are also arranged.Many student events throughout OHSU areopen to all students at the four OHSUschools. Members of Student Council alsoassist students when they first arrive inPortland by picking them up at the airport,

helping them find accommodations orfurniture and giving campus tours. Moreinformation on Student Council is availableon their Web site, clsu.cse.ogi.edu/council/or by e-mail at scouncil@admin.ogi.edu.

P E T S O N C A M P U S

The school enjoys the presence of well-behaved pets on our campus and has adetailed pet policy that can be found atwww.ogi.edu/policies/pets.html. We considerit a privilege, and not a right, to bring petsonto the campus with certain restrictions.The rights of students, employees andvisitors of the school are primary to those ofpets and pet owners. Following is asummary of the policy: Anyone with amedical condition, fear of animals or relatedcondition is responsible for notifying the petowner and the owner is obligated to respectthe individual’s concerns and requests. Petsare not allowed in specified areas of thecampus, including eating areas, classrooms,laboratories, restrooms and the library; theymust leashed outside a private office. Petsare allowed in private offices only when theowner posts a notice alerting people to thepresence of a pet; the pet does not bark,hiss or otherwise annoy others; the pet iscaged, on a leash or behind a gate wheneverleft unsupervised; and the owneraccommodates any individual who is notcomfortable with the pet. In addition,owners must clean up after their pet, petsmust be in good health with currentimmunizations, and animals in heat are notallowed. Students, faculty, staff or visitorswho violate the policy are notified that theirpet can no longer be brought to any part ofthe campus. Our policy does not apply toseeing/hearing or personal assistantanimals for individuals with disabilities.

O G I | O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G

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THE DEPARTMENT OF BIOCHEMISTRY AND

MOLECULAR BIOLOGY offers graduatestudy leading to M.S. and Ph.D.degrees. Students participate inresearch immediately upon enteringour program. This early exposure toresearch allows each student tobecome familiar with the variety ofactivities represented in thedepartment and aids the student inthesis research selection.R E S E A R C H A R E A S I N C L U D E :• Metallobiochemistry (with an emphasis on the

structure and function of metal ions in proteins,and mechanisms of metal trafficking in cells).

• Fungal, yeast and bacterial biochemistry.

• Ion transport across biological membranes (withan emphasis on molecular biology andreconstitution of cation or anion carriers).

The research experience at OGI is extensive.Much of the research is interdisciplinary,covering basic and applied aspects. Studentsare involved in all aspects of thedepartmental research program and haveready access to modern researchinstrumentation. As a result, our graduatesare well qualified for research careers inacademia, government and industry.

ADMISSION REQUIREMENTSAdmission requirements are the same as thegeneral requirements of the institution. Inaddition, Ph.D. applicants must submitgeneral GRE scores and a GRE subject scorefor one of the following tests: (a) biology, (b)chemistry, or (c) biochemistry, cell andmolecular biology. M.S. applicants are notrequired to submit GRE scores. Prospectivestudents should carefully examine the facultyresearch interests and departmentalresearch programs to determine whethertheir specific professional needs can befulfilled at OGI. Communication withindividual faculty members is encouragedbefore applying or enrolling.

DEGREE REQUIREMENTSM . S . P R O G R A M S

Two options are offered for the M.S. inbiochemistry and molecular biology.

N O N - T H E S I S O P T I O N

The non-thesis M.S. requires satisfactorycompletion of 44 credits, 28 in gradedcourses and 16 derived from an experimentalresearch project (BMB 610); and a writtenreport on the research. Graded coursesinclude 12 credits in BMB 527-528-529, and16 or more credits in advanced courses(BMB 532-544), student seminars (BMB 594or 596), and Special Topics (BMB 580). Theresearch for the non-thesis degree istypically a specific contribution to a largerproject, providing the student with extensivehands-on experience in biochemical andmolecular biological techniques. The non-thesis M.S. degree can be completed in oneyear of full-time study.

T H E S I S O P T I O N

The thesis M.S. is a research degree thatrequires satisfactory completion of 44credits, 20 of which are in graded courses(12 credits in BMB 527-528-529, 8 or morecredits in advanced courses), and a writtenthesis based on independent research (BMB700). The thesis M.S. degree can becompleted in 18 months of full-time study.

P H . D . P R O G R A M

The department offers a Ph.D. inbiochemistry and molecular biology. Ph.D.candidates are required to take the BMB527-528-529 biochemistry sequence andthree of the following core courses:

BMB 532 Bioenergetics andMembrane Transport 4 credits

BMB 533 Enzyme Structure, Functionand Mechanisms 4 credits

BMB 534 Instrumental Methodsin Biophysics I 4 credits

BMB 540 Advanced Molecular Biology 4 credits

BMB 542 Molecular Cell Biology 4 credits

Students must register for 12 credits perquarter. These credits typically includestudent seminars (BMB 594 or BMB 596),Department Seminar (BMB 591), andResearch (BMB 600 or BMB 800).

The qualifying examination for the Ph.D. isa comprehensive examination. It must becompleted within two years of entering theschool. An oral defense of the Ph.D.dissertation is required.

Department ofBiochemistry andMolecular Biology

www.bmb.ogi.edu

D E P A R T M E N T H E A D

Nin ian J . B lackburn

503 748-1384 E-mail: ninian@bmb.ogi.edu

D E P A R T M E N T A D M I N I S T R A T O R

Nancy Chr ist ie

503 748-1070E-mail: christie@bmb.ogi.edu

A D M I N I S T R A T I V E C O O R D I N A T O R

Terr ie Hadf ie ld

503 748-1071E-mail: hadfield@bmb.ogi.edu

B M B G E N E R A L I N Q U I R I E S

E-mail: info@bmb.ogi.edu503 748-1070

Ph.D. student Anthony Gaba is do ing researchon genet ic regu latory mechanisms.

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B M B | B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y

COURSE DESCRIPTIONSBMB 527 Biochemistry I: Proteins and EnzymesPrimary, secondary and tertiary structureof proteins; enzyme mechanisms; enzyme kinetics.

4 credits

BMB 528 Biochemistry II:Introduction to Molecular BiologyDNA replication, RNA synthesis and protein synthe-sis; genetic code; gene regulation. 4 credits

BMB 529 Biochemistry III:Metabolism and BioenergeticsMetabolism of carbohydrates, lipids and aminoacids; bioenergetics; photosynthesis; oxidativephosphorylation. 4 credits

BMB 532 Bioenergetics and Membrane TransportCritical evaluation of the chemiosmotic theory withspecific reference to oxidative phosphorylation,photophosphorylation and metabolite transport.Biochemical mechanisms of energy transductioncommon to bacterial and mitochondrial respiration,and bacterial and plant photosynthesis are reviewed.

4 credits

BMB 533 Enzyme Structure, Function and MechanismsProvides an in-depth analysis of the structural ori-gins of protein interactions and catalysis that arethe basis for biological function. The course devel-ops the basic principles of structural biologythrough an overview of X-ray crystal structures andfolding processes, acquainting the students withcomputational resources for protein structureanalysis. The structural foundation is expanded intoa detailed investigation of enzyme active sites,including the application of kinetic approaches tounderstanding enzymatic reaction mechanisms.

4 credits

BMB 534 Instrumental Methods in Biophysics ITheory and application of physical techniques toproblems in biochemistry. Optical, fluorescence, cir-cular dichroism, infrared and Raman spectroscopyof chromophoric groups. Magnetic susceptibility andnuclear magnetic resonance of metalloproteins.

4 credits

BMB 535 Instrumental Methods in Biophysics IIInvestigation of physical techniques particularlyuseful for studying metalloproteins. Electron para-magnetic resonance, electron spin echo, magneticcircular dichroism and X-ray absorption spec-troscopy. The course has significant “hands-on”exposure to both instrumentation and computersimulation techniques. 4 credits

BMB 537 Metals in BiochemistryComprehensive study of the chemistry and biochem-istry of metal ions in biological molecules and livingsystems. Topics include metalloprotein structure,metal ion specificity, biological oxidation mecha-nisms, metal ion catalysis in enzymes, metal iontransport and gene regulation. 4 credits

BMB 538 Coordination ChemistryStructures and stabilities of transition metal coordi-nation compounds with mono- and multi-dentate

ligands; coordination compounds as models for bio-logical metal centers; strategies for synthesis oftransition metal complexes. 4 credits

BMB 539 Chemical Group TheoryProperties of mathematical groups; symmetryprop-erties of molecules; symmetry groups, represen-tations, and character tables. Applications of grouptheory to the study of structure and spectroscopy oforganic and inorganic molecules; Hückel molecularorbital theory; ligand field theory; electronic spec-troscopy and vibrational spectroscopy. 4 credits

BMB 540 Advanced Molecular BiologyAn in-depth study of the molecular mechanisms gov-erning the replication, recombination, transcriptionand translation of genetic material. Emphasis is onexperimental approaches that have led to ourunderstanding of these fundamental processes.

4 credits

BMB 541 Molecular Genetics of DevelopmentA focused study of selected topics examining theregulation of gene expression during cellular differ-entiation. Emphasis is placed on the molecularnature of cell-cell interactions and the genetic con-trol of complex cellular responses to developmentaland environmental stimuli. 4 credits

BMB 542 Molecular Cell BiologyThe techniques of molecular biology have created anexplosion in knowledge of cell structure and func-tion. This course examines the following topics:cellular organization; cell signaling; cell differentia-tion; cell evolution. Knowledge of the cell is obtainedthrough combining core readings and lectures withstudent-led discussions of primary research papers.

4 credits

BMB 543 Current Topics in ProteomicsProteomics is an area of molecular biology whichaims to identify and map the total protein comple-ment of a genome. It expands the scope of biologicalinvestigation from studying single proteins to sys-tematically studying all proteins. Proteomics hasbroad applications in disease diagnosis, drug dis-covery and agriculture. The key technologies usedin proteomics are 2-dimensional gel electrophore-sis, mass spectrometry (ESI-MS, MALDI-TOF),imaging and database. This course will focus onelectrophoresis, mass spectrometry and applica-tions, using lectures, student seminars andliterature readings. 3 credits

BMB 544 Introduction to BioinformaticsPrimary literature of computational biology andhands-on experience in data manipulation fromlocal and remote databases. 3 credits

BMB 580 Special Topics in BiotechnologyExamination of current and past research papers ina specific area of biotechnology that is of mutualinterest to the student and the faculty member.Requires a written review paper or seminar presen-tation in one of the Student Seminar series.

Variable and repetitive credit

BMB 591 Department Seminar: Biochemistry/Molecular Biology 1 credit, repetitive

BMB 594 Metallobiochemistry Student SeminarPresentations and discussions of selected topicsfrom the recent literature and of ongoing researchprojects in the department. 2 credits, repetitive

BMB 596 Molecular Biology/Biochemistry Student SeminarPresentation and discussion of journal articles fromthe recent literature in molecular biology, geneticsand biochemistry. 2 credits, repetitive

BMB 600 ResearchSupervised research participation.

Variable and repetitive credit

BMB 610 Nonthesis ResearchSupervised research as a component of the non-thesis M.S. degree. Variable and repetitive credit

BMB 620 Professional InternshipThese courses provide the student with an opportu-nity to earn credit for relevant work experience inindustry. Students gain valuable industrial experi-ence that allows them to both apply the knowledgegained in the classroom and prepare for their futurecareers. Enrollment requires a faculty advisor andis limited by the number of internship opportunitiesavailable. Variable credit

BMB 700 M.S. Thesis ResearchResearch toward the thesis for the M.S. degree.

Variable and repetitive credit

BMB 800 Ph.D. Dissertation ResearchResearch toward the dissertation for the Ph.D. degree.

Variable and repetitive credit

RESEARCH PROGRAMSChemistry of Copper-Containing EnzymesIncreasing numbers of important enzymes areknown to contain copper at their active sites. Ofparticular interest are enzymes involved inbiogenic amine biosynthesis and metabolism(including important neuroactive amines such asnor-adrenaline and amphetamine); enzymesprotecting against oxidative cellular damagecaused by reduced oxygen metabolites; andenzymes catalyzing the biosynthesis ofneuropeptide hormones. A major goal is tounderstand the catalytic role of copper and themolecular mechanism of oxygen binding andutilization by these oxidase and oxygenaseenzymes. Blackburn

Spectroscopy of Copper ProteinsSpectroscopic techniques are used to probe thestructures of the copper sites in the nativeproteins and their complexes with substrates andinhibitors. Since the chemistry of the catalyticprocesses is generally centered on the Cu(I) formsof the enzymes, we are concentrating on thechallenging task of developing spectroscopic probesof the Cu(I) oxidation state, which is transparent tomost common spectroscopic techniques. Our workthus includes Fourier transform infrared, X-rayabsorption edge and EXAFS spectroscopies, andemphasizes the use of computer simulation of

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spectra on our Alpha workstation. Data for thelatter two techniques are collected at national andinternational synchrotron radiation facilities.Proteins under investigation include dopamine-ßhydroxylase, cytochrome c oxidase, hemocyanin,peptide amidating enzyme, Menkes and Wilson’sdisease proteins and copper chaperones.Blackburn

Radical Copper OxidasesRadical copper oxidases are a new class of redoxmetalloenzymes (including the fungal enzymesgalactose oxidase and glyoxal oxidase) containing aprotein free radical directly coordinated to acopper center. This free radical-coupled Cucomplex catalyzes the two-electron oxidation ofsimple alcohols and aldehydes and the reduction ofO2 to hydrogen peroxide, fueling extracellularperoxidases involved in lignin degradation. In theseproteins, the free radical is localized on a tyrosineresidue covalently crosslinked to a cysteinyl sidechain (a Tyr-Cys dimer). The catalytically activeenzyme is an intense green color, the result ofunusual optical spectra arising from electronictransitions within the copper radical complex. Lowenergy transitions in the near IR result frominterligand redox in this metal complex, ligand-to-ligand charge transfer (LLCT) processes that areclosely related to the electron transfer coordinatefor substrate oxidation. The active site metalcomplex is surprisingly flexible, twisting through apseudorotation distortion when exogenous ligandsbind, thereby modulating the basicity of a secondtyrosine ligand that serves as a general base incatalysis. Many of these aspects of electronicstructure and dynamics of the radical copperoxidases are the focus of active research.Whittaker

Manganese MetalloenzymesManganese is an essential element for life, forming the active site for a large number ofmetalloenzymes catalyzing hydrolytic or redoxreactions, including the photosynthetic oxygenevolving complex. We are interested in the Mnredox sites in Mn superoxide dismutase (MnSD,mononuclear Mn) and Mn catalase (MnC, dinuclearMn), enzymes that provide protection from toxicoxygen metabolites. The key question is: How dointeractions between the protein, metal ion andexogenous ligands tune the redox potential andchemistry of these complexes? We are combiningthe powerful tools of molecular biology withadvanced spectroscopic and computationalapproaches to explore the structure and dynamicsof Mn active sites. For MnSD, we find anunexpected temperature dependence for thestructures of anion complexes, which changecoordination as the temperature is raised. Thisthermal transition implies that the stability of theactive site structure is determined by dynamicalfeatures of the complex and that dynamicalexcitation may play an important role in controllingthe energetics of ligand binding and redox. A widerange of projects relating to the chemistry andbiology of Mn are in progress. Whittaker

Electronic Spectroscopy of BiologicalMetal ComplexesElectronic spectroscopy extends structural studiesof biomolecules beyond the atomic resolution ofX-ray crystallography to a level of structural detailthat directly relates to chemistry. The techniquesused in these studies span five decades of theelectromagnetic spectrum, from microwaves to theultraviolet and beyond. At the lowest energy,electron paramagnetic resonance (EPR)spectroscopy gives information on the electronicground state, defining the molecular orbital thatcontains the unpaired electron in a paramagneticcomplex. At higher energy, UV-visible absorptionspectroscopy excites orbital transitions betweenelectronic states, giving information oncharacteristic metal-ligand interaction energiesthat can be understood in terms of a ligand field ormolecular orbital analysis. Polarizationspectroscopy (linear dichroism, circular dichroismand magnetic circular dichroism) can give moredetailed information on ground and excited stateelectronic wave functions using geometric featuresof light to probe the active site. These experimentalapproaches can be complemented by spectroscopicmodeling and computational biology methods toprovide a detailed description of a metalloproteincomplex and its interactions. Whittaker

Mechanisms of Mammalian Chemical Communicationand Vomeronasal OlfactionChemical communication plays a significant role inlife strategies for many mammals. Our researchfocuses on chemical identification of pheromonesfunctioning during reproductive events in the Asianelephant, Elephas maximus. A female-to-malepreovulatory urinary sex pheromone, (Z)-7-dodecen-1-yl acetate, has been identified anddemonstrated to be robust in its synthetic form.This compound is also bioactive in manyLepidoptera, making it a good example ofconvergent evolution of structure and function.Biochemical studies have established the presenceof the pheromone in the serum, and future studieswill investigate its biosynthetic pathways.Considerable progress has been made onestablishing the proteins functioning as pheromonetransporters prior to signal transduction in theneuroreceptive cells of the vomeronasal organ.Radiolabeled analogs, competition experiments andmolecular biological studies have establishedunusual roles for elephant albumin and olfactorybinding protein. A second pheromonal system isactively being investigated. The facial temporalgland, breath and urine exude unusual chemicalcompounds during musth in Asian male elephants.These signals have a role in mate choice by femaleelephants, spatial distribution by male elephantsand other reactions by conspecifics. Utilizingseveral state-of-the-art gas chromatographic/massspectrometric techniques, we are identifyingspecific compounds that have a chemicalcommunication function, i.e., elicit behavioralresponses, and correlating the release of suchcompounds with serum androgen levels.Rasmussen

Vibrational Spectroscopy of MetalloproteinActive SitesWe are interested in the structural and functionalproperties of metal ions in enzymes and proteins,and we use electronic, vibrational (especially rR)and EPR spectroscopy to characterize metal-ionactive sites. Our laboratory has a sensitive, state-of-the-art Raman instrument: a fast spectrographwith a liquid N2-cooled CCD detector. We also use acombined FT-IR/FT-Raman instrument for proteinand model compound studies. Our research focuseson heme (iron porphyrin), nonheme-iron andcopper enzymes and the roles of their metal ions inenzymatic catalysis. Of particular interest is thebiochemistry of O2. Metalloproteins are involved inO2 binding (e.g., hemoglobin or hemocyanin) and inoxidative chemistry whereby O2 is reduced andsubstrates are oxygenated or oxidized. Theinvestigation of trapped reaction intermediates andmodel compounds helps us to unravel thesecomplex processes and to define reactionmechanisms. The availability of site-directedmutants permits the alterations in structures andreactivities to be studied. Loehr

Heme OxygenaseHeme oxygenase is a fascinating system that usesthe O2-binding affinity of its heme substrate in thecellular degradation of heme to open-chainbiliverdin. These studies are carried out with PaulR. Ortiz de Montellano’s group at U.C. SanFrancisco. The resting heme-heme oxygenaseenzyme substrate complex is much like myoglobin:The heme is linked to the enzyme by an iron-histidine bond and the iron exists mainly in asix-coordinate, high-spin state with an additionalwater ligand. The Fe-NHis bond was identified fromits resonance Raman vibration at 216 cm-1 in theFe(II)-heme complex. The absence of thisfingerprint frequency in the H25A mutant clearlyidentified His25 as the axial ligand. Remarkably,when imidazole was added to the inactive H25Apreparation, activity was fully restored. Ourcurrent efforts, in collaboration with Angela Wilksat University of Maryland, examine the structureand activity of several bacterial heme oxygenases.Loehr and Moënne-Loccoz

Oxygen Activation by Iron ProteinsSeveral diiron enzymes react with molecularoxygen to form powerful oxidizing agents importantin biology. Examples include (i) ribonucleotidereductase protein R2, which oxidizes tyrosine 122to its catalytically important neutral radical form;(ii) methane monooxygenase, whose hydroxylasecomponent oxidizes hydrocarbons to alcohols; (iii)plant desaturases, which oxidize fatty acids toolefins, e.g., stearoyl to oleoyl; and (iv) ferroxidasereactions, in which Fe2+ is oxidized to Fe3+. Acommon feature of these enzymes appears to bethe formation of an initial peroxo intermediateupon exposure of the reduced enzyme to O2. In therespiratory protein, hemerythrin, O2 binding isaccomplished by reduction to peroxide, and thisreaction is readily reversible. However, inribonucleotide reductase, peroxide is similarlyformed but decomposes irreversibly to a ferryl

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intermediate that is capable of carrying outoxidative chemistry. This dichotomy of behavior isreminiscent of the respiratory vs. peroxidasefunctions of different heme-containing proteins. Weare interested in determining common principlesthat influence the pathways of oxygen utilization.This problem is being approached by structuralelucidation of the iron sites in the proteinsthemselves and in model complexes, as well as bystudying mechanisms of their reactions withoxygen-containing substrates.Loehr and Moënne-Loccoz

Interaction of Nitric Oxide with MetalloproteinsNitric oxide (NO) is currently the subject of intenseinterest due to its role in a diverse range ofbiological processes. In mammals, it serves as asignaling molecule in the cardiovascular system.This discovery received the Nobel Prize forMedicine in 1998. In bacteria, NO is produced asan intermediate during denitrification — theprocess by which certain organisms convert nitratethrough to N2 or N2O. The production of NO is thefirst opportunity for fixed nitrogen to be lost fromthe soil to the atmosphere with implicationsranging from fertilizer loss to atmosphericpollution. Throughout biological NO-chemistry,proteins with Fe or Cu-containing active sites playa central role in generating and releasing NO aswell as in sensing and initiating chemistry inresponse to changes in NO-levels. Our research isaimed at investigating the structures andmechanisms of these metalloproteins through theuse of a variety of spectroscopic, biochemical andkinetic techniques. Andrew

Translational Control in Fungal AminoAcid BiosynthesisA greater understanding of many human healthissues relies on increased knowledge of how cellsexpress genetic information. Gene expression canbe controlled by regulating the synthesis andstability of functional RNA and protein. The goalof our research is to obtain a greaterunderstanding of how these mechanisms workusing the Neurospora crassa arg-2 andSaccharomyces cerevisiae CPA1 genes as models.These homologous genes encode the first enzymein arginine biosynthesis and they are negativelyregulated at both transcriptional andtranslational levels in response to the availabilityof arginine. An evolutionarily conserved upstreamopen reading frame (uORF) present in the5’-leader regions of these transcripts isresponsible for translational control. Synthesis ofthe uORF-encoded peptide causes ribosomes tostall when the level of arginine is high, blockingaccess of ribosomes to the translation initiationsite for the polypeptide encoding the argininebiosynthetic enzyme. Our current work is focusedon developing a molecular understanding of howsynthesis of this uORF-encoded peptide causesribosomes to stall, since this will provideimportant insights into the fundamental cellularprocess of protein synthesis. Sachs

Translational Control of Human Proto-OncogenesThe transcripts specified by many genes involvedin human cancers contain uORFs; these include the her-2 and bcl-2 proto-oncogenes. Usingmethods similar to those developed forunderstanding the roles of the uORFs of N. crassaarg-2 and S. cerevisiae CPA1 gene expression,we are examining the functions of thesemammalian uORFs, to better understand theirrole in controlling the expression of thesecritically important genes. Sachs

The Neurospora GenomeWe are part of a team that is sequencing andannotating the genome of Neurospora crassa (seewww.genome.wi.mit.edu/annotation/fungi/neurospora/),and are gearing up to apply this information tolarge-scale community-wide efforts in functionalgenomics. This is the first genome of a filamentousfungus that has been sequenced with public funds.The annotation of this sequence is provinginvaluable for understanding fungal genomeevolution; many fungi important for agricultureand medicine are closely related to N. crassa. Werecently began experiments aimed at cloning andanalyzing the telomeric regions of N. crassa andthe closely related pathogenic rice blast fungusMagnaporthe grisea because mounting evidenceindicates that genes near telomeres evolve morequickly and are frequently involved in pathogenicinteractions with hosts. Sachs

Regulation of Long Chain Fatty Acid Transport andOxidation in Mammalian Heart and LiverThe rate-limiting step in ß-oxidation is theconversion of long-chain acyl-CoA to acylcarnitine,a reaction catalyzed by the outer mitochondrialmembrane enzyme carnitine palmitoyltransferase I(CPTI) and inhibited by malonyl-CoA. Theacylcarnitine is then translocated across the innermitochondrial membrane by the carnitine/acylcarnitine translocase and converted back toacyl-CoA by CPTII. This reaction in intactmitochondria is inhibited by malonyl-CoA, the firstintermediate in fatty acid synthesis, suggestingcoordinated regulation of fatty acid oxidation andsynthesis. Although CPTII has been examined indetail, studies on CPTI have been hampered by aninability to purify CPTI in an active form fromCPTII. In particular, it has not been conclusivelydemonstrated that CPTI is even catalytically active,or whether sensitivity of CPTI to malonyl-CoA is anintrinsic property of the enzyme or is contained ina separate regulatory subunit that interacts withCPTI. To address these questions, the genes forhuman heart muscle M-CPTI and rat liver LCPTIand CPTII were separately expressed in Pichiapastoris, a yeast with no endogenous CPT activity.High levels of CPT activity were present in purifiedmitochondrial preparations from both CPTI- andCPTII-expressing strains. Furthermore, CPTIactivity was highly sensitive to inhibition bymalonyl-CoA while CPTII was not. Thus, CPTcatalytic activity and malonyl-CoA sensitivity arecontained within a single CPTI-polypeptide inmammalian mitochondrial membranes. Ourlaboratory is the first to describe the kinetic

characteristics for the yeast-expressed CPTIs, thefirst such report for a CPTI enzyme in the absenceof CPTII. Both yeast-expressed M-CPTI and L-CPTIare inactivated by detergent solubilization.However, removal of the detergent in the presenceof phospholipids resulted in the recovery ofmalonyl-CoA-sensitive CPTI activity, suggestingthat CPTI requires a membranous environment.CPTI is thus reversibly inactivated by detergents.We have isolated and sequenced the promoterregion of the gene for the human heart M-CPTI.We have mapped the malonyl-CoA and substratebinding sites in human heart M-CPTI and liverL-CPTI by deletion, site-directed mutagenesis andchemical modification studies using residue-specific reagents. Our deletion and point mutationanalyses have demonstrated that glutamate-3 andhistidine-5 are necessary for malonyl-CoAinhibition and binding of CPTI but not for catalysis.We will determine the structural basis for the highmalonyl-CoA sensitivity of M-CPTI by constructingchimeras between M-CPTI and L-CPTI and by site-directed mutagenesis. We will prepare milligramquantities of the expressed highly purified humanheart M-CPTI and liver L-CPTI for structuralcharacterization studies. Finally, we plan to studythe regulation of human heart M-CPTI geneexpression by hormonal, developmental and dietaryfactors. Our goal is to elucidate the molecularmechanism of the regulation of fatty acid transportand oxidation in mammalian cells. Woldegiorgis

Anaerobiosis of Bacillus subtilisA gram-positive soil bacterium, B. subtilis, ishighly amenable to genetic analysis and has beenused as a model system to study fundamentalmicrobiological research. In addition, B. subtilis ismedically and industrially important since itproduces a variety of antibiotics and extracellularenzymes. Although the organism has been widelyused, it has been mistakenly referred to as a strictaerobe until recently. Our studies, together withothers, have shown that B. subtilis is able to growunder anaerobic conditions by utilizing nitrate ornitrite as an alternative electron acceptor. In theabsence of terminal electron acceptors, itundergoes fermentative growth. Our research aimsinclude elucidation of the regulatory mechanismsthrough which the cells adapt to oxygen limitation.Molecular genetic and biochemical approaches areapplied. Nakano

ResD-ResE Two-Component SignalTransduction SystemBacteria often encounter sudden environmentalchanges. Cells cope with such changes by anelaborate network of adaptive responses. The two-component signal transduction system senses andthen processes information derived fromenvironmental changes so that the cell can choosethe appropriate adaptive response. This simplesignal transduction system is widespread inbacteria and also found in plants and lowereukaryotes. ResE is a histidine kinase and ResD isa response regulator of this large protein family.We have shown that ResD and ResE areindispensable for anaerobic respiration in

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B. subtilis. A specific signal derived by oxygenlimitation is recognized by the N-terminal inputdomain of the ResE kinase leading toautophosphorylation of a conserved histidineresidue in the C-terminal transmitter domain. Thisphosphoryl group is then transferred to aspartatein the conserved N-terminal domain of ResD,altering the activity of its C-terminal domain as atranscriptional activator. The ResD-ResE signaltransduction system is activated by oxygenlimitation or by addition of nitric oxide generators.The objectives of our studies are to determine howResE senses oxygen limitation or nitric oxide andhow anaerobically induced genes are activated byResD. Nakano

Flavohemoglobin (Hmp)Flavohemoglobin is a ubiquitous protein presentin organisms ranging from Escherichia coli toSaccharomyces cerevisiae. The N-terminal part ofthe protein has similarity to hemoglobin and theC-terminus is homologous to reductase with aflavin-binding domain. Recent studies showed thatflavohemoglobin is involved in detoxification ofnitric oxide. B. subtilis hmp was identified amonggenes, expression of which is induced by oxygenlimitation. The anaerobic induction of hmp requiresthe ResD-ResE signal transduction pairs andnitrite. The expression is also induced byexogenous nitric oxide through ResDE-dependentand -independent mechanisms. The detailedregulatory mechanism of hmp expression and itsfunctional role in anaerobiosis are underinvestigation. Nakano

Prokaryotic Signal Transduction/Gene RegulationBacteria can respond in variety of ways to agrowth-restricting environment. Prolongedexposure to a nutritionally poor environmentresults in the induction of antibiotic biosynthesis,functions required for cell motility and processes ofcellular differentiation that give rise to highlyresistant cell types. How cells respond tonutritional stress is profoundly influenced by celldensity. Extracellular signal molecules accumulatein the local environment of densely populated cellcultures and trigger antibiotic production anddevelopmental processes such as sporulation andgenetic competence. The objective of our researchis to understand, in molecular terms, theregulatory networks that cells utilize to choose themost appropriate response to harsh conditions. Inthe spore-forming bacterium, Bacillus subtilis,establishment of genetic competence is co-regulated with peptide antibiotic biosynthesis by acomplex network of signal transduction pathwaysthat utilize protein components common to allprokaryotic and most eukaryotic organisms. Zuber

Role of Chaperones/Proteases in the Controlof Gene ExpressionThere is growing evidence that protein complexesthat function in protein folding, remodeling anddegradation interact directly with the molecularmachinery that initiates gene expression. Inmammalian, fungal and bacterial cells, componentsof ATP-dependent protease complexes have been

implicated in the control of RNA polymeraseactivity through direct protein-protein interaction.In the spore-forming bacterium, Bacillus subtilis,developmentally regulated transcription during theearly stages of sporulation, genetic competencedevelopment and antibiotic biosynthesis isprofoundly affected by members of the heat shockprotein family that normally function aschaperones and multi-component proteases.Evidence from our studies indicates that theseproteins operate closely with RNA polymeraseduring the process of regulated transcriptioninitiation. Our work is aimed at determining thenature of these interactions and their effects onthe systems controlling bacterial developmentalprocesses. Zuber

The Mitochondrial ATP-sensitive K+ Channel(mitoKATP)MitoKATP resides in the inner membrane ofmitochondria where it serves to regulate thevolume of mitochondrial compartments and also totrigger cell signaling leading to cardioprotectionand gene transcription. We showed that mitoKATPmediates the actions of potassium channel openersand ischemic preconditioning to protect the heartagainst ischemia-reperfusion injury. We areworking to understand the mechanisms of thiseffect and the normal physiological role of mitoKATPin heart and brain. We introduced techniques forpurification and reconstitution of mitoKATP in lipidvesicles and use this preparation to study thetransport kinetics of the channel. We have purifiedthe mitoKATP subunits to homogeneity and will usethese to obtain the molecular structure ofmitoKATP. Garlid

Mitochondrial Uncoupling ProteinsOur laboratory was the first to demonstratereconstitutive activity of the new uncouplingproteins, UCP2 and UCP3, and we have long beenactive in the study of UCP1. Flux studies inproteoliposomes containing UCP have led to a newmechanism of UCP-mediated uncoupling, in whichthe fatty acid anion is transported by UCP and theprotonated fatty acid cycles spontaneously backacross the bilayer to deliver protons. Garlid

Mitochondrial Bioenergetics Progress in understanding mitochondrialbioenergetics has not kept pace with the enormousprogress in structure-function of the enzymes ofoxidative phosphorylation. This occurs at a timewhen understanding bioenergetics at thephysiological level is most needed, in view of theincreased recognition of the roles played bymitochondria in cell physiology andpathophysiology. A number of unresolved questionsrelating to the mechanism of energy conservationin mitochondria are being addressed by theoreticaland experimental approaches. Subjects beinginvestigated include the question of redox slip;volume activation of electron transport; and therole of the intermembrane space in regulatingenergy transfers between matrix and cytosol.Garlid

Biochemistry of Lignin DegradationLignin is the most abundant renewable aromaticpolymer, constituting approximately 25 percent ofwoody plant cell walls. Our multidisciplinaryresearch program aims to understand and exploitthe fungal degradation of this underutilizedresource. The metabolic pathways and enzymaticcomponents of the lignin degradative system areexamined using biochemical, enzymological andmolecular biological methods. Two novelextracellular heme peroxidases (lignin peroxidaseand manganese peroxidase) involved in thedegradation of lignin were discovered in ourlaboratory. Lignin peroxidase oxidizes a variety ofnonphenolic lignin model compounds and prioritypollutants. Manganese peroxidase oxidizes MnII toMnIII, which in turn oxidizes phenolic andnonphenolic substrates. The structures, activesites, mechanisms, catalytic cycles and regulationof these enzymes are being characterized in ourlaboratory and via collaborations usingspectroscopy, stopped-flow kinetics, proteinchemistry, enzymology, X-ray crystallography andbioorganic and molecular genetic methods.Recently, we developed a homologous expressionsystem for these peroxidases. This system allowsstructure/function studies by site-directedmutagenesis. Applications for lignin-degradingsystems include the more efficient utilization ofbiomass, nonpolluting forest products technologiesand toxic waste cleanup. We also are studyingseveral intracellular enzymes such as quinonereductases, ring-cleaving dioxygenases andreductive dehalogenases that are involved in ligninand pollutant degradation. Gold

Molecular Biology and Genetics of Phanerochaetechrysosporium and Its Lignin-Degrading SystemWe are isolating and sequencing the genesencoding components of the P. chrysosporiumlignin-degrading system. These include genesencoding lignin and manganese peroxidases, anovel quinone reductase and several other genes.We are analyzing the coding and promoterregions of these genes and studying theregulation of their transcription. We havediscovered that Mn peroxidase is regulated byMn ion, the substrate for the enzyme, as well asby nutrient nitrogen, heat shock and oxidativestress. Using reporter genes, we are elucidatingthe molecular mechanisms involved in Mnperoxidase gene regulation. We developed atranscriptional reporter system based on thegene encoding the green fluorescent protein fromthe jellyfish. Using this system, we aredelineating the sequences in the mnp genepromoter involved in the Mn regulation of Mnperoxidase transcription. Gold

Biodegradation of Aromatic PollutantsThe nonspecific and oxidative nature of the lignindegradation system of the fungus Phanerochaetechrysosporium enables this organism to degrade avariety of toxic aromatic pollutants, includingpolychlorinated phenols, polychlorinated dioxins,chlorophenoxyacetic acid and nitrotoluenes. We are

B M B | B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y | F A C U L T Y

examining the biochemical pathways, enzymes andregulatory mechanisms involved in the totaldegradation of these compounds. The fungusutilizes extracellular peroxidases as well asintracellular quinone reductases, reductivedehalogenases, and dioxygenases to carry outthese processes. We are attempting to characterizethese enzymes and their encoding genes to morefully understand the mechanisms involved in thedegradation of these pollutants. We discovered anovel reductive dechlorination system in white-rotfungi that removes chlorines from chlorinatedhydroquinones. This system is being examined bybiochemical and molecular biological methods. Gold

Enzymes Involved in Cellobiose OxidationCellulose constitutes 40 to 60 percent of plant cellwall material; its biotechnological conversion,initially to glucose and then to ethanol, can providean alternative source of energy. This applicationrequires a complete understanding of the variousenzymes involved in fungal cellulose degradation.Cellulose-degrading cultures of Phanerochaetechrysosporium produce a unique hemoflavoenzyme,cellobiose dehydrogenase (CDH), which oxidizescellobiose to cellobionolactone. We have purifiedCDH to homogeneity in high yields. The aminoacids responsible for heme ligation in CDH havebeen identified in our lab by site-directedmutagenesis, and in collaboration by solving thecrystal structure of CDH. In addition, the aminoacids in the flavin domain involved in the bindingand oxidation of cellobiose have been identified bysite-directed mutagenesis and kinetic studies. Gold

RESEARCH FACILIT IESThe department is well equipped to carry on a vigorous research program. Instruments andequipment available in the department include:

• Gas chromatograph/mass spectrometer

w i th computer data system

• High-reso lut ion mass spectrometer

• UV/VIS spectrometer

• Capi l lary co lumn gas chromatographs with f lame

ion izat ion detectors

• Four ier t ransform infrared spectrometers

• Four ier t ransform Raman spectrometer w i th

CW Nd:YAG laser

• X-band e lectron paramagnet ic

resonance spectrometer

• Ultrav io let/v is ib le/near- in f rared spectrophotometers

• Scanning f luorescence spectrophotometers

• Magnet ic c i rcu lar d ichro ism (MCD) spectrometer

• Diode array UV/VIS spectrophotometer

• Laser Raman spectrophotometer

• Raman spectrograph with CCD detector

• Ar, Kr, He-Cd, He-Ne, and dye lasers

• High-vacuum l ines

• Phosphor imager

• Contro l led atmosphere react ion chamber

• Super speed centr i fuges

• Ultracentr i fuges

• HPLCs

• FPLCs

• Fract ion co l lectors

• Liqu id sc int i l lat ion systems

• Gel e lectrophores is systems

• Laminar f low hoods for ster i le cu l ture

• Growth chambers

• Constant temperature rooms

• Light and e lectron microscopes

• Ultraf i l t rat ion systems

• Autoc laves

• Photographic fac i l i t ies

• Probe type son icators and extruder

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N I N I A N J . B L A C K B U R NProfessor and Department HeadPh.D., Inorganic ChemistryUniversity of Dundee,Scotland, U.K., 1975ninian@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Structure and function of oxidaseand oxygenase metalloenzymes;spectroscopy of metal sites inproteins with emphasis on EPR,EXAFS, absorption edge and FTIRspectroscopies; coordinationchemistry and biochemistry ofcopper. Biochemistry of metaltrafficking in cells.

R E P R E S E N TAT I V E P U B L I C AT I O N SF.C. Rhames, N.N. Murthy, K.D. Karlin

and N.J. Blackburn, “Isocyanide Bindingto the Copper(I) Centers of theCatalytic Core of PeptidylglycineMonooxygenase (PHMcc),” J. Biol.Inorg. Chem., 6, pp. 567-577, 2001.

S. Jaron and N.J. Blackburn,“Characterization of a Half-ApoDerivative of PeptidylglycineMonooxygenase. Insight into theReactivity of Each Active Site Copper,”Biochemistry, 40, pp. 6867-6875,2001.

N.J. Blackburn, F. C. Rhames, M.Ralle and S. Jaron, “Major Changesin Copper Coordination AccompanyReduction of PeptidylglycineMonooxygenase: Implications forElectron Transfer and the CatalyticMechanism,” J. Biol. Inorg. Chem.,5, pp. 341-353, 2000.

J.F. Eisses, J.P. Stasser, M. Ralle,J.H. Kaplan and N.J. Blackburn,“Domains I and III of Human CopperChaperone for Superoxide DismutaseInteract via a Cysteine-BridgedDicopper(I) Cluster,” Biochemistry,38, pp. 7337-7342, 2000.

N.J. Blackburn, M. Ralle, R. Hassettand D.J. Kosman, “SpectroscopicAnalysis of the Trinuclear Cluster in theFet3 Protein from Yeast, a MultinuclearCopper Oxidase,” Biochemistry, 39,pp. 2316-2324, 2000.

C O L I N A N D R E WResearch Assistant ProfessorPh.D., Chemistry University of NewcastleUpon Tyne, 1992candrew@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Bioinorganic chemistry; structure,function and spectroscopy ofmetalloenzymes; generation,mobilization and sensing of nitricoxide by metalloproteins; redox-active copper proteins.

R E P R E S E N TAT I V E P U B L I C AT I O N SC.R. Andrew, E.L. Green, D.M. Lawson

and R.R. Eady, “Resonance RamanStudies of Cytochrome c’ Support theBinding of NO and CO to Opposite Sidesof the Heme: Implications for LigandDiscrimination in Heme-Based Sensor,”Biochemistry, 40, pp. 4115-4122,2001.

D.M. Lawson, C.E.M. Stevenson,C.R. Andrew and R.R. Eady,“Unprecedented Proximal Binding ofNitric Oxide to Heme: Implications forGuanylate Cyclase,” EMBO J., 19,pp. 5661-5671, 2000.

J.P. Hannan, S.L. Davy, G.R. Moore,R.R. Eady and C.R. Andrew, “Effect ofNickel(II) Substitution on the ResonanceRaman and NMR Spectra of Alcaligenesxylosoxidans azurin II: Implications forAxial-Ligand Bonding Interactions inCupredoxin Active Sites, Biol. Inorg.Chem., 3, pp. 282-291, 1998.

C.R. Andrew, J. Han, T. den Blauuwen,G. van Pouderoyen, E. Vijgenboom,G. W. Canters and J. Sanders-Loehr,“Cysteine Ligand Vibrations areResponsible for the Complex ResonanceRaman Spectrum of Azurin,” Biol. Inorg.Chem., 2, pp. 98-107, 1997.

C.R. Andrew and J. Sanders-Loehr,“Copper-Sulfur Proteins: UsingRaman Spectroscopy to PredictCoordination Geometry [Review], Acc.Chem. Res., 29, pp. 365-372, 1996.

K E I T H D . G A R L I DProfessorM.D., The Johns HopkinsUniversity Schoolof Medicine, 1961Dr. technicae norwegiensis,Physical ChemistryNorwegian Instituteof Technology, 1987garlid@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

The structure-function of themitochondrial ATP-sensitiveK+ channel (mitoKATP) andits role in cardioprotectionand cardiac physiology; thestructure-function of uncouplingproteins; mitochondrial andcellular bioenergetics.

R E P R E S E N TAT I V E P U B L I C AT I O N SR. Bajgar, S. Seetharaman, A.J.

Kowaltowski, K.D. Garlid and P. Paucek,“The ATP-Sensitive Potassium Channelof Brain Mitochondria,” J. Biol. Chem.,276, pp. 33369-33374, 2001.

A.J. Kowaltowski, S. Seetharaman,P. Paucek and K.D. Garlid, “BioenergeticConsequences of Opening the ATP-Sensitive K+ Channel of HeartMitochondria,” Am. J. Physiol. HeartCirc. Physiol., 280, pp. H649-H657,2001.

K.D. Garlid, M. Jaburek and P. Jezek,“Mechanism of Uncoupling ProteinAction,” Biochem. Soc. Trans., 29,pp. 803-806, 2001.

K.D. Garlid and P. Paucek, “TheMitochondrial Potassium Cycle,”IUBMB Life, 52, pp. 153-158, 2001.

K.D. Garlid, M. Jaburek, P. Jezek andM. Varecha, “How Do UncouplingProteins Uncouple?” Biochim. Biophys.Acta, 1459, pp. 383-389, 2000.

M I C H A E L H . G O L DInstitute ProfessorPh.D., BiochemistryState University of New Yorkat Buffalo, 1970mgold@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Biochemistry; molecularbiology; genetics of fungi;fungal degradation of ligninand environmental pollutants;structure and function ofnovel peroxidases; structureexpression and regulation offungal genes; biotechnology.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.D. Sollewijn Gelpke, J. Lee

and M.H. Gold, “Lignin PeroxidaeOxidation of Veratryl Alcohol: Effectsof the Mutants H82A, Q222A, W171Aand F267L,” Biochemistry, 41,pp. 3498-3506, 2002.

G.V.B.Reddy and M.H. Gold,“Purification and Characterizationof Glutathione Conjugate Reductase:A Component of the Tetrachlorohydro-quinone Reductive DehalogenaseSystem from Phanerochaetechrysosporium,” Arch. Biochem.Biophys., 391, pp. 271-277, 2001.

F.A.J. Rotsaert, B. Li, V. Renganathanand M.H. Gold, “Site-directedMutagenesis of the Heme Axial Ligandsin the Hemoflavoenzyme, CellobioseDehydrogenase,” Arch. Biochem.Biophys., 390, pp. 206-214, 2001.

H.L. Youngs, M.D. Sollewijn Gelpke,D. Li, M. Sundaramoorthy and M.H.Gold, “The Role of E39 in MnII Bindingand Oxidation by ManganesePeroxidase from Phanerochaetechrysosporium,” Biochemistry, 40,pp. 2243-2250, 2001.

B. Ma, M.B. Mayfield and M.H. Gold,“The Green Fluorescent Protein GeneFunctions as a Reporter of GeneExpression in Phanerochaetechrysosporium,” Appl. Environ.Microbiol., 67, pp. 948-955, 2001.

F A C U L T Y | B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y | B M B

FACULTY

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B M B | B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y | F A C U L T Y

T H O M A S M . L O E H RProfessor EmeritusPh.D., Inorganic ChemistryCornell University, 1967loehr@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Metallobiochemistry; biologicalrole of transition metals;molecular and electronicstructures of metalloenzyme activesites; chemistry of O2 metabolism;metal-oxo intermediates;resonance and FT Raman, FT-IR,and EPR spectroscopy.

R E P R E S E N TAT I V E P U B L I C AT I O N SL.K. Lightning, H. Huang, P. Moënne-

Loccoz, T.M. Loehr, D.J. Schuller,T.L. Poulos and P.R. Ortiz deMontellano, “Disruption of an ActiveSite Hydrogen Bond Converts HumanHeme Oxygenase-1 into a Peroxidase,”J. Biol. Chem., 276, pp. 10612-10619,2001.

J. Hirst, S.K. Wilcox, J. Ai, P. Moënne-Loccoz, T.M. Loehr and D.B. Goodin,“Replacement of the Axial HistidineLigand with Imidazole in Cytochromec Peroxidase. 2. Effects on HemeCoordination and Function,”Biochemistry, 40, pp. 1274-1283,2001.

J. Baldwin, W.C. Voegtli, N. Khidekel,P. Moënne-Loccoz, C. Krebs, B.A. Ley,B.H. Huynh, T.M. Loehr, A. C.Rosenzweig and J.M. Bollinger, Jr.,“Rational Reprogramming of theR2 Subunit of Escherichia coliRibonucleotide Reductase into a Self-Hydroxylating Monooxygenase,” J. Am.Chem. Soc., 123, pp. 7017-7030, 2001.

E.L. Green, S. Taoka, R. Banerjeeand T.M. Loehr, “Resonance RamanCharacterization of the Heme Cofactorin Cystathionine Beta-Synthase.Identification of the Fe-S(Cys) Vibrationin the Six-Coordinate Low-Spin Heme,”Biochemistry, 40, pp. 459-463, 2001.

Y. Liu, L. Koenigs Lightning,H.-w. Huang, P. Moënne-Loccoz,D.J. Schuller, T.L. Poulos, T.M. Loehrand P.R. Ortiz de Montellano,“Replacement of the Distal Glycine 139Transforms Human Heme Oxygenase-1into a Peroxidase,” J. Biol. Chem., 275,pp. 34501-34507, 2000.

P I E R R E M O Ë N N E - L O C C O ZAssistant ProfessorPh.D., BiophysicsUniversity of Pierre & Marie Curie,Paris VI, 1989ploccoz@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Structure-function relationshipswithin proteins. Metallo- andheme-proteins. Spectroscopicstudies of enzyme-active sites andtheir cofactors. Reactionintermediates within catalysis.

R E P R E S E N TAT I V E P U B L I C AT I O N SR.A. Ghiladi, K.R. Hatwell, K.D. Karlin,

H.-w. Huang, P. Moënne-Loccoz,C. Krebs, B.H. Huynh, L.A. Marzilli,R.J. Cotter, S. Kaderli and A.D.Zuberbuhler, “Dioxygen Reactivity ofMononuclear Heme and CopperComponents Yielding a High-SpinHeme-Peroxo-Cu Complex,” J. Am.Chem. Soc., 123, pp. 6183-6184, 2001.

K. Auclair, P. Moënne-Loccoz andP.R. Ortiz de Montellano, “Roles of theProximal Heme Thiolate Ligand inCytochrome P450cam,” J. Am. Chem.Soc., 123, pp. 4877-4885, 2001.

P. Moënne-Loccoz, O.-M.H. Richter,H.-w. Huang, I. Wasser, R.A. Ghiladi,K.D. Karlin and S. de Vries, “NitricOxide Reductase from Paracoccusdenitrificans Contains an Oxo-BridgedHeme/Non-Heme Diiron Center,” J. Am.Chem. Soc., 122, pp. 9344-9345, 2000.

A. Wilks and P. Moënne-Loccoz,“Identification of the Proximal LigandHis-20 in Heme Oxygenase (HmuO)from Corynebacterium diphtheriae.Oxidative Cleavage of the HemeMacrocycle Does Not Require theProximal Histidine,” J. Biol. Chem.,275, pp. 11686-11692, 2000.

P. Moënne-Loccoz, C. Krebs,K. Herlihy, D.E. Edmondson, E.C. Theil,B.H. Huynh and T.M. Loehr, “TheFerroxidase Reaction of FerritinReveals a Diferric mu-1,2 BridgingPeroxide Intermediate in Common withOther O2-Activating Non-Heme DiironProteins,” Biochemistry, 38, pp. 5290-5295, 1999.

M I C H I K O M . N A K A N OResearch Associate ProfessorPh.D., Cell BiologyUniversity of Tokyo, 1976mnakano@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Anaerobiosis of Bacillus subtilis;oxygen-controlled gene regulation;two-component signal transductionsystem; transcriptional activation;nitrate/nitrite reductases;flavohemoglobin; anaerobicelectron transport; nitric oxidesignaling.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.M. Nakano and Y. Zhu, “Involvement

of the ResE Phosphatase Activity inDown-Regulation of ResD-ControlledGenes in Bacillus subtilis DuringAerobic Growth,” J. Bacteriol., 183,pp. 1938-1944, 2001.

M.M. Nakano, Y. Zhu, M. LaCelle,X. Zhang and F.M. Hulett, “Interactionof ResD with Regulatory Regions ofAnaerobically Induced Genes inBacillus subtilis,” Mol. Microbiol.,37, pp. 1198-1207, 2000.

M.M. Nakano, F. Hajarizadeh, Y. Zhuand P. Zuber, “Loss-of-functionMutations in yjbD result in ClpX-and ClpP-independent CompetenceDevelopment in Bacillus subtilis. Mol.Microbiol., 42, pp. 383-394, 2001.

M.M. Nakano and P. Zuber,“Anaerobiosis,” in Bacillus subtilis andIts Closest Relatives, A.L. Sonenshein,J.A. Hoch and R. Losick, eds., AmericanSociety for Microbiology, Washington,DC, pp. 393-404, 2001.

M.M. Nakano, “Induction of ResDE-dependent Gene Expression in Bacillussubtilis in Response to Nitric Oxide andNitrosative Stress,” J. Bacteriol., 184,pp. 1783-1787, 2002.

P E T E R P A U C E KResearch Assistant ProfessorDr.Rer.Nat., Biophysics andChemical PhysicsPalacky University(Czech Republic), 1988Ph.D., Biological ScienceThe Academy of Sciencesof the Czech Republic, 1991paucek@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Molecular biophysics ofmitochondrial cation transportersand channels, with emphasis onNa+/Ca2+ antiporter and the ATP-dependent K+ channel in cardiacand brain mitochondria; receptorproperties and their roles incellular signaling, bioenergeticsand pharmacology.

R E P R E S E N TAT I V E P U B L I C AT I O N SR. Bajgar, S. Seetharaman,

A.J. Kowaltowski, K.D. Garlid andP. Paucek, “Identification andProperties of a Novel Intracellular(Mitochondrial) ATP-SensitivePotassium Channel in Brain,” J. Biol.Chem., 276, pp. 3369-33374, 2001.

K.D. Garlid and P. Paucek, “TheMitochondrial Potassium Cycle,”IUBMB Life, 52, pp. 153-158, 2001.

G.J. Grover, A.J. D’Alonzo,K.D. Garlid, N.J. Lodge, P.G. Sleph,R.B. Darbenzio, T.A. Hess, M.A. Smith,P. Paucek and K.S. Atwal,“Pharmacologic Characterization ofBMS-101-05, a Mitochondrial KATPOpener with No Peripheral Vasodilatoror Cardiac Action Potential ShorteningActivity,” J. Pharmacol. Exp. Ther.,297, pp. 1184-1192, 2001.

A.J. Kowaltowski, S. Seetharaman,P. Paucek and K.D. Garlid, “BioenergeticConsequences of Opening the ATP-Sensitive K+ Channel of HeartMitochondria,” Am. J. Physiol. HeartCirc. Physiol., 280, pp. H649-H657,2001.

M. Jaburek, V. Yarov-Yarovoy,P. Paucek, W. Li and K.D. Garlid,“State-Dependent Inhibition of theMitochondrial KATP Channel byGlyburide and 5-Hydroxydecanoate,”J. Biol. Chem., 273, p. 1357, 1998.

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M A R T I N A R A L L EResearch ScientistPh.D., ChemistryUniversity of Bonn,Germany, 1993ralle@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Metallobiochemistry; structure-function analysis ofmetalloenzymes. Spectroscopiccharacterization of coppertransporters such as Wilson’s andMenkes disease protein, usingextended X-ray absorption finestructure spectroscopy (EXAFS).Cloning, overexpression andcharacterization of proteinsinvolved in copper transport in themammalian cell.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.F. Eisses, J.P. Stasser, M. Ralle,

J.H. Kaplan and N.J. Blackburn,“Domains I and III of Human CopperChaperone for Superoxide DismutaseInteract via a Cysteine-BridgedDicopper(I) Cluster,” Biochemistry,38, pp. 7337-7342, 2000.

N.J. Blackburn, M. Ralle, R. Hassettand D.J. Kosman, “SpectroscopicAnalysis of the Trinuclear Cluster in theFet3 Protein from Yeast, a MultinuclearCopper Oxidase,” Biochemistry, 39,pp. 2316-2324, 2000.

M. Ralle, M.L. Verkhovskaya,J.E. Morgan, M.I. Verkhovsky,M. Wikstrom and N.J. Blackburn,“Coordination of CuB in Reducedand CO-liganded States of Cytochromebo3 from Escherichia coli. Is ChlorideIon a Cofactor?” Biochemistry, 38,pp. 7185-7194, 1999.

N.J. Blackburn, M. Ralle, E. Gomez,M.G. Hill, A. Pastuszyn, D. Sandersand J.A. Fee, “Selenomethionine-substituted Thermus thermophilusCytochrome ba3: Characterization ofthe CuA Site by Se and Cu K-EXAFS,”Biochemistry, 38, 7075-7084, 1999.

M. Ralle, M.J. Cooper, S. Lutsenkoand N.J. Blackburn, “The MenkesDisease Protein Binds Copper via Novel2-Coordinate Cu(I)-Cysteinates in theN-Terminal Domain,” J. Am. Chem.Soc., 120, pp. 13525-13526, 1998.

L . E . L ( B E T S ) R A S M U S S E NResearch ProfessorPh.D., NeurochemistryWashington University(St. Louis), 1964betsr@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Mammalian chemocommunication:the transport, olfactory andvomeronasal organ reception of(Z)-7-dodecenyl acetate, the sexpheromone of the Asian elephant;the origin and synthesis of (Z)-7-dodecenyl acetate; identificationand function of pheromones andchemical signals of the elephant-unique temporal gland.

R E P R E S E N TAT I V E P U B L I C AT I O N SL.E.L. Rasmussen, H.S. Riddle and

V. Krishnamurthy, “Mellifluous Maturesto Malodorous in Musth,” Nature, 415,pp. 975-976, 2002.

L.E.L. Rasmussen and G. Wittemyer,“Chemosignaling of Musth by IndividualWild African Elephants (Loxodontaafricana): Implications for Conservationand Management,” Proc. Royal Soc.London, 269, pp. 853-860, 2002.

L.E.L. Rasmussen, J. Lazar,D.R. Greenwood and G.D. Prestwich,“Albumin-An Ideal Pheromone Carrier,”Chem. Senses, 26, p. 1102, 2001.

L.E.L. Rasmussen, “Source and CyclicRelease Pattern of (Z)-7-DodecenylAcetate, the Preovulatory Pheromoneof the Female Asian Elephant,” Chem.Senses, 26, pp. 611-623, 2001.

L.E.L. Rasmussen. “ElephantOlfaction,” ChemoSenses, 2,pp. 4-5, 1999.

L.E.L. Rasmussen and T.E. Perrin.“Physiological Correlates of Musth:Lipid Metabolites and ChemosignalComposition,” Physiol. Behav., 67,pp. 539-549, 1999.

L.E.L. Rasmussen. “ChemicalCommunication: An Integral Part ofFunctional Asian Elephant (Elephasmaximus) Society, Ecoscience, 5,pp. 410-426, 1998.

M AT T H E W S . S A C H SAssociate ProfessorPh.D., BiologyMassachusetts Institute ofTechnology, 1986msachs@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Mechanisms of translationaland transcriptional control thatregulate the expression of theNeurospora crassa arg-2 andSaccharomyces cerevisiaeCPA1 genes; translational control of human proto-oncogenes;fungal genomes.

R E P R E S E N TAT I V E P U B L I C AT I O N SD.D. Perkins, A. Radford and

M.S. Sachs, The NeurosporaCompendium: Chromosomal Loci.Academic Press, 2001.

H.S. Kelkar, J. Griffiths, M.E. Case,S.F. Covert, D.A. Hall, C. Keith,J.S. Oliver, M.J. Orbach, M.S. Sachs,J.R. Wagner, M.J. Weise, J.K.Wunderlich and J. Arnold, “TheNeurospora Crassa Genome: LibrariesSorted by Chromosome,” Genetics,157, pp. 979-990, 2001.

A. Gaba, Z. Wang, T. Krishnamoorthy,A.G. Hinnebusch and M.S. Sachs,“Physical Evidence for DistinctMechanisms of Translational Control by Upstream Open Reading Frames,”EMBO J., 20, pp. 6453-6463, 2001.

P. Fang, Z. Wang and M.S. Sachs,“Evolutionarily Conserved Features ofthe Arginine Attenuator Peptide Providethe Necessary Requirements for itsFunction in Translational Regulation,”J. Biol. Chem., 275, pp. 26710-26719,2000.

A.P. Geballe and M.S. Sachs,“Translational Control by UpstreamOpen Reading Frames,” in TranslationalControl of Gene Expression,N. Sonenberg, J.W. B. Hershey andM.B. Mathews, eds., Cold SpringHarbor Laboratory Press, New York,pp. 595-614, 2000.

J O A N N S A N D E R S - L O E H RProfessor EmeritusPh.D., BiochemistryCornell University, 1969

R E S E A R C H I N T E R E S T S

Investigation of the role ofmetal ions in proteins byresonance Raman spectroscopy;oxygen activation andmetabolism; active-site structuresand redox reactions of ironproteins, copper proteins andquinone-containing proteins.

R E P R E S E N TAT I V E P U B L I C AT I O N SC.S. Farmer, D.M. Kurtz, Jr.,

Z.J. Liu, B.C. Wang, J. Rose, J. Ai andJ. Sanders-Loehr, “The CrystalStructures of Phascolopsis gouldiiWild Type and L98Y Methemerythrins:Structural and Functional Alterationsof the O2 Binding Pocket,” J. Biol.Inorg. Chem., 6, pp. 418-429, 2001.

M.L. Alvarez, J. Ai, W. Zumft,J. Sanders-Loehr and D.M. Dooley,“Characterization of the Copper-SulfurChromophores in Nitrous OxideReductase by Resonance RamanSpectroscopy: Evidence for SulfurCoordination in the Catalytic Cluster,”J. Am. Chem. Soc., 123, pp. 576-587,2001.

J. Xiong, R.S. Phillips, D.M. Kurtz, Jr.,S. Jin, J. Ai and J. Sanders-Loehr, “TheO2 Binding Pocket of Myohemerythrin:Role of a Conserved Leucine,”Biochemistry, 39, pp. 8526-8536,2000.

K.S. Lyle, P. Moënne-Loccoz, J. Ai,J. Sanders-Loehr, T.M. Loehr andB.G. Fox, “Resonance Raman Studiesof the Stoichiometric Catalytic Turnoverof a Substrate-Stearoyl-Acyl CarrierProtein �9 Desaturase Complex,”Biochemistry, 39, pp. 10507-10513,2000.

T. Rasmussen, B.C. Berks, J. Sanders-Loehr, D.M. Dooley, W.G. Zumft andA.J. Thomson, “The Catalytic Center inNitrous Oxide Reductase, CuZ, is aCopper-Sulfide Cluster,” Biochemistry,39, pp. 12753-12756, 2000.

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B M B | B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y | F A C U L T Y

J A M E S W. W H I T TA K E RAssociate ProfessorPh.D., BiochemistryUniversity of Minnesota, 1983jim@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Electronic structures anddynamics of metalloenzyme activesites; spectroscopic andcomputational approaches tobiomolecular structure;metalloenzyme mechanisms;enzyme engineering; biology ofmetal ions.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.M. Whittaker and J.W. Whittaker,

“Characterization of RecombinantBarley Oxalate Oxidase Expressed byPichia pastoris,” J. Biol. Inorg. Chem.,7, pp. 136-145, 2002.

V.V. Barynin, M.M. Whittaker,S.V. Antonyuk, V.S. Lamzin,P.M. Harrison, P.J. Artymiuk andJ.W. Whittaker, “Crystal Structure ofManganese Catalase from Lactobacillusplantarum,” Structure, 9, pp. 725-738,2001.

M.M. Whittaker and J.W. Whittaker,“Catalytic Reaction Profile for AlcoholOxidation by Galactose Oxidase,”Biochemistry, 40, pp. 7140-7148,2001.

R.A. Edwards, M.M. Whittaker,J.W. Whittaker, E.N. Baker andG.B. Jameson, “Outer Sphere MutationsPerturb Metal Reactivity in ManganeseSuperoxide Dismutase,” Biochemistry,40, pp. 15-27, 2001.

M.M. Whittaker and J.W. Whittaker,“Expression of Recombinant GalactoseOxidase by Pichia pastoris,” ProteinExpr. Purif., 20, pp. 105-111, 2000.

M.M. Whittaker and J.W. Whittaker,“Recombinant Superoxide Dismutasefrom a Hyperthermophilic Archaeon,Pyrobaculum aerophilium,” J. Biol.Inorg. Chem., 5, pp. 402-408, 2000.

G E B R E TAT E O S W O L D E G I O R G I SAssociate ProfessorPh.D., Nutritional BiochemistryUniversity of Wisconsin-Madison, 1976gwoldeg@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Regulation of carnitinepalmitoyltransferase I; regulationof long-chain fatty acid transportand oxidation in mammalian cells;regulation of cell metabolism andsignaling by long-chain acyl CoAesters; mitochondrial ion transportand bioenergetics.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. Nicot, J. Relat, G. Woldegiorgis,

D. Haro and P.F. Marrero, “Pig LiverCarnitine Palmitoyltransferase I:Chimera Studies Show That Both theN- and C-terminal Regions of theEnzyme Are Important for the UnusualMalonyl CoA Sensitivity,” J. Biol.Chem., 277, pp. 10044-10049, 2002.

C. Nicot, F.G. Hegardt, G. Woldegiorgis,D. Haro and P.F. Marrero, “Pig LiverCarnitine Palmitoyltransferase I,with low Km for Carnitine and HighSensitivity to Malonyl-CoA Inhibition,is a Natural Chimera of Rat Liver andMuscle Enzymes,” Biochemistry,40, pp. 2260-2266, 2001.

J. Dai, H. Zhu, J. Shi andG. Woldegiorgis, “Identification byMutagenesis of Conserved Arginineand Tryptophan Residues in Rat LiverCarnitine Palmitoyltransferase IImportant for Catalytic Activity,”J. Biol. Chem., 275, pp. 22020-22024,2000.

J. Shi, H. Zhu, D.N. Arvidson andG. Woldegiorgis, “The First 28N-Terminal Amino Acid Residues ofHuman Heart Muscle CarnitinePalmitoyltransferase I are Essentialfor Malonyl CoA Sensitivity and High-Affinity Binding,” Biochemistry, 39,pp. 712-717, 2000.

L. Abu-Elheiga, W.R. Brinkley,L. Zhong, S.S. Chirala, G. Woldegiorgisand S.J. Wakil. “The SubcellularLocalization of Acetyl-CoA Carboxylase2,” Proc. Natl. Acad. Sci. USA, 97,pp. 1444-1449, 2000.

P E T E R Z U B E RProfessorPh.D., MicrobiologyUniversity of Virginiapzuber@bmb.ogi.edu

R E S E A R C H I N T E R E S T S

Regulation of prokaryotic geneexpression and development inresponse to stress; signaltransduction; regulation andmechanism of peptide antibioticbiosynthesis; regulation of geneticcompetence in Bacillus subtilis.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.M. Nakano, S. Nakano and P. Zuber,

“Spx (YjbD), a Negative Effector ofCompetence in Bacillus subtilis,Enhances ClpC-MecA-ComKInteraction,” Mol. Microbiol., 44,pp. 1341-1350, 2002.

P. Zuber, “A Peptide Profile of theBacillus subtilis Genome,” Peptides,22, pp. 1555-1577, 2001.

P. Zuber, “Specificity ThroughFlexibility,” Nat. Struct. Biol., 7,pp. 1079-1081, 2000.

J. Liu and P. Zuber, “The ClpXProtein of Bacillus subtilus IndirectlyInfluences RNA PolymeraseHoloenzyme Composition and DirectlyStimulates SigmaH-DependentTranscription In Vitro,” Mol. Microbiol.,37, pp. 885-897, 2000.

G. Zheng, R. Hehn and P. Zuber,“Mutational Analysis of the sbo-albLocus of Bacillus subtilis:Identification of Genes Required forSubtilosin Production and Immunity,”J. Bacteriol., 182, pp. 3266-3273,2000.

M.M. Nakano, Y. Zhu, J. Liu,D.Y. Reyes, H. Yoshikawa and P. Zuber,“Mutations Conferring Amino AcidResidue Substitutions in the Carboxy-Terminal Domain of RNA PolymeraseAlpha Can Suppress clpX and clpP withRespect to Developmentally RegulatedTranscription in Bacillus subtilis,”Mol. Microbiol., 37, pp. 869-884, 2000.

M.M. Nakano, G. Zheng and P. Zuber,“Dual Control of sbo-alb OperonExpression by the Spo0 and ResDESystems of Signal Transduction UnderAnaerobic Conditions in Bacillussubtilis,” J. Bacteriol., 182, pp. 3274-3277, 2000.

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JOINT FACULTY

D A V I D R . B O O N EEnvironmental BiologyPortland State University

J A M E S M . C R E G GKeck Graduate Instituteof Applied Life Sciences

B E R N A R D A . F O XEarle A. Chiles Research InstituteProvidence Medical Center

S T E P H E N B . H A L LPulmonary and CriticalCare MedicineOregon Health & Science University

J A M E S F. P A N K O WEnvironmental Scienceand EngineeringOGI School of Science& Engineering

R I C H A R D L . S T O U F F E ROregon National PrimateResearch Center andDept. of Physiologyand PharmacologyOregon Health & Science University

P A U L G . T R AT N Y E KEnvironmental Scienceand EngineeringOGI School of Science& Engineering

ADJUNCT FACULTY

G . D O Y L E D A V E SConsultant

K E N T H E R M S M E Y E ROregon Regional PrimateResearch Center

J A M E S K . H U R S TWashington State University

G E O R G E D . O L S E NOregon Health & Science University

V. R E N G A N AT H A NConsultant

C A R L C . W A M S E RPortland State University

RESEARCH ASSOCIATES

M A R T I N J A B U R E KPh.D., Biochemistryand Molecular BiologyOGI School of Science& Engineering

M A L AYA L A M S R I D H A RPh.D., Organic ChemistryIndian Institute of Science

M E I M . W H I T TA K E RPh.D., BiochemistryUniversity of Minnesota

G U O L U Z H E N GPh.D., Food MicrobiologyUniversity of Arkansas

SENIOR STAFF

D E E P A L I D AT TAM.Sc., ZoologyDelhi University, India

K A I T L I N G R A M M E RB.S., GeologyUniversity of Alaska-Fairbanks

M A R Y M AY F I E L D - G A M B I L LB.S., MicrobiologyOregon State University

S H U N J I N A K A N OB.S., Molecular BiologyNagoya University, Japan

C R A I G S E M R A DB.S., PhysicsStanford University

M I C H E L L E T R E B E RB.S., Biological SciencesCalifornia PolytechnicState University

Z E N E N G W A N GPh.D., BotanyPeking University

F A C U L T Y | B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y | B M B

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THE DEPARTMENT OF BIOMEDICAL

ENGINEERING, currently underdevelopment, is one of thepromising outcomes of the mergerof Oregon Health & ScienceUniversity and the OGI Schoolof Science & Technology. Themerger, which took place on July1, 2001, created the OGI Schoolof Science & Engineering, wherethe Department of BiomedicalEngineering is housed. Formationof the department has beenapproved, the curriculum iscurrently under development,and recruitment has begun for adepartment head and additionalfaculty. Admission to the Ph.D.program is expected to begin nolater than the fall of 2003.

The program of study will include a corecurriculum, electives tailored to specificareas of research, and hands-on research inexisting or new laboratories within OHSU.Our vision is to build a nontraditional, first-rate biomedical research and educationalprogram that will prepare students andworking professionals for careers inacademia or industry.

The existing program in BiomedicalEngineering offered through OGI’sDepartment of Electrical and ComputerEngineering (ECE) will be incorporated intothe new department. See ECE section fordetails on this program.

OVERVIEWThe interface between the rapidly changingfields of health, science and technology is afrontier where developments of greatimportance to human health are emerging.Advances in these high-tech areas arecreating new ways for technology to supporthealth care. Although traditionalbioengineering areas continue to beimportant, recent scientific and technologicaladvances in computational neuroscience,

tissue engineering, sensor technology,molecular biology, functional genomics,biomaterials, and biological and medicalinformatics, together with Oregon’spioneering spirit, will enable us to definea unique bioengineering program tosupport future clinical medicine and healthcare delivery.

Biomedical engineering incorporates manyfields, including various engineeringdisciplines, basic science and clinicalscience. The Department of BiomedicalEngineering will be multidisciplinary entitybringing these fields together in amultifaceted culture with a unified vision forresearch and training. These characteristicswill position us to capitalize not only onexisting strengths and collaborations but alsoon opportunities in emerging areas at theinterface between medicine and engineering.

RESEARCHB I O M E D I C A L O P T I C S

Research in Biomedical Optics is focused onthe development of uses for lasers and lightin medicine and biology. Examples of ongoingapplications in this well-established researchprogram include the use of lasers in clinicaldiagnosis, nondestructive evaluation oftissues, optical imaging of disease, and light-activated chemotherapy for cancer. Facilitiesinclude those for both clinical application andbasic research.

C A R D I O VA S C U L A R B I O E N G I N E E R I N G

Cardiovascular bioengineering (CBE) is agrowing area of interest at OHSU. The CBEprogram will encompass the major areas ofcardiovascular biology using engineeringtools for investigation. These will includecardiac and vessel behavior, computationalfluid dynamics, electrocardiography andelectrical signal processing, laserthrombolysis, 4-D embryo modeling,functional magnetic resonance imaging,ultrasound technology and shear stress geneexpression modeling.

G E N O M I C S

Genomics is the study of all the nucleotidesequences in the chromosomes of anorganism, including structural genes,regulatory sequences and noncoding DNAsegments. The term genomics is alsopopularly used to include the study of

Department ofBiomedical Engineering

www.bme.ogi.edu

I N T E R I M D E P A R T M E N T H E A D Misha Pave l

503 748-1155E-mail: pavel@ece.ogi.edu

G E N E R A L I N Q U I R I E S

503 748-1261

Facu l ty member Xubo Song stud iesb iomedica l imag ing .

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B M E | B I O M E D I C A L E N G I N E E R I N G

relationships between gene structure andbiological function on a genome-wide scale.The phenotype of an individual or organism isdependent on the information stored in thechromosomal DNA and expressed duringdevelopment. Mutations in the germ-line DNAmay cause inherited disease or abnormaldevelopment. Perturbations in generegulation during development and adulthoodmay lead to physiological changes anddisease. Genomic research in the Departmentof Biomedical Engineering involves theidentification of the genetic bases of inheriteddiseases such as Alzheimer’s and Parkinson’sdisease, and the genome-wide study of genesand their functions using state-of-the-arttechniques such as expression profiling withhigh-density microarrays.

I M A G I N G

Magnetic resonance imaging has emerged asa powerful tool for basic and clinicalresearch on the biology of normal andabnormal tissue function, as well as for thediagnosis and treatment of disease. Inconjunction with the OHSU Advanced ImagingResearch Center, core faculty in biomedicalengineering will be hired with researchspecializations in MR physics, pulse sequencedesign, image analysis, and tissue structureand tissue dynamics. In addition, a widerange of faculty across the OHSU campusapply a variety of imaging techniques to theirbasic and clinical research in areas such asneuroscience, cardiology and oncology. Thus,students will have opportunities to developresearch and applications in a variety ofimaging research settings.

I N F O R M AT I C S

Informatics activities at OHSU are wideranging. Currently they include: managingand analyzing gene expression data,programs in medical informatics andoutcomes research, database research,networks and embedded systems andtechniques for 3-D visualization. The BMEdepartment will serve as a focus fordeveloping technologies that leverage thisexpertise in such areas as computationalbioengineering, medical visualization,integration of genomic and medicalinformation, home health networking andhybrid instrumentation. BME will alsocontribute to existing curriculain bioinformatics.

N E U R O E N G I N E E R I N G

Basic neuroscience research, clinicalneurology and neurosurgery are strongprograms within OHSU. The existence of adepartment of biomedical engineering in thiscenter of neuroscience research and clinicalmedicine creates rich opportunities forbiomedical engineers. They can work withneuroscientists and clinicians to applyemerging scientific knowledge in thedevelopment of processes and devices neededfor the diagnosis, assessment and treatmentof neurological disorders and diseases.Ongoing research opportunities range fromvery basic molecular biophysics and modelingto systems analysis to drug delivery systems,neuroprosthetics and neurosurgical devices.

P O I N T- O F - C A R E B I O M E D I C A L E N G I N E E R I N G

Research in this area is focused on thedevelopment of health care delivery systemssuitable for use in homes, assisted livingfacilities and other residential settings.Application areas include processes andtechnologies for the monitoring, evaluationand treatment of people disabled by aging,chronic disease or disability. Researchchallenges include the development ofunobtrusive sensors, wireless communicationof multi-rate signals, processing and fusion ofsignals from multitudes of noisy sensors, andubiquitous perceptual interfaces.

R E H A B I L I TAT I O N A N D B I O M E C H A N I C S

Many diseases and disorders of muscle, boneand nervous system result in treatment,immobilization, healing and thenrehabilitation. Basic and applied research inthe Department of Biomedical Engineeringfocuses on the normal and abnormal controlof movement and musculoskeletal biology.This research is multidisciplinary and highlycollaborative with both clinical and basicscience departments at OHSU. Currentlyactive research by our faculty has resulted inthe development of novel therapeutic devicesand procedures that are tested on patientgroups provided by collaborating clinicians.

T I S S U E E N G I N E E R I N G A N D B I O M AT E R I A L S

Research in tissue engineering andbiomaterials is represented by amultidisciplinary group of materialsscientists, biomedical and tissue engineers,chemists, physiologists, dentists andphysicians. Faculty projects include the

following research: physical biomechanics ofdental and orthopedic implants,computational biomechanics of dentalimplants, dental restorations and vascularstents, dissolution and volatilization fromdental alloys, noninvasive and nondestructiveevaluation of engineered tissues, laserwelding of tissues, natural, protein-basedbiomaterials, polymer mechanics,micromechanics of biocomposites, thermalanalysis, tribology, collagen and otherbiocomposites, skin scaffolds, bone healingand vascular grafts.

FACULTY

A N T Ó N I O B A P T I S TA , P H . D .

N I N I A N B L A C K B U R N , P H . D .

K I M B U R C H I E L , M . D .

P A U L C O R D O , P H . D .

D A V I D D A W S O N , P H . D .

J . J O B FA B E R , M . D . , P H . D .

J A C K L . F E R R A C A N E , P H . D .

B R A H M N . G O L D S T E I N , M . D .

D A N H A M M E R S T R O M , P H . D .

H Y N E K H E R M A N S K Y, P H . D .

M O N I C A H I N D S , P H . D .

J A M E S H O O K , P H . D .

FAY H O R A K , P H . D .

M A R W A N J A B R I , P H . D .

S T E V E J A C Q U E S , P H . D .

J E R I J A N O W S K Y, P H . D .

S E A N J . K I R K P AT R I C K , P H . D .

T O D D L E E N , P H . D .

J A N E M A C P H E R S O N , P H . D .

D A V I D M A I E R , P H . D .

E D W A R D N E U W E LT, M . D .

A L F R E D L . N U T TA L L , P H . D .

M I S H A P A V E L , P H . D .( I N T E R I M D E P A R T M E N T H E A D )

R O B E R T J . P E T E R K A , P H . D .

S C O T T P R A H L , P H . D .

S U S A N P R I C E , M . D .

P. H E M A C H A N D R A R E D D Y, P H . D .

P AT R I C K R O B E R T S , P H . D .

W I L L I A M R O B E R T S , P H . D .

D A V I D J . S A H N , M . D .

R O N S A K A G U C H I , D . D . S . , P H . D .

M A R I E S H E A , M . S .

X U B O S O N G , P H . D .

K E N T L . T H O R N B U R G , P H . D .

G A R Y W E S T B R O O K , M . D .

F A C U L T Y | B I O M E D I C A L E N G I N E E R I N G | B M E

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THE DEPARTMENT OF COMPUTER SCIENCE

AND ENGINEERING has an internationallyacclaimed research program. Thebreadth and depth of the research isapparent in the research projects andresearch centers listed below, and inthe educational program.Four degrees are offered: Master of Sciencein Computer Science and Engineering, Masterof Science in Computational Finance, OregonMaster of Software Engineering, and Doctorof Philosophy in Computer Science andEngineering. In addition, we offer certificatesin Computational Finance, Applied Computingand Oregon Master of Software Engineering.

ADMISSION REQUIREMENTSAdmission requirements are the same as thegeneral requirements of the institution.General aptitude GRE scores are required,except in cases of advanced placementadmission for M.S. students (see below). Acandidate must hold a bachelor’s degree incomputer science, mathematics, engineering,one of the biological or physical sciences orone of the quantitative social sciences.Candidates with a degree in a field other thancomputer science must have completedcourses in the following subject areas:

• An introduction to programming in ahigh-level language

• Data structures*

• Discrete mathematics*

• Logic design and computer organization

• Calculus or other college-level mathematics

*APC 515, Data Structures and DiscreteMathematics, may be taken to meetthe prerequisite.

A D VA N C E D P L A C E M E N T A D M I S S I O N S F O R M . S . S T U D E N T S

Students who are currently studying at theOGI School and have earned 12 credits incomputer science classes are exempt fromthe GRE and TOEFL requirements. Only twoletters of recommendation are required; allother admissions requirements remain thesame. The CSE courses must include at leasttwo, preferably three, courses from the M.S.Core (list follows). Students must earn anoverall Grade Point Average of 3.0 and a B orbetter in each M.S. Core class to be eligibleto apply through Advanced Placement:

CSE 500 Introduction to Software Engineering

CSE 511 Principles of Compiler Design

CSE 513 Introduction to Operating Systems

CSE 514 Introduction to Database Systems

CSE 521 Introduction to Computer Architecture

CSE 532 Analysis and Design of Algorithms

CSE 533 Automata and Formal Languages

If a student applies to the ComputationalFinance program through advancedplacement, the 12 credits earned mustinclude two courses from the Finance Core,together with relevant CSE, ECE, APC orFIN courses.

DEGREE REQUIREMENTSA Student Program Committee (SPC) thatprovides academic advising is assigned foreach matriculating student. The SPC alsoapproves the application of courses towardthe student’s degree requirements.

A maximum of 21 credits earned beforematriculation at OGI may be applied towardthe master’s degree. This may include up to12 credits transferred from other institutions(up to 18 from Portland State University, theUniversity of Oregon or Oregon StateUniversity) and credits taken at OGI prior tomatriculation.

The program of study for each master’sFstudent may be tailored to meet individualneeds by the SPC. Students are particularlyencouraged to include special-topic courses(CSE 58X) relevant to their interests.

CSE M.S. PROFESSIONAL INTERNSHIP OPTION

Participation is limited by available industrialinternships. Students declaring this option mustcomplete 45 credits of course work and up to anadditional 3 credits of a professional internship(CSE 620).

M A S T E R O F S C I E N C E I N C O M P U T E R S C I E N C EA N D E N G I N E E R I N GAll CSE M.S. students must complete the M.S. coreof 21 credits:

M.S. CSE CORE COURSES

CSE 500 Introduction to Software Engineering 3 credits

CSE 511 Principles of Compiler Design 3 credits

CSE 513 Introduction to Operating Systems 3 credits

CSE 514 Introduction to Database Systems 3 credits

CSE 521 Introduction to Computer Architecture 3 credits

CSE 532 Analysis and Design of Algorithms 3 credits

CSE 533 Automata and Formal Languages 3 credits

Department of Computer Science

and Engineeringwww.cse.ogi.edu

D E P A R T M E N T H E A D

James Hook

503 748-1169E-mail: james.hook@cse.ogi.edu

D E P A R T M E N T A D M I N I S T R A T O R

Dana Director

503 748-1358E-mail: danad@cse.ogi.edu

A C A D E M I C C O O R D I N A T O R

Shir ley Kapsch

503 748-1255E-mail: kapsch@cse.ogi.edu

A C A D E M I C D E P A R T M E N T S E C R E T A R Y

Barbara Mosher

503 748-1151E-mail: bmosher@cse.ogi.edu

C S E G E N E R A L I N Q U I R I E S

503 748-1151E-mail: csedept@cse.ogi.edu

CSE scient ists are using the robotic-control led"Timbot" to test software that may one day guiderobotic vehic les such as cars, buses or a irplanes.

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C S E | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G

M . S . T H E S I S O P T I O N

Students choosing the thesis option mustsubmit and defend a master’s thesis and mayapply up to 12 credits of thesis research(CSE 700) toward the 45-credit requirement.

1. M.S. CSE CORE (listed above)

2. CSE 700 M.S. THESIS (maximum 12 credits)

3. ELECTIVES (12 credits), as directed by the thesisadvisor or SPC

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

M . S . N O N - T H E S I S O P T I O N S

Students choosing the non-thesis M.S. CSEoption must complete 15 courses and aminimum of 45 credits; up to six credits ofnon-thesis research (CSE 610) may beincluded, with the approval of the student’sStudent Program Committee (SPC). Studentsmatriculated prior to Winter Quarter 2002are exempt from the 15-course requirement.

NINE AREAS OF EMPHASIS

Students pursuing the non-thesis option maychoose one of the nine areas of emphasisdefined below or consult their SPC to define acustom program.

ADAPTIVE SYSTEMS

1. M.S. CSE CORE (listed above)

2. ADAPTIVE SYSTEMS CORE (12 credits)

Required:

CSE 547 Statistical Pattern Recognition 3 credits

CSE 560 Artificial Intelligence 3 credits

Choose two:

CSE 540 Neural Network Algorithmsand Architecture 3 credits

CSE 545 Advanced Neural and Adaptive Algorithms 3 credits

CSE 546 Data and Signal Compression 3 credits

CSE 548a Statistical Computing I 2 credits

CSE 550 Spoken Language Systems 3 credits

CSE 562 Natural Language Processing 3 credits

CSE 564 Human-Computer Interaction 3 credits

CSE 568 Empirical Research Methods 3 credits

ECE554 Adaptive Signal Processing 4 credits

3. SUGGESTED ELECTIVES (12 credits)

CSE 563 Multiagent Systems 3 credits

CSE 569 Scholarship Skills 3 credits

CSE 58X appropriate special topics course

(or) any CSE class not already taken

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

COMPUTATIONAL FINANCE

1. M.S. CSE CORE (listed above)

2. COMPUTATIONAL FINANCE CORE (16 credits)

Required (choose four):

FIN 541 Principles of Modern Finance 4 credits

FIN 544 Investment and Portfolio Management 4 credits

FIN 551 Options and Futures I 4 credits

FIN 552 Options and Futures II 4 credits

FIN 561 Risk Management 4 credits

FIN 573 Financial Time-Series Analysis 4 credits

3. SUGGESTED ELECTIVES (8 credits)

CSE 509 Object-Oriented Programming 3 credits

CSE 540 Neural Network Algorithms Architecture 3 credits

CSE 544a Probability and Statistics I 2 credits

CSE544b Probability and Statistics II 2 credits

CSE 545 Advanced Neural and Adaptive Algorithms 3 credits

CSE 546 Data and Signal Compression 3 credits

CSE 547 Statistical Pattern Recognition 3 credits

CSE 548a Statistical Computing I 2 credits

CSE 548b Statistical Computing II 2 credits

CSE 549D Applied Business Forecasting 4 credits

CSE 555a Mathematical Methods 2 credits

CSE 555b Stochastic Calculus 2 credits

CSE 556a Simulation 2 credits

CSE 556b Modern Optimization Techniques 2 credits

CSE 564 Human-Computer Interaction 3 credits

CSE 568 Empirical Research Methods 3 credits

CSE 58X Special Topics

ECE 525 Analytical Techniques in Process and Communication 4 credits

ECE 555 Engineering Optimization 4 credits

(or) any CSE class not already taken

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

COMPUTER SECURITY

1. M.S. CSE CORE (listed above)

2. COMPUTER SECURITY CORE (15 credits)

Required:

CSE 503 Software Engineering Processes 3 credits

CSE 524 TCP/IP Internetworking Protocols 3 credits

CSE 527 Principles and Practices of System Security 3 credits

CSE 58X Cryptography 3 credits

CSE 58X Building Secure Systems 3 credits

3. SUGGESTED ELECTIVES (9 credits)

CSE 515 Distributed Computing Systems 3 credits

(or) any CSE class not already taken.

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

DATA-INTENSIVE SYSTEMS

1. M.S. CSE CORE (listed above)

2. DATA-INTENSIVE SYSTEMS CORE (12 credits)

Choose four:

CSE 515 Distributed Computing Systems 3 credits

CSE 526 Modern Operating System Design 3 credits

CSE 541 Database Implementation 3 credits

CSE 542 Object Data Management 3 credits

CSE 58X Informational Retrieval and the Internet 3 credits

CSE 58X Any special topics course in the database area

One course from the System Software Core

One course from the Software Engineering Core or theSoftware Engineering for Industry Professionals Core

3. SUGGESTED ELECTIVES (12 credits)

Any CSE class not already taken.

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

HUMAN-COMPUTER INTERFACES

1. M.S. CSE CORE (listed above)

2. HUMAN-COMPUTER INTERFACES CORE (18 credits)

Required:

CSE 560 Artificial Intelligence 3 credits

CSE 564 Human-Computer Interaction 3 credits

Choose four:

CSE 547 Statistical Pattern Recognition 3 credits

CSE 561 Dialogue 3 credits

CSE 562 Natural Language Processing 3 credits

CSE 563 Multi-Agent Systems 3 credits

CSE 567 Developing User-Oriented Systems 3 credits

CSE 568 Empirical Research Methods 3 credits

CSE 58X Any special topics course appropriate to this area

ECE 58X Hidden Markov Models forSpeech Recognition 4 credits

ECE 58X Structure of Spoken Language 4 credits

3. SUGGESTED ELECTIVES (6 credits)

CSE 507 Logic Programming 3 credits

CSE 515 Distributed Computing Systems 3 credits

CSE 540 Neural Network Algorithms & Architecture 3 credits

CSE 569 Scholarship Skills 3 credits

(or) any CSE class not already taken.

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

SOFTWARE ENGINEERING

1. M.S. CSE CORE (listed above)

2. SOFTWARE ENGINEERING CORE (15 credits)

Required:

CSE 503 Software Engineering Processes 3 credits

CSE 504 Object-Oriented Analysis and Design 3 credits

CSE 509 Object-Oriented Programming 3 credits

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C O M P U T E R S C I E N C E A N D E N G I N E E R I N G | C S E

MST 512 Project Management 3 credits

CSE 564 Human-Computer Interaction 3 credits

CSE 567 Developing User-Oriented Systems 3 credits

3. SUGGESTED ELECTIVES (9 credits)

Any CSE class not already taken

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

SOFTWARE ENGINEERING FOR INDUSTRY PROFESSIONALS

1. M.S. CSE CORE (listed above)

2. SOFTWARE ENGINEERING FOR INDUSTRYPROFESSIONALS CORE (15 credits)

Required:

OMSE 511 Managing Software Development 3 credits

OMSE 521 Using Metrics and Models 3 credits

OMSE 531 Software Requirements Engineering 3 credits

OMSE 533 Software Design Techniques 3 credits

Choose one:

CSE 564 Human-Computer Interaction 3 credits

CSE 567 Developing User-Oriented Systems 3 credits

3. SUGGESTED ELECTIVES (9 credits)

Any CSE course not already taken.

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

SPOKEN LANGUAGE SYSTEMS

1. M.S. CSE CORE (listed above)

2. SPOKEN LANGUAGE SYSTEMS CORE (12-16 credits)

Choose three:

CSE 550 Spoken Language Systems 3 credits

CSE 561 Dialogue 3 credits

CSE 562 Natural Language Processing 3 credits

ECE 541 Speech Processing 3 credits

ECE 545 Speech Systems 4 credits

ECE 58X Hidden Markov Models forSpeech Recognition 4 credits

ECE 58X Speech Synthesis 4 credits

ECE 58X Structure of Spoken Language 4 credits

Choose one of the following or one more from theabove list:

CSE 540 Neural Network Algorithms & Architectures 3 credits

CSE 545 Advanced Neural & Adaptive Algorithms 3 credits

CSE 547 Statistical Pattern Recognititon 3 credits

CSE 560 Artificial Intelligence 3 credits

CSE 564 Human Computer Interaction 3 credits

CSE 568 Empirical Research Methods 3 credits

ECE 540 Auditory & Visual Processing by Human& Machine 4 credits

ECE 544 Introduction to Signals, Systems andInformation Processing 4 credits

ECE 551 Introduction to Digital Signal Processing 4 credits

ECE 552 Digital Signal Processing II 4 credits

ECE 554 Adaptive Signal Processing 4 credits

3. SUGGESTED ELECTIVES (8-12 credits)

Courses in the Spoken Language Systems core, or any CSEclasses not already taken.

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

SYSTEMS SOFTWARE

1. M.S. CSE CORE (listed above)

2. SYSTEMS SOFTWARE CORE (12 credits)

Choose four:

CSE 515 Distributed Computing Systems 3 credits

CSE 524 TCP/IP Internetworking Protocols 3 credits

CSE 526 Modern Operating System Design 3 credits

CSE 527 Principles and Practices of System Security 3 credits

CSE 541 Database Implementation 3 credits

CSE 58X Internet Technology 3 credits

CSE 58X Multi-Media Networking 3 credits

CSE 58X Any special topics courses appropriateto this area

3. SUGGESTED ELECTIVES (12 credits)

Any course in the Systems Software area core or anyCSE class not already taken.

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

MASTER OF SC IENCE IN COMPUTAT IONAL F INANCE

C O M P U TAT I O N A L F I N A N C E P R O G R A M D I R E C T O RDav id Baster f ie ld

503 748-1153E-mail: basterfield@cse.ogi.edu

P R O G R A M A D M I N I S T R AT O RShel ly Char les

503 748-1257E-mail: shelly@cse.ogi.edu

The M.S. in Computational Finance is aninterdisciplinary program offering studentsthe flexibility to learn technical skills directlyrelevant to quantitative and computationalwork in the finance industry. A professionalinternship track is available (see below).

The student must obtain 48 credits, consist-ing of 24 credits from the finance core and24 credits from elective courses. Certificatein Computational Finance available uponcompletion of four of these courses.

1. M.S. IN COMPUTATIONAL FINANCE CORE (24 CREDITS)

FIN 541 Principles of Modern Finance 4 credits

FIN 544 Investment and Portfolio Management 4 credits

FIN 551 Options and Futures I 4 credits

FIN 552 Options and Futures II 4 credits

FIN 561 Risk Management 4 credits

FIN 573 Financial Time Series Analysis 4 credits

2. BREADTH REQUIREMENT (21 CREDITS)

Students may take elective finance courses andelectives from other departments at OGI. However,the breadth requirement for the degree is that atleast 20 electives must come from at least two ofthe non-finance tracks. The course lists for eachtrack are representative, not exhaustive. Studentsmay request approval to substitute other OGIcourses in place of those listed below.

A. ADVANCED TRAINING IN FINANCE

FIN 547 Global Markets and Foreign Exchange 2 credits

FIN 576 Financial Markets and Trading 2 credits

FIN 558 Advanced Numerical Computing in Finance 2 credits

FIN 58X Special topics in Computational Finance

B. APPLIED COMPUTING(Applied Computing Certificate available upon completionof four of these courses)

APC 500a Introduction to Visual Basicfor Applications 2 credits

APC 500b Advanced Visual Basic for Applications 2 credits

APC 501a Accelerated Development withVisual Basic I 2 credits

APC 501b Accelerated Development withVisual Basic II 2 credits

APC 503a Introduction to Perl Programming 2 credits

APC 503b Web Development with Perl 2 credits

APC 505a Applications Programming in C++ I 2 credits

APC 505b Applications Programming in C++ II 2 credits

APC 506a Advanced Applications Programmingin C++ 2 credits

APC 506b Numeric Programming in C++ 2 credits

APC 508a Applications Programming in Java I 2 credits

APC 508b Applications Programming in Java II 2 credits

APC 511 Computational Tools 2 credits

C. COMPUTER SCIENCE

CSE 500 Principles of Software Engineering 3 credits

CSE 504 Object-Oriented Analysis and Design 3 credits

CSE 509 Object-Oriented Programming 3 credits

CSE 514 Introduction to Database Systems 3 credits

D. APPLIED MATHEMATICS, STATISTICS ANDMACHINE LEARNING

CSE 540 Neural Network Algorithmsand Architectures 3 credits

CSE 544a Probability and Statistics I 2 credits

CSE 544b Probability and Statistics II 2 credits

CSE 547 Statistical Pattern Recognition 3 credits

CSE 548a Statistical Computing I 2 credits

CSE 548b Statistical Computing II 2 credits

CSE 549D Applied Business Forecasting 4 credits

CSE 555a Mathematical Methods 2 credits

CSE 555b Stochastic calculus 2 credits

CSE 556a Simulation 2 credits

CSE 556b Modern Optimization Techniques 2 credits

C S E | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G

ECE 525 Analytical Techniques in StatisticalSignal Processing 4 credits

ECE 544 Introduction to Signals, Systems andInformation Processing 4 credits

ECE 550 Linear Systems 4 credits

ECE 554 Adaptive Signal Processing 4 credits

ECE 555 Engineering Optimization 4 credits

E. MANAGEMENT SCIENCE

MST 501 Managerial & Financial Accounting forScience & Technology 4 credits

MST 502 Financial Management 4 credits

MST 512 Project Management 3 credits

MST 520 Managing in Science and Technology 4 credits

MST 540 International Management in Scienceand Technology 3 credits

M A S T E R O F S C I E N C E , C O M P U TAT I O N A L F I N A N C EP R O F E S S I O N A L I N T E R N S H I P P R O G R A M

Participation in this program option is limitedby available industrial internships. Forstudents declaring this option, the breadthrequirement courses must come from at leastone of the tracks listed above, plus FIN 620,Professional Internship in Finance.

O R E G O N M A S T E R O F S O F T W A R EE N G I N E E R I N G ( O M S E )

P R O G R A M A D V I S O R

Dick Fa i r ley, CSE Professor

503 748-1558E-mail: fairley@cse.ogi.edu

OGI School of Science & Engineering,Portland State University, Oregon StateUniversity and the University of Oregonjointly offer the Oregon Master of SoftwareEngineering (OMSE) degree to meet theneeds of software professionals. Thecurriculum emphasizes the technical andleadership aspects of software engineering,teamwork and communication skills, and thebusiness aspects of developing industrial-strength software. Admission requirementsinclude a B.S. with pre-foundation courses inprogramming, discrete mathematics, datastructures, operating systems and computerarchitecture as well as two years of softwaredevelopment experience. Courses may betaken on a non-admitted basis. For additionalinformation, see www.omse.org.Oregon Master of Software Engineeringstudents will take the following courses:

OMSE 500 Principles of Software Engineering 3 credits

OMSE 511 Managing Software Development 3 credits

OMSE 512 Understanding the Software Business 3 credits

OMSE 513 Professional Communication Skills forSoftware Engineers 3 credits

OMSE 521 Using Metrics and Models to SupportQuantitative Decision Making 3 credits

OMSE 522 Modeling and Analysis of Software Systems 3 credits

OMSE 525 Software Quality Analysis 3 credits

OMSE 531 Software Requirements Engineering 3 credits

OMSE 532 Software Architecture and Domain Analysis 3 credits

OMSE 533 Software Design Techniques 3 credits

OMSE 535 Software Implementation and Testing 3 credits

OMSE 551 Strategic Software Engineering 3 credits

OMSE 555 Software Development Practicum I 3 credits

OMSE 556 Software Development Practicum II 3 credits

Electives: Any two CSE or OMSE classes notalready taken. 6 credits

O R E G O N G R A D U AT E E N G I N E E R I N GI N T E R N S H I P P R O G R A M

For information and availability regarding theOGI School’s Department of Computer Scienceinternships, please contact the department.

C O O P E R AT I V E C O M P U T E R S C I E N C E P R O G R A M S

The OGI School has establishedundergraduate/graduate cooperativeprograms with Lewis & Clark College, PacificUniversity, Reed College and WillametteUniversity. These programs allow selectedundergraduate students to enter the master’sprogram in computer science and engineeringat the beginning of their senior year. In twoyears of residence at OGI, the student cansimultaneously fulfill requirements for thebachelor’s degree at the undergraduateinstitution and the master’s degree at OGI.

PH.D. PROGRAM The Ph.D. program is strongly orientedtoward preparation for research. Eachstudent has the opportunity to work closelywith a faculty research advisor throughouthis or her residency at OGI. A student mustsatisfy the institutional requirements for thePh.D.

Candidacy is satisfied in three parts:

F O U N D AT I O N R E Q U I R E M E N T S : Students are requiredto take six foundation courses. Particularly well-prepared students can waive some of thesecourses by passing an examination on the coursematerial.

A R E A R E Q U I R E M E N T S : Students choose threecourses within one area and three courses out ofthat area, as outlined below.

R E S E A R C H S K I L L S A S S E S S M E N T: Students arerequired to take CSE 569, Scholarship Skills, andto pass the research proficiency examination

(RPE), which requires a written and oralpresentation of a research paper. The RPE usuallytakes place in the spring quarter of the secondyear of residence.

Ph.D. students must obtain a grade of B orbetter in each required course. Requiredcourses should be completed by the end ofthe second year. The doctoral dissertationwill document a significant, original researchcontribution and must be of publishablequality in both content and presentation.

The faculty strongly recommends thatstudents prepare a formal thesis proposalbetween 9 and 18 months before the Ph.D.defense. The proposal is not a candidatescreening tool, but instead a means to ensurean acceptable level of intellectual vigor andmaturity. Starting in the second year, thefaculty strongly recommends that studentsdeliver yearly research talks. The RPE,presentation at the student researchsymposium, the thesis proposal and talks atrefereed conferences satisfy thisrequirement. Practice talks for conferencepapers should be open for commentary.

The program of study for each Ph.D. studentis tailored to meet individual needs andinterests. Each student’s Student ProgramCommittee provides academic advising and isin direct control of the student’s program ofstudy. The SPC will work with the student toset and review goals on a twice-yearly basis.Students must write a progress report for allSPC meetings except the first one. EachPh.D. student’s academic progress isreviewed by the entire faculty annually.

FOUNDATION REQUIREMENTS (18 CREDITS)

Required:

CSE 513 Introduction to Operating Systems 3 credits

CSE 521 Introduction to Computer Architecture 3 credits

CSE 532 Analysis and Design of Algorithms 3 credits

CSE 533 Automata and Formal Languages 3 credits

Choose one programming language course:

CSE 502 Functional Programming 3 credits

CSE 507 Logic Programming 3 credits

CSE 509 Object-Oriented Programming 3 credits

CSE 531 Foundations of Semantics 3 credits

Choose one interactive and adaptivesystems course:

CSE 540 Neural Network Algorithmsand Architectures 3 credits

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CSE 560 Artificial Intelligence 3 credits

CSE 564 Human-Computer Interaction 3 credits

AREA REQUIREMENTS (18 CREDITS)

Three courses from one of the following six areas,and three other courses not from that area and notalready taken:

ADAPTIVE SYSTEMS AND APPLICATIONS

CSE 540 Neural Network Algorithmsand Architectures 3 credits

CSE 545 Advanced Neural and Adaptive Algorithms 3 credits

CSE 546 Data and Signal Compression 3 credits

CSE 547 Statistical Pattern Recognition 3 credits

CSE 568 Empirical Research Methods 3 credits

FIN 573 Financial Time Series Analysis 4 credits

ECE 540 Auditory and Visual Processing byHuman and Machine 4 credits

ECE 553 Control Systems: Classical, Neuraland Fuzzy 4 credits

ECE 554 Adaptive Signal Processing 4 credits

HUMAN-COMPUTER INTERACTIVE SYSTEMS

CSE 550 Spoken Language Systems 3 credits

CSE 560 Artificial Intelligence 3 credits

CSE 561 Dialogue 3 credits

CSE 562 Natural Language Processing 3 credits

CSE 563 Multiagent Systems 3 credits

CSE 564 Human-Computer Interaction 3 credits

CSE 567 Developing User-Oriented Systems 3 credits

CSE 568 Empirical Research Methods 3 credits

CSE 58X Special Topics: Computer Graphics variable

ECE 540 Auditory and Visual Processing by Humanand Machine 4 credits

ECE 58X Hidden Markov Models forSpeech Recognition 4 credits

ECE 58X Structure of Spoken Language 4 credits

PROGRAMMING LANGUAGES AND SOFTWARE ENGINEERING

CSE 500 Introduction to Software Engineering 3 credits

CSE 502 Functional Programming 3 credits

CSE 503 Software Engineering Processes 3 credits

CSE 504 Object-Oriented Analysis and Design 3 credits

CSE 507 Logic Programming 3 credits

CSE 509 Object-Oriented Programming 3 credits

CSE 511 Principles of Compiler Design 3 credits

CSE 512 Compiling Functional Languages 3 credits

CSE 518 Software Design and Development 3 credits

CSE 530 Introduction to Mathematical Logic 3 credits

CSE 531 Foundations of Semantics 3 credits

CSE 567 Developing User-Oriented Systems 3 credits

SYSTEMS SOFTWARE

CSE 509 Object-Oriented Programming 3 credits

CSE 510 Software Tools 3 credits

CSE 514 Introduction to Database Systems 3 credits

CSE 515 Distributed Computing Systems 3 credits

CSE 524 TCP/IP Internetworking Protocols 3 credits

CSE 526 Modern Operating System Design 3 credits

CSE 527 Principles and Practices of System Security 3 credits

CSE 541 Database Implementation 3 credits

CSE 542 Object Data Management 3 credits

THEORY

CSE 530 Introduction to Mathematical Logic 3 credits

CSE 531 Foundations of Semantics 3 credits

CSE 534 Computability and Intractability 3 credits

CSE 535 Categories in Computer Science 3 credits

RESEARCH SKILLS REQUIREMENT (3 CREDITS)

CSE 569 Scholarship Skills 3 credits

Research Proficiency Exam

COURSE DESCRIPTIONSCSE 500 Introduction to Software EngineeringSoftware engineering is concerned with the ways inwhich people conduct their work activities and applytechnology to produce and maintain softwareproucts and software-intensive systems. Issues ofconcern include specification, design, implementa-tion, verification, validation and evolution ofsoftware artifacts. Related topics include softwaremetrics, project management, configuration man-agement, quality assurance, peer reviews, riskmanagement and process improvement. This coursepresents an integrated view of these topics andrelated issues. It is an essential course for anyoneworking in development, maintenance, managementor related areas in a software organization.

3 credits

CSE 502 Functional ProgrammingIn functional programming, we shift our focus fromdata objects and their representations to functionsthat act on data. Programs are formulated as com-positions of functions, rather than as sequences ofstatements. This leads to a programming methodol-ogy that is quite different from that learned in usingstatement-oriented languages. This course intro-duces the student to functional notation, recursion,higher-order functions, reasoning about functionsand polymorphic-type systems. Functional program-ming languages are known for their increasedproductivity and reliability, due in part to the higherlevels of abstraction provided by functional lan-guages. Course is taught by lecture with smallweekly programming assignments. Experience isgained by programming in the functional languageHaskell or one of its close derivatives. Recentadvances in functional programming languagesallow them to use updatable state in a safe mannerand to cause effects on the real world. Students gainexperience by writing programs using these featuresto program interactive window-based programsusing an embedded “widget” library. 3 credits

CSE 503 Software Engineering ProcessesThis course is concerned with examining and

improving the software development processes,including the technical, managerial and culturalprocesses, used by organizations to develop andmaintain high-quality software systems in a timelyand economical manner. Various process models,including the SEI Capability Maturity Models, theISO SPICE model, the Team Software Process, andthe Personal Software Process are studied and con-trasted. Tailoring of process models to fit localsituations and various approaches to softwareprocess improvement are presented. Studentsselect and complete term projects that address top-ics in software process improvement. 3 credits

CSE 504 Object-Oriented Analysis and DesignThis course presents an integrated set of techniquesfor software analysis and design based on object-oriented concepts. The techniques focus onproducing the artifacts and work products,expressed in UML, appropriate for the analysis anddesign phases of the software development lifecycle.We adopt a use case model for requirements and aresponsibility-driven approach for the developmentof object models. Design patterns and frameworksare also emphasized. Note that CSE 509 Object-Oriented Programming is intended as a follow-oncourse for CSE 504. 3 credits

CSE 507 Logic ProgrammingLogic programming is an attempt to construct com-puter languages with completely declarativesemantics: The programmer only states “what”should be done; the interpreter or compiler mustdecide “how.” This course examines existing logicprogramming languages, notably Prolog; providesthe foundations in logic and theorem provingfor such languages, and covers implementation oflogic programming languages. Other topics mayinclude an introduction to modal logic and intuition-istic logic. 3 credits

CSE 509 Object-Oriented ProgrammingThis course provides a rigorous introduction to theconcepts behind object-oriented programming. It isfor students who are already familiar with the con-cept of object-orientation and with object-orientedanalysis and design techniques. One way to learnthis background material is by taking CSE 504,Object-Oriented Analysis and Design. In CSE 509,students gain a thorough understanding of incre-mental programming, type-safety, polymorphism,encapsulation and set-based abstraction, and applythese concepts through a variety of programmingprojects. We study several programming languages,including Java and Smalltalk, so students areexposed to different realizations of these conceptsand gain an appreciation for the programming lan-guage design space. We also look at publishedobject-oriented design patterns and see how theycan be implemented in different object-oriented pro-gramming languages. Students are required to readappropriate research papers, complete severalshort programming assignments, complete a sub-stantial programming project and write some shortessays. Prerequisite: CSE 504 or equivalent.

3 credits

CSE 511 Principles of Compiler DesignThis course introduces the basics of building a com-

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piler using a multiphase translation process. It cov-ers lexical analysis, parsing and translation toabstract syntax using modern parser generatortechnology. It discusses binding of identifiers andsymbol table organization, and a variety of interme-diate representations that are suitable for back-endanalysis. It investigates back-end transformationsand optimizations for a number of languages. Othertopics include type checking, static analysis andbasic run time support. Compiling is essentially aprocess of symbolically manipulating program rep-resentations represented by tree and graph-likedata structures. Because of this, we will use toolsthat facilitate symbolic manipulation and definitionof such structures as parser and lexical generators,and tools for generating code from pattern-baseddescriptions. Prerequisite: CSE 533. 3 credits

CSE 512 Compiling Functional LanguagesA project-oriented course on the theory and designof a compiler for a typed, functional programminglanguage. Topics include understanding a formaldefinition of programming language semantics, com-piling pattern analysis, lifting abstractions,continuation-passing style of implementation,abstract machines, code generation and addressassignment, register allocation and assignment ongeneral-register machines, run-time storage admin-istration, data-flow analysis and code improvement.Prerequisite: CSE 511. 3 credits

CSE 513 Introduction to Operating SystemsA study of the design and implementation of modernoperating systems. The course concentrates onoperating system kernel design and includes the fol-lowing topics: concurrent processes, interprocesscommunication, synchronization, scheduling,resource allocation, memory management, the con-cept of virtual memory and the required underlyinghardware support, secondary storage management,file systems and security. We will use the Linuxoperating system to ground the discussion ofabstract concepts. Interested students will beencouraged to read the Linux source code for dis-cussions in class. 3 credits

CSE 514 Introduction to Database SystemsA survey of database fundamentals emphasizing theuse of database systems. Topics include databasedesign, data dependencies and normalization, sec-ondary storage structures, SQL, relational algebra,query processing, query optimization, transactions,recovery and embedded SQL. This course focuses onrelational database systems and the SQL query lan-guage. Students participate in a project to design,populate and query a database. Prerequisites: Datastructures, discrete mathe-matics and mathemati-cal logic. 3 credits

CSE 515 Distributed Computing SystemsThis course concentrates on distributed computingfrom a systems software perspective. Major topicsinclude communications middleware (remote proce-dure call, remote method invocation and causalbroadcast), operating system support, distributedfile systems, distributed transaction processing,load balancing, distributed programming languagesand systems, fault-tolerance and replication algo-

rithms, distributed timing issues and distributedalgorithms. Prerequisites: CSE 513, Introduction toOperating Systems. (Also a basic understanding ofcomputer communications problems and protocols.)

3 credits

CSE 518 Software Design and DevelopmentContemporary, object-oriented software design,using the Java programming language. An introduc-tion to the eXtreme Programming softwaredevelopment methodology, which is based upon theprinciple that change is inevitable and successfulsoftware designs undergo continual evolution.Techniques to be covered include program refactor-ing, automated unit testing, pair programming,participatory design and managing short productdevelopment cycles. These principles and tech-niques will be illustrated in a term-length projectthat provides design and implementation experience.

3 credits

CSE 521 Introduction to Computer ArchitectureThis course provides a broad introduction to com-puter architecture. It covers a large amount ofmaterial in moderate depth, providing a good under-standing of the basic issues in computer systemdesign. Specifically, the course covers instructionset design, pipelining, the memory heirarchy, I/Osystems, networking issues and multiprocessors.Example systems include the Intel x86, MIPS andDEC Alpha processors. Prerequisites: Experiencewriting software, preferably with some C or assem-bler programming. NOTE: Computer architecturehas become a quantitative science, so there will beconsiderable algebraic manipulation involved in theperformance analysis component of the course.

3 credits

CSE 522 Advanced Computer ArchitectureThis course is a follow-up to CSE 521. It coversadvanced computer architecture topics such as SMP(Shared Memory Multiprocessors) and NUMA (Non-Uniform Memory Access) Architectures. It alsolooks at new trends in designing high-performanceclusters with examples. Specific topics to be coveredinclude: fundamentals of parallel architectures(communication paradigms, programming models,etc.), snoopy-based multiprocessors (cachecoherency, bus designs, multilevel caches, etc.),directory-based multiprocessors (NUMA and hybridarchitectures), interconnection networks (routing,switch designs, virtual lanes, etc.). Examples ofcommercial and prototype architectures such asIBM NUMAQ, InfiniBandTM and ServerNet.Prerequisite: CSE 521. 3 credits

CSE 524 TCP/IP Internetworking ProtocolsThis course provides an overview of the structureand algorithms used in the TCP/IP networking pro-tocols that make up the foundation of the Internet.Protocols and technologies covered will include anintroduction to the link layer, ARP, IP, ICMP, UDP,TCP, routing protocols and application protocols andsystems like the DNS, NFS, SMTP, FTP, HTTP andmulticasting protocols and applications. Providesarchitectural insight into protocol design issues andoperating system implementation techniques, typi-cally in terms of the Berkeley UNIX socket

programming model. Provides socket programmingexperience with the client/server model. Providesexperience reading Internet RFC’s and/or drafts.Prerequisites: Familiarity with the functions of amodern multiuser operating system such as is cov-ered in CSE 513 or PSU’s CS 533; familiarity with Cprogramming on modern UNIX computers. 3 credits

CSE 526 Modern Operating System DesignThis course includes an in-depth study of modernoperating system design. The course is based on acollection of recent research papers and includes anemphasis on evaluating the papers in addition tounderstanding the systems they describe. Topicsinclude micro-kernel operating systems, lightweightinterprocess communication, extensible operatingsystems, file systems, mobile computing, work-sta-tion clusters, adaptive resource management andOS support for multimedia systems. Prerequisites:CSE 513 and CSE 521. 3 credits

CSE 527 Principles and Practices of System SecurityIn the Internet age, host system security is essentialand difficult. This course explains the principles andpractices of securing host systems. Students learnthe principles of how to build secure systems andhow various real systems succeed and fail in livingup to these principles. We will study various securi-ty-enhancing technologies, in each case relating thesecurity enhancement to the principles of securesystems. Prerequisite: CSE 513. 3 credits

CSE 530 Introduction to Mathematical LogicProvides a theoretical foundation for the logic ofcomputation. Propositional and first-order predicatecalculi, soundness and completeness, incomplete-ness and incomputability, the Church-Turing thesis,term-rewriting systems and application to programverification. 3 credits

CSE 531 Foundations of SemanticsFormal semantics aims to answer two importantquestions: 1) when are two programs equal? and 2)when does a program faithfully implement a mathe-matical specification? The course exploresdenotational semantics, operational semantics andprogram logic, studying how they are related andhow they can answer the motivating questions.Programming language concepts, such as impera-tive programming, functional programming,call-by-name, call-by-value and continuations, arecontrasted and explained in terms of their semanticfoundations. Key concepts include full abstractionand the use of least fixed point constructions tosolve recursive equations. The course is designed forstudents interested in the mathematical foundationsof programming languages and programming logics.Prerequisite: Discrete mathematics. 3 credits

CSE 532 Analysis and Design of AlgorithmsAn introduction to the design and analysis of algo-rithms. The course covers design techniques, suchas dynamic programming and greedy methods, aswell as fundamentals of analyzing algorithms forcorrectness and time and space bounds. Topicsinclude advanced sorting and searching methods,graph algorithms and geometric algorithms. Otherareas vary from year to year and may include com-

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putational geometry, matrix manipulations, stringand pattern matching, set algorithms, polynomialcomputations and the fast Fourier transform.Prerequisites: Data structures and discrete mathe-matics. 3 credits

CSE 533 Automata and Formal LanguagesAutomata theory introduces fundamental modelsthat are used over and over again in computer sci-ence for programming languages, in compilerconstruction and in algorithms. These models are avaluable part of the repertoire of any computer sci-entist or engineer. This course introducesprogressively more powerful models of computation,starting with finite automata and moving throughcounter, stack and Turing machines. It also presentsthe regular, context-free, recursive and recursivelyenumerable languages and shows how they corre-spond to the various models of computation and togeneration mechanisms such as regular expressionsand grammars. The emphasis is on understandingthe properties of these models, the relationshipsamong them and how modifications such as nonde-terminism and resource bounds affect them. Thecourse includes application of these con-cepts toproblems arising in other parts of computer science.Prerequisite: Discrete mathematics. 3 credits

CSE 534 Computability and IntractabilityComputability and complexity theory identify class-es of languages based on characteristics ofmachines that recognize them. The course presentselementary results from recursive function theory,including recursive and recursively enumerablesets, and degrees of undecidability. Using recursiontheory as a model, it develops the classical resultsof complexity theory, including time and space com-plexity classes, hierarchy theorems and elementaryresults from parallel complexity. The course con-cludes by studying classes of problems that areprovably intractable, with a particular emphasis onNP-complete problems. Prerequisite: CSE 532 orCSE 533. 3 credits

CSE 535 Categories in Computer ScienceCategory theory provides a powerful and concisenotation for abstract properties of functions.Originally developed for algebraic topology, it hasfound widespread application in computer science.This course introduces the basic notions of categorytheory, including functors, natural transformations,products, sums, limits, colimits, monads andadjunctions. These concepts are illustrated withexamples from computer science and mathematics,including the relationship between Cartesian closedcategories and the lambda-calculus. Familiarity withdiscrete mathematics is an essential prerequisite.

3 credits

CSE 540 Neural Network Algorithms and ArchitecturesThis course introduces the fundamentals of connec-tionist and neural network models. Paradigms forsupervised, unsupervised and reinforcement learn-ing are covered. Topics include LMS andbackpropagation algorithms, network optimizationtechniques, theoretical and practical tools toaddress generalization and complexity control, prin-cipal components and independent component

analysis, mixture models and clustering. The courseaims to develop the student’s statistical understand-ing of the use of neural network techniques.Applications to classification, time series predic-tion, regression and data clustering are treatedusing real world data. 3 credits

CSE 541 Database ImplementationThis course provides hands-on experience imple-menting database management systems. Typicaltopics discussed include benchmarking, transactionprocessing, file and index implementation, buffermanagement, concurrency control, recovery, queryoptimization and a variety of query processing algo-rithms. The data model to be implemented, and thecomputer architecture to be used, will changebetween offerings. Prerequisite: CSE 514. Thiscourse is offered at Portland State University asCS 545. 3 credits

CSE 542 Object Data ManagementA variety of products for managing object data haveemerged in the marketplace. Object-oriented data-base systems and persistent programminglanguages have been joined by object-relationaldatabases and middleware component technologies,such as Enterprise Java Beans. Other storageengines, such as LDAP and XML servers, have anobject flavor. This course begins with the conceptsin types, data models and languages that underlieobject data management. It then looks at exampleprototype and commercial systems, and examinesdesign dimensions such as data model, persistence,encapsulation, hierarchies, query languages andtransactions. It touches on application developmentand data management issues and concludes withtreatment of software architecture, implementationand benchmarking techniques. Students will do aproject using a commercial product. Prerequisite:CSE 514 or other introductory database course.

3 credits

CSE 544a Probability and Statistics IThis course introduces probability and statisticalinference. It examines such topics as the elementsof probability, exploratory data analysis, samplingtheory, hypothesis testing, linear regression, good-ness-of-fit tests and maximum likelihood estimation.The primary analysis tools for this course are S-PLUS, SAS or MATLAB. Prerequisites: Knowledge ofcalculus, linear algebra and basic differential equa-tions. 2 credits

CSE 544b Probability and Statistics IIThis course explores further concepts in probabilityand statistical inference and builds on the materialcovered in FIN 521. The course examines topicssuch as Bayesian inference, nonparametric testsand design of experiments. The primary analysistools for this course are S-PLUS, SAS or MATLAB.Prerequisite: CSE 544a, Probability and Statistics I,or equivalent. 2 credits

CSE 545 Advanced Neural and Adaptive AlgorithmsAn advanced treatment of architectures and algo-rithms for pattern recognition, regression,timeseries prediction and datamining. Typical topicsinclude convergence, effects of noise, optimizationmethods, probabilistic framework (including

Bayesian estimation), generalization ability and reg-ularization and pruning, Hebbian learning andclustering and density modeling. Prerequisite: CSE540 or instructor permission. 3 credits

CSE 546 Data and Signal CompressionThe need for signal and data compression is ubiqui-tous in image, video and speech processing, financeand computational science. Where data storesbecome very large (e.g. video, finance, earth sci-ence), the need is not met by simple lossless filecompression schemes, and we must turn to sophis-ticated coding techniques. This course addressesboth the theoretical basis and practical algorithmsfor data and signal compression. Topics include loss-less entropy-based coding, including Huffman andLempel-Ziv, and lossy compression techniquesincluding scalar quantizers, transform coding(Karhunen-Loeve, DCT and nonlinear transformcodes), predictive coding, vector quantization, adap-tive codes and wavelets. The relation betweencompression schemes and probabilistic data model-ing is emphasized in conjunction with eachtechnique. Application to speech, image and videocoding are discussed. Students will have the oppor-tunity to design compression schemes for suchdiverse applications as earth science data, finance,speech or video, depending on their interests.Prerequisites: Undergraduate calculus, introductoryprobability and statistics, some programming expe-rience. 3 credits

CSE 547 Statistical Pattern RecognitionTheory and practice of statistical pattern recogni-tion. Students will learn fundamental theory andpractices that are common to a broad range of pat-tern recognition applications and technologies, andapply principles to real-world examples. Theemphasis is on developing theoretical and practicaltools that provide grounding in pattern recognitionproblems and methods, rather than on showcasingparticular technologies. The course will benefitthose whose work may use any of a variety of recog-nition technologies in broad-ranging applicationssuch as speech and image processing, data mining,finance. Topics include: random vectors, detectionproblems (binary decision problems), likelihoodratio tests, ROC curves, parametric and non-para-metric density estimation, classification models,theoretical error bounds and practical error estima-tion through cross-validation. Maximum likelihoodand Bayesian parameter esti-mation, model-basedclustering, feature extraction for dimensionalityreduction and for classification. 3 credits

CSE 548a Statistical Computing IThis course introduces modern applied statistics.Topics will be selected from distributions and datasummaries, density estimation, generalized linearmodels, modern nonlinear regression, robust statis-tics, factor analysis, linear and nonlinearclassifiers. The goal is to provide a solid under-standing of practical statistical inference methodsand proficiency in using modern statistical tools.The primary analysis tools for this course are S-PLUS or SAS. Prerequisite: CSE 544a, Probabilityand Statistics I, and CSE 555a, MathematicalMethods, or equivalent. 2 credits

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CSE 548b Statistical Computing IIThis course explores further concepts in modernapplied statistics and builds on the material coveredin CSE 548a. The course examines topics such asBayesian classifiers, cluster analysis, decisiontrees, ensemble learning methods and cross-valida-tion techniques. The goal is to provide a solidunderstanding of practical statistical inferencemethods and proficiency in using modern statisticaltools. The primary analysis tools are S-PLUS, SAS orMATLAB. Prerequisite: CSE 548a, StatisticalComputing I, or equivalent. 2 credits.

CSE 549D Applied Business ForecastingThis Web-based course in applied business fore-casting emphasizes generating and implementingbusiness forecasts. It is designed for students whowant to know how forecasts are actually developedand utilized, emphasizing modern statistical meth-ods widely used to generate business forecasts.Specific applications to business include forecastingsales, production, inventory, macroeconomic factorssuch as interest rates and exchange rates, and otheraspects of both short- and long-term business plan-ning. Topics include a statistical review, dataconsiderations, model selection, moving averagesand exponential smoothing, regression analysis,time-series decomposition, Box-Jenkins (ARIMA)models, optimal forecast combination and forecastimplementation. The course utilizes MicrosoftExcel-based ForecastX Software for Windows, whichaccompanies Wilson and Keating’s BusinessForecasting (McGraw Hill-Irwin, 4th Edition).Prerequisite: Knowledge of basic statistics andregression analysis is highly recommended butnot required. 4 credits

CSE 550 Spoken Language SystemsSpoken language systems are already beingdeployed to help people find flight information, tradestock, access e-mail and learn traffic conditions.With the continuing advancements in speech tech-nology, more information and services will becomereadily available. A simple cell phone will be enoughto hook into the information age. This course teach-es the fundamentals of spoken language systems.These systems include components for speechrecognition, natural language under-standing, dia-logue management, text generation, speechsynthesis and agent architecture. We will examinealternative approaches for doing each of these tasksin terms of their benefits and limitations in buildinga complete system. Students will combine thesetechnologies to build working spoken dialogue sys-tems, ranging in complexity from simplefill-in-the-slot dialogues, to mixed initiative dia-logues, where the user and system work together toaccomplish some task. Class projects will be doneusing the CSLU toolkit, Tcl/Tk, and VoiceXML.

3 credits

CSE 555a Mathematical Methods This course reviews the essential mathematicalmethods required for quantitative analysis in engi-neering and finance. It examines a selection oftopics such as multivariate calculus, differentialequations and mathematical optimization. The focus

is on explaining the key mathematical results and,by means of examples and assignments, showinghow they may be applied in engineering and finance.Prerequisites: Knowledge of calculus, linear algebraand basic differential equations. 2 credits

CSE 555b Stochastic CalculusThis course explores the essential mathematicalconcepts underlying stochastic calculus (continuousstochastic processes). We will cover topics such asstochastic processes, Ito integrals, Ito calculus,martingales and stochastic control. The focus is onexplaining the key mathematical results and, bymeans of examples and assignments, showing howthey may be applied in engineering and finance.Prerequisites: CSE 555a, Mathematical Methods, andCSE 544a, Probability and Statistics I, or equivalent.

2 credits

CSE 556a SimulationThis course introduces modern, advanced numericalmethods for quantitative work in engineering,finance and operations research, focusing on MonteCarlo Simulation. Topics covered include pseudo-random and quasi-random number generators,continuous-time and discrete-event simulation, gen-eration of stochastic processes, variance reductiontechniques, bootstrapping, jackknife and other sta-tistical techniques. Students will learn the scienceand art of effectively applying these techniques.Grading will be based on assignments and a groupproject, and these will involve programming in MAT-LAB. The assignments, project and examples inclass will be drawn from practical problems inengi-neering and finance. Prerequisites: Programmingexperience, and CSE 544a, Probability and StatisticsI, or equivalent. 2 credits.

CSE 556b Modern Optimization TechniquesThis course introduces modern, advanced numericalmethods for quantitative work in engineering,finance and operations research, focusing on opti-mization techniques. We will briefly reviewtraditional methods, such as hill-climbing anddynamic programming, and study in detail newheuristic techniques such as genetic algorithms, dif-ferential evolution, simulated annealing, and antcolony and swarm optimization. Students will beintroduced to mathematical modeling, and will learnthe science and art of effectively applying thesetechniques. Grading will be based on assignmentsand a group project, and these will involve program-ming in MATLAB. The assignments, project andexamples in class will be drawn from practical prob-lems in engineering and finance. Prerequisites:Programming experience and CSE 555a, Mathe-matical Methods, or equivalent. 2 credits

CSE 560 Artificial IntelligenceThis course surveys the foundations and applica-tions of symbolic approaches to artificialintelligence. The approach emphasizes the formalbasis of automated reasoning and includes an intro-duction to programming in Prolog. Fundamentalscovered include search, knowledge representation,automated inference, planning, nonmonotonic rea-soning and reasoning about belief. Applications

include expert systems, natural language processingand agent architectures. 3 credits

CSE 561 DialogueThis course provides an in-depth treatment of themajor theories of dialogue, including finite-state,plan-based and joint action theories. Dialogue isexamined at a level general enough to encompassconversations between humans, between humanand computer, and among computers, while at thesame time being precise enough to support imple-mentations. The course introduces basic speech acttheory, planning and reasoning through a number ofclassic papers. Plan-based theories are examined indetail, including their incorporation into spoken dia-logue systems and their potential effects uponspeech recognition components. Students will devel-op dialogue components and integrate them intoworking systems. Prerequisite: CSE 560. 3 credits

CSE 562 Natural Language ProcessingAn introduction to artificial intelligence techniquesfor machine understanding of human language. Thecourse introduces key aspects of natural language,along with the analyses, data structures and algo-rithms developed for computers to understand it.Computational approaches to phonology, morpholo-gy, syntax, semantics and discourse are covered.Programming assignments are written in Prolog.Prerequisite: CSE 560 or equivalent. 3 credits

CSE 563 Multiagent SystemsThis course covers the emerging theory and practiceof multiagent systems: semi-autonomous, semi-intelligent distributed computing systems that canbe organized ad hoc to meet the immediate needs ofa user. The course covers a variety of individual andmultiagent architectures, including the Contract Netprotocol, distributed blackboard systems and mobileagents. Also discussed are principles for buildingnetworks of heterogeneous agents, ranging fromsimple rule-based systems to databases andhumans. In order to collaborate to solve a user’sproblem, agents need to communicate. We examineagent communication languages, including KQMLand FIPA, as well as the underlying general speechact theories. Students learn how to model these sys-tems formally and will develop and programindividual agents that can participate in a multia-gent system. 3 credits

CSE 564 Human-Computer InteractionThis course emphasizes the experience of comput-ing, which centers on an understanding of real usersand the specific tasks they need to accomplish whencomputing. In the pursuit of optimal user support,an interdisciplinary approach to system design andevaluation is stressed. The course reviews currentresearch viewpoints and activities in the field ofhuman-computer interaction, surveys key researchchallenges and discusses trends in next-generationsystem design. Students gain hands-on experienceby critiquing existing interfaces, as well as hearingreports from experts in industry on the state of thefield. An introduction to this topic is essential foreveryone working in the field of computer science.

3 credits

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CSE 567 Developing User-Oriented SystemsThis course explores a range of issues and methodsneeded to design and evaluate user-oriented soft-ware applications. Topics focus on field andethnographically based design studies, participatorydesign methods, user laboratory studies and usabil-ity testing. The purpose is to have access to a rangeof methods that help uncover opportunities, break-downs and interactions that affect the design anduse of developing systems. Students are challengedto evaluate the underlying perspectives of theapproaches and decide which approach or combina-tion of approaches works best for particularproblems. They apply the methods in field and class-room exercises and produce a real-world project orpaper using course methods. The intended result isto make students more effective not only at gather-ing relevant user-based information, but also atintegrating it into the development process.

3 credits

CSE 568 Empirical Research MethodsThis course introduces principles of experimentaldesign and data analysis for empirical research.Topics include the goals and logic of experimentaldesign, hypothesis formation and testing, probabili-ty and sampling theory, descriptive statistics,correlation and regression, basic parametric andnonparametric tests of statistical significance (e.g.,Binomial, t-test, chi-square, analysis of variance),standard designs for single- and multi-factor exper-iments, and strategies of scientific investi-gation(e.g., Exploratory vs. Directed). The course is fun-damental for anyone who plans to conductindependent research or needs to evaluate critical-ly the research of others. Students participate indesigning and analyzing data to answer scientificquestions and present the results of these activitiesboth orally and in writing. 3 credits

CSE 569 Scholarship SkillsScientific results have little value if they are notcommunicated clearly or are disconnected fromprior work in a field. This course teaches students toresearch, write, present and review effectively forthe computer sciences. It emphasizes learning bydoing, and students have frequent writing and pres-entation assignments. Students learn how to locateand organize background materials, how to writeclearly about technical topics, how to organize Webcontent, the structure and stylistic conventions ofscientific documents (such as conference abstracts,journal papers, theses and proposals), how to pre-pare and deliver short and long presentations, therefereeing process, and how to prepare and respondto a review. This course is required for Ph.D. stu-dents and strongly recommended for master’sstudents, especially those pursuing the thesisoption. It also is useful for professionals who mustwrite or speak to a technical audience. 3 credits

CSE 58X Special TopicsUnder this number, we offer courses of particularrelevance to the research interests of faculty or instate-of-the-art subjects of interest to the community.

CSE 600 ResearchSupervised research activity.

Variable and repetitive credit.

CSE 610 Non-thesis ResearchSupervised research for up to 6 credits as a compo-nent of the non-thesis master’s degree. Students arerequired to produce concrete research deliverables,including a final report equivalent to a CSE techni-cal report. Each 3 credits of CSE 610 may count asone class to fulfill the M.S. non-thesis graduationrequirements.

CSE 620 Professional InternshipThese courses provide an opportunity to earn creditfor relevant work experience in industry. Studentsgain valuable industrial experience that allows themto both apply the knowledge gained in the classroomand prepare for careers in computer science. Awritten report must be submitted to the CSE facultyadvisor at the end of the experience. Enrollmentrequires a faculty advisor and is limited by the num-ber of internship opportunities available.

1 to 3 credits per quarter

CSE 700 M.S. Thesis ResearchResearch toward the thesis for the M.S. degree.

Variable and repetitive credit

CSE 800 Ph.D. Dissertation ResearchResearch toward the dissertation for the Ph.D. degree.

Variable and repetitive credit

FIN 541 Principles of Modern FinanceThis course examines the theory and practice ofmodern corporate finance, stressing the six centralconcepts in finance: Net Present Value, CapitalAsset Pricing Model, Efficient Capital Markets,Value Additivity (Capital Structure Theory), OptionTheory and Agency Theory. Topics include discount-ed cash flow analysis, capital budgeting, capitalstructure theory, mean-variance portfolio theory,arbitrage-pricing theory, Black-Scholes option pric-ing and real options. In addition, students will learnthe nuances of valuing a business. The principal goalof the course is to provide an intuitive foundation ofmodern finance upon which the student can applyadvanced computational techniques. This is accom-plished through interaction between the text,instructor, case studies, MATLAB assignments andstudent presentations/discussions. 4 credits

FIN 544 Investment and Portfolio ManagementThis course applies quantitative investment analysisin a systematic attempt to outperform the marketbenchmark. Accordingly, it begins with the tools oftraditional investment analysis, such as asset valu-ation, efficient markets, mean-variance portfoliotheory, efficient set mathematics, CAPM and APT,and proceeds to the new discipline of active portfo-lio management. Specifically, the course examinesadvanced quantitative portfolio management proce-dures that are increasingly employed by portfolioand money managers worldwide. Topics includeadvanced risk modeling, forecasting exceptionalreturns, constructing and implementing active port-folios, hedge portfolios, and observing and refiningportfolio performance. This course requires outsidecase studies using MATLAB and BARRA On-Campus.

4 credits

FIN 547 Global Markets and Foreign ExchangeThis course surveys the modern paradigms in inter-national finance. Specifically, the course examines

the theory linking the world’s various foreignexchange, money and securities markets, emphasiz-ing global investment and risk management. Topicsinclude spot and forward FX markets, FX options,interest rate parity, purchasing power parity,exchange rate theory, global investing, global FX riskmanagement and emerging markets. Course assign-ments make use of MATLAB. 2 credits

FIN 551 Options and Futures IThis course introduces the trading, pricing and risk-management applications of financial derivatives,including futures, swaps and option contracts.Emphasis is on pricing models, including arbitragepricing theory, risk-neutral valuation and Black-Scholes analysis. Topics covered include futures andswap pricing, methods for pricing American-styleoptions, hedging and speculation using derivatives,Ito calculus, portfolio insurance, option tradingstrategies, dynamic hedging strategies and numeri-cal methods. Course assignments require use ofMATLAB. 4 credits

FIN 552 Options and Futures IIA continuation of FIN 551, Options and Futures I,this course examines derivative pricing modelssince Black-Scholes, models for the term structureof interest rates and relevant numerical methods.Emphasis is on pricing fixed-income derivatives,credit derivatives and exotic options using numeri-cal solution methods such as finite differencemethods, lattice methods and Monte Carlo simula-tion. Equilibrium and no-arbitrage term structuremodels for interest rates are presented, fromVasicek through Heath-Jarrow-Morton. In addition,we examine the issues of model calibration and esti-mation. The course builds on the concepts ofstochastic calculus that were covered in FIN 551.Additional topics include arbitrage pricing, equiva-lent martingale measures and risk neutralvaluation. Course assignments require the use ofMATLAB. Prerequisite: FIN 551 Options andFutures I, or permission of instructor. 4 credits

FIN 558 Advanced Numerical Computing in FinanceThis course introduces the major numerical meth-ods needed for quantitative work in finance, focusingon derivatives pricing and fixed income applications.Topics include binomial and trinomial methods,finite difference solution of partial differential equa-tions, Crank-Nicholson methods for various exoticoptions, treatment of discrete dividends, projected-SOR method for American options, numericalmethods for stochastic differential equations, ran-dom number generators, Monte-Carlo methods forEuropean and least-squared Monte-Carlo methodsfor American options. The course is lab oriented.Prerequisite: FIN 552, Options and Futures II, orpermission from instructor. 2 credits

FIN 561 Risk ManagementThis course explores various aspects of quantitativerisk management. Emphasis is on evaluating finan-cial risk using value-at-risk (VAR) models andinvestigating the growing markets for credit riskderivatives. In addition, applications to energy riskmanagment and insurance are discussed. Specifictopics include sources and measurement of riskexposure, methods for calculating value at risk,

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extreme value theory, credit risk management, andimplementation and evaluation of risk manage-mentsystems. Course assignments use MATLAB.

4 credits

FIN 573 Financial Time-Series AnalysisThis course reviews advanced time-series techniquesand their application to the analysis and forecastingof financial time-series. Emphasis is on multivariateand nonlinear methods applied to high-frequencyfinancial data. Topics include ARIMA models,GARCH models, martingales and random walks, sto-chastic trends, co-integration and error-correctionsmodels. The primary analysis tool is S-PLUS.Prerequisite: CSE 548a, Statistical Computing I, orpermission from instructor. 4 credits

FIN 576 Financial Markets and TradingThis course surveys the structure and dynamics offinancial markets, the behavior of financial priceseries, and trading techniques. Topics include mar-ket microstructure, market efficiency anddocumented anomalies, noise traders and boundedrationality, properties of high-frequency data, non-linear price behavior, speculative bubbles andcrashes, market psychology and technical tradingsystems. The course draws upon the academic liter-ature and the practitioners’ lore. Students useMATLAB, S-PLUS and extensive data resources toanalyze price behavior and build and test simpletechnical trading systems. Prerequisites: FIN 541,Principles of Modern Finance, and FIN 573,Financial Time Series Analysis. 2 credits

FIN 58X Special Topics in Computational FinanceUnder this number we offer courses of particularrelevance to the research interests of faculty or instate-of-the-art topics of interest to the community.Special topics are offered intermittently;

Credits vary

FIN 620 Professional Internship in FinanceThis course provides an opportunity to earn creditfor relevant work experience in finance and relatedindustries. It enables students to enhance theirunderstanding of the practical realities of modernfinance, including such areas as corporate treasuryoperations, investment analysis, portfolio manage-ment, risk management, derivatives pricing,forecasting and trading. Students gain valuableindustrial experience that allows them both to learnto apply knowledge gained in the classroom and toprepare for careers in finance. Enrollment requiresthe instructor’s permission and is limited by thenumber of internship opportunities available.

1-3 credits

A P P L I E D C O M P U T I N G C O U R S E SThese courses may be applicable to the Master inComputational Finance or as a prerequisite for theMaster in Computer Science and Engineering or theOregon Master of Software Engineering.

APC 500a Introduction to Visual Basic for Applications This course introduces Visual Basic for Applicationsas a tool for rapid application development, cus-tomization and system integration in Windowsenvironments. The course focuses on combining VBA

with Microsoft Office. Topics covered includeObject-Oriented Programming, the structure of theVBA programming language and built-in functions,enhancing recorded macros using VBA code, intro-ducing the MS Office object models. Prerequisite:Experience with MS Excel and Access and knowl-edge of a programming language. 2 credits

APC 500b Advanced Visual Basic for ApplicationsApply the power of Visual Basic programming to cre-ate highly functional applications, enabling infinitelevels of automation, customization and integration.This course allows students with knowledge of VBAbasics to expand their skills in advanced analysisand data manipulation, developing and customizingMS Office applications, and integrating them withexisting systems. Additional topics include modelingwith MS Excel and MS Access database program-ming. Prerequisite: APC 500a, Introduction to VisualBasic for Applications, or equivalent. 2 credits

APC 501a Accelerated Development with Visual Basic IThis course uses Visual Basic 6.0 and Visual Basicfor Applications as tools to introduce the concepts ofrapid application development, systems integrationand customization on Windows platforms. Thecourse focuses on the structure and elements of thelanguages, and covers basic analysis and designtechniques. Assignments involve practical work withthese software tools, using applications from indus-try/business as case studies. This fast-paced courseis intended for experienced programmers wishing toaugment their skills with knowledge of Visual Basic.Prerequisites: Programming experience with C, C++or Java (APC 500 is not a prerequisite for thiscourse). 2 credits

APC 501b Accelerated Development with Visual Basic IIThis course builds further on the concepts intro-duced in APC 501a. While studying Visual Basic,students will gain an understanding of the architec-ture of Windows applications and create COMcomponents, ActiveX controls and executable pro-grams. Students will also learn how to apply basicanalysis and design techniques, and how to makeuser interfaces friendly and efficient. Assignmentsinvolve practical work with these software tools,using applications from industry/ business as casestudies. This fast-paced course is intended for expe-rienced programmers wishing to augment theirskills with knowledge of Visual Basic. Prerequisites:APC 501a, Accelerated Development with VisualBasic I, or equivalent. 2 credits

APC 503a Introduction to Perl ProgrammingThis course introduces students to the Perl pro-gramming language, and is based on RandalSchwartz’s popular O’Reilly Nutshell book, LearningPerl. The course covers the structure and elementsof the language (variables, control structures, fileI/O, regular expressions, objects and built-in func-tions), focusing on the items needed to accomplishmany common programming tasks. The course issuitable for students in engineering, managementand finance who wish to learn how to write typicalcommand-line programs in Perl. Prerequisite:Knowledge of a programming language and the UNIXoperating system. 2 credits

APC 503b Developing Web Applications with PerlThis course explores how to develop database-drivenweb applications using CGI and Perl. Topics includeHTML refresher, basics of CGI (forms, actions,dynamic forms and sticky fields), advanced CGI(authentication, cookies, client-pull refresh and ses-sions), CGI security, persistent storage mechanisms(client-side and server-side), and an overview ofPerl database access (with SQL). On completion,students will be able to develop web applicationswith server side automation. Prerequisite: APC503a, Introduction to Perl programming, or equiva-lent and knowledge of HTML. Knowledge of SQL isstrongly recommended. 2 credits

APC 505a Applications Programming in C++ IThis course introduces programming in C++, whichis used widely for developing engineering and busi-ness applications. It introduces the C++ languageand talks about fundamental concepts such as class-es, composition and inheritance, polymorphism,virtuals, overloading, overriding and streams. Thecourse is suitable for students in engineering, man-agement and finance who wish to gain anunderstanding of the language. On completion, stu-dents will be in a position to contribute to the designand development of systems using the basic featuresin C++. Assignments include writing programs anda programming project. Prerequisite: Knowledge ofa programming language. 2 credits

APC 505b Applications Programming in C++ IIThis course builds further on the concepts intro-duced in APC 505a. Topics include abstract classes,pure virtuals, exceptions, operator overloading,templates and a brief introduction to design pat-terns. The course is suitable for students inengineering, management and finance who wish togain an understanding of the language. On comple-tion, students will be in a good position to use thesefeatures for design and development of systemsusing C++. Assignments include writing programsand a programming project. Prerequisite: APC 505a,Applications Programming in C++ I, or equivalent.

2 credits

APC 506a Generic Programming and the C++ StandardTemplate LibraryGeneric programming is a paradigm that expressesalgorithms and data structures in a broadly adapt-able, interoperable form that results in efficientsoftware construction. This course will introduceC++ templates and the concepts fundamental togeneric programming. We will then explore thedesign and use of the C++ Standard TemplateLibrary (STL). The course is suitable for students inscience, commercial software development andfinance who wish to further their understanding ofthis important paradigm in C++ programming.Assignments will include writing programs that usethe STL as well as classes that implement their owngeneric programming features. Prerequisite: APC505b, Applications Programming in C++ II, or equiv-alent. Although the course will not focus onobject-oriented development, a good understandingof object-oriented principles is important for stu-dents to compare and contrast to their

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understanding of generic programming as taught inthis course. 2 credits

APC 506b Numerical Programming in C++This course explores techniques for the effective andefficient implementation of numerical methods usingC++. The C++ language is often used in high-performance systems and applications, but therehave also been challenges to its use in performancecritical applications where fast performance andhigh degrees of accuracy are primary goals. Topicsinclude floating point computation and approxima-tions, partial evaluation and expression templates,matrix factorization and the use of some popularC++ numeric libraries. The course is suitable forstudents in science, industrial engineering andfinance who need to know how to use C++ mosteffectively for numeric programming. Prerequisite:APC 505b, Applications Programming in C++ II,or equivalent. 2 credits

APC 508a Applications Programming in Java IThis course introduces Java 2 technology andobject-oriented programming. Topics include thesoftware development process, learning the Javasyntax and libraries, and the writing of object-ori-ented Java programs that include arrays,inheritance, overloaded methods, polymorphism andcontainment. Assignments include writing pro-grams, applets and a final project using the JavaGUI. Pre-requisite: Knowledge of a programminglanguage. 2 credits

APC 508b Applications Programming in Java IIThis course is designed for students comfortable withthe Java language and writing programs in Java. Itfocuses on more advanced Java topics, including theSwing toolkit, stream I/O, multi-threading, network-ing and writing client/server applications.Assignments include a series of programs leading upto a project designing a distributed socket-basedclient and server. Prerequisites: APC 508a,Applications Programming in Java I, or equivalent.

2 credits

APC 511 Computational Tools forEngineering and FinanceThis course introduces essential programming skillsneeded for engineering and finance. It provides acomprehensive introduction to computing in MAT-LAB. MATLAB topics include language features,handling vectors, matrices and cells, programmingin MATLAB (functions and script files), 2D and 3Dgraphics, using key toolboxes, developing a graphi-cal user interface and other advanced features.Examples and assignments in MATLAB will be usedas a vehicle for introducing topics in numericalanalysis, including some standard methods, numer-ical precision, and convergence and algorithmcomplexity. Some classes may be held in the com-puter lab. Programming assignments focus on thepractical use of MATLAB. Short course offeredselected mornings from September 10 to 23, 2002.Prerequisite: Knowledge of a programming language.

2 credits

APC 515 Data Structures and Discrete MathThis course covers fundamental topics in data struc

tures and discrete mathematics. The topics are pre-sented in an integrated manner that provides thediscrete math foundations for data structures andcomputing applications of discrete mathematicsconcepts. Topics include stacks, queues, linked lists,trees, algorithms for searching and sorting, finitestate automata, and concepts of computability anddecidability. Topics from discrete math include setsand various types of relations (functions, graphs,trees, lattices), recursion and inductive proofs,boolean logic, relational algebra, predicate calculus,series and limits, and asymptotic behavior ofsearching and sorting algorithms. Programmingexercises are assigned throughout the course.Prerequisites: APC 505 or equivalent knowledge of Cor C++. 3 credits

O R E G O N M A S T E R O F S O F T W A R E E N G I N E E R I N GC O U R S E O F F E R I N G S

OMSE 500 Principles of Software EngineeringThis course introduces software engineering. Itfocuses on understanding the software engineeringprocess and its attendant problems as manifest inreal development projects. The course comparesand contrasts different models of the software engi-neering process and approaches to processimprovement. It includes the analysis of where andhow things go wrong motivated by case studies. Thiscourse is intended as a leveling course for enteringstudents who have not had prior instruction in soft-ware engineering and may be waived for studentswith an equivalent senior-level or master’s-levelcourse or equivalent work experience. Prerequisite:Knowledge of programming. Relevant work experi-ence required. 3 credits

OMSE 511 Managing Software DevelopmentThis course provides the knowledge and skills need-ed to plan, organize, lead and control softwareprojects. Topics include planning and estimating,measuring and controlling, and achieving results inenvironments that include a great deal of ambiguityand contradictory information. Quantitative meas-ures and risk management will be emphasized.Students will prepare project plans for real or hypo-thetical software projects, to include effort, cost andschedule estimates and risk management plans.Prerequisite: OMSE 500. 3 credits

OMSE 512 Understanding the Software BusinessThis course provides a familiarity with the businessand economic aspects of software companies andother high-technology companies that develop soft-ware. Topics include fundamental macro-economicconcepts, basic accounting and financial principlesand methods, basic business law, and the functionsand role of marketing in enterprises that developsoftware products or products that include soft-ware. Prerequisite: OMSE 500. 3 credits

OMSE 513 Professional Communication Skillsfor Software EngineersThis course covers the skills necessary for appro-priate professional conduct and effectivecommunication in a professional setting. It includestechnical writing, making effective presentations,conducting effective meetings, conflict resolution,

team and decision-making skills and professionalethics. Prerequisite: OMSE 500. 3 credits

OMSE 521 Using Metrics and Models to SupportQuantitative Decision MakingThis course provides the knowledge and skills need-ed to apply quantitative tools based on metrics andmodels of the software product and developmentprocess to make decisions under uncertainty. Topicscovered will include measurement concepts, deci-sion-making under uncertainty, and model andmetric development for the software developmententerprise. Prerequisite: OMSE 500. 3 credits

OMSE 522 Modeling and Analysis of Software SystemsAbstract models are used to formalize specificationsof software systems. Formalized reference specifi-cations serve as a basis for the design of softwareimplementations and for validating critical proper-ties of software systems. This course provides thefundamental mathematical concepts needed tounderstand abstract models of software and to rea-son about them as well as examples of how they areapplied. Prerequisite: OMSE 500.

3 credits

OMSE 525 Software Quality AnalysisThis course covers processes, methods and tech-niques for developing quality software, for assessingsoftware quality and for maintaining quality. Coursematerial emphasizes the tradeoffs between softwarecost, schedule time and quality; the integration ofquality into the software development process; for-mal review and inspection methods; principles oftesting and test planning; module design for testa-bility; and maintaining quality while supportingexisting software. Prerequisite: OMSE 500.

3 credits

OMSE 531 Software Requirements EngineeringThis course covers the principles, tools and tech-niques for requirements elicitation, specificationand analysis. The focus is on understanding the roleof requirements in system development and mainte-nance, goals of the requirements phase, essentialdifficulties of specifying requirements for real sys-tems, and effective methods, tools and techniques.The course covers techniques for formally modelingand specifying software requirements with hands-onexperience as well as the role of prototyping in val-idating requirements. Prerequisite: OMSE 500.

3 credits

OMSE 532 Software Architecture and Domain AnalysisThis course covers the principles and methods of thearchitectural design of complex software systems. Itincludes a survey of the major architectural styles,strengths and weaknesses of each style, and trade-offs among them; application of domain analysis toidentifying and capturing common architecture insoftware domains (e.g., product lines); the impact ofplatform dependence and independence on architec-tural decisions; and the relation of softwarearchitecture to requirements and its effects ondownstream design. Students will examine domainanalysis and the architectural design processand products in context including the effect of deci-sions on function, quality, cost and schedule.Prerequisite: OMSE 500. 3 credits

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OMSE 533 Software Design TechniquesThis course covers the principles of software designand a survey of design methods, techniques andtools. In-depth and hands-on study of at least onemethod such as object-oriented design as applied toa realistic industrial problem. It examines theeffects of design decisions on the functional andnonfunctional properties of the software (e.g., easeof understanding, maintainability, reuse) and howsoftware engineering principles are applied to makeappropriate trade-offs. Students also examine thedesign process and products in context, includingthe effect of design decisions on function, quality,cost and schedule. Prerequisite: OMSE 500. CSEstudents may not receive credit for both CSE 504and OMSE 533 because there is significant overlapin content. 3 credits

OMSE 535 Software Implementation and TestingThis course covers the principles of implementingand verifying computer software. Implementationtopics include coding style, packaging principles,reuse, testability and maintainability. Verificationtopics include structural (white box) testing andtechniques for code verification. Also covers verifi-cation and integration of foreign code, testingtechnique and how to apply them, including code-based and specification-based testing, hands-onapplication of the testing process, including testcase generation, and test adequacy, test validation,test execution and automation. Prerequisite:OMSE 500. 3 credits

OMSE 551 Strategic Software EngineeringWhereas traditional software engineering focuseson the development and maintenance of individualsystems, strategic software engineering addressesthe development of multiple systems over time.Recent work has shown that significant gains in pro-ductivity, cost and schedule can result fromsystematic improvement of a company’s overall soft-ware development process and systematic reuse oflife-cycle products over multiple developments. Thiscourse covers the principles, methods and tools forsuch strategic software development, includinglong-term process modeling and improvement,developing programs as instances of families of sys-tems, and systematic approaches to code generationand the reuse of non-code products, includingrequirements and design. Prerequisites: all previousOMSE courses. 3 credits

OMSE 555 Software Development Practicum I 3 credits

OMSE 556 Software Development Practicum IIThe development practicum enables students toapply the knowledge and skills gained in othercourses as they synthesize a solution to a signifi-cant, realistic and practical problem. Students workin teams to analyze a problem, develop a softwareconcept, plan a software development effort, definerequirements and implement a solution. Each offer-ing of the practicum will include at least one hour oflecture per week. Students will work closely withOMSE program faculty and, where possible, review-ers from industry to apply advanced software

engineering techniques to a disciplined developmentof a realistic product and evaluate the results.Software development artifacts created as part ofthe practicum will become part of the student’s pro-fessional portfolio. Contents of the portfolio includesuch products as the concept definition, cost esti-mate, project plan and schedule, formalrequirements specification, test plan, software qual-ity assurance plan, software architecture, softwaredesign, implementation artifacts, test results andmetrics collected. The portfolio contents provideexamples of the student’s professional capabilities.

3 credits

RESEARCH PROGRAMSThe specific research projects under way at anygiven time depend upon current interests and obli-gations of faculty, students and research sponsors.

Agent-Based SystemsThis project is designing a new agent communica-tion language (AGENTTALK) and multiagentarchitecture. Unlike DARPA’s current language(KQML), the language offers a true semantics, andprovably correct dialogue protocols, based on jointintention theory. The Adaptive Agent Architecture,a successor to our earlier Open AgentArchitecture, offers platform and application inter-operability, facilitated communication, properconcurrent operation, dynamic reconfigurability offacilitators, and separation of data and control.Quickset has been reimplemented to use this archi-tecture, gaining a more robust capability forsupporting human-human collaboration, multime-dia and dynamic adaptation to processingenvironments. Cohen

Constructing Software from SpecificationsResearch in formal methods for software engineer-ing has been concerned primarily with softwarespecification. This research explores the next step:given a declarative specification, to generate prac-tical and efficient software by the technologies ofprogram transformation and specialization. Wehave demonstrated a new software developmentmethod in which software components areconstructed from executable specifications bytyped, staged functional programs and atranslation directed by an interface specificationthat determines data representations. Systematictechniques for proving the semantic validity of rep-resentations for data types are explored. Kieburtz, Hook, Sheard, Launchbury

Digital GovernmentDOT is collaborating with the U.S. Forest Service,Bureau of Land Management, Fish and WildlifeService and other government agencies to build aforest information portal for the AdaptiveManagement Area (AMA) program. The AMAsdevelop and test innovative approaches to forestmanagement. We are developing an informationmodel called Metadata++ to locate documents anddocument fragments along several dimensions andto search for documents based on “similarity

search” between locations. The forest project alsoincludes participants from the MST and ESEdepartments at OGI, from the University of Nevada,Las Vegas, and from the private sector.Delcambre, Maier, Toccalino, Phillips, Steckler,Koch, Tolle, Landis, Palmer

Domain-Specific LanguagesA domain-specific language can provide a declara-tive programming interface for specialists in anapplication domain who are not primarily softwareengineers. A well-designed domain-specificlanguage improves productivity, reduces the inci-dence of programming errors and furnishes aneasily understood medium for documentation of asoftware artifact. A barrier to the widespreadadoption of domain-specific languages is the inher-ent difficulty of language design andimplementation. We are developing semantics com-binators to allow rapid implementation ofdeclarative, domain-specific languages. We are alsopursuing staged implementations as a means ofefficiently embedding a domain-specific languageinto a broad-spectrum functional language frame-work. Sheard, Hook, Kieburtz, Launchbury

Functional Programming LanguagesFunctional programming languages are based uponthe idea that programs can be designed as mathe-matical functions with logical properties.Functional abstraction is a powerful and flexiblemeans of constructing concise programs. PacSoftfaculty have a continuing interest in techniques foranalysis and efficient implementation of functionalprogramming languages, including ML and Haskell.These techniques include staged programming, par-tial evaluation, effects encapsulation with monads,automatic program transformation and advancedtype systems. Black, Hook, Jones, Kieburtz, Launchbury, Sheard

Machine Learning and Adaptive SystemsOur work in machine learning, neural computation,evolutionary computation, adaptive systems andcognition includes theoretical, algorithmic andpractical aspects. Research in theory,architectures and algorithm design includes super-vised, unsupervised, and reinforcement learning,genetic algorithms, generalization theory (modelselection and pruning, invariant learning, theoreti-cal characterization), stochastic optimization, localand mixture models, time series, control, and con-text-sensitive learning. Practical applicationdomains include speech and image processing,medical screening technology, environmental fore-casting and observation systems, anomalydetection for aeronautics, aircraft control, sensorfusion and finance. We explore applications of evo-lutionary computation for design optimization,automatic programming, and modeling of evolution-ary systems.Hermansky, Leen, Mitchell, Moody, Pavel, Song, Wan

Multimodal SystemsMultimodal interfaces enable more natural andefficient interaction between humans and machinesby supporting multiple coordinated channels

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through which input and output can pass. TheCenter for Human-Computer Communication isengaged in empirical investigation of multimodalinteraction. This informs our research and develop-ment of architectures for multimodal languageprocessing, work which draws on a range of fieldssuch as cognitive science, natural languageprocessing, multimedia, user interface design,speech recognition, gesture recognition and visualparsing. The Quickset system developed at CHCCsupports multimodal pen/voice interaction withcomplex visual/spatial displays, such as maps.Cohen, Oviatt

Natural Language DialogueThe performance of speech recognition systemsimproves significantly when the spoken languageunderstanding system can predict the next utter-ance. Accordingly, we are performing perceptualstudies of dialogue and building models of human-human and human-computer dialogue in order todevelop computational models of conversation thatcan be used to track and predict spoken language.This work is based on speech-act theory,multiagent architectures and models ofspontaneous speech. Cohen, Heeman, Oviatt

Net Data ManagementWe believe that data management systems of thefuture must stress data movement over data stor-age. NIAGARA is an initial effort, conducted withthe University of Wisconsin, to move beyond disk-centric data management to net-centric systems.Current work includes algebras and special opera-tors for XML, exploiting stream semantics forefficient processing, and data-query hybrids fordistributed query evaluation. Maier, DeWitt, Naughton

Neurobiological ModelingThe brain handles a continuous temporal flow ofsensory information. At the microscopic level of thesynapses, the relevant signals are the small vari-able electrophysiological events called synapticpotentials. When learning occurs, there is a changein the relative weighted value of these synapticpotentials. At the macroscopic level of a functionalregion of the brain, the relevant variables are sys-tems properties of the response to large numbersof cellular inputs. The system needs to optimize thetrade-off between accuracy, which may take sometime to establish, and adaptability, which oftenrequires rapid adjustment to changes in the senso-ry environment. This collaborative projectcombines statistical adaptive system approacheswith tools from computational biology and experi-mental neurophysiology. The present focus is onmodeling adaptation in a sensory-motor system inweakly electric mormyrid fish. The modeling formsa bridge between microscopic dynamics andmacroscopic system behavior. This project involvesa novel aspect of modeling emphasizing statisticalproperties of then-synaptic adaptation in the pres-ence of noise, and making testable predictionsabout how noise can affect the accuracy of thefish’s stored signal memories. Leen, Roberts

Operating SystemsOur operating systems-related research focusesprimarily on adaptive systems software and itsapplication in distributed, mobile and multimediacomputing environments. Several large projectsare currently under way in the areas of qualityof service control, adaptive resource managementand dynamic specialization for enhanced perform-ance, survivability and evolvability oflarge software systems.Black, McNamee, Steere, Walpole

Query OptimizationOur work on query optimization and evaluationdeals with both general frameworks and specifictechniques for different data model and query lan-guage features. Columbia is a C++-based,top-down framework for construction of cost-basedquery optimizers. We are currently examiningpruning techniques for searching, transforms forcollection-valued attributes and nested queries,and “multiplex” query optimization for efficientlyoptimizing groups of queries. Columbia is a jointproject with Portland State University.Maier, Shapiro

Speech RecognitionThe goal of Large Vocabulary Continuous SpeechRecognition research is to enable normal humanspeech as an input device in next-generation com-puters alongside today’s keyboard and mouse input.This technology can be used by itself for dictationand command control applications. It can also formpart of a powerful information processing systemwhen used together with information retrieval andnatural language understanding systems. Theresearch focuses include accurate acoustic model-ing, speaker adaptation, confidence measure andrejection, and modeling spontaneous speech.Yan, Heeman

Spoken Language SystemsSpoken language systems make it possible for peo-ple to interact with computers using speech, themost natural mode of communication. A spokenlanguage system combines speech recognition, nat-ural language understanding and human interfacetechnology. It functions by recognizing the person’swords, interpreting the words in terms of the con-text and goals of the task, and providing anappropriate response to the user. We are involvedin the analysis and development of various compo-nents of such systems, ranging from empiricalstudies of human dialogues through the construc-tion of interactive systems to the development ofabstract models of behavior.Cohen, Oviatt, Heeman, van Santen

Superimposed Information andSuperimposed ApplicationsWe are interested in providing typical databasesystem capabilities in an environment where we donot own or manage the underlying, base informa-tion. We seek to develop a superimposed layer ofinformation that can reference selectedinformation from the base layer and can also add

new information to highlight, interconnect, elabo-rate or annotate the selected information. We havedefined an architecture for building superimposedapplications and have implemented our first tool:SLIMPad, a scratchpad application that allowsusers to easily create “scraps” that referenceselected items from the base layer and organizescraps into bundles. The tendency to use scrapsand bundles to organize our thoughts is commonpractice, as confirmed by our observationalresearch team that is studying how clinicians seekand use information in a hospital intensive-careunit. Observational team: Gorman, Ash, Lavelle;computer science team: Delcambre, Maier

RESEARCH CENTERS C E N T E R F O R H U M A N - C O M P U T E R C O M M U N I C AT I O N

Kimberly Tice, Center Administrator503 748-7806ticeki@cse.ogi.edu

The Center for Human-Computer Communication isdedicated to realizing a vision of transparent infor-mation and service access. Research projects arebroadly interdisciplinary, and includecollaborations with numerous universities, federalresearch laboratories, and the Data-IntensiveSystems Center at the OGI School.

Research activities focus on:

• Multimodal human-computer interaction thatallows people to state their needs using speech,writing and gestures, and that providesmultimedia output.

• User-centered design of next-generationinterface technology, including spoken languageand multimodal interfaces, and interfaces formobile and multimedia technology.

• Intelligent agent technologies — softwaresystems that help users accomplish tasks andcan reason about how and where to carry outusers’ requests in a worldwide distributedinformation environment.

• Collaboration technologies to support human-human communication, and collaborativedecision making among groups of people.

CHCC organizes an annual Distinguished LectureSeries on the Future of Human-ComputerInteraction. World-class researchers are invited toshare current topics.

Dr. Philip Cohen and Dr. Sharon Oviatt are co-directors of the center. Other center faculty includeDr. Peter Heeman, and Dr. Misha Pavel. For moreinformation, visit CHCC’s Web pages atwww.cse.ogi.edu/CHCC/.

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C S E | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G

P A C I F I C S O F T W A R E R E S E A R C H C E N T E R

Kelly Atkinson, Center Administrator503 748-1336kelly@cse.ogi.edu

Sheri Dhuyvetter, Center Administrator503 748-1476sherid@cse.ogi.edu

The Pacific Software Research Center (PacSoft) isa team of faculty, students and professionalresearch staff who study mathematically basedtechniques for the specification, development andvalidation of complex computer software. Our goalsare to explore and test new techniques that cansupport the development of software products inwhich clients can have high confidence.

PacSoft’s approach to software specification anddevelopment is grounded in functionalprogramming, type theory and formal semanticsof programming languages. Our research methodsextend from theoretical investigation throughprototype software tool development to experi-ental validation.

Much of our work during the past decade hasfocused on techniques for the design andimplementation of domain-specific languages.A domain-specific language is able to express theabstractions and operations used in a particularengineering domain, in terms familiar to domainexperts. One domain in which this work hasdemonstrated considerable success is the designof complex microarchitectures for high-performance microprocessors.

The Hawk project has exploited abstraction andequational specification techniques from functionalprogramming languages to produce a new kind ofhardware specification language. A microarchitec-ture specification written in Hawk can be directlyexecuted as a simulation, symbolically manipulatedas a hardware algebra, or submitted to formal veri-fication of its properties by model checking or by atheorem prover.

Among current PacSoft projects is Programatica,an exploration of computer-supported techniquesfor developing property-certified programs (“pro-gramming as if properties mattered”). ProjectTimber is developing new means of programmingembedded applications that involve both time-criti-cal and critical-rate tasks.

Dr. Tim Sheard is the director of the Center. DrRichard Kieburtz is the founding director. Otherfaculty members of PacSoft are Dr. James Hook,Dr. Mark Jones and Dr. John Launchbury of theOGI School, and Dr. Andrew Tolmach of PortlandState University. The Center employs six postdoc-toral researchers and has numerous visitors eachyear. Research by PacSoft scientists is supportedby grants and contracts from the National ScienceFoundation, DARPA, the National Security Agency,Intel Corp. and Compaq. For additionalinformation, visit the PacSoft Web site,http://www.cse.ogi.edu/PacSoft/.

D ATA B A S E A N D O B J E C T T E C H N O L O G Y L A B O R AT O R Y

Jo Ann Binkerd, Center Administrator503 748-1112binkerd@cse.ogi.edu

The Database and Object Technology Lab (DOT)conducts theoretical and applied research relatedto database management and object-oriented sys-tems. Query processing is a long-term focus,particularly query optimization frameworks as wellas design, optimization and evaluation of object-oriented query languages. Another area of interestis scientific data management, most recently insupport of multidisciplinary studies in forestcanopy science. DOT research includes conceptualmodeling, including semantic and object-orienteddatabase models, models for object-oriented analy-sis and design, and models for superimposedinformation. Other topics include data dissemina-tion, focusing particularly on information utilityand superimposed information management.Superimposed information enhances the utility andvalue of existing data sources by layering smallamounts of information over them. We are examin-ing superimposed information in connection withimproving accessibility of medical records.

Dr. Dave Maier of the OGI School is the directorof DOT. Additional DOT-affiliated faculty membersare Dr.Crispin Cowan, Dr. Lois Delcambre, allof OGI, and Dr. Leonard Shapiro of PortlandState University.

S Y S T E M S S O F T W A R E L A B O R AT O R Y

Cynthia Pfaltzgraff, Center Administrator503 748-7109pfaltz@cse.ogi.edu

The Systems Software Lab (SySL) is a center forresearch spanning the areas of distributed andmobile computing, operating systems, networkingand wide-area-network-based information manage-ment systems. SySL focuses on the development ofadaptive systems that utilize techniques such asfeedback control, specialization, domain-specificlanguages, and quality of service management toenable them to operate effectively in today’s rapid-ly evolving and widely heterogeneous distributedenvironments. We emphasize the real-world appli-cability of our research results and we continue tobuild distributed and scalable prototype systemsfor application areas such as multimedia comput-ing and communications, active networks,Internet-based information management, and sur-vivable distributed systems. We collaborate closelywith industry sponsors such as Intel and IBM, andhave strong federal funding from DARPA and NSF.Dr. Jonathan Walpole is the director of SySL.Additional SySL-affiliated faculty are Drs. Wu-chiFeng, Wu-chang Feng, Andrew Black and DavidSteere of the OGI School, and Dr. Molly Shor ofOregon State University.

FACILIT IESThe Department of Computer Science andEngineering provides a state-of-the-art computingenvironment designed to support the needs ofresearch and education. The computing facilitiesstaff has a wide range of skills that allow the com-puting environment at CSE to be flexible andresponsive in meeting the department’schanging needs.

Support for central services such as mail, dial-upaccess, video conferencing, database access andfile and printer sharing, as well as access toInternet and Internet2 services, is distributedacross a group of Sun computers and a NetworkAppliance file server that comprise the core sup-port environment.

While Sun computers are highly visible at CSE,both Intel- and Alpha-based machines runningWindows or Linux are mainstays of our researchactivities. The generous support of our industryand government research partners allows CSE tomaintain a high-quality computing infrastructurecapable of supporting a high degree of heterogene-ity as required for high-quality research.

In all, a facilities staff of eight supports almost 400computer systems, X terminals and peripheraldevices spanning multiple networks using a varietyof automated techniques, many developed internal-ly, to cope with the high degree of complexityinherent in such a heterogeneous environment.

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FACULTY

J A M E S H O O KAssociate Professor andDepartment HeadPh.D., Computer ScienceCornell University, 1988james.hook@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Domain-specific languages,formal methods and functional programming.

R E P R E S E N TAT I V E P U B L I C AT I O N SW. Harrison, T. Sheard and J. Hook,

“Fine Control of Demand in Haskell,”Proceedings of the Sixth InternationalConference on the Mathematics ofProgram Construction, Dagstuh,Germany, July 2002.

J. Hook, E. Meijer and D. Leijen,“Client-side Web scripting in Haskell,”in proceedings of Practical Applicationsof Declarative Languages, January1999.

J. Hook, E. Meijer and D. Leijen,“Haskell as an Automation Controller,”in Advanced Functional Programming,Swierstra, Henriques and Oliveira, eds.,Springer Verlag, LNCS, Vol.1608.

T. Widen and J. Hook, “SoftwareDesign Automation: Language Designin the Context of Domain Engineering,”Sere 98, June 1998.

J. Bell, F. Bellegarde and J. Hook,“Type-driven Defunctionalization,”ICFP 97, June 1997.

R. Kieburtz, F. Bellegarde et al.,“Calculating Software Generators fromSolution Specifications,” TAPSOFT 95,Springer-Verlag, LNCS, May 1995.

F. Bellegarde and J. Hook,“Substitution: A Formal MethodsCase Study using Monads andTransformations,” Science of ComputerProgramming, 22 (2-3), p. 287, 1994.

J. Bell, J. Hook et al., “SoftwareDesign for Reliability and Reuse: AProof-of-Concept Demonstration,” TRI-Ada 94 Proceedings, ACM Press,November 1994.

D A V I D B A S T E R F I E L DAssistant Professorand Computational FinanceProgram DirectorPh.D., Decision TheoryUniversity of Manchester, 1984basterfield@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Numerical computing,simulation, optimization,genetic algorithms, informationsystems, time series analysisand computational finance.

R E P R E S E N TAT I V E P U B L I C AT I O N SD. Basterfield, “Error bounds on Tree

methods for Calculating OptionsPrices,” paper presented atComputational Finance 2000, June2000.

D. Basterfield, T. Bundt andG.Murphy, “The Stable ParetianHypothesis and the Asian CurrencyCrisis,” paper presented atComputational Finance 2000,June 2000.

A N D R E W P. B L A C KProfessorD. Phil. University of Oxford(Balliol College), Englandblack@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Programming languages;distributed systems; streaminginfrastructure for wide-areanetworks; object-orientedlanguages and systems;programming environments; andthe ways in which all of theseareas interrelate.

R E P R E S E N TAT I V E P U B L I C AT I O N SA. P. Black, J. Huang and J. Walpole,

“Reifying Communication at theApplication Level,” Oregon GraduateInstitute, Department of ComputerScience and Engineering, Beaverton,Oregon, Technical Report CSE-01-006,May 2001.

C. Pu, A. Black, C. Cowan, J. Walpoleand C. Consel, “Microlanguages forOperating System Specialization,”Proc. First ACM SIGPLAN Workshopon Domain-Specific Languages, Paris,pp. 49-57, January 1997.

C. Pu, T. Autrey, A.P. Black, C. Consel,C. Cowan, J. Inouye, L. Kethana,J. Walpole and K. Zhang, “OptimisticIncremental Specialization:Streamlining in a CommercialOperating System,” Proceedings of the15th ACM Symposium on OperatingSystems Principles, December 1995.

A.P. Black and M.P. Immel,“Encapsulating Plurality,” Proceedingsof European Conference on Object-Oriented Programming, July 1993.

R.K. Raj, E.D. Tempero, H.M. Levy,A.P. Black, N.C. Hutchinson and E. Jul,“Emerald, A General PurposeProgramming Language,” SoftwarePractice & Experience, 21 (1), p. 91,January 1991.

A.P. Black and Y. Artsy, DigitalEquipment Corp., “ImplementingLocation Independent Invocation,” IEEETrans. on Parallel and DistributedSystems, 1 (1), p. 107, January 1990.

T H O M A S B U N D TAssociate ProfessorPh.D., EconomicsMichigan State University, 1985bundt@cse.ogi.edu

R E S E A R C H I N T E R E S T S

International monetary theoryand empirical models of exchangerate determination, time-seriesanalysis and forecasting andpedagogical tools in finance.Professor Bundt has also writteninstructional manuals (distancelearning courses) in managerialeconomics, business forecastingand e-business valuations.

R E P R E S E N TAT I V E P U B L I C AT I O N ST. Bundt, T.F. Cosimano and

J.A. Halloran, “DIDMCA and BankMarket Risk: Theory and Evidence,”Journal of Banking and Finance, 16,pp. 1179-1193, 1992.

T. Bundt and J.H. Bergstrand,“Currency Substitution and MonetaryAutonomy: The Foreign Demand forU.S. Demand Deposits,” Journal ofInternational Money and Finance, 9,pp. 325-334, 1990.

T. Bundt and R. Schweitzer,“Deregulation, Deposit Markets,and Banks’ Costs of Funds,” TheFinancial Review, 24 (3), pp. 417-430,August 1989.

T. Bundt, J.S. Chiesa and B.P. Keating,“Common Bond Type and Credit UnionBehavior,” Review of Social Economy,47 (1), pp. 27-42, Spring 1989.

T. Bundt and A. Solocha, “Debt,Deficits and the Dollar,” Journal ofPolicy Modeling, 10 (4), pp. 581-600,October 1988.

P H I L C O H E NProfessor, Co-DirectorCenter for Human-ComputerCommunicationPh.D., Computer ScienceUniversity of Toronto, 1978pcohen@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Multimodal interfaces, human-computer interaction, naturallanguage processing, dialogue,delegation technology, cooperatingagents, communicative action,applications to mobile computing,information management, networkmanagement, manufacturing.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Kumar, P. Cohen and H. Levesque,

“The Adaptive Agent Architecture:Achieving Fault-Tolerance UsingPersistent Broker Teams,” in theFourth International Conference onMultiagent Systems (ICMAS 2000),Boston, July 2000.

S. Kumar and P. Cohen, “Towardsa Fault-Tolerant Multiagent SystemArchitecture,” in the FourthInternational Conference onAutonomous Agents (Agents 2000),Barcelona, June 2000.

D. McGee, P. Cohen and L. Wu,“Something from Nothing: Augmentinga Paper-based Work Practice withMultimodal Interaction,” Proceedingsof the Designing Augmented RealityEnvironments Conference, ACM Press,pp. 71-80, Copenhagen, April 2000.

S. Oviatt and P. Cohen, “MultimodalInterfaces That Process What ComesNaturally,” Communications of theACM, Vol. 43, No. 3, pp. 45-53,March 2000.

L. Wu, S.L. Oviatt and P. Cohen,“Multimodal Integration — AStatistical View,” IEEE Transactions onMultimedia, Vol. 1, No. 4, pp. 334-341,December 1999.

P. Cohen, D. McGee, S.L. Oviatt,L. Wu, J. Clow, R. King, S. Julier andL. Rosenblum, “Multimodal Interactionsfor 2D and 3D Environments,” IEEEComputer Graphics and Applications,pp.10-13, July-August 1999.

C R I S P I N C O W A NAssistant Research ProfessorPh.D., Computer ScienceUniversity of Western Ontario,1995crispin@cse.ogi.edu

R E S E A R C H I N T E R E S T S

System security and survivability,operating systems, distributedsystems, computer architecture,optimism, programming languages.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. Wright, C. Cowan, S. Smalley,

J. Morris and G. Kroah-Hartman,“Linux Security Modules: GeneralSecurity Support for the LinuxKernel:, Eleventh USENIX SecurityConference, 2002.

C. Cowan, S. Beattie, C. Wrightand G. Kroah-Hartman, “RaceGuard:Automatic Adaptive Detection andPrevention of Buffer-Overflow Attacks,”Tenth USENIX Security Conference,2001.

C. Cowan, M. Barringer, S. Beattie,G. Kroah-Hartman, M. Frantzen andJ. Lokier, “FormatGuard: AutomaticAdaptive Detection and Prevention ofBuffer-Overflow Attacks,” TenthUSENIX Security Conference, 2001.

D. McNamee, J. Walpole, C. Cowan,C. Pu, C. Krasic, P. Wagle, C. Consel,G. Muller and R.Marlet, “SpecializationTools and Techniques for SystematicOptimization of Systems Software,”ACM Transactions on ComputerSystems, Vol. 19, No. 2, May 2001.

C. Cowan, C. Pu, D. Maier, H. Hinton,J. Walpole, P. Bakke, S. Beattie,A. Grier, P. Wagle and Q. Zhang,“Stackguard: Automatic AdaptiveDetection and Prevention of Buffer-Overflow Attacks,” Seventh USENIXSecurity Conference, 1998.

C. Cowan and H. Lutfiyya,“A Wait-Free Algorithm for OptimisticProgramming: HOPE Realized,”16th International Conference onDistributed Computing Systems(ICDCS’96), Hong Kong, 1996.

C. Cowan, T. Autrey, C. Krasic,C. Pu and J. Walpole, “Fast ConcurrentDynamic Linking for an AdaptiveOperating System,” in the InternationalConference on Configurable DistributedSystems (ICCDS’96), Annapolis, 1996.

L O I S D E L C A M B R EProfessorPh.D., Computer ScienceUniversity of SouthwesternLouisiana, 1982lmd@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Superimposed information,database system data models,scientific data management.

R E P R E S E N TAT I V E P U B L I C AT I O N SM. Weaver, L. Delcambre and

D. Maier, “A SuperimposedArchitecture for Enhanced Metadata,”DELOS Workshop on Interoperabilityin Digital Libraries, held in conjunctionwith European Conference on DigitalLibraries (ECDL 2001), Darmstadt,Germany, September 2001.

S. Bowers and L. Delcambre, “AGeneric Representation for ExploitingModel-Based Information,” ETAIJournal, Linköping Electronic Articlesin Computer and Information Science,ISSN 1401-9841, Vol. 6, nr 006, 2001,www.ep.liu.se/ea/cis/2001/006/.

L. Delcambre, D. Maier, S. Bowers,L. Deng, M. Weaver, P. Gorman, J. Ash,M. Lavelle and J. Lyman, “Bundles in Captivity: An Application ofSuperimposed Information,”Proceedings of the IEEE InternationalConference on Data Engineering,Heidelberg, Germany, April 2001.

S. Bowers and L. Delcambre.“Representing and Transforming Model-based Information,” in Proceedings ofthe International Workshop on theSemantic Web, in conjunction withECDL 2000, Lisbon, September 2000.

P. Gorman, J. Ash, M. Lavelle,J. Lyman, L. Delcambre, D. Maier,S. Bowers and M. Weaver, “Bundlesin the Wild: Tools for ManagingInformation to Solve Problems andMaintain Situation Awareness,”Library Trends 49 (2), Fall 2000.

D. Maier and L. Delcambre,“Superimposed Information for theInternet,” in Proc. of the ACM SIGMODWorkshop on the Web and Databases(WebDB ‘99), pp. 1-9, June 1999.

L. Delcambre and D. Maier, “Modelsfor Superimposed Information,” inAdvances in Conceptual Modeling(ER ‘99), Vol. 1727, Lecture Notes inComputer Science, pp. 264-280,November 1999.

R I C H A R D E . ( D I C K ) FA I R L E YProfessor and Associate Deanof Graduate EducationPh.D., Computer ScienceUCLA, 1971dfairley@cse.ogi.edu

R E S E A R C H I N T E R E S T S

All aspects of softwareengineering, including but notlimited to systems engineering ofsoftware-intensive systems,software process modeling andprocess improvement, softwarerequirements engineering,software design, software qualityengineering, software metrics,software project management,software cost and scheduleestimation, software riskmanagement, and softwareengineering policies, procedures,standards and guidelines.

R E P R E S E N TAT I V E P U B L I C AT I O N S“Software Project Management,”

Encyclopedia of Computer Science,Groves Dictionaries, 2001.

“Software Estimation Risk,”Encyclopedia of Software Engineering,Vol. 2, John Wiley and Sons, 2000.

R. Fairley, “A Process-OrientedApproach to Software ProductImprovement,” PROFES’99 ConferenceProceedings, Oulu, Finland, June 1999.

R. Fairley, “The Concept of Operations— The Bridge from OperationalRequirements to Technical Specifica-tions,” Annals of Software Engineering,Vol. 3, Amsterdam, September 1997.

R. Fairley, “Standard for Concept ofOperations Documents,” IEEE Standard,Vol. 1362, IEEE Computer Society, 1997.

R. Fairley, “Standard for SoftwareProject Management Plans,” IEEEStandard, Vol. 1058, IEEE ComputerSociety, 1997.

R. Fairley, “Risk-Based CostEstimation,” Proceedings of the11th COCOMO Users Group,Los Angeles, November 1996.

R. Fairley, “Some Hard Questionsfor Software Engineering Educators,”keynote presentation, CSEE 95Proceedings, ACM Conference onSoftware Engineering Education,New Orleans, March 1995.

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W U - C H A N G F E N GAssistant ProfessorPh.D., Computer ScienceUniversity of Michigan, 1999wuchang@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Scalable Internet systemsInternet congestion controland queue management, wirelessnetworking, programmablenetwork infrastructure.

R E P R E S E N TAT I V E P U B L I C AT I O N SW. Feng, D. Kandlur, D. Saha and

K. Shin, “Blue: An AlternativeApproach to Active QueueManagement,” NOSSDAV 2001,June 2001.

W. Feng, D. Kandlur, D. Saha andK. Shin, “Stochastic Fair Blue: A QueueManagement Algorithm for EnforcingFairness,” INFOCOM 2001, April 2001.

W. Feng, D. Kandlur, D. Saha andK. Shin, “A Self-Configuring REDGateway,” INFOCOM 1999, May 1999.

W. Feng, D. Kandlur, D. Saha andK. Shin, “Adaptive Packet Marking forMaintaining End-to-End Throughput ina Differentiated Services Internet,”IEEE/ACM Transactions on Networking,Vol. 7, No. 5, October 2001.

W. Feng, D. Kandlur, D. Saha andK. Shin, “Understanding and ImprovingTCP Performance over Networks withMinimum Rate Guarantees,” IEEE/ACMTransactions on Networking, Vol. 7, No.2, pp. 173-187, April 1999.

W U - C H I F E N G

Associate Professor Ph.D., Computer ScienceUniversity of Michigan, 1996wuchi@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Networking, multimediasystems, multimedia networking,video coding, middlewareservices and massively scalablestreaming infrastructures.

R E P R E S E N TAT I V E P U B L I C AT I O N SA.S. Tosun and W. Feng, “On Error

Preserving Video Encryption Algorithmsfor Wireless Transmission,” inProceedings of the ACM Multimedia2001, October 2001.

W. Feng and M. Liu, “ExtendingCritical Bandwidth AllocationTechniques for Stored Video DeliveryAcross Best-Effort Networks,”International Journal of CommunicationSystems, Vol. 14, pp. 925-940,September 2001.

A.S. Tosun and W. Feng, “LightweightSecurity Mechanisms for Wireless VideoTransmission,” in Proceedings of theIEEE International Conference onInformation Technology: Coding andComputing 2001, Las Vegas, April2001.

A.S. Tosun and W.Feng, “On ImprovingQuality of Video for H.263 overWireless CDMA Networks,” inProceedings of the IEEE WirelessCommunications and NetworkingConference, Chicago, September 2000.

A. Agarwal, W. Feng and C. Wolfe,“A Multi-Differential Video CodingAlgorithm for Robust VideoConferencing,” in Proceedings ofthe SPIE Voice, Video and DataCommunications Conference, Boston,November 2000.

A.S. Tosun, A. Agarwal and W. Feng,“Providing Efficient Support forLossless Video Transmission andPlayback,” in 10th InternationalWorkshop on Network and OperatingSystems Support for Digital Audioand Video, Chapel Hill, North Carolina,June 2000.

J U L I A N A F R E I R EAssistant Professor Ph.D., Computer ScienceState University of New Yorkat Stony Brook, 1997 juliana.freire@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Databases and knowledge-basesystems, information integration,management of semi-stuctureddata, Web information systemsand Internet applications.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Freire, J.R. Haritsa, M. Ramanath,

P. Roy and J. Siméon, “StatiX: zmakingXML Count,” ACM SIGMOD Internation-al Conference on Management of Data,pp. 181-192, 2002.

M. Benedikt, J. Freire and P.Godefroid, “VeriWeb: AutomaticallyTesting Dynamic Web Sites,” Inter-national World Wide Web Conference(WWW), 2002.

P. Bohannon, J. Freire, P. Roy andJ. Siméon, “From XML Schema toRelations: A Cost-based Approach toXML Storage,” IEEE InternationalConference on Data Engineering(ICDE), pp. 64-75, 2002.

J. Freire, D.F. Lieuwen and J.J.Ordille, “Integrating Network Devices ina Metadirectory: The MetaCommexperience,” Information Systems27(3), pp. 193-217, 2002.

J. Freire, B. Kumar and D.F. Lieuwen,“WebViews: Accessing Personalized WebContent and Services,” InternationalWorld Wide Web Conference. (WWW),pp. 576-586, 2001.

V. Anupam, J. Freire, B. Kumar andD.F. Lieuwen, “Automating Web Naviga-tion With the WebVCR,” ComputerNetworks 33(1-6), pp. 503-517, 2000.

H. Davulcu, J. Freire, M. Kifer and I.V.Ramakrishnan, “A Layered Architecturefor Querying Dynamic Web Content,” ACMSiGMOD International Conference onManagement of Data, pp. 491-502, 1999.

J. Freire, T.Swift and D.S. Warren.“Beyond Depth-First Strategies:Improving Tabled Logic ProgramsThrough Alternative Scheduling,”Journal of Functional and LogicProgramming 1998(3), 1998.

J. Freire, T. Swift and D.S. Warren,“Taking I/O Seriously: ResolutionReconsidered for Disk,” InternationalConferrence on Logic Programming(ICLP), pp. 198-212, 1997

P E T E R A . H E E M A NAssistant ProfessorPh.D., Computer ScienceUniversity of Rochester, 1997heeman@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Spontaneous speech recognition,modeling disfluencies andintonation, dialogue management,collaboration, spoken dialoguesystems, natural languageprocessing.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Strayer and P. Heeman, “Dialogue

Structure and Mixed Initiative,’’ Secondworkshop of the Special Interest Groupon Dialogue, Aalborg, Denmark,September 2001.

P. Heeman and J. Allen, “ImprovingRobustness by Modeling SpontaneousSpeech Events,” in J. Junqua andG. van Noord, eds., Robustness inLanguage and Speech Technology,Kluwer Academic Publishers, 2000.

K. Ward and P. Heeman,“Acknowledgments in Human-ComputerInteraction,” in Proceedings of the 1stConference of the North AmericanChapter of the Association forComputational Linguistics, Seattle,May 2000.

P. Heeman, “Modeling Speech Repairsand Intonational Phrasing to ImproveSpeech Recognition,” in IEEE Workshopon Automatic Speech Recognition andUnderstanding, Keystone, Colorado,December 1999.

P. Heeman and J. Allen, “SpeechRepairs, Intonational Phrases andDiscourse Markers: Modeling Speakers’Utterances in Spoken Dialog,”Computational Linguistics, Vol. 25-4,1999.

P. Heeman, “POS Tags and DecisionTrees for Language Modeling,” inProceedings of the Joint SIGDATConference on Empirical Methods inNatural Language Processing and VeryLarge Corpora, College Park, Maryland,June 1999.

P. Heeman, M. Johnston, J. Denneyand E. Kaiser, “Beyond StructuredDialogues: Factoring Out Grounding,”in Proceedings of the InternationalConference on Spoken LanguageProcessing ICSLP-98, Sydney,December 1998.

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M A R K P. J O N E SAssociate ProfessorD.Phil., ComputationUniversity of Oxford, 1992mpj@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Programming language designand implementation, programmingparadigms, module and componentsystems, type theory, semantics,program transformationand analysis.

R E P R E S E N TAT I V E P U B L I C AT I O N SMark P. Jones , “Type Classes with

Functional Dependencies,” inProceedings of the 9th EuropeanSymposium on Programming, ESOP2000, Berlin, Germany, Springer-VerlagLNCS 1782, March 2000.

M.P. Jones, “First-class Polymorphismwith Type Inference,” in Proceedings ofthe 24th Annual ACM SIGPLAN-SIGACTSymposium on Principles ofProgramming Languages, Paris,January 1997.

M.P. Jones, “Using ParameterizedSignatures to Express ModularStructure,” in Proceedings of the23rd Annual ACM SIGPLAN-SIGACTSymposium on Principles ofProgramming Languages, St.Petersburg Beach, Fla., January 1996.

M.P. Jones, “Simplifying andImproving Qualified Types,” inProceedings of FPCA ‘95: Conferenceon Functional Programming Languagesand Computer Architecture, La Jolla,Calif., June 1995.

M.P. Jones, “A System of ConstructorClasses: Overloading and ImplicitHigher-order Polymorphism,” Journalof Functional Programming, 5, 1,Cambridge University Press, January1995.

S. Liang, P. Hudak and M.P. Jones,“Monad Transformers and ModularInterpreters,” in Conference Recordof POPL’95: 22nd ACM SIGPLAN-SIGACT Symposium on Principles ofProgramming Languages, SanFrancisco, January 1995.

M.P. Jones, Qualified Types: Theoryand Practice, Cambridge UniversityPress, November 1994.

R I C H A R D B . K I E B U R T ZProfessor Ph.D., Electrical EngineeringUniversity of Washington, 1961dick@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Functional programming, programtransformation, domain-specificlanguages, program verification,high-confidence software

R E P R E S E N TAT I V E P U B L I C AT I O N SR. B. Kieburtz, “Real-time Reactive

Programming for EmbeddedControllers,” QAPL 2001,September 2001.

R. B. Kieburtz, “A Logic for RewritingStrategies,” Strategies ’01, June 2001.

R. B. Kieburtz, “Defining andImplementing Closed Domain-SpecificLanguages,” SAIG ’00, September 2000.

R. B. Kieburtz, “Taming Effects withMonadic Typing,” in Proc.3rdInternational Conf. on FunctionalProgramming, ACM Press, April 1998.

R. B. Kieburtz, “Reactive FunctionalProgramming,” in PROCOMET’98,pp. 263-284, Chapman and Hall,June 1998.

R.B. Kieburtz, L. McKinney, J. Bell,J. Hook, A. Kotov, J. Lewis, D. Oliva,T. Sheard, I. Smith and L.Walton,“A Software Engineering Experiment inSoftware Component Generation,” inProceedings of the 18th InternationalConference on Software Engineering,Berlin, March 1996.

R.B. Kieburtz, F. Bellegarde, J. Bell,J. Hook, J. Lewis, D. Oliva, T. Sheard,L. Walton and T. Zhou, “CalculatingSoftware Generators from SolutionSpecifications,” TAPSOFT ’95, Springer-Verlag, series LNCS, 915, 546, 1995.

R.B. Kieburtz, “Programming withAlgebras,” Advanced FunctionalProgramming, E. Meijer and J.Jeuring,eds., Springer-Verlag, Series LNCS,Vol. 925, 1995.

R.B. Kieburtz, “Results of the SDRRValidation Experiment,” PacificSoftware Research Center SoftwareDesign for Reliability and Reuse: PhaseI Final Scientific and Technical Report,Vol. VI, CDRL No. 0002.11, February1995.

J O H N L A U N C H B U R YProfessorPh.D., Computing ScienceUniversity of Glasgow, 1990jl@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Functional programminglanguages, semantics-basedprogram analysis, programtransformation and partialevaluation.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Lewis, M. Shields, E. Maijer and

J.Launchbury, “Implicit Parameters,”Implicit Parameters, ACM Principlesof Programming Languages, 2000.

J. Matthews and J. Launchbury,“Elementary Microarchitecture Algebra,”Computer Aided Verification, 1999.

J. Launchbury, J. Lewis and B. Cook.“On embedding a microarchitecturedesign language within Haskell,”International Conference on FunctionalProgramming, ACM, 1999.

J. Launchbury and A. Sabry,“Axiomatization and Type Safety ofMonadic State,” Proc. ACMInternational Conference on FunctionalProgramming, 1997.

J. Launchbury and R. Paterson,“Parametricity and Unboxing withUnpointed Types,” Proc. EuropeanSymposium on Programming,Linkoping, 1996.

J. Launchbury and S.P. Jones, “Statein Haskell,” J. of Lisp and SymbolicComputation, December 1995.

J. Launchbury and S.P. Jones, “LazyFunctional State Threads,” in Proc.SIGPLAN Programming LanguagesDesign and Implementation, Orlando,Fla., 1994.

A. Gill, J. Launchbury and S.P. Jones,“A Short Cut to Deforestation,” in Proc.SIGPLAN/SIGARCH FunctionalProgramming and ComputerArchitecture, Copenhagen, 1993.

J. Launchbury, “A Natural Semanticsfor Lazy Evaluation,” in Proc. SIGPLANPrinciples of Programming Languages,Charleston, S.C., 1993.

J. Hughes and J. Launchbury,“Projections for Polymorphic First-Order Strictness Analysis,” inMathematical Structures in ComputerScience, 2, p. 301, C.U.P., 1992.

T O D D K . L E E NProfessorPh.D., PhysicsUniversity of Wisconsin, 1982tleen@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Machine learning, local andmixture models, invariance,stochastic learning, withapplications to sanomalydetection, environmental systemsmonitoring, and data coding.Modeling neurobiological systems.

R E P R E S E N TAT I V E P U B L I C AT I O N S

R. Sharma, T.K. Leen and M. Pavel,“Bayesian Image Sensor Fusion UsingLocal Linear Generative Models,”Optical Engineering, 40, p. 1364, 2001.

C. Archer and T.K. Leen, “The CodingOptimal Transform,” in Proceedings ofthe Data Compression Conference2001, IEEE Computer Press, 2001.

C. Archer and T.K. Leen, “FromMixtures of Mixtures to AdaptiveTransform Coding,” in T. Leen,T. Dietterich, V. Tresp, eds., Advancesin Neural Information ProcessingSystems 13, MIT Press, 2001.

W. Wei, T.K. Leen and E. Barnard,“A Fast Histogram-BasedPostprocessor that Improves PosteriorProbability Estimates,” NeuralComputation, 11, p. 1235, 1999.

T.K. Leen, B. Schottky and D. Saad,“Optimal Symptotic Learning:Macroscopic Versus MicroscopicDynamics, Physical Review E, 59,p. 985, 1999.

T.K. Leen and J.E. Moody, “StochasticManhattan Learning: Time-EvolutionOperator for the Ensemble Dynamics,”Physical Review E, 56, p. 1262, 1997.

N. Kambhatla and T.K. Leen,“Dimension Reduction by LocalPrincipal Component Analysis,”zNeural Computation, 9, p. 1493, 1997.

T.K. Leen, “From Data Distribution toRegularization in Invariant Learning,”Neural Computation, 7, p. 974, 1995.

T.K. Leen, “A Coordinate-IndependentCenter Manifold Reduction,” PhysicsLetters, A-174, p. 89, 1993.

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D A V I D M A I E RProfessorPh.D., Electrical Engineeringand Computer SciencePrinceton University, 1978maier@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Database systems (includingobject-oriented databasemanagement systems, queryprocessing, scientific informationmanagement, superimposedinformation and net datamanagement), object-oriented andlogic programming languages,algorithms, bioinformatics andhealth information technology.

R E P R E S E N TAT I V E P U B L I C AT I O N SL. Shapiro, D. Maier, P. Benninghoff,

K. Billings, Y. Fan, K. Hatawal, B.Vanceand Q.Wang, “Exploiting Upper andLower Bounds in Top-down QueryOptimization,” Proceedings of the 5thInternational Conference on DatabaseEngineering and Applications (IDEAS2001), Grenoble, France, July 2001.

J. Shanmugasundaram, K. Tufte,D. DeWitt, J. Naughton and D. Maier.“Architecting a Network Query Enginefor Producing Partial Results,” in TheWorld Wide Web and Databases (ThirdInternational Workshop WebDB 2000),Lecture Notes in Computer Science,Vol. 1997, Springer-Verlag, 2001.

L. Delcambre, D. Maier, S. Bowers,L. Deng, M. Weaver, P. Gorman, J. Ash,M. Lavelle and J. Lyman, “Bundles inCaptivity: An Application ofSuperimposed Information,”Proceedings of the IEEE InternationalConference on Data Engineering,Heidelberg, Germany, April 2001.

P. Gorman, J. Ash, M. Lavelle,J. Lyman, L. Delcambre, D. Maier,S. Bowers and M. Weaver, “Bundles inthe Wild: Tools for ManagingInformation to Solve Problems andMaintain Situation Awareness,”Library Trends 49 (2), Fall 2000.

L. Fegaras and D. Maier, “OptimizingObject Queries Using an EffectiveCalculus,” ACM Transactions onDatabase Systems 25 (4), December2000.

J O H N M AT T H E W SAssistant Professor Ph.D., Computer Science Oregon Graduate Institute, 2000 johnm@cse.ogi.edu

Formal verification, theoremproving, model checking,specification languages,functional and constraint logicprogramming languages.

R E P R E S E N TAT I V E P U B L I C AT I O N SL. Lamport, J. Matthews, M. Tuttle

and Y. Yu, “Specifying and VerifyingSystems With TLA+,” Tenth ACMSIGOPS European Workshop: Can wereally depend on an OS?, Saint-Emilion,France, September 2002 (to appear).

S. Krstic and J. Matthews, “VerifyingBDD Algorithms through MonadicInterpretation,” Proceedings of theThird International Workshop onVerification, Model Checking andAbstract Interpretation, Venice, Italy,January 2002.

J. Matthews, “Recursive FunctionDefinition over Coinductive Types,”Proceedings of the 12th InternationalConference on Theorem Proving inHigher Order Logics, Nice, France,September 1999, LNCS Vol. 1690.

J. Matthews and J. Launchbury,“Elementary MicroarchitectureAlgebra,” Proceedings of the 11thInternational Conference on ComputerAided Verification, Trento, Italy, July1999, LNCS Vol. 1633.

B. Cook, J. Launchbury, and J.Matthews, “Specifying SuperscalarMicroprocessors in Hawk,” Workshopon Formal Techniques for Hardwareand Hardware-like Systems, Marstrand,Sweden, June 1998.

J. Matthews, J. Launchbury, and B.Cook, “Microprocessor Specification inHawk,” Proceedings of the IEEEInternational Conference on ComputerLanguages 1998, Chicago, May 1998.

M E L A N I E M I T C H E L LAssociate Professor Ph.D., Computer Science University of Michigan, 1990 mitchell@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Artificial intelligence, machinelearning, cognitive science andcomplex systems. Computermodeling of perception andanalogy-making. Theory andapplications of evolutionarycomputation. Collectivecomputation in spatially extendedsystems such as cellular automataand neural models. History ofscience and technology.

R E P R E S E N TAT I V E P U B L I C AT I O N SL. Pagie and M. Mitchell, “A compari-

son of evolutionary and coevolutionarysearch,” to appear in InternationalJournal of Computational Intelligenceand Applications, in press.

M. Mitchell, “Analogy-making as aComplex Adaptive System,” in L. Segeland I. Cohen, eds., Design Principlesfor the Immune System and OtherDistributed Autonomous Systems,Oxford University Press, 2001.

M. Mitchell, “Can Evolution ExplainHow the Mind Works? A Review of theEvolutionary Psychology Debates.”Complexity, 3 (3), pp. 17-24, 1999.

E. van Nimwegen, J.P. Crutchfield andM. Mitchell, “Statistical Dynamics ofthe Royal Road Genetic Algorithm,”Theoretical Computer Science, 229 (1),pp. 41-102, 1999.

M. Mitchell, “A Complex-SystemsPerspective on the ‘Computation vs.Dynamics’ Debate in Cognitive Science,”in M. A. Gernsbacher and S. J. Derry,eds., Proceedings of the 20th AnnualConference of the Cognitive ScienceSociety — Cogsci98, pp. 710-715, 1998.

J.P. Crutchfield and M. Mitchell, “TheEvolution of Emergent Computation,”Proceedings of the National Academy ofSciences, USA, 92 (23), p. 10742, 1995.

M. Mitchell, J.P. Crutchfield and P.T.Hraber, “Dynamics, Computation, andthe ‘Edge of Chaos’: A Re-examination,”in G. Cowan, D. Pines and D. Melzner,eds., Complexity: Metaphors, Models,and Reality, Addison-Wesley, 1994.

J O H N E . M O O D YProfessorPh.D., Theoretical PhysicsPrinceton University, 1984moody@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Computational finance, timeseries analysis, analysis offinancial markets, forecastingand statistical learning theoryand algorithms. Applicationsof machine learning to problemsin finance, economics andthe sciences.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Moody and M. Saffell, “Learning

to Trade via Direct Reinforcement,”IEEE Transactions on Neural Networks,Vol. 12, No. 4, July 2001.

J. Moody and H. Yang, “TermStructure of Interactions of ForeignExchange Rates,” in Y. S. Abu-Mostafa,B. LeBaron, A. W. Lo and A. S. Weigend,eds., Computational Finance 1999,MIT Press, 2000.

V. Tresp and J. Moody, “PredictingBlood Glucose Metabolism in Diabetics:A Machine Learning Solution,” IEEETransactions on BioMedicalEngineering, 1999.

J.Moody, L. Wu, Y. Liao and M.Saffell, “Performance Functions andReinforcement Learning for TradingSystems and Portfolios,” Journal ofForecasting, Vol. 17, pp. 441-470,1998.

J. Moody and L. Wu, “HighFrequency Foreign Exchange Rates:Price Behavior Analysis and ‘TruePrice’ Models,” Chapter 2, C. Dunis andB. Zhou, eds., Nonlinear Modelling ofHigh Frequency Financial Data, WileyFinancial Publishing, 1998.

T. Leen and J. Moody, “StochasticManhattan Learning: Time-EvolutionOperator for the Ensemble Dynamics,”Physical Review E, 1997.

J. Moody and T. Rognvaldsson,“Smoothing Regularizers for ProjectiveBasis Function Networks,” in M.C.Mozer, M.I. Jordan and T. Petsche, eds.,Advances in Neural InformationProcessing Systems, 9, MIT Press,1997.

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S H A R O N L . O V I AT TProfessorCo-Director for Center for HumanComputer CommunicationPh.D., Experimental PsychologyUniversity of Toronto, 1979oviatt@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Multimodal and spoken languagesystems, modality effects incommunication (speech, writing,keyboard, etc.), communicationmodels, telecommunications andtechnology-mediatedcommunication, mobile andinteractive systems, human-computer interaction, empiricallybased design and evaluation ofhuman-computer interfaces,cognitive science andresearch methodology.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. L. Oviatt, “Multimodal Interfaces,”

in J. Jacko and A. Sears, eds.,Handbook of Human-ComputerInteraction, Lawrence Erlbaum Assoc.,invited book chapter to appear in 2002.

S. L. Oviatt, P. R. Cohen, L. Wu,J. Vergo, L. Duncan, B. Suhm, J. Bers,T. Holzman, T. Winograd, J. Landay,J. Larson and D. Ferro. “Designing theUser Interface for Multimodal Speechand Gesture Applications: State-of-the-art Systems and Research Directions,”Human Computer Interaction, 15 (4),pp. 263-322, 2000. Reprinted inJ. Carroll, ed., Human-ComputerInteraction in the New Millennium,Addison-Wesley Press, 2001.

S. L. Oviatt, “Multimodal SystemProcessing in Mobile Environments,”Proceedings of the 13th Annual ACMSymposium on User Interface SoftwareTechnology UIST’2000, pp. 21-30,2000.

S. L. Oviatt, “Multimodal SignalProcessing in Naturalistic NoisyEnvironments,” in B. Yuan, T. Huangand X. Tang, eds., Proceedings of theInternational Conference on SpokenLanguage Processing ICSLP’2000,Vol. 2, pp. 696-699, Beijing, China:Chinese Friendship Publishers.

S. L. Oviatt, “Taming RecognitionErrors with a Multimodal Architecture,”Communications of the ACM, 43 (9),pp. 45-51, (special issue on“Conversational Interfaces”),September 2000.

C A LT O N P UProfessorPh.D., Computer ScienceUniversity of Washington, 1986calton@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Transaction processing,distributed databases, scientificdatabases, parallel anddistributed operating systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SL. Liu and C. Pu, “An Adaptive Object-

Oriented Approach to Integration andAccess of Heterogeneous InformationSources,” International Journal onDistributed and Parallel Databases,5 (2), April 1997.

K.L. Wu, P.S. Yu and C. Pu,“Divergence Control for Epsilon-Serializability,” IEEE Transactions onKnowledge and Data Engineering,9 (2), March-April 1997.

J. Biggs, C. Pu, A. Groeninger andP.E. Bourne, “pdbtool: An InteractiveBrowser and Geometry Checker forProtein Structures,” Journal of AppliedCrystallography, 29 (4), 1996.

L. Liu, C. Pu, R. Barga and T. Zhou,“Differential Evaluation of ContinualQueries,” Proceedings of the 16thInternational Conference on DistributedComputing Systems, Hong Kong, May1996.

K. Ramamrithan and C. Pu, “AFormal Characterization of EpsilonSerializability,” IEEE Transactions onKnowledge and Data Engineering, 7 (6),December 1995.

C. Pu, T. Autrey, A.P. Black, C. Consel,C. Cowan, J. Inouye, L. Kethana,J. Walpole and K. Zhang, “OptimisticIncremental Specialization:Streamlining a Commercial OperatingSystem,” Proceedings of the 15thSymposium on Operating SystemsPrinciples, December 1995.

R. Barga and C. Pu, “A Practical andModular Implementation Techniqueof Extended Transaction Models,”Proceedings of the 21st InternationalConference on Very Large Data Bases,Zurich, September 1995.

K. Ramamrithan and C. Pu, “AFormal Characterization of EpsilonSerializability,” IEEE Transactions onKnowledge and Data Engineering, 7 (3),June 1995.

T I M S H E A R DAssociate Professor, DirectorPacific Software Research CenterPh.D., Computer andInformation ScienceUniversity of Massachusettsat Amherst, 1985sheard@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Functional programming, softwarespecification, program generation,meta-programming and staging.

R E P R E S E N TAT I V E P U B L I C AT I O N ST. Sheard, “Accomplishments and

Research Challenges in Meta-Programming,” Second InternationalWorkshop on Semantics, Applicationsand Implementation of ProgramGeneration (SAIG 2001), LNCS 2196,Florence, Italy,September 2001.

T. Sheard, “Generic Unification viaTwo-Level Types and ParameterizedModules,” Sixth ACM SIGPLANInternational Conference on FunctionalProgramming (ICFP’01), ACM Press,Florence, Italy, September 2001.

T. Sheard, Z. Benaissa and E. Pasalic,“DSL Implementation Using Staging andMonads,” Usenix, Second Conference onDomain Specific Languages. Austin,Texas. October 1999.

W. Taha, Z. Benaissa and T. Sheard,“Multi-Stage Programming:Axiomatization and Type Safety,” 25thInternational Colloquium on Automata,Languages and Programming, July1998.

M. Shields, T. Sheard and S. PeytonJones, “Dynamic Typing as Staged TypeInference,” ACM-SIGPLAN-SIGACTSymposium on Principles ofProgramming Languages (POPL ’98),San Diego, January 1998.

T. Sheard, “A Type-Directed, On-Line,Partial Evaluator for a PolymorphicLanguage,” ACM-SIGPLAN Conferenceon Partial Evaluation and Semantics-Based Program Manipulation,Amsterdam, June 1997.

W. Taha and T. Sheard, “Multi-Stage Programming with ExplicitAnnotations,” ACM-SIGPLANConference on Partial Evaluationand Semantics-Based ProgramManipulation, Amsterdam, June 1997.

C L Á U D I O T. S I LVAAssociate ProfessorPh.D., Computer ScienceState University of New Yorkat Stony Brook, 1996csilva@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Computer graphics, scientificvisualization, appliedcomputational geometry, high-performance computing.

R E P R E S E N TAT I V E P U B L I C AT I O N SW. Corrêa, J. Klosowski and C. Silva,

“Out-Of-Core Sort-First ParallelRendering for Cluster-Based TiledDisplays,” 4th Eurographics Workshopon Parallel Graphics and Visualization,2002 (to appear).

M. Alexa, J. Behr, D. Cohen-Or, S.Fleishman, C. Silva and D. Levin,“Computing and Rendering Point SetSurfaces,” IEEE Transactions onVisualization and Computer Graphics,2002 (to appear).

R. Farias and C. Silva, “Out-Of-CoreRendering of Large UnstructuredGrids,” IEEE Computer Graphics andApplications, 21(4), pp. 42-50, 2001.

P. Lindstrom and C. Silva, “A MemoryInsensitive Technique for Large ModelSimplification,” IEEE Visualization2001, pp. 121-126.

J. El-Sana, N. Sokolovsky and C. Silva,“Integrating Occlusion Culling withView-Dependent Rendering,” IEEEVisualization 2001, pp. 371-378.

J. Klosowski and C. Silva, “ThePrioritized-Layered ProjectionAlgorithm for Visible Set Estimation,”IEEE Transactions on Visualization andComputer Graphics, 6(2), pp. 108-123,2000.

B. Wei, C. Silva, E. Koutsofios, S.Krishnan and S. North. “VisualizationResearch with Large Displays,” IEEEComputer Graphics and Applications,20(4), pp. 50-54, 2000.

J. Comba, J. Klosowski, N. Max, J.Mitchell, C. Silva and P. Williams, “FastPolyhedral Cell Sorting for InteractiveRendering of Unstructured Grids,”Computer Graphics Forum, 18, pp.367-376, 1999.

F. Bernardini, J. Mittleman, H.Rushmeier, C. Silva and G. Taubin, “TheBall-Pivoting Algorithm for SurfaceReconstruction,” IEEE Transactions onVisualization and Computer Graphics,5(4), pp. 349-359, 1999.

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D A V I D C . S T E E R EAssistant ProfessorPh.D., Computer ScienceCarnegie Mellon University, 1997dcs@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Operating systems, mobilecomputing, distributedinformation systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SD.C. Steere, A. Goel, J. Gruenberg,

D. McNamee, C. Pu and J. Walpole,“A Feedback-driven ProportionAllocator for Real-Rate Scheduling,”Operating Systems Design andImplementation, February 1999.

J. Walpole, C. Krasic, L. Liu, D. Maier,C. Pu, D. McNamee and D.C. Steere,“Quality of Service Semantics forMultimedia Database Systems,”Proceedings Data Semantics 8:Semantic Issues in Multimedia SystemsIFIP TC-2 Working Conference, Rotorua,New Zealand, January 1999.

D. McNamee, D. Revel, D.C. Steereand J. Walpole, “Adaptive Prefetchingfor Device Independent File I/O,” inProceedings of Multimedia Computingand Networking 1998 (MMCN98),January 1998.

D.C. Steere, “Exploiting the Non-Determinism and Asynchrony of SetIterators to Reduce Aggregate File I/OLatency,” in Proceedings of the 16thACM Symposium on Operating SystemsPrinciples, October 1997.

D.C. Steere and J. Wing, “SpecifyingWeak Sets,” in Proceedings of the 15thInternational Conference on DistributedComputing Systems, pp. 414-421,Vancouver, B.C., June 1995.

M. Satyanarayanan, H.H. Mashburn,P. Kumar, D.C. Steere and J.J. Kistler,“Lightweight Recoverable VirtualMemory,” ACM Transactions onComputer Systems, 12 (1), pp. 33-57,February 1994. Corrigendum: ACMTransactions on Computer Systems, 12(2), pp. 165-172, May 1994.

M. R. Ebling, L.B. Mummert and D.C.Steere, “Overcoming the NetworkBottleneck in Mobile Computing,” inProceedings of the First Workshop onMobile Computing Systems andApplications, pp. 34-36, Santa Cruz,Calif., December 1994.

J O N AT H A N W A L P O L EProfessorPh.D., Computer ScienceUniversity of Lancaster, 1987walpole@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Adaptive systems softwareand its application in distributed,mobile and multimediacomputing environments andenvironmental observation andforecasting systems. Quality ofservice specification, adaptiveresource management anddynamic specialization forenhanced performance,survivability and evolvability oflarge software systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SA. Goel, B. Krasic, K. Li and

J. Walpole, “Supporting Low-LatencyTCP-Based Media Streams,” inProceedings International Workshopon Quality of Service (IWQoS), 2002.

A. Black, R. Koster, J. Huang,J. Walpole and C. Pu, “Infopipes: AnAbstraction for Multimedia Streaming,”to appear in ACM / Springer-VerlagMultimedia Systems Journal, 2002.

K. Li, C. Krasic, J. Walpole, M. Shorand C. Pu, “The Minimal BufferingRequirements of Congestion ControlledInteractive Multimedia Applications,”in Proceedings of the 8th InternationalWorkshop on Interactive DistributedMultimedia Systems - iDMS 2001,Lancaster, UK, September 2001. Alsopublished in Springer-Verlag`s LectureNotes in Computer Science SeriesLNCS 2158, pp. 181-192.

R. Koster, A.Black, J. Huang,J. Walpole and C. Pu, “ThreadTransparency in Information FlowMiddleware,” in ProceedingsMiddleware 2001 — IFIP/ACMInternational Conference onzDistributed Systems Platforms,Heidelberg, Germany, November 2001.Also appears as OGI Technical ReportCSE-01-004.

D. McNamee, J. Walpole, C. Cowan,C. Pu, C. Krasic, P. Wagle, C. Consel,G. Muller and R. Marlet, “SpecializationTools and Techniques for SystematicOptimization of Systems Software,”ACM Transactions on ComputerSystems, Vol. 19, No. 2, pp. 217-251,May 2001.

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C S E | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G | F A C U L T Y

JOINT FACULTY

D R . A N T Ó N I O B A P T I S TA

Environmental Scienceand EngineeringOGI School of Science& Engineering

D R . F R A N C O I S E B E L L E G A R D E

University of FrancheComte, France

D R . D A N H A M M E R S T R O M

Electrical andComputer EngineeringOGI School of Science& Engineering

D R . H Y N E K H E R M A N S K Y

Electrical andComputer EngineeringOGI School of Science& Engineering

D R . J O D Y H O U S E

Electrical andComputer EngineeringOGI School of Science& Engineering

D R . M I S H A P A V E L

Electrical andComputer EngineeringOGI School of Science& Engineering

D R . L E O N A R D S H A P I R O

Department of Computer SciencePortland State University

D R . X U B O S O N G

Electrical andComputer EngineeringOGI School of Science& Engineering

D R . A N D R E W T O L M A C H

Department of Computer SciencePortland State University

D R . J A N P. H . VA N S A N T E N

Electrical andComputer EngineeringOGI School of Science& Engineering

D R . E R I C W A N

Electrical andComputer EngineeringOGI School of Science& Engineering

D R . Y O N G H O N G YA N

Electrical andComputer EngineeringOGI School of Science& Engineering

PART-TIME FACULTY

D R . F R A N Ç O I S E B E L L E G A R D E

University of Franche Comte, France

D R . C H A R L E S C O N S E L

University of Bordeaux

D R . D A V I D G . N O V I C K

University of Texas, El Paso

ADJUNCT FACULTY

D R . L O U G I E A N D E R S O N

Gemstone Systems Inc.

M R . J O N B AT C H E L L E R

Synopsys, Inc.

M R . R O B E R T B A U E R

Rational Software Corp.

D R . C . M I C B O W M A N

Intel Corporation

D R . T E D B R U N N E R

Tektronix Inc.

D R . C H R I S T O P H E R D U B AY

Oregon Health &Science University

D R . E A R L E C K L U N D

Objective Technology Group

M R . R O Y H A L L

Crisis in Perspective

D R . D A V I D H A N S E N

George Fox University

D R . J A M E S L A R S O N

Intel Corporation

M R . S C O T T LY M A N

Merix Corporation

D R . E R I C M E I J E R

Microsoft

D R . G I L N E I G E R

Intel Corporation

M R . S A N J E E V Q A Z I

Intel Corporation

M S . N I V R U T I R A I

Intel Corporation

M R . R A M A K R I S H N A S A R I P A L L I

Network Elements

M R . D A N S A W Y E R

OGI School of Science& Engineering

M R . B R U C E S C H A F E R

Oregon College of Engineeringand Computer Science

M R . R A N D A L S C H W A R T Z

Stonehenge Consulting

D R . TAT I A N A S H U S T E R M A N

Rensselaer Polytechnic Institute

D R . R I C H A R D S P R O AT

AT&T Labs, New Jersey

M S . E L I S A B E T H S U L L I VA N

TruSec Solutions

D R . A N D R E W T O L M A C H

Portland State University

M R . R O B E R T U VA

Ambling Software, Inc.

M R . P E R R Y W A G L E

Computer Science and EngineeringOGI School of Science& Engineering

D R . M A Z I N Y O U S I F

Intel Corporation

48

Ph.D. student B i l l Meyer works in thesemiconductor character izat ion lab.

The primary mission of theDEPARTMENT OF ELECTRICAL AND

COMPUTER ENGINEERING is to provideinnovative and quality graduateeducation, research and technologytransfer in the areas of intelligentsignal processing, semiconductormaterials and devices, computerand systems engineering andbiomedical engineering.To meet these goals, the department offers awide variety of formal courses in our focusareas as well as in specific research areas.The curriculum for each student isdetermined in part by his or her academicbackground and interest, and is set afterdiscussion with a faculty advisor.

The major fields of research activity in thedepartment are:

• Advanced Lithography

• Atmospheric Optics

• Biomedical Engineering

• Biomedical Optics

• Biomorphic Engineering

• Digital Signal Processing

• Display Technology, including Thin FilmTransistors and Phosphors

• Electro-Optic Systems

• Home Health Research and Engineering

• Human Information Processing

• Human-Machine Interface

• Image and Video Processing

• Information Fusion

• Machine Learning

• Micro-Electrical-Mechanical Analysis (MEMS)

• Neural Networks Optical Remote Sensing

• Pattern Recognition

• Processing for Ultra Shallow Device Technology

• Robotics

• Semiconductor Electronic Devices

• Semiconductor Materials, Characterizationand Processing

• Speech Recognition, Enhancement and Synthesis

• Sensors

• Systems Dynamics

• Technology Transfer

• Transient Thermal Processing

• VLSI Architecture for Intelligent Computing

The research activities of the departmentcreate a number of opportunities for studentsto participate, via M.S. and Ph.D. thesisresearch or student projects, in the researchof most of the faculty. Students may becomeinvolved in relatively fundamentalinvestigations (such as semiconductormaterials characterization and processing) orin advanced engineering applications (suchas video display technology or signal/imageprocessing). In all cases, the emphasis is onscientific and engineering investigationshaving well-defined goals and real utility inan atmosphere resembling that of a workingresearch development laboratory. Thedepartment has close ties to local industry,particularly Intel. The academic program,while rigorous, is innovative and individuallyplanned to meet each student’s needs. Thelimited number of students in residenceassures close attention to each student andprogress at a rate determined by thestudent’s ability and effort.

D E P A R T M E N T S E M I N A R S

The ECE department and other localeducational and corporate organizations hostinvited talks and seminars on topics ofinterest in the field of electrical engineering.Although not required for graduate credit, werecommend that all ECE students attendthese informative meetings. Seminarschedules are generally posted in thedepartment each quarter. Additionally, theECE department and Portland StateUniversity’s Department of Electrical andComputer Engineering jointly sponsor thePortland Area Semiconductor Seminar Series(PASSS) and the Information SciencesSeminar Series (ISSS). These seminars arefree of charge and offer an opportunity tomeet leading local and nationally recognizedEE professionals and learn about the latesttechnical advancements in the high-technology industry.

ADMISSIONS REQUIREMENTSThe Department of Electrical and ComputerEngineering at the OGI School offers both aMaster of Science degree and Ph.D in

Department of Electrical

and Computer Engineering

www.ece.ogi.edu

I N T E R I M D E P A R T M E N T H E A D

John Carruthers

503 748-1616E-mail: carruthers@ece.ogi.edu

D E P A R T M E N T A D M I N I S T R A T O R

Don Johansen

503 748-1315E-mail: johansen@ece.ogi.edu

A C A D E M I C C O O R D I N A T O R

Barbara O lsen

503 748-1418E-mail: bolsen@ece.ogi.edu

A D M I N I S T R A T I V E C O O R D I N A T O R

Joan S ims

503 748-1144E-mail: jsims@ece.ogi.edu

E C E G E N E R A L I N Q U I R I E S

503 748-1130E-mail: ecedept@ece.ogi.edu

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Electrical Engineering. Students must havea Master of Science degree acceptable tothe ECE department to be considered forthe Ph.D. program. The M.S. degree may befrom the OGI School or another acceptableinstitution of higher education.

Admission requirements are the same asthe general OGI School requirements. TheTOEFL is required of all international studentapplicants for both the M.S. and Ph.D.programs. However, the GRE is not requiredfor the part-time M.S. program or the full-time M.S. program in the ECE department. Itis recommended for M.S. students who maywant to apply for the Ph.D. at a later date.The GRE is required for all applicants to thePh.D. program.

Prerequisite: B.S. or M.S. in physics,applied physics, engineering physics,electrical engineering or equivalent. Sincemodern electrical engineering programs arebroad and diverse, students withundergraduate degrees in appliedmathematics as well as other branches ofengineering are encouraged to apply.

DEGREE REQUIREMENTSM A S T E R O F S C I E N C E ( M . S . ) P R O G R A M

The M.S. program is designed to enableprofessionals or recent graduates to adaptquickly to the changing needs of their fields.ECE’s M.S. program offers three degreeoptions for full-time and part-time students.The M.S. degree requires 48 credits. It maybe obtained with a non-thesis option, a non-thesis project option or a thesis option. Allcourses, non-thesis research and thesisresearch must be taken for graded credit tobe counted toward the M.S. degree. Coursestaken outside of the OGI School’s ECEdepartment must also be taken for gradedcredit; Pass/No Pass is not acceptable.Courses taken from other OGI Schooldepartments or from other institutions mustbe approved by both the student’s facultyadvisor and the ECE departmentadministrator. A minimum grade pointaverage of 3.0 must be maintainedthroughout the degree program. A student’scourse of study should be reviewed andapproved by a faculty advisor. Students arelimited to 12 credits per quarter unless theyobtain a waiver from their advisor.

N O N - T H E S I S O P T I O N

The non-thesis option requires completion ofat least 48 credits of graded courses. Whilestrongly encouraged to focus on courseswithin the ECE department, students maytake up to 24 credits of course work in otherOGI academic departments, provided thecourses fall within the degree requirementsset by the ECE department. For studentsseeking an M.S. degree in ElectricalEngineering, a minimum of 24 credits ofcourse work must be taken from the OGISchool’s ECE department curriculum. Allcourses, regardless of school department,must be taken for graded credit.

N O N - T H E S I S P R O J E C T O P T I O N

The non-thesis project option requirescompletion of at least 48 graded credits,comprising at least 40 credits of course workand at least 8 credits of research (ECE 610).The research project is more limited in scopethan a thesis and may include experimentalwork, a critical literature review or a specificcontribution to a larger project. For the non-thesis project the student must submit awritten report to satisfy the research graderequirements. In selecting this option thestudent must work with a faculty advisor toformulate an appropriate project.

T H E S I S O P T I O N

The M.S. thesis option requires completion ofat least 32 credits of graded course work andat least16 credits of graded research (ECE700). The thesis is an original independentwork resulting in publication. The student willwork with a faculty member to select coursesand design an appropriate thesis researchprogram. A thesis committee is assigned toguide and advise the research program. Thestudent must submit the thesis in writing anddefend it orally. Thesis research creditsearned toward an M.S. degree must begraded. At a minimum, the thesis committeemust include three OGI School faculty, oneperson from outside the OGI School, and anyother committee members deemed practical.All thesis committee members must holdPh.D. degrees.

S U M M E R P R O J E C T S

Although not required, students may want toconsider taking at least one project coursefor the M.S. degree. Because most facultyuse the summer to do research, it is an idealtime to do a project. In addition, there may

often be summer internships available atlocal companies, which also qualify. Thedepartment is not required to provideprojects for students, but usually there aremany opportunities. Projects can involve realimplementation and often are done in a teamsetting, making them ideal preparation for acareer in engineering. Projects are done asSpecial Topics courses, ECE 580-ECE, andthey are graded. The specifics of a projectare the responsibility of the sponsoringfaculty member. Industrial adjunct facultymay also advise projects.

T R A N S F E R C R E D I T S

Up to 12 credits from accredited institutionsmay be transferred to the OGI School.Students may petition for transfer of up to 18credits from the following institutions:Portland State University, Oregon StateUniversity and the University of Oregon.Students petitioning for acceptance oftransfer credits should provide (1) writtenrequest, (2) detailed course descriptions frominstitution catalogs and/or web site, and (3)original transcript(s) verifying credit hoursand grades earned.

Upon approval from the department head,students may apply a maximum of 21 creditsfrom other OGI School departments towardtheir degree. Acceptance of all transfercredits will be subject to review and approvalby the ECE department’s CurriculumCommittee. In certain cases, preapproval oftransfer credit courses is recommended toavoid transfer of courses not relevant todepartment’s academic program. Transfercredits will not replace the degree/creditrequirement of 24 credits of graded coursesfrom the OGI School’s ECE departmentcurriculum. Cross-listed courses may not beused as part of these 24 credits.

P H . D . P R O G R A M

The OGI School offers a Ph.D. degreeprogram in Electrical Engineering from theECE department. Admission to the Ph.D.program generally requires a prior M.S. inElectrical Engineering, Computer Engineeringor a related field, whether from the OGISchool or another institution. Upon entry intothe program a Student Program Committee(SPC) of three faculty members is formed.The student discusses feasible researchareas and eventual research directions withthe committee and together they chart an

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individualized course of study to prepare thestudent for the qualifying exam.

The qualifying exam may be written or oralor both, at the discretion of the SPC, and mayadditionally involve a formal researchproposal. It is usually taken within 12months of enrolling in the program, and maybe scheduled at any time of year. The amountof course work to be completed before takingthe qualifying exam depends on theindividual’s level of preparation at entry. Atminimum, three graded courses from the OGISchool’s ECE department must be completedbefore taking the exam.

After passing the qualifying exam, thestudent works with the SPC to develop aresearch plan specifically for thedissertation. Ph.D. students are requiredto make annual reports to the SPC on thestatus of their research, and may be calledupon to deliver timely research presentationsas the work progresses. The dissertationitself must constitute a significant researchcontribution and must be of publishablequality. The Ph.D. degree is granted followingthe presentation of an acceptabledissertation and successful oral defense.

There is a two-year residency requirementfor Ph.D. students.

ECE CURRICULUM FOCUS AREASStudents may focus exclusively withinone area of specialization or may combinetwo or more focus areas into a broadercourse of study.

• Semiconductor Devices, Materialsand Processing

• Signal, Speech and Image Processing

• Communications and Networking

• Computer Engineering and Design

• Biomedical Engineering

Students should refer to the ECEdepartment’s 12-month Curriculum Plan tolearn what courses may be offered in the2002-2003 academic year. There arerecommended core courses and tracks formost focus areas.

S E M I C O N D U C T O R D E V I C E S , M AT E R I A L SA N D P R O C E S S I N GECE offers a broad spectrum of courses insemiconductor synthesis, processing, device

physics and integrated circuits. Courses aredesigned to prepare the student for growth areasin semiconductor-based technology. Specificgroupsof courses are designed to provide a strong,cohesive and marketable body of knowledge indevice processing, device physics and design,and integrated circuit design. Students may tailorcourse selections to create unique specializationsin preparation for careers in this importanttechnology field.

SEMICONDUCTOR DEVICES, MATERIALS AND PROCESSING

Recommended core classes

1. ECE 515 Introduction to Semiconductors

2. ECE 580-DOE Statistical Process Control and DOE

3. Choose one device class from:

ECE 512 Advanced MOSFET Analysis I: DC Models

ECE 516 Fundamental Semiconductor Device Structures

ECE 580-OSD Operation of Semiconductor Devices

The following course tracks are recommended for anyone whowishes to specialize in a particular area of microelectronics.

SEMICONDUCTOR DEVICES/CIRCUITS

ECE 512 Advanced MOSFET Analysis I: DC Models

ECE 513 Advanced MOSFET Analysis II: Dynamic Models

ECE 514 MOSFET Modeling for VLSI Circuit Design

ECE 516 Fundamental Semiconductor Device Structures

ECE 517 Advanced Semiconductor Devices: Structuresand Materials

ECE 571 Analog Integrated Circuit Design

ECE 572 Digital Integrated Circuit Design

ECE 574 CMOS Digital VLSI Design I

ECE 575 CMOS Digital VLSI Design II

SEMICONDUCTOR PROCESSING AND MATERIALS

ECE 535** Thin Film Deposition and Applicationsin Semiconductors

ECE 560 Microelectronic Device Fabrication I

ECE 561 Microelectronic Device Fabrication II

ECE 562 Microelectronic Device Fabrication III

ECE 563* Plasma Processing of Semiconductors I

ECE 568 Failure and Reliability in Microelectronics

ECE 580-EMI Electroplating for Microelectronic Interconnects

ECE 580-MPE Modern Photolithographic Engineering

ECE 580-RFD** Reliability and Failure of Electronic Devices,Packages and Assemblies

ECE 580-SMVI Simulation and Modeling of VLSI Interconnect

ECE 580-TP Technology of Photoresists

SEMICONDUCTOR MATERIALS AND DEVICE CHARACTERIZATION

ECE 565 Analytical Scanning Electronic Microscopy

ECE 566 Focused Ion Beam Technology

ECE 567 Transmission Electronic Microscopy

ECE 568 Failure and Reliability in Microelectronics

ECE 569** Electronic Materials andDevice Characterization

MEMS AND SENSORS

ECE 580-CCM Capstone Course — MEMS andMicrosensors Project

ECE 580-FSM Fundamentals of Sensors and MEMS Fabrication

ECE 580-ISM Introduction to Sensor Microfabrication

ECE 580-MEM Microelectromechanical Systems

ECE 580-SSE Semiconductor Sensors

The following classes are required for Ph.D. students and areelectives for MS students. However, these are recommendedfor MS students planning to continue with our Ph.D. program.

ECE 507 Introduction to Electromagnetics forModern Applications

ECE 508 Electromagnetics for Modern Applications II

ECE 509 Electromagnetics for Modern Applications III

ECE 510* Introduction to QM for Electrical andComp. Eng.

ECE 511* Advanced QM for Electrical and Comp. Eng.

*May be offered in alternating years,beginning 2002-03

** May be offered in alternating years,beginning 2003-04

SIGNAL, SPEECH AND IMAGE PROCESSING

This focus area consists of recommended corecourses, with open slots that allow extra coursesfor specialization in one of several related areas.

The recommended basic core curriculum:Choose 4:

• ECE 541** Signal Processing for Multimedia Applications

• ECE 550 Linear Systems

• ECE 551 Introduction to Digital Signal Processing

• ECE 554 Adaptive and Statistical Signal Processing

• ECE 555 Engineering Optimization

• PSU-ECE563-663 Introduction to Information Theory

Several specializations are possible:

SPEECH SYSTEMSRequired:

• ECE 545 Introduction to Speech Systems

Choose 3:

• ECE 540 Auditory and Visual Processing by Humanand Machine

• ECE 580- Hidden Markov Models for Speech RecognitionHMM

• ECE 580-SSL Structure of Spoken Language

• ECE 580-SSY Speech Synthesis

• CSE 550 Spoken Language Systems

• CSE 564 Human-Computer Interaction

IMAGE PROCESSINGChoose 3:

• ECE 540 Auditory and Visual Processing by Humanand Machine

• ECE 542 Introduction to Image Processing

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• ECE 543 Introduction to Digital Video Processing

MACHINE LEARNINGChoose 4:

• ECE 580-HMM Hidden Markov Models for Speech Recognition

• CSE 540 Neural Network Algorithms and Architecture

• CSE 547 Statistical Pattern Recognition

• CSE 560 Artificial Intelligence

• CSE 58X Machine Learning

Other recommended classes:

• ECE 526 Introduction to Communication

• ECE 527 Introduction to Digital Communication

• ECE 552 Digital Signal Processing II

• ECE 580- Applied Functional AnalysisAFA**

• ECE 580-BSP Biomedical Signal Processing

• CSE 546 Data and Signal Compression

Prerequisites include ECE 544, Introduction toSignals, Systems and Information Processing; andECE 525, Analytical Techniques in StatisticalSignal Processing and Communications, orequivalent classes. In addition, students shouldhave a basic competency in probability, complexvariables and linear algebra. If a student doesnot possess these competencies, he or she shouldtake undergraduate courses in these areas atPortland State University to attain proficiency.It’s recommended that the student also performan M.S. project of 4-8 credits.

** May be offered in alternating years,beginning 2003-04

COMMUNICATIONS AND NETWORKING

Job opportunities in communications and computernetworking are exploding. This field is enjoyingcontinuous growth because of the rapid progress ofwireless communications, optical fiber technology,media-rich communication and the need to movelarger and larger amounts of information globally.

The basic core curriculum consists of:

• ECE 526 Introduction to Communication

• ECE 527 Introduction to Digital Communication

• ECE 580-CN Introduction to Computer Networks

• ECE 580- Digital Fiber-Optic Communication SystemsDCS**

• ECE 580-WCSI Wireless Communications Systems I

There are several specializations:

COMMUNICATION SIGNAL PROCESSING

• ECE 541** Signal Processing for Multimedia Applications

• ECE 551 Introduction to Digital Signal Processing

• ECE 552 Digital Signal Processing II

• ECE 554 Adaptive and Statistical Signal Processing

NETWORKING AND MULTIMEDIA COMMUNICATION

• ECE 541** Signal Processing for Multimedia Applications

• ECE 543 Introduction to Digital Video Processing

• ECE 580-IE Internet Engineering

• ECE 580-MC Multimedia Communications

COMMUNICATION SYSTEMS

• ECE 550 Linear Systems

• ECE 574 CMOS VLSI Design

• ECE 575 Advanced CMOS VLSI Design

• ECE 580-AC Analog CMOS Design

• ECE 580-DDC Design of Digital Communication Circuits

• PSU ECE Introduction to digital subscriber line (DSL)510-OC6

It’s recommended that students perform an M.S.project (of at least 8 credits) that involves acommunication application.

COMPUTER ENGINEERING AND DESIGN

Computer engineering is a hybrid program utilizingelectrical engineering and computer sciencecourses. It involves the engineering aspects ofhardware and software as well as the underlyingtheory of computation.

The Computer Engineering focus area consists ofone track with recommended core courses, withopen slots that allow extra courses forspecialization in one of several related areas.

The recommended core assumes knowledge ofbasic logic design, circuits and C programming.If a student does not possess these competencies,it’s recommended that he or she take under-graduate courses in these areas at Portland StateUniversity to attain proficiency.

The basic recommended core curriculum is:

• ECE 559 Design with Programmable Logic

• ECE 573 Advanced Logic Design

• ECE 574 CMOS VLSI Design

• ECE 575 Advanced CMOS VLSI Design

There are several specializations:

CIRCUITS

• ECE 500 Introduction to Electronicsand Instrumentation

• ECE 515 Introduction to Semiconductors

• ECE 558 High Speed Interconnect Design

• ECE 572 Digital IC Design

• ECE 580- Selected Topics in Analog IC DesignACD

• PSU-ECE Low Power IC Design510-6

• PSU-ECE Digital Integrated Circuit Design II (Test)526

• OSU-ECE 527 VLSI System Design

SIGNAL PROCESSING

• ECE 542 Introduction to Image Processing

• ECE 551 Introduction to Digital Signal Processing

• ECE 552 Digital Signal Processing II

• ECE 554 Adaptive and Statistical Signal Processing

• ECE 580-BSP Biomedical Signal Processing Communication

COMMUNICATION

• ECE 526 Introduction to Communication

• ECE 580-AC Analog CMOS Design

• ECE 580-CN Introduction to Computer Networks

• ECE 580- Wireless Communication Systems IWCSI

• CSE 524 TCP/IP Networking Protocols

COMPUTER ARCHITECTURE

• ECE 580-COD Computer Organization

• CSE 521 Introduction to Computer Architecture

• CSE 522 Advanced Computer Architecture

• CSE 526 Introduction to Operating Systems

• OSU-ECE 527 VLSI System Design

Students are encouraged to perform an M.S.project (of at least 8 credits) that involves design.

BIOMEDICAL ENGINEERING

Biomedical engineering is a rapidly developing,broad field of study at the interface betweenengineering and basic biology and medicine, suchas biomedical signal processing, imaging, sensing,biomaterials, information technology,bioinformatics and many other areas. The ECEbiomedical engineering program collaborates withother departments in the OGI Schools of Scienceand Engineering, Medicine, Dentistry and Nursingto offer students a variety of research andclassroom opportunities to acquire breadth anddepth of knowledge and expertise in this field.

In particular, ECE currently has a core of expertisein two areas, Biomedical Optics and TissueEngineering, providing research opportunities andcourses in optical sensing, imaging and imageanalysis, laser-tissue interactions, biomechanicsand tissue engineering. Research activities areexpanding to cover biomedical sensors andinstrumentation, biomedical signal processing andanalysis, computational neuroscience, data-miningand technology in health care delivery. The latterincludes intelligent rehabilitation and assistivetechnologies for future health care delivery insmart homes (home health) using wearable sensorsand networked devices, exploiting intelligent datafusion and incorporating the latest results infunctional genomics.

Because of the diversity of the field, each studentis encouraged to devise a program tailored to hisor her specific career objectives. Courses availablerange from introductory courses in biology andmedicine, biomedical sensors and instrumentation,biomedical optics and laser-tissue interactions,biomaterials, biomechanics, neuroscience,

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molecular engineering, audio and video processingby humans and machines, biomedical signalprocessing, biological pattern recognition and data-mining, bioinformatics and medical informatics.To be prepared for the challenge, students areexpected to take, in addition to specific biomedicalengineering courses, a number of basic engineeringcourses in statistical signal analysis, andrecognition, digital signal processing, imageprocessing, pattern recognition, databases andinformation retrieval.

Note: Students electing this focus area areencourage to consult with their advisor as to whichrecommended courses are most appropriate fortheir goals.

ECE 500 Introduction to Electronics and Instrumentation

ECE 525 Analytical Techniques in Statistical Signal Processing & Communications

ECE 532* Biomedical Optics I: Tissue Optics

ECE 533* Biomedical Optics II: Laser Tissue Interactions

ECE 534* Biomedical Optics III: Engineering Design

ECE 540 Auditory and Visual Processing by Humanand Machine

ECE 541** Signal Processing for Multimedia Engineering

ECE 542 Introduction to Image Processing

ECE 551 Introduction to Digital Signal Processing

ECE 552 Digital Signal Processing II

ECE 554 Adaptive and Statistical Signal Processing

ECE 580-CLI Computational Approaches to Laser Interaction with Biological Tissues

ECE 580-CLT Computational Approaches to LightTransport in Biological Tissues

ECE IB1 Biomaterials I

ECE IB2 Biomaterials II

ECE 580-ONE Optical Non-Destructive Evaluation

ECE 580-PGO Physical and Geometric Optics

Other OGI School Courses

CSE 514 Introduction to Database Systems

CSE 540 Neural Network Algorithms and Architectures

CSE 544 Introduction to Probability andStatistical Inference

CSE 547 Statistical Pattern Recognition

CSE 548 Statistical Computing

CSE 564 Human-Computer Interaction

ESE 500 Introduction to Discrete Methods

ESE 550 Environmental Microbiology

ESE 570 Principles of Toxicology and Risk Assessment

*May be offered in alternating years,beginning 2002-03

** May be offered in alternating years,beginning 2003-04

COURSE DESCRIPTIONS ECE 500 Introduction to Electronicsand InstrumentationReview of fundamental electronics components anddesign: passive components, transistor circuits, opamps, RC circuits, frequency domain and timedomain response. Feedback theory, op amp limita-tions, precision op amp circuits. Noise, interference,grounding, and shielding. Phase-locked loops, lock-in amplifiers. Practical advice on componentselection and circuit design. Equipment and circuitdemonstrations in class. Homework includes Pspicecircuit simulation problems. 4 credits

ECE 507 Introduction to Electromagnetics forModern ApplicationsThis series (ECE 507-509) cover essentials of elec-tromagnetic theory for modern practitioners in suchareas of engineering and applied science as semi-conductor devices; IC design; optics, lasers andoptoelectronics; wireless and optical communica-tions; electronic displays; electron and ion beamtechnology; vacuum electronic devices; and variousbiomedical applications. The course is practicallyoriented and presents both analytical and numericalmethods. The first course introduces basic experi-mental laws and theoretical concepts. Laplace andPoisson equations for static electric and magneticpotentials. Basic properties of electromagneticmaterials. Maxwell equations for static and time-varying fields. Wave equations and Poyntingtheorem. Finite-difference numerical solution ofboundary-value problems. Prerequisite: Someundergraduate electromagnetism, calculus throughordinary and partial differential equations, somevector calculus, or consent of instructor. 4 credits

ECE 508 Electromagnetics for Modern Applications IIThis course introduces additional mathematicaltools and covers topics basic to circuit design, semi-conductor device operation, IC design, optics,transmission lines and antenna design. Waves inconductors and skin effect are included. Retardedpotentials for time-varying fields. Electromagneticsof lumped-element circuit theory. Plane wave prop-agation, reflection and refraction. Polarizationstates and Stokes parameters. Analytical methodsfor boundary-value problems and numerical solutionby boundary-element method. Introductory (TEM)field theory of transmission lines and its relation tocircuit model. Prerequisite: ECE 507 and some lin-ear algebra or consent of instructor. 4 credits

ECE 509 Electromagnetics for Modern Applications IIIThis course covers advanced transmission-line andwaveguide field theory for high speed interconnects,microwave and optical waveguides; resonant cavi-ties for frequency control and lasers; and radiationbasics for communications and optics. Topicsinclude TE and TM transmission-line and waveguidemodes. Field theory of multiple-conductor transmis-sion lines: Modes, coupling, crosstalk andtermination. Dielectric waveguides. Resonant cavi-ties. Radiation from antennas and apertures.Additional topics as time permits, chosen from:electromagnetic properties of materials; variational

formulation of field problems and finite elementnumerical solution; analytical and numerical calcu-lation of charged-particle motion in electromagneticfields; suggestions of students. Prerequisite: ECE508 and some linear algebra or consent of instructor.

4 credits

ECE 510 Introduction to Quantum Mechanics forElectrical and Computer EngineersCourses ECE 510-511 present basic quantum theo-ry for understanding practical applications such assolid state devices, lasers and other optoelectronicdevices, properties of electronic materials, band-gap engineering, quantum effects due to shrinking ICfeature sizes, quantum-dot and quantum-welldevices and quantum computing. The first courseintroduces basic concepts and results essential tounderstanding solid-state band structure, devicesbased on tunnelling and quantum-well devices.Topics include a review of classical mechanics. TheSchroedinger equation, postulates of QuantumMechanics and basic Hilbert-Dirac formalism. Thefree particle. One-dimensional quantum-well boundstates and tunneling through potential barriers.Bloch functions in periodic potentials and the originof solid-state band structure. Prerequisite: Calculusthrough ordinary and partial differential equations,or consent of instructor. 4 credits

ECE 511 Advanced Quantum Mechanics for Electricaland Computer EngineersThis course covers two- and three-dimensionalapplications and introduces new physical phenome-na, mathematical formulations and tools essentialfor understanding materials science, lasers, solidstate devices, quantum optics and quantum comput-ing. Covered are two- and three-dimensionalquantum wells. The simple harmonic oscillator andalgebraic methods. Angular momentum and spin.Matrix formulation of Quantum Mechanics. Atomicstructure. Approximation methods, including per-turbation theory. Interaction of matter andelectromagnetic waves. Prerequisite: ECE 510 plussome linear algebra, or consent of instructor.

4 credits

ECE 512 Advanced MOSFET Analysis I: DC Models“No IC designer’s education is complete withoutdetailed exposure to MOS transistor operation andmodeling” (J.Tsividis). This is the first part of athree-course sequence addressing this importantneed. Starting with contact potentials and proper-ties of semiconductor surfaces, we analyze (withinthe charge sheet and depletion approximations), thecharges and potentials in MOS capacitors fromaccumulation to flat band to inversion (including therole of oxide charge). With these results we discussvarious MOSFET dc current models based on thegradual channel approach: Symmetric (body-refer-enced) models and the concept of extrapolatedpinch-off potential, source-referenced models andthe concept of extrapolated threshold voltage(including body effect); more compact models forstrong inversion and for sub-threshold behavior(weak inversion); interpolation models for moderateinversion. The compact models are then modified ina semi-empirical way to describe the effects of ion

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implanted channels (including buried channels), aswell as those due to small channel dimensions(channel length modulation, effective modification ofthreshold voltage in short and narrow channels,velocity saturation, series resistance effects, thinoxide/shallow deletion effects). Breakdown andpunch-through are discussed qualitatively.Prerequisites: basic electrostatics, semiconductorsand circuits. 4 credits

ECE 513 Advanced MOSFET Analysis II: Dynamic Models.Based on ECE 512 the dynamic large-signal andsmall-signal models of MOSFET operation aredeveloped for digital and analogue applicationsrespectively: Large-signal modeling is analyzed indetail for quasi-static operation (neglecting transit-time effects) in terms of the charges flowing in andout of all four MOSFET terminals covering the vari-ous charge conditions in the semiconductor(accumulation to inversion); non-quasi-static model-ing is introduced to include transit-time effects inhigh-speed applications and is illustrated for achannel in strong inversion. Small-signal modelingfor the description of equivalent circuit elementsstarts with a simplified quasi-static analysis atlowand medium frequencies at all channel conditions(weak to strong inversion). Then this model isextended to high frequencies in a complete quasi-static mode that includes transcapacitors at highestfrequencies near gain cut-off. Non-quasi-staticmodeling is discussed and applied to channels instrong inversion. Finally, noise models are devel-oped to supplement the derived equivalent circuitswith the proper noise source elements. Pre-requisite:ECE 512. 4 credits

ECE 514 MOSFET Modeling for VLSI Circuit DesignA comprehensive study of state-of-the-art compactmodels used in circuit simulators for VLSI designand their underlying physics. Topics coveredinclude: high speed and high frequency (non-quasi-static) models, quantum effects, high field andhydrodynamic effects. Substrate current and gatecurrent modeling with applications for reliabilitymodeling in circuit simulators and circuit designimpact. Discussion of device scaling issues, funda-mental limits to mos device and circuit per-formance. A review of novel device architectures forfuture mos devices, in particular SOI devices, dou-ble gate devices, their physics and operation interms of analytic models. Study of parameterextraction, optimization and device characterizationtechniques required for developing compact models.Development of statistical and mismatch models forthe mosfet. Radio frequency models for the mosfetand S parameter characterization. Review and com-parison of existing mosfet models such as BSIM4,EFLKV, PCIM. Implementation of mos models in cir-cuit simulators. Project work will include evaluatingvarious models in SPICE, and their impact on cir-cuits, as well as understanding device operationusing a 2D device simulator (MINIMOS) and a cou-pled 1D Schrodinger-Poisson Solver (SPIN).

4 credits

ECE 515 Introduction to Electronic MaterialsThe fundamental properties and concepts needed tounderstand electronic materials are introduced in

this course. We begin with crystals, their structureand bonding, and thermal properties. We thenexamine electron interactions in metal and semi-conductor crystals. The physics behind the energybandgap in semiconductors are examined, and usedultimately to derive the energy band structure,effective mass and equilibrium carrier statistics.Next, we use these statistics to define carrier trans-port in semiconducting materials. Finally, we studyand understand dielectrics and insulators, magneticproperties, superconductivity and the opticalresponse of semiconductors. This course is recom-mended if you have never taken a semiconductordevice course (or if you need a refresher). The mate-rials covered will provide you with background forother semiconductor device, processing and charac-terization courses offered at OGI. Although quantummechanics is not required, taking the course willhelp achieve a more advanced understanding of theconcepts discussed in this class. 4 credits

ECE 516 Fundamental Semiconductor Device Structures Semiconductor bulk, junction and surface proper-ties. We develop the fundamentals of semiconductorstructures, bulk defects, mechanisms affectingelectron/hole transport at low and high electricfields, junction formation/stability (p-n, metal-semiconductor, and metal-insulator) and relation-ships between semiconductor properties and deviceperformance. The underlying concepts of minoritycarrier and majority carrier devices are expoundedand clarified. 4 credits

ECE 517 Advanced Semiconductor Devices:Structures and Materials The complex interplay between materials proper-ties, fabrication technologies and device perform-ance is examined in the context of elucidating suchcurrent technology developments as silicon on insu-lator (SOI), high-K dielectrics, SiGe heterojunctions,heterojunction bipolar transistors (HBT), pseudo-morphic high electron mobility transistors(PHEMT), Vertical Cavity Surface Emitting Lasers(VCSEL), quantum dots, single electron transistorsand organic semiconductors. 4 credits

ECE 520 Transmissionline-Line TheoryMaxwell’s equations, field analysis of transmissionlines, circuit analysis of transmission lines (telegra-pher’s equations, equivalent circuit models),microstrip, stripline, signal integrity (transientresponse, impedance mismatch, reflections, bouncediagrams), skin effect, dispersion, discontinuities(bends, vias), multiconductor transmission lines inmultilayered dielectric systems ([L] and [C] matri-ces). Numerical analysis of multiconductortransmission-line networks (method of momentstechnique); Crosstalk. 4 credits

ECE 521 Microwave Engineering ConceptsTraveling waves and transmission-line concepts;Time harmonic transmission-line equations; Smithchart (construction and applications), impedancematching networks, impedance transformation,matrix representation of multiport transmission-linenetworks ([S], [Z], [Y], and chain matrices), [S]parameters properties, matrix conversions ([Z] to[S] and vice-versa); numerical analysis of transmis-

sionline discontinuities at microwave engineeringfrequencies (Finite Difference Time Domain, FDTDtechnique). 4 credits

ECE 525 Analytical Techniques in Statistical SignalProcessing and CommunicationsDevelopment of the mathematical techniques need-ed to analyze systems involving random variablesand/or stochastic processes with particular applica-tion to communications and instrumentation. Topicsinclude Bayes Theorem (discrete and continuousforms), Tchebycheff inequality, Chernoff bound, cen-tral limit theorem, stationary processes and linearsystems, mean square estimation, Poisson process,Gaussian process, Markoff process and series rep-resentations. MATLAB and the MATLAB StatisticsTool Box are used in this course. 4 credits

ECE 526 Introduction to CommunicationAn overview: sources, channels and limits to com-munication, signals and spectra, distortionlesstransmission, linear and nonlinear distortion, trans-mission loss. Random Signals: probability andrandom variables, probability functions, statisticalaverages, probability models, random processes,random signals. Signal transmission with noise:noise models, signal-to-noise ratio, pulse detectionand matched filters. Analog communication: band-pass systems and signals, double-sided amplitudemodulation (AM), modulators and transmitters, sup-pressed-sideband amplitude modulation, frequencyconversion and demodulation, frequency/phasemodulation (FM/PM), transmission bandwidth anddistortion, generation and detection of FM/PM, interference, receivers for FM/PM, frequencydivision multiplexing, a case study of analog com-munication systems, noise in analog communicationsystems. 4 credits

ECE 527 Introduction to Digital CommunicationIntroduction to communications systems, compo-nents, signals and channels, sampling, quantization,pulse amplitude modulation (PAM), pulse code mod-ulation (PCM), quantization noise, time divisionmultiplexing, delta modulation. Digital communica-tions: baseband signals, digital PAM, eye diagram,equalization, correlative coding, error probabilitiesin baseband digital transmission, bandpass trans-mission, digital amplitude shift keying (ASK),frequency shift keying (FSK), phase shift keying(PSK) and quadrature shift keying (QPSK), errorprobabilities in bandpass digital transmission, acase study of digital commmunication systems.Introduction to information theory: fundamental lim-its in communications, channel capacity andchannel coding, signal compression. 4 credits

ECE 532 Biomedical Optics I: Tissue OpticsLight propagation in tissue: This course treats lighttransport in scattering and absorbing media such asbiological tissue. Light transport is modeled using avariety of theories and computational techniques,including Monte Carlo simulations and approximatesolutions of the radiative transport equation.Steady-state and time-dependent problems aretreated. Spectroscopy and fluorescence measure-ments are introduced. Optical imaging techniquesare presented. Students learn the basics required

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for design of optical devices for therapy and diag-nostics. Course offered every other year; nextsession, academic year 2002-03. 4 credits

ECE 533 Biomedical Optics II: Laser-Tissue InteractionsPhysics of laser-tissue interactions: The coursetreats the immediate physical processes thataccompany the absorption of light by biological tis-sues, including photochemical reactions, heatingand tissue coagulation, vaporization, creation ofplasmas and production of stress waves in tissue.Such processes are modeled using finite-differencetechniques. Applications in medicine and biology arediscussed. Prerequisites: ECE 532 or permission ofinstructor. Course offered every other year; nextsession, academic year 2002-03. 4 credits

ECE 534 Biomedical Optics III: Engineering DesignStudents work as a team in preparing five businessplans throughout the quarter. Each business plan isdevoted to a potential medical device or protocolusing optical technologies. The team is divided intoa CEO, scientific officer, marketing manager, regu-latory affairs manager and manufacturing manager.The roles are rotated among the students for eachbusiness plan. Feasibility studies are conducted in alaboratory exercise designed by the students. Theteam formally presents a business plan every twoweeks. Prerequisites: ECE 532 and ECE 533, orpermission of instructor. Course offered every otheryear; next session, academic year 2002-03.

4 credits

ECE 535 Thin Film Deposition and Applications inSemiconductor FabricationCovers thin film deposition topics, such as thermalevaporation, plasma deposition, chemical vapordeposition (CVD and MOCVD), molecular beam epi-taxy (MBE), atomic layer epitaxy (ALE),electrochemical deposition and electroless deposi-tion. Thin film deposition forms the basis formanufacture of modern integrated circuits; a knowl-edge of methods available for thin film deposition isessential for IC process engineers. Course isdesigned to cover the theory and applications ofmain deposition techniques in use or being consid-ered for future IC fabrication processes. 4 credits

ECE 536 Surface Science for Semiconductor TechnologyThe study of gas-solid surface science with empha-sis on understanding semiconductor systems andthe mechanisms of epitaxial growth of semiconduc-tor films by molecular beam epitaxy (MBE),metal-organic molecular beam epitaxy (MOMBE),atomic layer epitaxy (ALE), etc. The study of ther-mal desorption, surface diffusion. Surface electronicproperties such as work function. Physical absorp-tion, the growth of multilayer films and theapplication of this phenomena to the study of theBET equation as a tool for the determination of sur-face area. 4 credits

ECE 540 Auditory and Visual Processing by Humanand MachineInteraction between humans and machines could begreatly enhanced by machines that could communi-cate using human sensory signals such as speechand gestures. Knowledge of human information pro-cessing, including audition, vision and their

combination, is, therefore, critical in the design ofeffective human-machine interfaces. The courseintroduces selected phenomena in auditory andvisual perception and motor control. Students learnhow to interpret empirical data, incorporate thesedata in models, and apply these models to engineer-ing problems. The anthropomorphic (humanlike)signal processing approach is illustrated on engi-neering models of perceptual phenomena. 4 credits

ECE 541 Signal Processing for Multimedia ApplicationsThe course covers the concept of signal as a carrierof information and basic principles of processing ofcognitive signals. Using speech as an example ofcognitive signal, it goes through fundamentals ofhuman speech production and perception, proper-ties of speech signal and some techniques for signalprocessing for multimedia engineering. Emphasis ison active research in auditory modeling that exploitsspecial properties of speech to improve perform-ance of speech technology in practical applications.The course is intended for those who have a goodundergraduate-level knowledge of mathematics andphysics but who need an introduction to or refresh-ing of fundamental concepts of signals, systems andhuman information processing to master specializedmultimedia topics in speech and image processing,classification and transmission. 4 credits

ECE 542 Introduction to Image ProcessingThis course covers basic image processing princi-ples and techniques with a brief introduction tomachine vision. Students acquire theoretical andworking knowledge of image processing approaches,including image representation, transform methods,image filtering, multiresolution representation, edgedetection, texture characterization and motionanalysis. This course demonstrates application ofthese methods to image enhancement, imagerestoration and image compression, with emphasison image quality metrics based on human visualperception. Selected areas in machine visioninclude image segmentation, elementary techniquesin pattern recognition and object representation.Numerous examples show how to apply these tech-niques. Prerequisite: ECE 551. 4 credits

ECE 543 Introduction to Digital Video ProcessingThis course introduces digital video processing formultimedia systems. It begins with video capture,image formation, analog and digital video signalsand standards, and spatio-temporal sampling.Subsequent topics include motion estimation, seg-mentation and tracking, video filtering and videostandards conversion. Students are familiarizedwith video compression techniques and standards(JPEG, MPEG2, H.261, H.263) and model-basedvideo quality estimation. Students will gain workingknowledge of these video techniques through classprojects. Familiarity with digital signal processingand transform methods is desirable. Prerequisite:ECE 542. 4 credits

ECE 544 Introduction to Signals, Systems andInformation ProcessingThis course provides the essential mathematicaltools and analytical techniques for the analysis ofcontinuous-time and discrete-time systems. Basic

signal and system characteristics — linearity, time-invariance, convolution and correlation — are firstexamined from the time domain perspective. Wethen proceed to study a family of transforms —Fourier Series, Fourier Integral Transform, LaplaceTransform, Discrete Time Fourier Transform (DTFT),Discrete Fourier Transform (DFT) and z-Transform— which take the study of these systems to a deep-er level and introduce useful properties that thetime perspective alone does not reveal. Basic appli-cations in information processing, communicationand control fill out the mathematically derivedresults. A greater portion of the syllabus in ECE 544is allotted to continuous time signals/systems thanto discrete time signals/systems, because the latterare taken up in detail in other information process-ing courses, particularly ECE 551. A goal of thepresentation in ECE 544 is to impart the essentialunity of all the transforms and the almost perfectcorrespondence of approach in continuous-time anddiscrete-time contexts. The student becomes a well-equipped practitioner who knows the way aroundthe entire territory. This course is a useful prereq-uisite or co-requisite to ECE 551 and all othercourses in the information processing area.

4 credits

ECE 545 Speech SystemsSpeech is one of the most natural means for com-munication and carries information from manysources. The explosive growth of communicationsand computer technologies puts new demands ontechniques for machine extraction of informationcontent of speech signals, for its storage or trans-mission, and for reconstruction of the speech signalfrom its parametric representation. The course cov-ers techniques for processing the speech signal usedfor speech coding and synthesis, enhancement ofdegraded speech, speech recognition, speakerrecognition and language identification. 4 credits

ECE 550 Linear SystemsThis course introduces the State Variable represen-tation of linear dynamical systems and studies alarge body of State Space techniques to reveal bothinner structure and external behavior of the systemsmodeled in this way. The course develops and usesa general framework for treating time-varying linearsystems. Major emphasis is placed, however, on thetime-invariant systems, whose structure anddynamics are investigable and knowable to theutmost detail. Both continuous-time and discrete-time linear systems are explicitly studied. Thecourse provides a strong body of foundational mate-rial, which is utilized either explicitly or implicitly invirtually all applications-specific areas pertaining tosystem analysis/design and signal/information pro-cessing. The major topics covered are: canonicalrealizations, equivalent systems, canonical transfor-mations, canonical decompositions, solution of stateequations, stability, controllability and observability,design of asymptotic observers, state-feedback com-pensation schemes. The Linear Quadratic Regulatorand Kalman Filter are also introduced. The LinearAlgebra material required for this study — matricesas linear operators, solutions of sets of linear equa-tions, eigenvalues and eigenvectors, eigenstructure

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factorizations and spectral decompositions — arepresented and developed concurrently, as needed.The relevant differential equations material will alsobe concurrently reviewed. 4 credits

ECE 551 Introduction to Digital Signal ProcessingThe representation and processing of signals andsystems in the discrete or digital domain is the pre-ferred mode in today’s computer and informationdriven technologies. DSP provides the core buildingblock from cell phones to modems, HDTV to videoconferencing, and speech recognition to MP3 audio.This classes covers the fundamental concepts andmathematics including representation and analysisof discrete time signals and systems, Z-Transforms,Discrete-Time Fourier Transform (DTFT) and theDiscrete Fourier Transform (DFT), sampling andwindowing techniques pertaining to discrete timeprocessing of continuous signals, analysis anddesign of recursive (IIR) and non-recursive (FIR)digital filters, and applications of the Fast FourierTransform (FFT) to convolution, spectral analysisand audio processing. Prerequisite: ECE 544 orequivalent. 4 credits

ECE 552 Digital Signal Processing IIThis follow-up course to ECE 551 examines severalwidely used advanced signal processing. Topicsinclude computational complexity considerations inDSP algorithm development; multirate signal pro-cessing; filterbanks and wavelets and theirapplication in audio and image processing (e.g.MPEG standards). Topic coverage is weightedtoward the interests of the students enrolled.

4 creditsECE 554 Adaptive and Statistical Signal Processing

The field of adaptive filters and systems constitutesan important part of statistical signal processing. Anadaptive system alters or adjusts its definingparameters in such a way that it improves perform-ance through contact with the environment.Adaptive filters are currently applied in suchdiverse fields as communications, control, radar,seismology and biomedical electronics. This coursewill cover the theory and applications of adaptivelinear systems. Topics include Wiener filters, leastsquares, steepest descent, LMS, RLS, Newton’smethod, FIR and IIR adaptive structures and Kalmanfilters. Applications covered include noise cancel-ing, signal enhancement, adaptive control, adaptivebeam-forming, system identification and adaptiveequalization. The theory also lays the foundation forstudy in nonlinear signal processing with neural net-works and will be introduced in the later half of theclass. This course should be of interest to electricaland computer engineers specializing in signal pro-cessing and the information sciences. This courseshould also be taken as background for additionalclasses offered in artificial neural networks, con-nectionist models and machine learning. Pre-requisites: ECE 551 plus an undergraduate levelcourse in probability and statistics. 4 credits

ECE 555 Engineering OptimizationIssues of optimization appear in virtually every areaof engineering and applied research. Most practi

tioners tend merely to rely on “canned” routineswhen optimization needs to be performed. But suc-cessful optimization entails both science and art —deep mathematical derivations and formal conver-gence proofs on the one hand, conventionalengineering “folklore and experiential” rules ofthumb on the other. Through this course you will beable to choose intelligently among available opti-mization strategies, customize given algorithms toyour own specific applications, and even write yourown routines entirely from scratch. After reviewingsome necessary mathematical fundamentals fromlinear algebra and multivariable calculus, includingLagrange multipliers and Kuhn-Tucker conditions,the following topics will be covered: unconstrainedand constrained nonlinear multivariable optimiza-tion, via direct-search and gradient-based methods,including pattern search, simplex search, conjugategradient, variable metric, feasible directions, cut-ting plane, gradient projection and penalty functionmethods. Algorithms for specially structured prob-lems, such as linear programming, quadraticprogramming, integer programming, geometric pro-gramming. Methods that utilize random heuristics,including: genetic algorithm, dynamic evolution andsimulated annealing. Time permitting, dynamic pro-gramming and the optimal control problem will beintroduced. 4 credits

ECE 557 Computer-Aided Analysis of CircuitsThis course covers the algorithms and techniquesfor formulation and solution of circuit equations forlarge-scale VLSI circuits. Topics include equationformulation, linear AC and DC networks, linear tran-sient networks and stability analysis. Solution ofnonlinear DC and transient problems. Frequencydomain (AWE) techniques for VLSI interconnections,Sensitivity analysis, harmonic balance, circuit opti-mization and statistical design. The implementationof device models in circuit simulators and conver-gence issues is covered. Assignments stresscomputer-aided implementation techniques and useof simulators such as PSPICE. 4 credits

ECE 558 High Speed Interconnect DesignElectrical analysis, design and validation of inter-connect for digital buses operating at speeds greaterthan 1 GHz. Key topics include transmission-lineanalysis and tools, digital signals and timing analy-sis, measurement equipment and techniques, lossyand coupled transmission lines, advanced signalingtechniques, design tools and methodology. A designproject is used to give students practical insight intohigh-speed bus design problems. 4 credits

ECE 559 Design with Programmable LogicProgrammable logic, such as FPGA and PLDdevices, has become a major component of digitaldesign. This course discusses design tools and tech-niques for creating logic designs usingprogrammable logic. A design is first created inVerilog, a high-level Register Transfer Level (RTL)language, and simulated. Synthesis to a program-mable logic device is then performed. In addition,common problems of poor routing and placementare discussed while presenting the student with acomprehensive understanding of the operation of

synthesis tools. The course has a strong project ori-entation. Students will take several designs fromconcept to RTL verification and synthesis, then toprogrammable device implementation. A commer-cial set of software tools will be used. Prerequisite:ECE 573 or consent of instructor. 4 credits

ECE 560 Microelectronic Device Fabrication IThis course is the first in a full-year, three-termsequence that treats both the science and practiceof modern microelectronic fabrication. The princi-ples of crystal growth and wafer preparation, ionimplantation, doping and diffusion, and oxidationare all covered. Emphasis is placed on understand-ing the basic chemistry, physics and materialscience of wafer processing. This includes crystalstructure and defects, heterogeneous chemicalreactions, the thermodynamics and kinetics of diffu-sion, etc. In addition, the practical implementationof these processes is discussed. This includesrealistic process flows, physical metrology, devicestructure and electrical behavior, trade-offs, etc.The course is intended to serve both workingprocess engineers and matriculating graduatestudents. 4 credits

ECE 561 Microelectronic Device Fabrication IIThe second class of this series emphasizes metal-lization and dielectrics. Metallization issues includesilicides, barrier layers, interconnects (e.g., Cu),multilevel metallization, and low k dielectrics. Thisis followed by discussion of deposition and proper-ties of different dielectric films. Finally, processingissues of epitaxial growth and properties of SOIdevices are covered. Class assignments includecomputer simulation of device fabrication. 4 credits

ECE 562 Microelectronic Device Fabrication IIIThis class starts with electron beam, x-ray and pho-tolithography, including discussion of resisttechnology (e.g., chemically amplified resists). Thisis followed by fundamentals and applications ofplasmas for etching and deposition (e.g., high-densi-ty plasmas), including plasma damage. Other topicsconsidered are process integration, which includesseveral devices such as BiCMOS, and memories.Finally yield and reliability statistics as related tomicroelectronic device fabrication are discussed.Class assignments include computer simulation ofdevice fabrication and testing. 4 credits

ECE 563 Plasma Processing of Semiconductors IFundamental plasma properties. Plasma produc-tion, properties and characterization. DC and RFplasmas. Sputtering. Sputtering as a depositionprocess for the growth of thin films. Multicomponentfilms. Plasma etching. 4 credits

ECE 565 Analytical Scanning Electron Microscopy (SEM)This course introduces the operation and theory ofSEM and covers sources, lenses, accelerating volt-age, detectors, image formation, beam-specimeninteractions, beam-produced signals, the combinedeffects of signal-to-noise ratio and spot size in deter-mining resolution, and stereo imaging SEM. Theprocess of specimen preparation, metallo-graphicgrinding and focused ion beam-produced transversecross sections, planar sections, coating techniques

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for nonconductors, sampling of powders and isola-tion of contaminants are among the topics. Studentsare encouraged to work on materials they provide.The course covers the operation of energy disper-sive X-ray detectors, qualitative analysis,quantitative analysis, elemental mapping, spectrumartifacts and contaminant and compound identifica-tion. The lecture portion of this course can bepresented on site at companies wihin a six-weekperiod. Corresponding lab sessions are done at OGI.A project requiring operation of the SEM at the stu-dents’ convenience during the remainder of thequarter and a written report are the basis fora grade. 4 credits

ECE 566 Focused Ion Beam TechnologyThis course covers operation and theory of a FIBworkstation, including ion sources, acceleratingvoltage, electrostatic lenses, beam-material interac-tions, resolution, beam intensity distribution, beamproduced signals, detectors, metal and oxide depo-sition and enhanced etch. FIB-produced site-specific SEM transverse cross sections, the locationand sectioning of micron and sub-micron scalestructures on the surface and buried in multilayeredstacks or bulk materials, cross sections in metals,semiconductors, ceramics, and composites are cov-ered. The location and sectioning of micron andsubmicron surface and buried structures to createelectron transparent foils with little or no damage inmetals, semiconductors, ceramics and composites,and artifacts of specimen preparation are present-ed. Ion beam lithography and microfabrication ofstructures on the micron and sub-micron scales arealso covered. This course uses a combination of lec-tures and hands-on practice to cover these topics.The lecture portion of this course can be presentedon site at companies wihin a six-week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the FIB at thestudents convenience during the remainder of thequarter and a written report are the basis fora grade. 4 credits

ECE 567 Transmission Electron MicroscopyElectron microscopy is a continually evolving disci-pline that has developed a wide range of techniquesto solve specific problems. This course is designedto help the student develop a broad appreciation andknowledge of the important techniques for theanalysis of crystalline and amorphous materials.Modern transmission electron microscopes can givethe investigator detailed information of crystalstructure, crystal defects and quantitative localchemistries on a nanometer scale. This informationis often critical to the understanding of materialproperties. Principles, methods and application oftransmission electron microscopy to crystallinematerials are covered, as well as the constructionand design of electron microscopes, electron dif-fraction, reciprocal lattice and Ewald Sphereconstruction. Kinematic and dynamic theories ofimage formation will be introduced. Combining lec-tures with hands-on laboratory practice, studentswill be instructed in the use of sample preparationequipment and an analytical transmission electronmicroscope. Students will be expected to carry out

basic experiments on selected materials that illus-trate fundamental concepts of the lecture. Thelecture portion of this course can be presented onsite at companies wihin a six-week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the SEM at the student’sconvenience during the remainder of the quarterand a written report are the basis for a grade.

4 credits

ECE 568 Failure and Reliability in MicroelectronicsThe failure and reliability of microelectronicsdepends on the stability of thin films and the purityof the bulk semiconductors. Contamination, filmthickness, diffusion and phase changes all drivemechanisms of failure. Characterization of a faileddevice depends on analysis of thin film structure,crystalline structures, contaminant identificationand microchemistry. This requires a variety ofmicroanalytical techniques involving the SEM, TEMand FIB. This course covers the potential defects,failure mechanisms and the methodology used toanalyze them. Case studies also are discussed. Thelecture portion of this course can be presentedon site at companies within a six-week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the SEM at the studentsconvenience during the remainder of the quarterand a written report are the basis for a grade.

4 credits

ECE 569 Electronic Materials andDevice CharacterizationThis class is designed for engineers and scientistswho wish to understand the basic principles behindthe electrical and optical techniques used to char-acterize semiconductor materials and devices.These techniques are crucial in determining thecauses of failure in semiconductor devices. Amongthe parameters covered are contact resistance, car-rier mobility and lifetime, defects, oxide andinterface trapped charges, as well as series resist-ance, channel length/width, threshold voltage andhot carriers in MOSFETs. This class includes somelab time. 4 credits

ECE 571 Analog Integrated Circuit DesignDesign techniques for analog-integrated circuits.Silicon bipolar and JFET analog integrated circuitdesign. Technology overview, device structures,Ebers-Moll equations, hybrid-pi model. Single-stageamplifiers, current sources, active loads, outputstages. Operational amplifiers, frequency response,feedback, stability. Design project. 4 credits

ECE 572 Digital Integrated Circuit DesignDesign techniques for digital integrated circuits.Silicon bipolar and MOS digital integrated circuitdesign. Technology overview, device structures,modeling. Standard logic families. NMOS and CMOSlogic design. Regenerative circuits and memory.Design project. 4 credits

ECE 573 Introduction to Computer Logic DesignThis course constitutes a basic introduction to thedesign and implementation of computer logic. Basicprinciples of discrete logic are presented, includingBoolean algebra, finite-state machine theory, mini-

mization and optimization. Students will apply logicdesign theory to actual PLD (Programmable LogicDevices) and FPGA (Field Programmable GateArray) devices. In addition, students will learn thebasics of the Verilog hardware description language.Though some of this material is generally found inundergraduate curriculums, this course covers thismaterial in greater depth and at a pace appropriatefor graduate credit. This course or its equivalent isa prerequisite to all other ECE Electronics Designcourses. Prerequisite: the C programming language.

4 credits

ECE 574 CMOS Digital VLSI Design IThis introduction to CMOS digital IC design coversbasic MOS transistor theory; operation of basicCMOS inverter; noise margins; switch level model-ing of MOS devices; capacitive characteristics ofMOS devices; introduction to device fabrication,design rules and layout issues; power consumption;gate design/transistor sizing; pass transistors andcomplimentary pass transistor logic; dynamic domi-no and precharge/discharge circuits; memoryelement design (RAM/ROM/flip-flops) and subsys-tem design (adders, multipliers, etc.). Anunderstanding of basic digital design concepts isassumed. Lab exercises use industry-standarddesign tools. Laboratories include circuit validationand characterization. Prerequisite: ECE 573.

4 credits

ECE 575 CMOS Digital VLSI Design IIConcentration on advanced digital VLSI circuitdesign techniques. Architecture and micro-architec-ture of VLSI components, clocking schemes,input/output circuits, and special functional blockssuch as random access memories, read only memo-ries and programmable logic arrays. The coursecovers design tradeoffs, especially considering cost,power and performance. The course devotes a con-siderable amount of time to layout, parasitics andperformance verification. Introduction to design andverification tools with hands-on experience.Prerequisites: ECE 574, familiarity with MOS tran-sistor operation; computer architecture andorganization; logic design. 4 credits

ECE 577 Principles for Technology Development andIntroduction to ManufacturingA project-oriented course on management proce-dures and key underlying concepts for effectivemanufacturing technology planning and develop-ment; an introduction to commercial production in acompetitive environment. While emphasis is onsemiconductor technology, most principles andmethodology are generally applicable to both hard-ware and software technology management. Issuesof technology strategic planning, process definitionand characterization, decision making, technologytransfer, product definition, yield and reliabilityimprovement, and concurrent engineering areexplored to identify effective management approach-es to shorten time-to-volume production, reduce riskand minimize engineering effort. 4 credits

ECE 580-XXX Special Topics Under this number, we offer courses of particular rel-evance to the research interests of faculty or in

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state-of-the-art subjects of interest to the community.Individual course descriptions are listed here. SpecialTopic courses are subject to change and are offeredintermittently. For course descriptions for SpecialTopics offered during the current term, please viewhttp://ece.ogi.edu/special.html.

ECE 580-AC Analog CMOS Integrated Circuit Design

ECE 580-ACD Selected Topics in Analog IC Design

ECE 580-AFA Introduction to Functional Analysis andits Application

ECE 580-BSP Biomedical Signal Processing

ECE 580-CCM Capstone Course — MEMS andMicrosensors Project

ECE 580-CLI Computational Approaches to LaserInteraction with Biological Tissues

ECE 580-CLT Computational Approaches to Light Transportin Biological Tissues

ECE 580-CN Introduction to Computer Networks

ECE 580-COD Introduction to Computer Organizationand Design

ECE 580-DCS Digital Fiber Optic Communication Systems

ECE 580-DDC Design of Digital Communication Circuits

ECE 580-DOE Statistical Process Control and DOE

ECE 580-ECE Special Topics in Electrical andComputer Engineering

ECE 580-EMI Electroplating forMicroelectronic Interconnects

ECE 580-FSM Fundamentals of Sensors andMEMS Fabrication

ECE 580-HMM Hidden Markov Models for Speech Recognition

ECE 580-IB1 Biomaterials I

ECE 580-IB2 Biomaterials II

ECE 580-IE Internet Engineering

ECE 580-IN Introduction to Nanomaterials

ECE 580-ISM Introduction to Sensor Microfabrication

ECE 580-LCD Introduction to Liquid Crystal Displays

ECE 580-MC Multimedia Communications

ECE 580-MCM Materials Characterization for MicroelectronicDevice Fabrication

ECE 580-MEC Microwave Engineering Concepts

ECE 580-MEM Micro-Electro-Mechanical Systems

ECE 580-MPE Modern Photolithographic Engineering

ECE 580-ONE Optical Non-destructive Evaluation

ECE 580-OSD Operation of Semiconductor Devices

ECE 580-PGO Physical and Geometric Optics

ECE 580-RFD Reliability and Failure of Electronic Devices,Packages, and Assemblies

ECE 580-SLD Statistical Learning and Data Mining

ECE 580-SMVI Simulation & Modeling of VLSI Interconnect

ECE 580-SSE Semiconductor Sensors

ECE 580-SSL Structure of Spoken Language

ECE 580-SSY Speech Synthesis

ECE 580-TP Technology of Photoresists

ECE 580-WCS Wireless Communication Systems

ECE 591 Independent StudyMay be taken only during student’s final quarter ofgraduate program for a maximum of 3 credits.Student works with professor on selected topic(s).Requires preapproval of professor, ECE depart-ment, as well as formal agreement between studentand professor outlining objectives and expectationsof independent study topic.

ECE 600 Prequalifying Ph.D. ResearchSupervised research participation. PrequalifyingPh.D. research prior to passing ECE departmentqualifying exam. Variable and repetitive credit

ECE 610 MS Nonthesis Project ResearchSupervised research for up to eight credits as acomponent of the non-thesis M.S. degree. Studentsare required to produce cogent research deliver-able(s) including, but not limited to, a final reportequivalent to an EE project paper. This researchclassification requires approval of the departmenthead and the student’s SPC.

Variable and repetitive credit

ECE 620 Professional InternshipThis course provides the student with an opportuni-ty to earn credit for relevant work experience inindustry. Students gain valuable industrial experi-ence that allows them to both apply the knowledgegained in the classroom and prepare for careers.Students on F-1 or J-1 visas must obtain prior writ-ten approval for internships from OGI’s Office ofInternational Students & Scholars before enrollingin ECE 620. Enrollment requires a faculty advisorand is limited by the number of internships avail-able. Variable and repetitive credit

ECE 700 M.S. ThesisResearch toward the thesis for the M.S. degree.

Variable and repetitive credit

ECE 800 Ph.D. DissertationResearch toward the dissertation for the Ph.D.degree. Variable and repetitive credit

RESEARCH CENTERS C E N T E R F O R B I O L O G I C A L LY I N S P I R E DI N F O R M AT I O N E N G I N E E R I N G ( C B I I E )Science and engineering have achieved greatadvances in automating and creating informationprocessing and analysis tools. Microelectronics,programming, signal processing and informationtheory underpin these achievements. Modernmicroprocessors and those that will be producedover the next decade will provide huge computation-al power, enabling new information processingapplications. By the end of the decade, manufactur-ers will be routinely manufacturing chips with overone billion transistors.

Many information-processing applications involvehuge amounts of real-world data that have to beprocessed and analyzed for making decisions. Thecomplexity of the analysis is often beyond the cur-rent techniques and methodologies of science andengineering. Yet natural evolution has producedvery sophisticated information processing systems,

and the information analysis performed by the humanbrain, or even by the brains of simple animals, is farsuperior to what currently can be achieved by state-of-the-art human-developed techniques.

A new research area now coalescing is devoted toconsolidating and refining existing solutions andfinding better solutions to these transformationproblems. The term Intelligent Signal Processing(ISP) is used to describe algorithms and techniquesthat involve the creation, efficient representationand effective utilization of complex models ofsemantic and syntactic relationships. Even the mostprimitive biological systems perform complex ISP. Inaddition, biological computing is robust in the pres-ence of faulty and failing hardware and isfundamentally asynchronous. Biological computingis energy efficient, consists of networks of sparselyconnected and sparsely activated nodes and requiresonly moderate levels of computational precision.

We believe that the merging of neuroscience andsemiconductor engineering is creating what AndyGrove, ex-CEO of Intel, refers to as a strategicinflection point. Therefore, the mission of the Centerfor Biologically Inspired Information Engineering isto harvest biology for solutions to real-world infor-mation engineering and Intelligent Signal Processingproblems and leverage the incredible functionaldensity of GSI (Giga-Scale Integrated) Silicon. Thecenter was established in 2001 and currently con-sists of two professors, Dan Hammerstrom andMarwan Jabri, and their staff and graduate stu-dents. The center currently receives funding fromNASA, NSF, SRC, ONR and Intel.

Current projects focus on:

• Computational models of sensorimotor control;

• High-level visual feature extraction usingunsupervised learning techniques;

• Top-down/Bottom up sensory fusion andsensorimotor control;

• Simulation of large-scale networks on PC clusters;

• Mapping computational neurobiology to FPGAsand eventually custom silicon;

• Understanding the issues involved in scalingneural models to very large configurations; and

• Pulse-based analog circuit design

C E N T E R F O R I N F O R M AT I O N T E C H N O L O G Y ( C I T ) Digital signal processing has made a significantimpact on human lives since its introduction sever-al decades ago. Industries are shifting emphasisfrom instrumentation and manufacturing to multi-media and communications services. Wide arrays oftechnologies, ranging from digital telephones tothe ability to accurately predict the behavior of com-plex systems, rely on elegant mathematicalconcepts and on the power of digital computers.Even the most advanced techniques, however, fail tocarry out many tasks that are effortlessly performedby humans.

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The mission of the Center for InformationTechnology (CIT) is to support the development anddeployment of signal-processing systems that wouldemulate and surpass human information processingcapabilities. CIT activities focus on the “human-like,” or anthropic, processing side of informationsystems. The anthropic signal processing is the syn-thesis of robust signal-processing techniques thatexceed the performance of standard classical signal-processing methods by appealing to human-like processing strategies and capabilities. Thisunique combination of engineering and human infor-mation processing strategies is strengthened byrecent incorporation of OGI into Oregon Health &Science University.

The center’s efforts focus on several target-engineer-ing systems, including robust feature extraction forspeech recognition systems, speech qualityenhancement in cellular communications, automat-ic target detection and identification, and a forwardvisibility system for aviation. These projects aresupported by basic research on several key sup-porting technologies, including neural networks,prediction, image and speech representation, infor-mation fusion and the incorporation of priorknowledge in adaptive systems.

Within the OGI School, CIT provides a natural com-plement to other centers, including the Center forSpoken Language Understanding and its Center forHuman-Computer Communication. CIT complimentsCSLU by developing advanced signal processingtechniques used in Signal Processing for MultimediaEngineering. In a similar way, CIT is developingsolutions to a variety of signal-processing problemsin natural communication using images, sound andgestures. CIT is an important component in the ECEdepartment’s focus on intelligent signal processing.

C E N T E R F O R S P O K E N L A N G U A G EU N D E R S TA N D I N G ( C S L U )The research program of the Center for SpokenLanguage Understanding (CSLU) encompasses abroad range of speech technologies. Such researchis inherently multidisciplinary, and the centerbrings together a team with expertise in signal pro-cessing, speech recognition, speech synthesis,dialogue modeling, natural language processing,multimodal systems, linguistics and human-comput-er interaction.

These groups focus on specific problem areas suchas: robust methods for enhancing speech in noisyenvironments; large vocabulary recognition of con-tinuous speech, as in broadcast news; unit selectionand voice conversion for more realistic speech syn-thesis; robust parsing and interpretation of spokenand multimodal input; modeling of disfluencies inspontaneous speech; and effective methods for dia-log management.

An important new direction of CSLU is basic speechtechnology research with a medical or educationalfocus. For example, CSLU obtained a three-yeargrant from the National Science Foundation to workon innovative voice transformation technologies tomake speech spoken by people suffering fromdysarthria more intelligible. CSLU also works on

new technologies that is used for creating multi-modal, interactive reading tutors for children withreading or hearing problems. Plans are under way toexpand this focus into analysis of speech from autis-tic children, stuttering and apraxia, as well asanalysis of non-native speakers learning English.

CSLU is also highly active in the development anddistribution of a wide variety of software systems(the “CSLU Toolkit”) and language resources, includ-ing corpora of transcribed telephone and cellularspeech data for over 20 languages.

Professor Jan van Santen is the director of OGI’sCenter for Spoken Language Understanding. Thecenter is co-directed by Professors Peter Heeman,John-Paul Hosom, Yonghong Yan and Eric Wan.Other center faculty include Professors Todd Leen,Hynek Hermansky and Xubo Song. The centerreceives support from government agencies includ-ing NSF, DARPA, NIH and ONR, as well as industrialsources. For additional information, visit the CSLUweb site: http://cslu.cse.ogi.edu.

RESEARCH PROGRAMSAdvanced LithographyLithography is the key technology pacing the evolu-tion of microelectronics, and maskless lithographyis of particular interest for the future as opticalmasked schemes reach the end of their capability. Inparticular massively parallel arrays of electronemitters can be used to achieve practical through-puts for direct-write e-beam systems. Research isongoing to develop a viable multibeam electronsource technology for use in large scale manufac-turing of semiconductor devices. By usingsemiconductor technology in combination with newcathode materials and approaches, it should be pos-sible to generate arrays allowing significantlyenhanced printing speed and improved patternfidelity. Berglund, McCarthy

Atmospheric OpticsThe use of laser systems to transmit signals throughthe atmosphere for purposes of communication,radar, recognition and designation is severely limit-ed by scattering caused by turbulence andparticulates such as water droplets or dust.Turbulence, which causes shimmer on a hot day andmakes stars seem to twinkle, results in the randomsteering, spreading and breaking up (scintillation) ofa laser beam. Particulate scattering that severelyattenuates the received signal also causes depolar-ization and multiple path effects such as pulsestretching and scrambling of the signal.Experimental studies, in conjunction with concur-rent theoretical work, are contributing significantlyto fundamental understanding of the effects ofatmospheric turbulence on laser beam, specklepropagation and its application to optical remotesensing. Holmes

Biomedical OpticsThe program in Biomedical Optics prepares the stu-dent to use lasers and light to measure, image,modify and machine materials, with emphasis onbiological materials but with broad application to a

variety of materials. The program offers a series ofcourses and labs on tissue optics, laser-tissue inter-actions and engineering design, with electivecourses in optics, spectroscopy, optical fibers, bio-mechanics, imaging and image analysis, opticalmeasurement techniques, and computational meth-ods for simulating light transport through andinteraction with biological materials. Students havethe opportunity to work in the hospital-basedresearch laboratories at the Oregon Medical LaserCenter at Providence St. Vincent Medical Center andthe Biomedical Optics Laboratory on the OHSUMedical Center campus. Jacques, Kirkpatrick, Prahl, Song

Electronic Materials An active research program in electronic materialsgrowth and characterization focuses on demands ofthe ever-shrinking microelectronic devices. Themain materials growth technique investigated isatomic layer deposition, which allows growth ofhighly conformal thin films, one atomic layer at atime. Materials investigated using this approachinclude thin gate dielectrics, including nanolami-nates and metallic films, which include copper seedlayers and barrier metals. Another area of researchinvolves electrodeposition of copper films for micro-electronic device interconnect applications. Thefocus of this investigation is to determine thecorrelation between the bath chemistry and thephysical properties of the films and their electromi-gration lifetimes. Freeouf, McCarthy, Solanki

Image, Video Processing and AnalysisOur interest in image and video processing coversboth low-level processing and high-level analysis.Recently, we have been developing image and videoanalysis techniques that are on the boundarybetween machine learning and computer vision. Weuse insights from statistics, stochastic systems andinformation theory to produce new algorithms forlongstanding problems. The goal is to understandthe fundamentals of these problems and to achieveperformance that is more robust, accurate and effi-cient. Current projects include information fusion,the incorporation of contextual information forimage recognition, model-based image segmenta-tion, enhancement and 3D reconstruction, andBayesian integrated motion analysis for autonomousnavigation. Song, Pavel

Neural Networks and Adaptive Systems Neural computation and adaptive systems are stud-ied from both theoretical and practical standpoints.Current research in theory, architecture and algo-rithm design includes deterministic and stochasticnetwork dynamics, learning algorithms (supervised,unsupervised and reinforcement), generalizationtheory (including model selection and pruning,invariant learning), context-sensitive learning, sig-nal processing, time series analysis and control. Inaddition, a major research thrust is the developmentof robust recognition algorithms based on informa-tion fusion. Practical application domains includeadaptive signal processing, pattern recognition,speech recognition, image processing, control sys-tems, macroeconomics and finance. Jabri, Leen, Moody, Pavel, Song, Wan

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Optical Remote SensingAnalytical and experimental studies are exploringthe use of the interaction of electromagnetic radia-tion and turbulence to measure winds andturbulence. Recent efforts include analytical,numerical and experimental work on a CO2, opticalheterodyne system for remote measurement ofatmospheric cross winds and strength of turbulence.Holmes

Speech and Speaker Recognition in AdverseCommunication Environments.Our research on acoustic processing of speechfocuses on human-like processing of speech in real-istic telecommunications environments to ensurereliable recognition of speech in adverse conditions,like those encountered in the current mobile cellu-lar telephony. Speech is a special signal that evolvedto be heard well. Subsequently, it is likely thathuman hearing represents the optimized way of itsprocessing and understanding, and emulatinghuman hearing may help improve speech technolo-gy. This spurred our interest in modeling human-likeprocessing of speech by modern discrete signal pro-cessing techniques. Our research includes aspectsof digital signal processing and of statistical patternrecognition as well as aspects of human hearingpsychology and physiology. Hermansky

Speech SynthesisSpeech is the most natural and efficient means bywhich individuals may access most information, andthe need for speech-based interfaces is growing ascomputing gradually moves off the desktop and intomobile devices. Since most online information isrepresented as ASCII text, the automatic conversionof text to speech provides a critical component invoice-based systems. Text-to-speech synthesis (TTS)has the further advantage of providing textual infor-mation to people who are visually impaired orfunctionally illiterate. This is an interdisciplinaryfield that draws elements from linguistics, computerscience, machine learning, human perception anddigital signal processing. At CSLU, we conductresearch at all levels of TTS, ranging from signal processing to statistical modeling of intonation andtext analysis of e-mail messages. We further workon special applications such as small footprint TTSand speech synthesis for individuals with speechproblems. Van Santen

VLSI Architecture for Intelligent ComputingSome of the most important problems in computinginvolve teaching computers to act in a more intelli-gent manner. Key to this is the efficientrepresentation of knowledge or contextual informa-tion. In this project a variety of highly parallelalgorithms are being studied, including neuromor-phic structures, with the intent of enhancing therepresentation and manipulation of knowledge insilicon. Hammerstrom, Jabri

R E S E A R C H FA C I L I T I E S

The department has a completecomplement of electronic measuring,recording, amplifying, signal generating,data processing and servicing gear,with associated power supplies andcomponent stocks. Additional facilitiesand equipment include:

C O M P U T I N G R E S O U R C E S

• Windows 2000 computer lab with workstationsand server

• Sun Enterprise 3500 departmental computer server

• Unix lab with Solaris workstations and X-terminals

• 8 Node Beowulf Computer Cluster

C I R C U I T D E S I G N

• Computer design lab with eight stations, eachconsisting of a PC workstation, an Altera UP1board, Altera Nios development board, TI DSPdevelopment board

• VLSI and FPGA circuit design software

• Digital television lab

M AT E R I A L S A N D E L E C T R O N I C C H A R A C T E R I Z AT I O N

• Far-infrared Fourier spectrometer

• Parallel f ield-vibrating sample magnetometer

• X-ray diffraction generator and cameras

• Facil ity for electronic transport and luminescencemeasurements as a function of temperature

• Visible, ultraviolet and infrared gas, solid state anddye lasers

• C-V, I-V measurement facil ities

• Electrical characterization (Hall)

• Recombinaion Lifetime System suitable for bulk andthin fi lm studies

• Two spectroscopic ell ipsometry systems, 250-750 nmand 140-300 nm

• Process and device two-dimensional simulators, three-dimensional simulators, Monte Carlo simulators

• Work function and high intensity photo-currentstabil ity measurement equipment

M I C R O S C O P Y

• Inverted and upright optical photomicroscopes

• Field electron and ion microscopes

• Focussed Ion Beam micromachining andmicroforming capabil ities

• Analytical scanning electron microscope —Heating, straining specimen stage

• Analytical scanning/transmission electronmicroscopes — Heating specimen stage

• High-resolution electron and ion microprobes

• Scanning auger microprobe microscopy

• Scanning confocal microscopy

• Ion mill, chemical jet-mill ing, sample preparationfacil ities, microtome

• Complete JCPDF x-ray and electron powderdiffraction database

• Electron diffraction and image simulation program

• Digital video capture for in-situ microscopy experiments

S E M I C O N D U C T O R A N D L C DFA B R I C AT I O N T E C H N O L O G Y

• Photolithographymask generation andexposure systems

• Semiconductor metall ization

• Sputter etching

• Wet etching facil ities

• Sputter deposition systems

• Pulsed UV-laser processing system

• Atomic layer epitaxy deposition system

• Liquid crystal display lab with pretilt, rubbing, andsingle-cell electro-optic characterization facil ities

• Electrochemical deposition

• Process simulators

S P E E C H A N D S P O K E N L A N G U A G E

• Whisperroom sound-isolation booth

• Mackie eight-channel mixing board

• Kay Elemetrics laryngograph

• High-quality condenser microphone

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A N T H O N Y E . B E L LAssociate ProfessorPh.D., Physical ChemistryUniversity of London, 1962bella@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Development of liquid metal fieldion sources; field ionization,surface physics and chemistry;field emission microscopy andenergy distribution measurements.Selected area processing formicrocircuit fabrication usingfocused electron beams. Direct-write electron-beam lithographyfor both mask making and ICfabrication using multiple photo-emitted electron beams. Plasmaprocessing for thin film depositionand etching. Field electronemissions and FED displays.Silver and tungsten metalization.Moisture evolution from oxidepassivation films.

R E P R E S E N TAT I V E P U B L I C AT I O N SA.E. Bell and D.F. Barofsky, “Field

Emission and Field Ionization,” inEncyclopedia of Applied Physics, 6,p. 379, 1993.

A.E. Bell, K. Jousten and L.W.Swanson, “High Field Ion Sources,”Rev. Sci. Intr., 61(1) Part II, p. 363,1990.

S. Rao, A.E. Bell, G.A. Schwind andL.W. Swanson, “Angular Distributionof Ions from a AuSi Liquid MetalSource,” J. Vac. Sci. Technol., A8(3),p. 2258, 1990.

S.. Rao, A.E. Bell, G.A. Schwindand L.W. Swanson, “A CombinationElectron/Ion Field Emission Source,”J. Vac. Sci. Technol., B7, p. 1793, 1989.

L.W. Swanson and A.E. Bell,“Liquid Metal Ion Sources,”I.G. Brown (Ed.), The Physicsand Technology of Ion Sources,John Wiley & Co., p. 313, 1989.

C . N E I L B E R G L U N DProfessorPh.D., Electrical EngineeringStanford University, 1964berglund@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Management of technology, andadvanced lithography forsemiconductor fabrication.

R E P R E S E N TAT I V E P U B L I C AT I O N SX. Ouyang, C.N.Berglund,

M.A. McCord and R.F. W. Pease, “High-Throughput High-Density Mapping andSpectrum Analysis of Transistor GateLength Variations in SRAM Circuits,”IEEE Trans. on Semi. Manuf., vol.14(4), pp. 318-329, November 2001.

X. Ouyang, C.N. Berglund,M.A. McCord and R.F.W. Pease,“Economical Sampling Algorithm UsingFourier Analysis for Mapping WaferCritical Dimension Variations,” J. Vac.Sci. Technol., B16(6), Nov.-Dec 1998.

L. Han, W. Wang, M.A. McCord,C.N. Berglund and R.F.W. Pease,“Practical Approach to Separating thePattern Generator-Induced Mask CDErrors from the Blank/Process-InducedMask CD Errors Using ConventionalMarket Measurements,” J. Vac. Sci.Technol., B15 (6), pp. 2243-2248,Nov.-Dec 1997.

C.N. Berglund, “Yield Loss From CDErrors Due to Finite-Sized Defects,”Microlithography World, pp. 12-14,Autumn 1996.

J. Ye, M. Takac, C.N. Berglund,G. Owen and R.F.W. Pease, “An ExactAlgorithm for the Self-Calibration ofPrecision X-Y Stages,” Conference onElectron, Ion & Photon BeamTechnology and Nanofabrication,May 1996.

M.T. Takac, J. Ye, M.R. Raugh,R,F.W. Pease, C.N. Berglund andG. Owen, “Self-Calibration in TwoDimensions: The Experiment,” 1996SPIE International Symposium onMicrolithography, March 1996.

W. Wang, J. Ye, A.B. Owen,C.N. Berglund and R.F.W. Pease,“Adaptive Metrology: An EconomicalStrategy for Judging the Acceptabilityof a Mask Pattern,” J. Vac. Sci.Technol., B13(6), Nov.-Dec. 1995.

J. Ye, C.N. Berglund and R.F.W. Pease,“Field Distortion CharacterizationUsing Linewidth or PitchMeasurement,” J. Vac. Sci. Technol.,B13(6), Nov.-Dec. 1995.

J O H N L . F R E E O U FProfessorPh.D., Physics, University ofChicago, 1973jfreeouf@ece.ogi.edu

R E S E A R C H I N T E R E S T S

The large and growingsemiconductor industry hasclearly established that to controlsomething you must be able tomeasure it. A major thrust of myresearch is to determine how tomeasure the specific parametersrequired to best understand andimprove our semiconductormaterials and devices. Typically,these measurements will involveincident photons; the output maybe either photons or someelectrical response.

R E P R E S E N TAT I V E P U B L I C AT I O N SS.G. Lim, S. Kriventsov, T.N. Jackson,

J.H. Haeni, D.G. Schlom, A.M.Balbashov, R. Uecker, J.L. Freeouf andG. Lucovsky, “Dielectric Functions andOptical Bandgaps of High-K Dielectricsfor Metal-Oxide-Semiconductor Field-Effect Transistors by Far UltravioletSpectroscopic Ellipsometry,” J. Appl.Phys., 91, p. 4500, 2002.

S.G. Lim, T.N. Jackson, W.C. Mitchel,R. Bertke and J.L. Freeouf, “OpticalCharacterization of 4H-SiC by FarUltraviolet Spectroscopic Ellipsometry,”Applied Physics Letters, 79, p. 162, 2001.

T. Holden, P. Ram, F.H. Pollak, J.L.Freeouf, B.X. Yang and M.C. Tomargo,“Spectral Ellipsometry Investigation ofZn Cd Se Lattice Matched to InP,”Physical Review B56, p. 4037, 1997.

M. Leibovitch, P. Ram, L. Malikova,F.H. Pollak, J.L. Freeouf, L. Kronik, B.Mishon, Y. Shapira, A.R. Clawson andC.M. Hanson, “Reflection AnisotropySpectroscopy, Surface PhotovoltageSpectroscopy, and ContactlessElectroreflectance Investigation of theInP/In0.53Ga0.47As (001)Heterojunction System,” J. Vac. Sci.Technol., B14, p. 3089, 1996.

J.L. Freeouf, N. Braslau andM. Wittmer, “Lifetime Measurements onSilicon on Insulator Wafers,” Appl.Phys. Lett., 63, p. 198, 1993.

M. Wittmer and J.L. Freeouf, “IdealSchottky Diodes on Passivated Silicon,”Phys. Rev. Lett., 69, p. 2701, 1992.

K E N T O N G R E G O R YAssociate ProfessorM.D., School of MedicineUniversity of Southern California,1980

R E S E A R C H I N T E R E S T S

Application of laser energy for thetreatment of altheroscleroticvascular disease, laserthrombolysis in acute myocardialinfarction and stroke, vascularsmooth muscle response to light,Elastin biomaterials for tissuereplacement and repair, and dye-targeted laser-tissue fusion.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.J. Girsky, K.W. Gregory, A. Shearin

and S.A. Prahl, “Photoacoustic DrugDelivery to Arterial Thrombus: A NewMethod for Local Drug Delivery,”American Heart Association, 69thAnnual Scientific Session, New Orleans,November 1996.

K.W. Gregory, “Laser Thrombolysis inAcute Myocardial Infarction,” CurrentReview of Interventional Cardiology(D. Holmes Jr. & P. Serruys), 3rdEdition, August 1996.

E.N. LaJoie, A.D. Barofsky,K.W. Gregory and S.A. Prahl, “WeldingArtifical Biomaterial with a PulsedDiode Laser and Indocyanine Green, “SPIE, Laser Tissue Interaction VI, S.L.Jacques, ed., San Jose, 1995.

H. Shangguan, L.W. Casperson,A. Shearin, K.W. Gregory and S.A.Prahl, “Photoacoustic Drug Delivery:The Effect of Laser Parameters onSpatial Distribution of Delivered Drug,”SPIE, Laser Tissue Interaction VI, S.L.Jacques, ed., San Jose, 1995.

K.W. Gregory and J.M. Grunkemeier,“Arterial Reconstruction using anElastin-based Biopolymer with DyeTargeted Diode Laser Fusion,”American Society for Laser Medicineand Surgery, 15th Annual Meeting,San Diego, April 1995.

FACULTY

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D A N H A M M E R S T R O MDoug Strain ProfessorPh.D., Electrical EngineeringUniversity of Illinois, 1977strom@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Biologically inspired computation.VLSI chip design for imageprocessing, digital video, signalprocessing and intelligent signalprocessing. Parallel computerarchitecture and micro-architecture. Technology transfer.

R E P R E S E N TAT I V E P U B L I C AT I O N SD. Hammerstrom, “Digital VLSI for

Neural Networks,” to appear in TheHandbook of Brain Theory and NeuralNetworks, Second Edition, MichaelArbib, ed., MIT Press.

D. Hammerstrom, “The ComingRevolution: The Merging ofComputational Neural Science andSemiconductor Engineering,” to appearin Toward Replacement Parts for theBrain, Ted Berger, ed., MIT Press.

D. Hammerstrom and D. Lulich,“Image Processing Using One-Dimensional Processor Arrays,”The Proceedings of the IEEE, 84(7),pp. 27-43, July 1996.

S. Rehfuss and D. Hammerstrom,“Model Matching and Single FunctionMultiple Data Computation (SFMD),”NIPS Proceedings, November 1995.

D. Hammerstrom, “A DigitalVLSI Architecture for Real WorldApplications,” An Introduction toNeural and Electronic Networks,S.F. Zornetzer, J.L. Davis, C. Lau andT. McKenna, eds., Academic Press,1995.

H Y N E K H E R M A N S K YProfessor and DirectorCenter for Information TechnologyDr. Eng., Electrical EngineeringUniversity of Tokyo, 1983hynek@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Communication between humanand machine; human perceptionand its computer simulation;speech production and perception;automatic recognition of speech,speech coding, synthesis andenhancement; identification andextraction of linguistic informationin realistic communicationenvironments.

R E P R E S E N TAT I V E P U B L I C AT I O N SH. Hermansky, “Human Speech

Perception: Some Lessons fromAutomatic Speech Recognition,” in Text,Speech, and Dialogue, Lecture Notes inArtificial Intelligence, Springer, 2001.

H. Hermansky, D.P.W. Ellis andS. Sharma, “Connectionist FeatureExtraction for Conventional HMMSystems,” in Proc. ICASSP’00, Istanbul,Turkey, 2000.

H. Hermansky and S. Sharma,“Temporal Patterns (TRAPS) in ASR ofNoisy Speech,” in Proc. ICASSP ‘99,Phoenix, March 1999.

H. Hermansky, “Should RecognizersHave Ears?” Speech Communication,(25), 1, pp. 3-27, Elsevier, Holland,August 1998.

H. Hermansky, “Modulation Spectrumin Speech Processing,” in SignalAnalysis and Prediction, ed. Prochazka,Uhlir, Rayner and Kingsbury,Birkhauser, 1998.

C. Avendano and H. Hermansky, “Onthe Properties of Temporal Processingfor Speech in Adverse Environments,”in Proceedings of 1997 Workshop onApplication of Signal Processing toAudio and Acoustics, Mohonk MountainHouse, New Paltz, N.Y., October 1997.

S. Tibrewala and H. Hermansky,“Multi-band and Adaptation Approachesto Robust Speech Recognition,” inProceedings of EUROSPEECH ‘97,Rhodos, Greece, September 1997.

J . F R E D H O L M E SProfessor EmeritusPh.D., Electrical EngineeringUniversity of Washington, 1968jfred@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Speckle propagation throughturbulence, optical remote sensingof wind and turbulence, electro-optic systems, instrumentationsignal processing and biomedicaloptics.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.F. Holmes, S.L. Jacques and

J.M. Hunt, “Adapting AtmosphericLidar Techniques to Imaging BiologicalTissue”, SPIE, Bios 2000 Conference,San Jose, January 2000.

M. Becker, J.F. Holmes andL. Meekisho, “InterdisciplinaryCurriculum Development in ElectronicsPackaging Using Course Segmentation,”ASEE 1998 Frontiers in EducationConference, Tempe, Ariz., November1998.

J.F. Homes and B.J. Rask, “RangeResolved, 3-D Optical Remote Sensingof Atmospheric Winds Using a CWLidar,” Advances in AtmosphericRemote Sensing with Lidar, A.Amsmann, P. Neuber, P. Rairoux, and U.Wandinger, eds., Springer-Verlag,Berlin, 1997.

J.F. Holmes, and C. Zhou, “PathResolved, Optical Remote Sensing ofthe Strength of Turbulence Using aPseudo Random Code Modulated CWLidar and Coherent OpticalProcessing,” 9th Conference onCoherent Laser Radar, Linkoping,Sweden, June 1997.

J.F. Holmes and B.J. Rask, “The Effectof Aerosol Speckle Phase Decorrelationon the Allowable Signal Averaging Timefor Coherent Optical Receivers,” SPIEAnnual Meeting, August 1996.

J.F. Holmes and B.J. Rask, “RangeResolved, 3-D, Optical Remote Sensingof Atmospheric Winds Using a CWLidar,” 18th International Laser RadarConference, Berlin, July 1996.

J.F. Holmes and B.J. Rask,“Optimum, Optical Local OscillatorLevels for Coherent DetectionUsing Photodiodes,” Appl. Opt., 34,February 1995.

J O H N - P A U L H O S O MAssistant ProfessorPh.D., Computer Scienceand Engineering,Oregon Graduate Institute ofScience & Technology, 2000hosom@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Automatic speech recognition(ASR). Time alignment ofphonemes. Acoustic-phoneticanalysis of speech. Assistivetechnology.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.P. Hosom, “Automatic Speech

Recognition,” in H. Bidgoli, S. B. Eom,A. Prestage, eds., Encyclopedia ofInformation Systems, San Francisco:Academic Press, 2002.

J.P. Hosom and R.A. Cole, “BurstDetection Based on Measurements ofIntensity Discrimination,” Proceedingsof ICSLP 2000, IV, pp. 564-567,October 2000.

P. Cosi and J.P. Hosom, “HighPerformance General Purpose PhoneticRecognition for Italian,” Proceedings ofICSLP 2000, II, pp. 527-530, October2000.

J.P. Hosom, R.A. Cole and P. Cosi,“Improvements in Neural-NetworkTraining and Search Techniques forContinuous Digit Recognition,”Australian Journal of IntelligentInformation Processing Systems,5 (4), pp. 277-284, Summer 1999.

R.A. Cole, B. Serridge, J.P. Hosom,A. Cronk and E. Kaiser, “A Platform forMultilingual Research in SpokenDialogue Systems,” Proceedings of theWorkshop on Multi-LingualInteroperability in Speech Technology(MIST), Leusden, The Netherlands,September 1999.

J.P. Hosom and M.Yamaguchi,“Proposal and Evaluation of a Methodfor Accurate Analysis of Glottal SourceParameters,” The Institute ofElectronics, Information andCommunication Engineers (IEICE)Transactions on Information andSystems, E77-D (10), pp. 1130-1141,October 1994.

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J O D Y H O U S EAssistant ProfessorSc.D., ElectricalEngineeringMassachusetts Instituteof Technology, 1998jhouse@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Electronic and photonic devicedesign for microsensorapplications with a currentconcentration on embeddedsensors and microfluidics.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. House, L. Williams, L. Newton-

Curtis and G. Borthwick, “AssessmentTool Development for SMET Programsfor Girls,” submitted to the Journal ofWomen and Minorities in Science andEngineering, expected publication June2002.

R. Ro, J. House and J. Hines, “AnEvolutionary Approach to ImprovedPerformance of Merged Companies,”NSF Design and ManufacturingResearch Conference. Puerto Rico,January 2002.

S. Gosavi, J.M. McCarthy, J.L. House,B.G. Scholte van Mast, G. Janaway,C.N. Berglund, “Stability Improvementat High Emission Densities for GoldThin-Film Photocathodes Use inAdvanced Electron Beam Lithography,”submitted to Journal of VacuumSciences and Technology B, June 2001.

J. Hines and J. House, “The Source ofPoor Policy: Controlling Learning Driftand Premature Consensus in HumanOrganization,” System DynamicsReview, 17(1), pp. 3-32, 2001.

J.H. Hines and J.L. House,“Management Fads & Poor Policies:A Year of Organization EvolutionResearch,” in NSF Design andManufacturing Research Conference.Tampa, 2001.

J. House, A. Kain, and J. Hines,“Evolutionary Algorithm: Metaphor forLearning.” in Genetic and EvolutionaryComputation Conference. Las Vegas:Morgan Kaufmann, 2000.

M A R W A N J A B R I Gordon and Betty MooreProfessor of MicroelectronicsPh.D., Electrical EngineeringUniversity of Sydney, 1988 marwan@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Artificial intelligence andintelligent signal processing. Theunderstanding of the principles bywhich humans and/or otherorganisms perceive theenvironment, process sensorysignals, reason, make decisionsand learn. The development andapplication of biologically inspiredinformation engineering. Thedesign of integrated systems forintelligent signal processing.

R E P R E S E N TAT I V E P U B L I C AT I O N S O. J.-M. D. Coenen,.M.P. Arnold,

T.J. Sejnowski and M.A. Jabri, “ParallelFiber Coding in the Cerebellum for Life-long Learning,” Autonomous Robots,vol 11:3, pp.291-7. Kluwer AcademicPublishers, The Netherlands, 2001.

B. Zhang, R. Coggins, M.A. Jabri,D. Dersch, and B. Flower, “Multi-resolution Forecasting for FuturesTrading Using Wavelet Decompositions,”IEEE Transactions on Neural Networks,vol. 12, no. 4, pp. 767-775, July 2001.

M.A. Jabri and R. Coggins, “Micro Power Adaptive Circuits forImplantable Devices,” Low Power-LowVoltage Circuits and System,E. Sanchez-Sinencio and AndreasAndreou, eds., IEEE Press,pp. 500-518, 1999.

R. Coggins and M.A. Jabri, “A LowComplexity Intracardiac ElectrogramCompression Algorithm,” IEEETransactions on BiomedicalEngineering, vol. 46, no. 1, pp. 82-91,January 1999.

J. Raymond, W. Wang and M.A. Jabri,“A Computational Model of the AuditoryPathway to the Superior Colliculus,” inBrain-like Computation and IntelligentInformation Systems, Shun-ichi Amariand Nikola Kasabov, eds., SpringerVerlag, pp. 81-104, 1998.

X.Q. Li and M.A. Jabri, “MachineLearning-based VLSI Cells ShapeFunction Estimation,” IEEETransactions on CAD for IntegratedCircuits and Systems, vol 17, no. 7, pp.613-623, 1998.

S T E V E N L . J A C Q U E SProfessorPh.D., Biophysicsand Medical PhysicsUniversity of California,Berkeley, 1984sjacques@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Biomedical optics and laser-tissueinteractions. Development ofdiagnostic and therapeutic devicesfor medicine and biology usingoptical technologies.

R E P R E S E N TAT I V E P U B L I C AT I O N SS.L. Jacques, J.C. Ramella-Roman

and K. Lee, “Imaging Skin Pathologywith Polarized Light,” J. Biomed. Opt.,in press, 2002.

J.A. Viator, G. Au, G. Paltauf, S.L.Jacques, S.A. Prahl, H. Ren, Z. Chenand J.S. Nelson, “Clinical Testing of aPhotoacoustic Probe for Port WineStain Depth Determination,” LasersSurg. Med., 30(2), pp. 141-8, 2002.

S.L. Jacques, N. Ramanujam,G. Vishnoi, R. Choe and B. Chance,“Modeling Photon Transport inTransabdominal Fetal Oximetry,”J. Biomed. Optics, 5, pp. 277-282,2000.

V.V. Vaidyanathan, S. Rastegar,T.W. Fossum, P. Flores, E.W. van derBreggan, N.G. Egger, S.L. Jacquesand M. Motamedi, “A Study ofAminolevulenic Acid-inducedProtoporphyrin IX FluorescenceKinetics in the Canine Oral Cavity,”Lasers Surg. Med., 26,pp. 405-414, 2000.

S.L. Jacques, J. Roman and K. Lee,“Imaging Superficial Tissues withPolarized Light,” Lasers Surg. Med.,26, pp. 119-129, 2000.

L.V. Wang, and S.L. Jacques,“Source of Error in Calculation ofOptical Diffuse Reflectance from TurbidMedia Using Diffusion Theory,” Comput.Methods Programs Biomed., 61(3), pp.163-70, 2000.

R O B E R T S . J A F F EInstructorPh.D., Electrical andComputer EngineeringPortland State University, 1988jaffe@ece.ogi.edu

A full-time instructor in ECE, Jaffeteaches in the areas of signals andsystems, applied mathematics andmathematical systems theory. Hisarea of specialization is linearsystems and robust control. Hereceived a Ph.D. in Electrical andComputer Engineering fromPortland State University in 1988.During an earlier career phasehe was a professor of philosophyand a researcher in the philosophyof education.

E C E | E L E C T R I C A L A N D C O M P U T E R E N G I N E E R I N G | F A C U L T Y

S E A N J . K I R K P AT R I C KAssociate ProfessorPh.D., BiomechanicsUnversity of Miami, 1992SKirkpatrick@providence.org

R E S E A R C H I N T E R E S T S

Development and application ofcoherent light techniques toaddress issues in biomaterialsscience and tissue mechanics.Laser speckle techniques are ofparticular interest. Recentinvestigations have focused on theevaluation of the micromechanicalbehavior of vascular, dermatologi-cal and skeletal tissues using novellaser speckle strain measurementmethods. Other interests includeexperimental investigations intothe micro-mechanics of syntheticbiomaterials used to replace oraugment damaged or pathologicaltissue.

R E P R E S E N TAT I V E P U B L I C AT I O N SS.J. Kirkpatrick and D.D. Duncan,

“Optical Assessment of TissueMechanics,” in V.V. Tuchin, ed., OpticalBiomedical Diagnostics, SPIE Press,Bellingham, Wash., 2002.

S.J. Kirkpatrick, D.A. Baker and D.D.Duncan, “Speckle Tracking of Low-frequency Surface Acoustic Waves forMechanical Characterization of Tissues,”Proceedings SPIE, p. 461, 2002.

S.J. Kirkpatrick ,M.T. Hinds and D.D.Duncan, “Laser Speckle Method forMeasurement of Cell and Cell SheetMechanics,“ Proceedings SPIE,p. 4617, 2002.

M.T. Hinds and S.J. Kirkpatrick,”Material Properties of EngineeredTissues Evaluated with NondestructiveMethods,” Proceedings SPIE, p. 4617,2002.

D.A. Baker, S.A. Prahl, S.J.Kirkpatrick and T.A. Moffitt,“Mechanical Properties of RepairedLiver Using an Argon Ion BeamCoagulator and Albumin,” ProceedingsSPIE, p. 4609, 2002.

I. Patrickeyev and S.J. Kirkpatrick,“Tissue Mechanical PropertiesEvaluated by Tracking SpeckleMotions,” Proceedings SPIE, 2002.

S.J. Kirkpatrick ,D.D. Duncan, D.A.Baker and J. Adams, “Surface Mechanicsof Biological Tissue Using LowFrequency Rayleigh Waves Detected byLaser Speckle,” Procceedings SPIE, 2002.

J A C K M C C A R T H YAssistant ProfessorPh.D., Materials Scienceand EngineeringOregon Graduate Institute ofScience & Technology, 1996jmcarthy@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Mechanisms of change in micro-electronic metallization andinsulator thin films, SEM and TEMin-situ testing to improve thin filmprocessing and reliability,multibeam electron lithography,development of focused ion beamprocesses for fabrication ofstructures on the micron, sub-micron and nano-scales to be usedin sensors and electromechanicaldevices, solid phase epitaxy,GaAs metallizations, materialscharacterization techniques usinganalytical electron microscopy andfocused ion beam technology.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Gosavi, J.M. McCarthy, J.L. House,

B. Scholte van Mast, G. Janawayand C.N. Berglund, “StabilityImprovement at High EmissionDensities for Gold Thin FilmPhotocathodes Used in AdvancedElectron Beam Lithographies,” 45thInternational Conference on Electron,Ion and Photon Beam Technology andNanofabrication, accepted forpublication in JVSTB, Nov.-Dec. 2001.

J.M. McCarthy, Z. Pei, M. Becker andD. Atteridge, “FIB MicromachinedSubmicron Thickness Cantilevers forthe Study of Thin Film Properties,” ThinSolid Films 358, pp. 146-151, 2000.

F. Radulescu and J.M. McCarthy,“The Effect of Stress in the PdGeMediated Solid Phase Epitaxial Growthof Ge on GaAs,” MRS SymposiumProceedings, Substrate Engineering forEpitaxy, 587, 1999.

F. Radulescu, J.M. McCarthy and E.Stach, “In-Situ Annealing TransmissionElectron Microscopy of Pd/Ge/Pd/GaAsInterfacial Reactions,” MRS SymposiumProceedings, Advances in MaterialsProblem Solving with the ElectronMicroscope, 589, 1999.

Z. Pei, J.M. McCarthy, C.N. Berglund,T.H.P. Chang, M. Mankos, K.Y. Leeand M.L. Yu, “Thin Film GatedPhotocathode for e-Beam Lithography,”J. Vac. Sci. Technol. B 17(6), p. 2814,1999.

M I S H A P A V E LProfessorPh.D., Experimental PsychologyNew York University, 1980pavel@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Analysis and modeling of complexbehaviors of biological systems,including visual and auditoryprocessing, pattern recognition,information fusion and decisionmaking. Development ofengineering systems mimickingthese abilities to supportmultimodal communicationbetween humans and machines(speech and video), machinevision, visually guided vehicularcontrol and virtual reality.Applications of these techniques tothe development of futurebiomedical and healthcaresystems, in particular point-of-care biomedical engineering.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Palmer, P. Verghese and M. Pavel,

“The Psychophysics of Visual Search,”Vision Research, 40, pp. 1227-1268,2000.

T. Arai, M. Pavel, H. Hermansky andC. Avendano, “Syllable Intelligibilityfor Temporally Filtered LPC CepstralTrajectories,” Journal of the AcousticalSociety of America, 105, pp. 2783-2791, 1999.

R.K. Sharma, T.K. Leen and M.Pavel,“Probabilistic Image Sensor Fusion,” inM.S. Kearns, S.A. Solla and D.A. Cohn,eds., Advances in Neural InformationProcessing Systems 11. Cambridge,Mass., MIT Press, 1999.

M. Pavel and H. Hermansky,“Information Fusion by Human andMachine,” in Proceedings of the FirstEuropean Conference on SignalAnalysis and Prediction, pp. 350-353,Prague, June 1997.

M. Pavel and H.A. Cunningham,“Eye Movements and the Complexityof Visual Processing,” in M.S. Landy,L.T. Maloney and M. Pavel, eds.,Exploratory Vision: The Active Eye,pp. 101-120, New York, Springer-Verlag, 1996.

H. Hermansky and M. Pavel,“Psychophysics of Speech EngineeringSystems,” Proceedings of the 13thInternational Congress on PhoneticScience, Stockholm, August 1995.

S C O T T A . P R A H LAssistant ProfessorPh.D., Biomedical EngineeringUniversity of Texas at Austin, 1988prahl@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Diagnostic and therapeuticapplications of light in medicine:laser thrombolysis noninvasiveoptical diagnostics, hemostasisand tissue repair.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.A. Viator, G. Au, G. Paltauf,

S.L. Jacques, S.A. Prahl, H. Ren,A. Chen, Z. and J.S. Nelson, “ClinicalTesting of a Photoacoustic Probe forPort Wine Stain Depth Determination,’’Lasers in Surgery and Medicine, vol.30, pp. 141-148, 2002.

J.J. Brazier, M. Yan, S.A. Prahl andY.C. Chen, :”Molecularly ImprintedPolymers Used as Optical Waveguidesfor the Detection of FluorescentAnalytes,’’ in MRS Proceedings ofMolecularly Imprinted Materials, vol.723, 2002.

G. Paltaulf, J.A. Viator, S.A. Prahl andS.L. Jacques, “Iterative ReconstructionMethod for Three-dimensionalOptoacoustic Imaging,’’ Journal ofAcoustic Society of America, submitted.

T.P.M.D. Baker, S.J. Kirkpatrick andS.A. Prahl, “Mechanical Properties ofCoagulated Albumin and FailureMechanisms of Liver Repaired Using anArgon Beam Coagulator with Albumin,’’J. Biomedical Materials Research(Applied Biomaterials), submitted.

R.F. Wolf, H. Xie, J. Petty, J.S. Teachand S.A. Prahl, “Argon Ion BeamHemostasis with Albumin followingLiver Resection,’’ Am. J. Surg.,submitted.

H. Xie, R.F. Wolf, J. Petty, A. Burke,J.S. Teach, K.W. Gregory and S.A. Prahl,“Hemostasis After Partial HepatectomyUsing Argon Beam Coagulation andConcentrated Albumin,’’ J. Trauma,submitted.

A.D. Janis, L.A. Buckley, A.N. Nyara,S.A. Prahl and K.W. Gregory, “AReconstituted in Vitro Clot Modelfor Evaluating Laser Thrombolysis,’’J. Thrombosis and Thrombolysis,submitted.

T.P. Moffitt and S.A. Prahl, “Sized-fiber Reflectometry for Measuring LocalOptical Properties,’’ IEEE JSTQE, vol.7, pp. 952-958, 2001.

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S H A N K A R R A N A N A VA R EAssociate Research ProfessorPh.D., Physical ChemistryUniversity of Missouri,St. Louis, 1983shankarr@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Nanotechnology: nanoparticles andphotoresists, dynamics of complexsystems, ferroelectric,antiferroelectric and amphitropicliquid crystals, flat panel displays,phase transitions and criticalphenomena.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. Di Meglio, S.B. Rananavare,

S. Sorenson, D.H. Thompson,“Bolaamphiphilic Phosphocholines:Structure and Phase Behavior inAqueous Media,” Langmuir, 16,p. 128, 2000.

V.G.K.M. Pisipati and S.B. Rananavare,“X-Ray Diffraction Studies of 100.14and 100.8,” Mol. Cryst. Liq. Cryst.,238, pp. 207-214, 1994.

J.H. Freed, A. Naveem andS.B. Rananavare, “ESR and LiquidCrystals: Statistical Mechanics andGeneralized Smoluchowski Equations,”Chapter 4, pp. 71-84, “ESR andMolecular Motions in Liquid Crystals,”“Thermodynamics of Liquid Crystalsand the Relation to MolecularDynamics: ESR Studies,” “ESR Studiesof Molecular Dynamics at PhaseTransitions in Liquid Crystals,” “ESRand Slow Motions in Liquid Crystals,”Chapters 12-15, pp. 271-402, TheMolecular Dynamics of Liquid Crystals,G. R. Luckhurst and C. A. Veracini, eds.,NATO ASI Series, Kluwer AcademicPublishers, The Netherlands, 1994.

S.B. Rananavare, V.G.K.M. Pisipatiand E.W. Wong, “The ACC MulticriticalPoint in Ferroelectric Liquid Crystals,”Phys. Rev. Lett., 72, p. 3558, 1994.

S.B. Rananavare, V.G.K.M. Pisipatiand E.W. Wong, “A Lifshitz Point inFerroelectric Liquid Crystals,” LiquidCrystal Materials, Devices andApplications III, R. Shashidhar, ed.,2175, pp. 108-119, SPIE-94, San Jose,February 1994.

V.G.K.M. Pisipati and S.B.Rananavare, “Interdigitated SmecticA and B Mesophases in HigherHomologues of 50.m Series,” LiquidCrystals, 13, pp. 757-764, 1993.

M I LT O N R . S C H O L LAssociate ProfessorPh.D., Materials Scienceand EngineeringOregon Graduate Center, 1987milts@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Micro-electro-mechanical systems(MEMS) and nano-electro-mechanical systems (NEMS) andtheir design and use, particularlythe mechanics, materials andinteraction of contacting surfaces,i.e. tribology of microsystems.Mimicry of organic biologicalmechanical sensory systems ininorganic manmade materials.Tribological systems ranging fromchemical mechanical polishing, tofiber-plate interactions in chiprefining and woodcutting, towheel-rail interactions.Tribological performance ofmaterials including abrasive anderosive wear, sliding behavior,rolling sliding conditions and theinteractions of the phenomenawith the working environment,focusing on surface response toexternal stimuli and mitigationtechniques to reduce or eliminatesurface damage.

R E P R E S E N TAT I V E P U B L I C AT I O N SM. Scholl, “Abrasive Wear of Titanium

Nitride Coatings,” Wear, vol. 203-204,pp. 57- 64, 1997.

M. Scholl, “Unique Thermal SprayCoatings by High Energy PlasmaSpraying,” Proceedings of theInternational Conference on Advancesin Welding Technology: Joining of HighPerformance Materials, Columbus,Ohio, November 1996.

D. Christensen, Y. Jia, M. Scholl,P. Clayton and S. Abubakr, “SurfaceDeterioration of Refiner Plates forThermo-Mechanical Pulping,”Proceedings of the 1994 PulpingConference, San Diego, pp. 193-203,TAPPI Press, Atlanta, 1994.

M. Scholl, “Plasma Spraying with WireFeedstock,” Proceedings of the 1994National Thermal Spray Conference,Boston, June 1994.

M. Scholl, C. Steinkamp and W.E.Wood, “Acoustic Emission Monitoring ofPlasma Sprayed Tubes,” EWI ResearchReport, 1994.

R A J S O L A N K IProfessorPh.D., PhysicsColorado State University, 1982solanki@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Atomic layer deposition, copperelectrodeposition andelectromigration, multilevelmetallization, high k gatedielectrics, inorganic and organicelectroluminescent devices,polysilicon thin film transistors.

R E P R E S E N TAT I V E P U B L I C AT I O N SH. Zhang and R. Solanki, “Atomic

Layer Deposition of High DielectricConstant Nanolaminates,”J. Electrochem. Soc., 63, p. 148, 2001.

B. Pathangey and R. Solanki, “AtomicLayer Deposition for Nanoscale ThinFilm Coatings,” Vacuum Tech. andCoatings, 1, p. 32, 2000.

R. Solanki, and B. Pathangey, “AtomicLayer Deposition of Copper SeedLayers,” Electrochem. and Solid-StateLetters, 3 , p. 479, 2000.

H. Zhang, R. Solanki, B. Roberdsk,G. Bai and I. Banerjee, “HighPermittivity Thin Film Nanolaminates,”J. Appl. Phys., 87, p. 1921, 2000.

A.T. Voutsas, M.A. Marmorstein andR. Solanki, “The Effect of LaserAnnealing Ambient on the Performanceof Excimer Laser Annealed Thin FilmTransistors,” J. Electrochemical Soc.,146, p. 3500, 1999.

R. Engelmann, J. Ferguson andR. Solanki, “Quantum Well ActivatedPhosphors — A New Concept forElectroluminescent Displays,” Appl.Phys. Lett., 70, p. 411, 1997.

J. Fogarty, W. Kong and R. Solanki,”Monte Carlo Simulation of High FieldElectron Transport in ZnS,” Solid-StateElectronics, 38, p. 653, 1995.

W. Kong and R. Solanki, “The Effect ofUltraviolet Radiation on a ZnS:Tb ThinFilm Electroluminescent Device,”J. of Appl. Phys., 75, p. 3311, 1994.

X U B O S O N GAssistant ProfessorPh.D., Electrical EngineeringCalifornia Instituteof Technology, 1999xubosong@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Digital image and videoprocessing, statistical patternrecognition, machine learning,sensor fusion, computer vision,information theory and coding,biomedical engineering.

R E P R E S E N TAT I V E P U B L I C AT I O N SX. Song, Y. Abu-Mostafa, J. Sill,

H. Kasdan and M. Pavel, “ImageRecognition by Fusion of ContextualInformation,” Information FusionJournal, 2002, under revision.

A. Adami, K. Yang, X. Song, M. Paveland D. Dirschl, “Model-based ImageProcessing and Analysis for FractureClassification,” Joint Meeting of theIEEE Engineering in Medicine andBiology Society (EMBS) and theBiomedical Engineering Society(BMES), 2002, submitted.

Y. Abu-Mostafa, X. Song, A. Nicholsonand M. Magdon-Ismail, “The BinModel,” IEEE Transactions onInformation Theory, 2001, underrevision.

X. Song, Y. Abu-Mostafa, J. Sill,H. Kasdan, “Image Recognition inContext: Application to MicroscopicUrinalysis,” in Advances in NeuralInformation Processing Systems,S.A. Solla, T.K. Leen and K.R. Muller,eds., MIT Press, pp. 963-969, 2000.

X. Song, “Contextual PatternRecognition with Applications toBiomedical Image Identification,”Ph.D. Thesis, California Institute ofTechnology, 1999.

X. Song, Y. Abu-Mostafa, J. Sill andH. Kasdan, “Incorporating ContextualInformation into White Blood Cell ImageRecognition,” in Advances in NeuralInformation Processing Systems,M.I. Jordan, M.J. Kearns and S.A. Solla,eds., MIT Press, pp. 950-956, 1998.

Y. Abu-Mostafa and X. Song, “Bin Model for Neural Networks,”in Proceedings of the InternationalConference on Neural InformationProcessing, S. Amari, L. Xu, L. Chan,I. King and K. Leung, eds., Springer, pp.169-173, 1996.

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J A N P. H . VA N S A N T E NProfessor and Center Directorof CSLUPh.D., Mathematical PsychologyUniversity of Michigan, 1979vansanten@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Speech timing, intonation, signalprocessing, statistical analysis oftext and speech corpora, and text-to-speech (TTS) system evaluation.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. van Santen and B. Möbius,

“A Model of Fundamental FrequencyContour Alignment,” in Intonation:Analysis, Modelling and Technology,Cambridge University Press,Cambridge, United Kingdom, 2000.

J. van Santen and C. Shih, “Segmentaland Suprasegmental Timing inAmerican English and ManadarinChinese,” Journal of the AcousticalSociety of America, pp. 1012-1026,2000.

J. van Santen and R. Sproat, “High-accuracy Automatic Segmentation,”Proceedings of EUROSPEECH 99,Budapest, Hungary, 1999.

J. van Santen, “Combinatorial Issuesin Text-to-speech Synthesis,”Proceedings of EUROSPEECH 97,Rhodes, Greece, 1997.

J. van Santen and A.L. Buchsbaum,“Methods for Optimal Text Selection,”in Proceedings Eurospeech 1997,Rhodes, Greece, 1997.

J. van Santen, “Prosodic Modellingin Text-to-speech Synthesis,” inProceedings Eurospeech, 1997,Rhodes, Greece, 1997.

J. van Santen, “Segmental Durationand Speech Timing,” in Y. Sagisaka,W.N. Campbell and N., Higuchi, eds.,Computing Prosody. New York,Springer, 1996.

J. van Santen, R.W. Sproat, J. Oliveand J. Hirschberg, eds., “Progress inSpeech Synthesis,” New York, Springer-Verlag, 1996.

E R I C A . W A NAssociate ProfessorPh.D., Electrical EngineeringStanford University, 1994ericwan@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Learning algorithms andarchitectures for neural networksand adaptive signal processing;applications to time-seriesprediction, speech enhancement,adaptive control, andtelecommunications.

R E P R E S E N TAT I V E P U B L I C AT I O N SE.A. Wan, and R. van der Merwe,

“The Unscented Kalman Filter,” inKalman Filtering and Neural Networks,S. Haykin, ed., Wiley Publishing, 2001.

E. Wan and A. Nelson, “Networks forSpeech Enhancement,” in Handbook ofNeural Networks for SpeechProcessing, S. Katagiri, ed., ArtechHouse, Boston, 1999.

E. Wan, and F. Beaufays,“Diagrammatic Methods for Derivingand Relating Temporal Neural NetworksAlgorithms,” in Adaptive Processing ofSequences and Data Structures,”Lecture Notes in Artificial Intelligence,M. Gori and C.L. Giles, eds., Springer-Verlag, 1998.

E. Wan and A. Nelson, “Neural DualExtended Kalman Filtering:Applications in Speech Enhancementand Monaural Blind Signal Separation,”IEEE Workshop on Neural Networksand Signal Processing, 1997.

E. Wan, “Adjoint LMS: An Alternativeto Filtered-X LMS and Multiple ErrorLMS,” ICASSP96, 3, pp. 1842-1845,1996.

E. Wan, “Time Series Prediction Usinga Neural Network with EmbeddedTapped Delay-Lines,” in Predicting theFuture and Understanding the Past,A. Weigend and N. Gershenfeld, eds.,SFI Studies in the Science ofComplexity, Proc., 17, Addison-Wesley,1993.

E. Wan, “Discrete Time NeuralNetworks,” Journal of AppliedIntelligence, 3(1), pp. 91-105, 1993.

E. Wan, “Neural NetworkClassification: A BayesianInterpretation,” IEEE Transactionson Neural Networks, 1(4), pp. 303-305,December 1990.

Y O N G H O N G YA N Associate Professor Ph.D., Computer Science and EngineeringOregon Graduate Institute, 1995. yan@cse.ogi.edu

R E S E A R C H I N T E R E S T S

Human-computer interface design,spoken language system, largevocabulary speech recognition,computer vision, real-timeembedded system and speechsignal processing.

R E P R E S E N TAT I V E P U B L I C AT I O N SX. Wu and Y. Yan, “Linear Regression

Under Maximum a Posteriori Criterionwith Markov Random Field Prior,” inProceedings IEEE ICASSP 2000, June2000.

C. Liu and Y. Yan, “Speaker ChangeDetection Using Minimum MessageLength Criterion,” in Proceedings of the6th International Conference on SpokenLanguage Processing, October 2000.

C. Zheng and Y. Yan, “EfficientlyUsing Speaker Adaptation Data,” inProceedings of the 6th InternationalConference on Spoken LanguageProcessing, October 2000.

Y. Yan, “Speech Recognition UsingCorrelation Generated Neural NetworkTarget,” IEEE Trans. on Speech andAudio Processing, May 1999.

E. Barnard and Y. Yan, “Toward NewLanguage Adaptation for LanguageIdentification,” Speech Communication,21(4), pp. 245-254, May 1997.

Y. Yan, E. Barnard and R.A. Cole,“Development of an Approach toAutomatic Language Identificationbased on Phone Recognition,” inComputer, Speech Language, vol. 10(1),pp. 37-54, January 1996.

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JOINT FACULTY

D R . R O B D A A S C HElectrical EngineeringPortland State University

D R . A N D R E W F R A S E RPortland State University

D R . T O D D L E E NComputer Science and EngineeringOGI School of Science& Engineering

D R . S H I H - L I E N L UIntel Corp.

D R . J O H N E . M O O D YComputer Science and EngineeringOGI School of Science& Engineering

D R . N E L S O N M O R G A NElectrical Engineering &Computer SciencesUniversity of California

D R . M I N G D E YA NChemistryPortland State University

ADJUNCT FACULTY

J O H N C . A B E L ELewis and Clark College

S H A R I A R S . A H M E DIntel Corp.

C H E D L E Y A O U R I R IIntel Corp.

A H M E D R A H H A L - A R A B IIntel Corp.

S H E K H A R B O R K A RIntel Corp.

S T E V E B R A I N E R DIntegrated Device Technology, Inc.

R O B C O N T O L I N INovellus

D O U G L A S C . D R A P E RPortland Community College

S T E P H E N R . E A R LYConsultant

Y O U S S E F A . E L - M A N S YIntel Corp.

R E I N H A R T E N G L E M A N NConsultant

D A V I D E VA N SSharp MicroelectronicsTechnology Inc.

W AY N E K . F O R DIntel Corp.

M A R K F R A N KConexant

H O W A R D H E C KIntel Corp.

D A E M A N N K I MPohang Institute of Science& Technology, Korea

R O Y K R A V I T ZRadisys Corporation

W I L L I A M A . M A C K I ELinfield College

V. D A K S H I N A M U R T YUniversity of Portland

K A R T I K R A O L

Intel Corp.

E D W A R D F. R I T Z , J R .Consultant

L A W R E N C E R U B YUniversity of California, Berkeley

LY N W O O D W. S W A N S O NFEI Co.

S T E W A R T S . TAY L O RMaxim

T H O M A S T H O M A SIntel Corp.

T R A N T H O N GMicrosystems Engineering, Inc.

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THE DEPARTMENT OF ENVIRONMENTAL

SCIENCE AND ENGINEERING (ESE) is oneof the oldest stand-aloneenvironmental science andengineering programs in the country,and offers graduate studies in water,soil and air sciences. Founded morethan 25 years ago, the department isknown for research and educationprograms that balance practicalapplications with fundamentalinvestigations of the physical,chemical and biological processesunderlying environmentalphenomena. The curriculum is highlyinterdisciplinary and is built on asolid foundation of fundamentalscience and engineering.The department offers graduate studiesleading to the degrees of Doctor ofPhilosophy (Ph.D.) and Master of Science(M.S.). The M.S. degree has both thesis andnon-thesis options. All of our programs maybe pursued full-time or part-time. Ph.D.students and M.S. thesis students participatein a program that includes both formalcourse work and research. The researchexperience is intensive, consisting oflaboratory, computational, theoretical and/orfield studies. Thesis students are involved inall aspects of departmental research andhave ready access to modern instrumentationand computers.

The Ph.D. program can be completed in fourto five years, and the M.S. thesis option takesapproximately two years to complete. TheM.S. non-thesis program can be completed in12 months.

Students in any of the degree programsmay concentrate their studies in thefollowing areas:

• Environmental Science and Engineering (ESE)(traditional program)

• Environmental Information Technology (EIT)

ADMISSION REQUIREMENTSApplications for admission to full-time andpart-time degree programs are invited from

persons with bachelor’s degrees in thephysical or biological sciences, mathematicsor engineering. Previous course work inchemistry, biology and mathematics (throughat least one year of calculus) is expected.

Requirements for admission to theDepartment of Environmental Science andEngineering are the same as the OGI Schoolof Science & Engineering’s admissionrequirements, except for the minimumTOEFL score. For applicants whose nativelanguage is not English, the departmentrequires TOEFL scores of at least 600 for thewritten test or 250 for the computer-basedtest. Students who earned undergraduate orgraduate degrees in the United States are notrequired to submit TOEFL scores. GRE generalaptitude scores are required for admission toall of the department’s M.S. and Ph.D.programs. A GRE subject examination scoremay also be submitted but is not required.

Completed Ph.D. applications should bereceived by February 15 for matriculation inthe fall of the same year. M.S. applicationsare accepted year-round, although most newM.S. students apply by July for matriculationin the fall. Prospective applicants for the Ph.D.program should examine the faculty researchprograms at http://www.ese.ogi.edu/people.htmlto determine whether their professionalgoals can be fulfilled in the department.Prospective students are encouraged to com-municate with individual faculty membersbefore applying.

DEGREE REQUIREMENTSDISTRIBUTION REQUIREMENTS

To achieve the necessary breadth in training,students in all programs take courses that cover arange of scientific disciplines and environmentalmedia. Five courses must be taken that satisfy thefollowing distribution requirements. No course cansatisfy more than one requirement.

At least one course must be taken from three ofthe following four discipline groups:

1. Applied Mathematics ESE 500; ESE 504; ESE 506; ESE 508

2. Chemistry ESE 510; ESE 511; ESE 514; ESE 516

3. Fluid Dynamics ESE 520; ESE 530; ESE 537; ESE 539

4. Biology ESE 550; ESE 554

At least one course must be taken from each of thefollowing environmental media groups:

1. Surface Waters ESE 520; ESE 530; ESE 537; ESE 539

2. Groundwater ESE 540; ESE 541; ESE 542; ESE 543

Students following the EIT track will in

Departmentof Environmental

Science andEngineering

www.ese.ogi.edu

D E P A R T M E N T H E A D

A n t ó n i o M . B a p t i s t a

503 748-1147E-mail: baptista@ese.ogi.edu

D E P A R T M E N T A D M I N I S T R A T O R

Therese Young

503 748-1247E-mail: tyoung@ese.ogi.edu

E S E G E N E R A L I N Q U I R I E S

E-mail: info@ese.ogi.edu

The Center for Coasta l and Land-Marg inResearch monitors estuar ine condit ions a longthe Oregon coast .

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E S E | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G

general have further requirements specific tothat track. The additional requirements willbe defined by the student’s SPC (StudentProgram Committee).

All full-time students are required to takeEnvironmental Science Seminar (ESE 599)each quarter except summer. However,this course does not count toward degreecredit requirements.

For all ESE educational programs, up to8 credits may be granted for courses takenin other OHSU departments. Up to 12quarter credits may be transferable fromother accredited institutions for graduatecourses comparable in content and level tocourses offered in the department. TheStudent Program Committee (SPC) decides on the appropriateness of internship andtransfer credits.

Transfer credits may not be used to reducethe annual tuition, but may allow for greaterflexibility in scheduling.

P H . D . I N E N V I R O N M E N TA L S C I E N C EA N D E N G I N E E R I N G

Students may complete the Ph.D. program inEnvironmental Science and Engineering(ESE) or Environmental InformationTechnology (EIT). The EIT program is a trackwithin the ESE department. Students whocomplete the EIT program receive theirdegree in Environmental Science andEngineering with a concentration in EIT.

Ph.D. students must complete the distribu-tion courses outlined above. Students mustalso complete additional courses for a total ofat least 52 credit hours of course work,selected with the approval of their SPC.

Ph.D. candidates must also pass a two-partcomprehensive exam. The first part is awritten examination covering four subjectareas selected by the department. The secondpart is the preparation and oral defense of aproposal that defines the student’s Ph.D.dissertation research. A written Ph.D. disser-tation with an oral defense is also required.

M . S . I N E N V I R O N M E N TA L S C I E N C EA N D E N G I N E E R I N G

M . S . T H E S I S O P T I O N S

Students may pursue M.S. thesis options inEnvironmental Science and Engineering(ESE) or Environmental Information

Technology (EIT). The EIT program is a trackwithin the ESE department. Students whocomplete the EIT program receive theirdegree in Environmental Science andEngineering with a concentration in EIT.

Students pursuing the M.S. thesis optionmust complete at least 45 credits. Thesecredits include the distribution requirementsoutlined above, additional courses selectedwith the approval of the SPC, and researchcredits. Master’s thesis research (ESE 700)is usually no more than 9 credits.Comprehensive examinations are notrequired of M.S. thesis students. However, awritten M.S. dissertation with an oral defenseis required.

M . S . N O N - T H E S I S O P T I O N S

Students may pursue the M.S. non-thesisoptions in Environmental Science andEngineering (ESE) or EnvironmentalInformation Technology (EIT). The EITprogram is a track within the ESEdepartment. Students who complete the EITprogram receive their degree inEnvironmental Science and Engineering witha concentration in EIT.

For the M.S. non-thesis degree, fivedistribution courses must be taken asoutlined above. Students must completeadditional courses for a total of at least 45credit hours, selected with the approval ofthe SPC. Up to 8 credits may be granted forapproved participation in non-thesis researchor approved work as an intern with a localcompany or government agency. Nocomprehensive examinations are required forthe non-thesis M.S. options.

DEGREE PROGRAMSE N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G( E S E ) ( T R A D I T I O N A L P R O G R A M )

The department offers Ph.D., M.S. thesis, andM.S. non-thesis options in EnvironmentalScience and Engineering (ESE). The ESEprogram is known for its research andeducation programs that balance practicalapplications with fundamental investigationsof the physical, chemical and biologicalprocesses underlying environmentalphenomena. The curriculum is highlyinterdisciplinary and is built on a solidfoundation of fundamental science andengineering. For more information, pleasesee http://www.ese.ogi.edu/curriculum.html.

E N V I R O N M E N TA L I N F O R M AT I O NT E C H N O L O G Y ( E I T )

The Environmental Information Technology(EIT) program is the newest program offeredwithin the Department of EnvironmentalScience and Engineering. The Ph.D. option inEIT began in Fall 2001, and the M.S. thesisand non-thesis options in EIT will begin inFall 2002. The EIT program combines theexpertise and course work found in ESE andin the Computer Science and Engineering(CSE) and Electrical and ComputerEngineering (ECE) departments at the OGISchool of Science & Engineering at OHSU.The goal of the EIT program is to combine adeep understanding of environmentalprocesses with mastery of sensing, modelingand information technology. Requirements forthe EIT program are the same as for the M.S.thesis and non-thesis options describedabove, except that students in the EITprogram complete approximately 20 percentof their course work in the CSE and ECEdepartments. The EIT curriculum includesfundamental courses, science courses,technology courses, elective courses andcapstone integrative courses. Electivecourses may include classes offered throughOHSU’s Medical Informatics program. Formore information on the EIT program and itscurriculum, see http://www.ese.ogi.edu/eit/.

T U I T I O N

Tuition for the full-time M.S. non-thesisprogram is $19,620 for the 2002-2003academic year, which is typically spreadequally over the first four quarters. A part-time non-thesis M.S. program is available tomeet the needs of working students, andinterested students are encouraged tocontact the Department of GraduateEducation for additional information. A $100deposit is required with the return of youracceptance to reserve your place in ourdepartment. This deposit is nonrefundableand will be applied toward your tuition.

COURSE OFFERINGSESE 500 Introduction to Discrete MethodsThis course is an introduction to discrete methodsfor environmental fluid dynamics. Lectures coverthe theory and application of methods for thenumerical solution of initial-value, boundary-valueand mixed initial-boundary-value problems.Prerequisite: Calculus. 4 credits

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ESE 504 Uncertainty AnalysisA survey of basic probability concepts followed byintroductions to several statistical advanced tech-niques that play an important role in environmentaldata analysis. Topics may include distribution func-tions, propagation of error, hypothesis testing,analysis of variance, experimental design, samplingtheory, regression analysis, time-series analysisand spatial statistics techniques. The course pro-vides a balance of theory and application usingenvironmental data sets. 4 credits

ESE 506 Environmental Systems AnalysisIntroduction to techniques of systems analysisapplied to environmental quality management.Emphasis is on development and application ofmathematical models with computer simulation andoptimization. Analysis includes efficient computa-tional algorithms and search techniques. Linear andseparable programming applied to evaluate man-agement alternatives. Applications to air, water,solid and hazardous waste management. Pre-requisites: Computer programming and calculus.

4 credits

ESE 508 Computational Fluid DynamicsThis course describes advanced topics in computa-tional fluid dynamics, including specialized discretemethods (e.g., for advection-dominated problems),formal analysis of stability and accuracy, and select-ed simulations of complex environmental andbiological systems. Prerequisites: Advanced calcu-lus and ESE 500. New for 2003-2004. 4 credits

ESE 510 Aquatic Chemistry General acid/base concepts (mono- and polyproticsystems); pH; making activity corrections; numeri-cal calculations; titration concepts as applied tonatural systems; buffer intensity; dissolved CO2chemistry; acidity and alkalinity in open CO2 sys-tems; minerals and their role in controlling naturalwater chemistry; solubility characteristics of oxideand hydroxides; introduction to redox chemistry innatural systems; pe-pH diagrams. 4 credits

ESE 514 Distribution and Fate of Organic PollutantsDiscussion of the physico-chemical processes thatcontrol the partitioning of organic chemicals inthe environment. This introductory course considersall environmental compartments, water, soil andair, and partitioning between those phases.Recommended prerequisite: ESE 510. 4 credits

ESE 516 Chemical Degradation and RemediationA thorough introduction to the transformation reac-tions that contribute to the fate of organicsubstances in the environment. The course coverspathways, mechanisms and kinetics of hydrolysis,oxidation, reduction, elimination, conjugation, etc.Treatment is balanced to reflect the importance ofthese processes in all types of environmental watersranging from engineered systems to groundwater,surface water, rain and fog. Recommended prepara-tion: ESE 511 and ESE 514. 4 credits

ESE 519 Air Pollution: Origins, Chemistry and ControlThis course will focus on tropospheric air pollutionwith particular emphasis on the urban and regionalscales. It will discuss the following items: basic

structure of the atmosphere and relevant meteoro-logical considerations; sources of tropospheric airpollutants; atmospheric photochemistry; the ozone,oxide of nitrogen and hydrocarbon chemical cycles;chemistry of toxic organic compounds in the atmos-phere; gas and aqueous phase chemistry of sulfurdioxide; size distributions, lifetimes, origins and for-mation mechanisms of aerosols; and control ofatmospheric emissions. 3 credits

ESE 520 Introduction to Environmental Observationand Forecasting SystemsThis course introduces environmental observationand forecasting systems and their applicationtoward the enhanced understanding and manage-ment of natural resources. Emphasis is on estuariesand coasts. Students are exposed to a novel, cross-disciplinary culture for understanding andinteracting with environmental systems. This cul-ture relies heavily on “real-time” generation ofmodeling and observational data, which are inte-grated and distributed through informationnetworks designed to bring the right environmentalinformation at the right time to the right user.Prerequisite: Instructor permission. 4 credits

ESE 522 Introduction to Spatial SciencesStudents will learn theoretical and practical appli-cations of geo-spatial sciences within the context ofEnvironmental Sciences and Engineering. Geo-graphic Positioning Systems (GPS) will be studiedwhile performing practical, hands-on laboratoryexperiments using the latest in GPS equipment.Classroom discussions will focus on relatinglocationon the Earth’s surface to a common graticule.Horizontal and vertical datum, theoretical spheroidsand ellipsoids, geoids and map projections will bediscussed. Spatial relationships, or analysis, of con-tinuous and categorical data will be addressedthrough the application of standard statistics andprobability. ARCVIEW, a popular Geographic Infor-mation System (GIS) software tool, will be stressed.

4 credits

ESE 523 Introduction to Remote Sensing ofthe EnvironmentThis course will explore the acquisition, analysisand visualization of remotely sensed data. Thephysics behind the collection of remotely senseddata will be introduced as will both airborne-plat-form and satellite-platform sensors. Fundamentalsof aerial photogrammetry, single-band, and multi-spectral and thermal infrared data will beaddressed. Concepts of image statistics, radiometricand geometric corrections, spatial filtering and spe-cial transformations like the Normalized DifferenceVegetation Index are explored. Supervised andUnsupervised classification schemes will be dis-cussed as will change detection. The coursepedagogy is designed to address the needs of theadvanced Environmental Science and Engineeringgraduate student. While there is no prerequisite, thecourse incorporates many topics from ESE 505,“Introduction to Spatial Science.” It is thereforerecommended that students unfamiliar with classifi-cation methods and the fundamental concepts ofGeographic Information Systems complete ESE 505or equivalent. 4 credits

ESE 530 Transport ProcessesAn introductory course in the physics of transportprocesses in the natural environment. The courseexamines heat, mass and momentum transport viaconservation principles and the Reynolds TransportTheorem, but strongly emphasizes the environmen-tal applications of these processes. Example studiesinclude atmospheric and oceanic circulation, flowand dispersion in rivers, and heat budgets for lakesand reservoirs. 4 credits

ESE 532 Modeling Coastal Circulation and Transport I This course introduces the students to the processof modeling coastal circulation and transport. Topicsinclude review of governing equations and of state-of-the-art models, in-depth analysis of selectedmodels, and hands-on solution of benchmark prob-lems. Prerequisites: ESE 500 or ESE 508, and ESE530. Contents revised for 2002-2003. 4 credits

ESE 533 Modeling Coastal Circulation and Transport IIThis course provides an advanced treatment ofcoastal circulation and transport modeling.Students are introduced to the detailed modeling ofcomplex estuarine, plume and continental shelfprocesses, through a combination of lectures andlabs focused on specific sites and processes.Prerequisites: ESE 532. Alternate years, contentsrevised for 2003-2004. 4 credits

ESE 537 Methods in OceanographyThis course covers the fundamentals of processingestuarine and coastal oceanographic data, includingtime series (e.g., surface elevation, currents andwinds) and data obtained from vessels (e.g., profileand bathymetric data). 2 credits

ESE 540 Groundwater and Watershed HydrologyHydrologic cycle, principles of unsaturated and sat-urated flow in the subsurface; characterization ofgroundwater/surface interactions, water balance,modeling of watershed-scale processes. 4 credits

ESE 541 Groundwater ModelingApplied groundwater modeling using finite differ-ence method. Introduction to numerical methods forsolving the partial differential equations for saturat-ed and unsaturated subsurface flow. Modelexecution and calibration. Prerequisite: ESE 540.Not offered 2002-2003. 4 credits

ESE 542 Contaminant HydrologyProcesses controlling subsurface contaminantmovement in porous and fractured media, includinggroundwater flow, dispersion, diffusion, sorptionand degradation. Parameter estimation, mathemati-cal and laboratory modeling of aquifers is alsocovered. 4 credits

ESE 543 Modeling in Contaminant HydrogeologyThis course is designed to be taken concurrentlywith ESE 542. It emphasizes the hands-on use ofcommon mathematical models for groundwater flowand transport (e.g., MODFLOW, RANDOMWALK,SUMATRA) to examine real groundwater contamina-tion problems. Prerequisite: ESE 542. Not offered2002-2003. 4 credits

ESE 550 Environmental MicrobiologyIntroduction to environmental microbiology, with

E S E | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G

emphasis on the role of microbes in the environmentand in remediation processes. Microbes and theirinteraction and activities in soil and aquatic envi-ronments will be discussed, as well as elementalcycling as influenced by microbes. Microbially medi-ated transformation of organic pollutants,transformation kinetics and remediation technolo-gies will be considered. In 2002-2003, may beoffered in combination with ESE 554. 4 credits

ESE 554 Biodegradation and BioremediationA process-oriented survey of microbially mediatedtransformations of organic pollutants. Transforma-tions occurring in the natural environment as wellas in remediation technologies are considered.Emphasis is on the pollutant properties, microbio-logical factors, and medium properties thatdetermine the pathways and kinetics of biodegrada-tion. Recommended preparation: ESE 550.

4 credits

ESE 560 Environmental Soil ScienceSoil physics, chemistry and microbiology; soil devel-opment, soil description and mapping, soils and landuse, agricultural and urban forestry; soil-plant rela-tionships for environmental restoration; soil processmodeling. Prerequisites: ESE 510 and ESE 550. Notoffered 2002-2003. 4 credits

ESE 562 Ecosystem EcologyPrinciples of ecology and of ecosystem process,description and measurement, with emphasis onecosystem health assessment. Simulation modelingof ecosystem processes; transport and transforma-tion. Not offered 2002-2003. 4 credits

ESE 570 Principles of Toxicology and Risk AssessmentThis course applies toxicological principles to bothhuman and ecological risk assessments. The princi-ples and methodologies for risk assessments arepresented within a regulatory context. Topicsinclude hazard identification, exposure assessment,dose-response relationships, deterministic andprobabilistic risk assessments, responses of variousreceptors to different contaminants, and environ-mental management decisions. 3 credits

ESE 58X Special TopicsTypically involves a scholarly and critical review ofan advanced scientific topic by one or more studentstogether with one or more faculty members.Requirements of the student typically include a writ-ten review paper and/or a seminar to be given aspart of ESE 599. Selection of this course for creditand the topic to be investigated must be approved bythe Student Program Committee.

Variable and repetitive credit

ESE 580 Ecosystem Management and RestorationThis course will provide an overview of ecosystemmanagement and restoration at the local and region-al scale. It will follow the hydrologic cycle fromupland watersheds through streams, rivers and estu-aries to the ocean and will track important systemparameters such as water flow and temperature.

4 credits

ESE 586 Environmental Law and RegulationA survey of environmental law and regulation essen-

tial to practicing scientists and engineers. Thecourse introduces the substance of environmentaland natural resource law and also weaves inprocess (such as rule making and permit writing)and practical skills (such as environmental manage-ment and negotiation). 3 credits

ESE 587 Clean Air Act Laws and RegulationsA thorough introduction to the Clean Air Act inits federal and state permutations, as well as thedetailed regulations guiding the act’s implementa-tion. The course focuses on the practical aspects ofstatutory and regulatory interpretation, applicationto specific facilities, and negotiation of Clean Air Actissues with EPA and the states. Not offered 2002-2003. 2 credits

ESE 589 Special Topics: Advanced Topics in FieldSampling and AnalysisAn intensive capstone course that integrates fieldprocesses with theory from previous lecture materi-al. Approximately one week is spent at site locationswhere students critically examine current tech-niques for collecting surface water, groundwaterand soil samples to characterize chemical, biologi-cal and physical properties. Laboratory methods foranalyzing organic and inorganic chemicals areincluded. Students work in teams on projects to col-lect and evaluate data, write reports and makerecommendations for future management of thesites. Anticipate overnight travel. Variable credit

ESE 598 Organization of Environmental Science andEngineering SeminarThis course is for the Ph.D. student responsible formanaging the weekly Environmental Science andEngineering Seminar series (ESE 599). Studentsenroll for this course with their advisor’s approval.

1 credit

ESE 599 Environmental Science SeminarWeekly seminars by invited guests on all aspects ofenvironmental science, and by ESE faculty and stu-dents on their research. Visitors are welcome.Schedules are available on the World Wide Web athttp://www.ese.ogi.edu/seminars/, or by request atinfo@ese.ogi.edu. 1 credit

ESE 600 ResearchResearch toward the dissertation for the Ph.D.degree before completing the comprehensive exam-inations. Variable and repetitive credit

ESE 610 Non-Thesis ResearchSupervised research as a component of the non-thesis M.S. degree. The plan of research and finaldeliverables must be approved by the research advi-sor and the Student Program Committee.Deliverables include a written report and/or semi-nar given as part of ESE 599. A maximum of 8credits from ESE 610 and ESE 620 may be appliedto a degree. Variable and repetitive credit

ESE 620 Professional InternshipThis course provides an opportunity to earn creditfor relevant work experience in industry. Studentsgain valuable experience that allows them both toapply the knowledge gained in the classroom and toprepare for their careers. Enrollment requires a

faculty advisor and is limited by the number ofinternship opportunities available. Internationalstudents need to submit appropriate paperwork forthe Immigration and Naturalization Service. A max-imum of 8 credits from ESE 610 and ESE 620 maybe applied to a degree.

Variable and repetitive credit

ESE 700 M.S. Thesis ResearchResearch toward the M.S. thesis degree.

Variable and repetitive credit

ESE 800 Ph.D. Dissertation ResearchResearch toward the dissertation for the Ph.D.degree after completing the comprehensive exami-nations. Variable and repetitive credit

RESEARCH PROGRAMSCascadia Subduction Zone TsunamisLarge tsunamis are believed to be locallygenerated in the Cascadia Subduction Zone (CSZ)every 200 to 600 years, based on geologicalrecords. The last large tsunami dates back about300 years, raising concerns about the protection ofcoastal communities in Oregon, Washington,California and British Columbia. The coastal impactof potential CSZ tsunamis is being investigatedthrough numerical modeling. The need to usegeological evidence on paleotsunamis as the sole,loose reference for model validation makes this anunusually interesting and challenging problem. TheOregon Department of Geology and MineralIndustry (DOGAMI) has incorporated our jointresearch results into the development of tsunamiinundation maps for the Oregon and Washingtoncoasts. Baptista, Chawla, external collaborators

CORIE: A Pilot Estuarine Observation andForecasting SystemSince 1996, we have been developing CORIE, anobservation and forecasting system for the ColumbiaRiver estuary (http://www.ccalmr.ogi.edu/CORIE).The motivation is twofold. First, the Columbia Riverand its near-shore plume are a dominantoceanographic feature of the northeastern PacificOcean and the focus of controversial ecosystemmanagement issues. CORIE represents a novel,promising and much-needed infrastructure forphysical and ecological research in this system.Second, we envision that multipurpose observationand forecasting systems will become central to themanagement of coasts and estuaries worldwide.The Columbia River estuary is a challengingnatural laboratory to test concepts and tools, andCORIE is a pilot system developed to anchor ourobservation and forecasting research.Baptista, Chawla, Zhang, Zulauf

Quality-Scalable Information Flow Systems forEnvironmental Observation and ForecastingRecent advances in computer power andconnectivity have fueled the development of real-time Environmental Observation and ForecastingSystems (EOFS). These systems will revolutionizethe way scientists share information about theenvironment and represent an unprecedentedopportunity to break traditional information

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barriers separating scientists from society atlarge. Incipient forms of EOFS are already in usein areas of strong social relevance, but they tendto be small-scale, application- and domain-specific, stand-alone systems. There is a needto evolve toward multipurpose, shared systemsdesigned to adapt flexibly to evolving needs ofinformation consumers. To meet this need, we haveassembled an interdisciplinary team, includingcomputer science and environmental scienceresearchers and a heterogeneous base of pilotusers. Our goals include (a) developing missingintegration concepts and technologies for EOFS,(b) closing the loop between environmental modelsand sensors, (c) using, evaluating and refining apilot EOFS, and (d) developing pilot multileveleducational programs. Baptista, Walpole, Maier,Leen, Feng and Feng

CORMIX Graphic User Interface and GISDatabase IntegrationThis project develops computer informationsystems for the CORMIX mixing zone water-qualitymodel. A fully interactive Windows-basedapplication is proposed, designed to give CORMIXadditional functionality, flexibility and power usingobject-oriented, rule-base technology for forms-based interactive data entry, flow classification,simulation logic description and GIS databaseintegration. Doneker

D-CORMIX Decision Support SystemThis project involves development, validation andscientific review of the D-CORMIX decision supportsystem. D-CORMIX is a physically based simulationmodel linked to a knowledge-based classificationsystem for predicting of water quality and sedimentdeposition impacts resulting from dredging. Thepurpose of the project is to assist water-qualitymanagers in performing waste load allocations forcontinuous dredge discharges. The methodologiesdeveloped in this project are also necessary forlong-term pollutant fate and transport studies byproviding information on initial boundaryconditions. This project also develops validationstudies and documentation for USEPA ScienceAdvisory Board (SAB) review of D-CORMIX. Doneker

CORMIX Documentation Development, WorkshopInstruction and Technical SupportOGI has a three-year cooperative agreement tomaintain, update and distribute the CORMIX usermanual, conduct technical training workshops onmixing zone models, and provide technicalassistance to CORMIX model users. The CORMIXwater-quality model has approximately 1,000 usersworldwide; their feedback through technicalsupport and training workshops directly supportscurrent model development activities. Doneker

Internal Circulation in Tidal Channels and StraitsThis project, funded by the Office of NavalResearch, seeks to use wavelet data analysistechniques and novel modeling strategies toimprove our conceptual understanding of estuarinecirculation and scalar transport. Continuouswavelet transforms allow resolution of timevariation in tidal processes in each frequency

band. The project is using this technique tounderstand estuarine internal circulation and shelfinternal tides in buoyant plumes. Modeling effortsuse symbolic mathematics software to provide abalance between the intuitive understanding andcompact nature of analytical solutions and thesuperior flexibility and accuracy of full-numericalsolutions. Jay

Contaminant Diffusion in ClayClay liners are often used in waste disposalfacilities to prevent the advective transport ofcontaminants into the surrounding groundwater.Even when advective transport is small, however,contaminant transport through liners may besignificant as the result of molecular diffusion. Thisphenomenon has been studied in the laboratoryand at actual waste disposal facilities to evaluateits roles in mass transport and groundwatercontamination. Johnson

Processes Controlling the Subsurface Transport ofDense Chlorinated SolventsThe uncontrolled release of chlorinated solvents isa common cause of serious groundwatercontamination in many parts of the world. It is inthis context that it is important to understand thephysical and chemical principles that govern themovement of these dense nonaqueous phase liquids(DNAPLs). Experiments under way at OGI and inconjunction with the University of Waterloo areexamining the behavior and remediation ofchlorinated solvents in the saturated andunsaturated zones. Johnson

Simulation of Subsurface Processes Using Very LargeScale Experimental AquifersMany important chemical, physical and biologicalprocesses are difficult to study in the laboratorybecause of problems of scaling. Many of theseprocesses are also difficult to characterize in thefield, because of the complex and uncontrollednature of environmental systems. For thesereasons, OGI has established the LargeExperimental Aquifer Program (OGI/LEAP). Atpresent, the facility consists of five large aquifersused to examine the movements of organic solventsand petroleum compounds in the unsaturated andsaturated porous media. Future LEAP aquifers willexamine inorganic geochemistry and theinteractions between chemical, biological andphysical processes in contaminated aquifers.Johnson and other faculty

Gas-Phase Transport in Unsaturated Porous MediaGas-phase transport is important in controllingmany subsurface processes, including respiration,pesticide behavior and contaminant volatilizationand movement. Laboratory experiments have beenconducted to determine diffusion rates of a varietyof organic compounds in porous media and thekinetics of adsorption and desorption for a varietyof soil types and a range of water contents. Johnson

Multi-Phase Monitoring of Gasoline Movement Usinga Very Large Physical Model (OGI/LEAP) Leaks from underground storage tanks (UST)represent a major ongoing source of groundwater

contamination. The rapid detection of leaks is,therefore, a major goal of UST legislation. TheOGI/LEAP facility is used to study the movement ofgasoline components in the vapor, aqueous andpure-product phases. This work will help establishwhich of a variety of leak-detection technologies isbest suited to detect leaks under a range ofenvironmental conditions. Johnson

Distribution of Organic Compounds Between the Gasand Urban Aerosol Particulate PhasesThe behavior of organic compounds in theatmosphere depends in large part on the extent towhich they partition from the gas phase to aerosolparticulate matter. Processes that are affected bythis partitioning process include precipitationscavenging of gases and particles as well as drydeposition of gases and particles. Fundamentalgas/solid sorption theory is being used toinvestigate important aspects of atmosphericgas/particle partitioning. The study involves theinvestigation of basic partitioning behavior of awide range of representative atmosphericcompounds (including alkanes and polycyclicaromatic hydrocarbons) on a variety ofrepresentative model particulate substrates,including elemental carbon, organic carbon, silicaand clay. Pankow

Thermodynamics of Inorganic Solid SolutionsThe manner in which inorganic solid solutionsbehave is one of the last major research frontiersin ambient temperature aqueous geochemistry.Coprecipitation of metal ions is well known innature, e.g., Sr2+ can form a solid solution incalcium carbonate (CaCO3[s]). Unfortunately, littleis known about the thermodynamics of such solidsolutions. That is, little is known about how theactivity coefficients of metal ions vary as a functionof composition in solid solutions of various types.The values of the activity coefficients are ofinterest because they control the extent to whichthe constituents in the solid solutions will besoluble in water, e.g., the extent to which a toxicmetal ion like Cd2+ that is present in calciumcarbonate will be soluble in water. In this work,activity coefficient values for a variety ofenvironmentally important divalent metal ions arebeing sought as a function of composition incalcium carbonate. Pankow

Fate and Effects of Fuel OxygenatesThe recent realization that oxygenated fueladditives such as MTBE are becoming widelydistributed groundwater contaminants has createda sudden and pressing demand for data on theprocesses that control their environmental fate.Ongoing work in this area includes modeling ofMTBE infiltration to the groundwater, laboratorystudies of MTBE biodegradation, and field studiesof several contaminated sites for MTBE and itspossible breakdown products. For more informa-tion on this work, see http://cgr.ese.ogi.edu/mtbe/.Pankow, Tratnyek, Johnson

Global Distributions and Mass Balances ofHalocarbons, Nitrous Oxide and Other Trace GasesGases such as CCl3F (F-11), CCl2F2 (F-12) CHClF2

E S E | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G

(F-22), CF4 (F-14), C2Cl3F3 (F-113), CH3CCl3,CH3Cl and N2O are being added to the atmosphereby various industrial processes and the public’s useof high-technology products. Such chlorine-containing compounds are believed to threaten theearth’s natural ozone layer high in the atmosphere(stratosphere). This research will systematicallyobtain a long-time series of concentrationmeasurements by a flask sampling system. Theresults are then interpreted with global massbalance models and sophisticated statisticaltechniques to quantify the sources and lifetimesof these gases in the environment. Such data arenow obtained from sites all over the worldextending from the Arctic Circle to the South Pole.Rasmussen

Studies of Past AtmospheresAtmospheric gases such as N2O, CO2, CO, CH3Cl,carbonyl sulfide (OCS), and CH4 are primarilyproduced by natural processes, but over the pastcentury human activities have been adding growingamounts to their natural abundance. This processcan upset the cycles of these gases and lead topossibly adverse environmental effects such as thewarming of the earth’s surface (N2O, CO2, CH4).When both natural and anthropogenic processescontribute to the current atmospheric abundanceof a trace gas, it is of interest to determine theamount which existed before human activities hadany effect. Perhaps the only realistic method todetermine the composition of the ancientatmosphere is to analyze the air in bubbles burieddeep in polar ice. The depth of the ice indicates theage of the air in the bubbles. By going far enoughback in time, the relationship between pastatmospheric composition and climate might befound. The novel and simple method of studying theold atmosphere of the earth is beset by manyproblems that complicate the relationship betweenthe gases in the bubbles and the composition of theold atmosphere. Theoretical and experimentalresearch for resolving these problems as well asthe measurement of trace gases are the majorgoals of this project. Rasmussen

Ocean-Air Exchange of GasesSome atmospheric gases are greatly influenced bythe earth’s oceans. For instance, a large amount ofthe atmospheric methyl chloride (CH3Cl) andmethyl iodide (CH3I) are produced in the oceans,possibly by biogenic processes. It has also beenshown recently that carbonyl sulfide (OCS) isproduced in the oceans and subsequently emittedto the atmosphere. On the other hand, man-madegases such as CCl3F (F-11) can dissolve in theoceans and thus be removed from the atmosphere.This research project is devoted to determining thesolubility of such gases in water and to modelingthe flux of gases into or out of the oceans. Theresults obtained are essential ingredients indetermining the sources and fates of atmospherictrace gases and in estimating the effects of humanactivities on the future warming of the earth ordepletion of the ozone layer. Rasmussen

Studies of Atmospheric MethaneConsiderable evidence has been accumulated

showing that methane (CH4) is increasing in theatmosphere, most likely as an indirect result ofgrowing human population. In the future, such anincrease of CH4 can lead to a global warming byenhancing the earth’s natural greenhouse effectand create more ozone and carbon monoxide in theatmosphere. However, it might also prevent someof the destruction of the stratospheric ozone layerby the manmade fluorocarbons 11 and 12. In thisproject, experimental and theoretical research isfocused on statistical trend analyses for the globalincrease of CH4, its seasonal variation, sources andsinks, models of its effect on the CO, O3, and OHcycles and its role in the future of the environment.Rasmussen

Development of Experimental Methods for TraceGas MeasurementsAt present, some 50 atmospheric gases can bemeasured at the Trace Gas Laboratory. Still, newmethods are needed to improve the accuracy andprecision of measurements and to satisfy thestringent demands of ultra-clean background airsampling. New methods are also being developedfor automated real-time analysis of many tracegases. Research programs include development ofgas chromatographic and mass spectrometricmethods for the analysis of trace gases. At present,GC/MS systems in the laboratory are being used toroutinely measure C2-C12 nonmethanehydrocarbons at tens of parts per trillion levels.Techniques for collecting and storing air and watersamples also are being developed. Rasmussen

Biogenic Sources of Atmospheric GasesLiving organisms produce and consume a variety ofgases and may therefore form an integral part ofthe global cycle of a trace gas. Selected plants andanimals, living in the sea or on land, are beingstudied to determine their role in the cycles of CH4,N2O, CH3CI, CH3I, isoprene and otherhydrocarbons. Rasmussen

The Global Cycle of Carbon Monoxide (CO)Based on 15 years of global sampling and theapplication of modern trend analysis techniques,our data have shown that CO increased in theatmosphere until around 1987 and has sincedeclined. These changes in CO have majorimplications for atmospheric chemistry and therole of biomass burning in causing global increasesof trace gases. Present research includes modelingof the global budgets, seasonal cycles and potentialenvironmental effects. Rasmussen

Methane Emissions from Rice FieldsMethane concentrations have nearly tripledcompared to the natural atmosphere of 300 yearsago (based on ice core analyses). The increase ofrice agriculture to sustain an increasing populationmay be a major contributor to the increase ofmethane during the last century. This researchprogram is designed to determine the role of riceagriculture in the global methane cycle. Fieldexperiments are being conducted in China,Indonesia and the U.S. Laboratory experiments andtheoretical research are being done at the GlobalChange Research Center (Portland State

University) in a comprehensive research program.This work includes modeling the production,oxidation and transport of methane in the ricepaddy ecosystem and measuring the controllingparameters. Rasmussen

Hydrocarbon Biodegradation in SoilPetroleum hydrocarbon contamination is prevalentin soils and groundwater. Efforts to clean up thisextensive petroleum contamination have promptedresearch into in-situ bioremediation. Depending onsite characteristics, in-situ hydrocarbonbiodegradation is a cost effective andenvironmentally sound remediation alternative orpartner to pump-and-treat and vacuum extractiontechnologies. We have studied the processes bywhich the biodegradation rates of organiccompounds can be optimized. Toccalino

Human-Health Assessment of Water QualityA national effort is under way with the U.S.Geological Survey’s National Water-QualityAssessment (NAWQA) program, in collaborationwith the U.S. Environmental Protection Agency(USEPA) and state agencies, to conduct a piloteffort to develop, test and refine concepts to moreeffectively communicate water-quality informationin a human-health context. The study includesdetermining how to effectively communicate thedata from this study in a human-health context toCongress, the media, the public, etc. Toccalino

Remediation of Halocarbon-Contaminated GroundwaterThere is enormous demand for improved ways toclean up aquifers that have been contaminatedwith halogenated hydrocarbon solvents like carbontetrachloride and TCE. Recent field-scale testshave shown that technologies based ondechlorination with granular iron may havesubstantial value. The goal of our research in thisarea is to provide a sound scientific basis fordesigning and operating such technologies bydetermining the mechanisms of dechlorination byiron and the geochemical and microbiologicalprocesses that affect the performance of thistechnique in the field. For more information on thiswork, see http://cgr.ese.ogi.edu/iron. Tratnyek

Remediation of Explosives-Contaminated GroundwaterThere are numerous facilities where militaryoperations have resulted in contamination ofgroundwater with explosives such as TNT andRDX. Both TNT and RDX react rapidly with zero-valent iron, suggesting that permeable reactivebarriers of zero-valent iron might be useful inremediation of these sites. However, the productsof these reactions with zero-valent iron may notpresent a satisfactory remediation end-point.Therefore, we are investigating the kinetics andmechanisms of this reaction in the experimentsperformed in the laboratory and in the field. Seehttp://cgr.ese.ogi.edu/iron/. Tratnyek and Johnson

Reduction Reactions of Organic Pollutants inAnaerobic EnvironmentsSome organic pollutants undergo rapid reduction inanaerobic sediments, soils and groundwaters.Despite the potential importance of this process,little is known about the natural reducing agents

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that are responsible for these reactions. In thisproject, assays are being developed to identify andquantify environmental reducing agents in situ.These assays will be used in kinetic studies ofimportant pollutant reduction reactions. Tratnyek

Oxidation Reactions of Organic PollutantsSome organic pollutants undergo rapid oxidation innatural waters, when catalyzed by sunlight, and intechnological systems, when chemical oxidants areadded to effect remediation. These reactions areusually mediated by “activated oxygen species”such as hydroxyl radical. We are studying thekinetics, mechanisms and products of thesereactions with a wide variety of contaminants. Theaim of this work is help assess the suitability ofvarious advanced oxidation technologies (AOTs) forremediation of groundwater, as well as to betterunderstand the fate of contaminants in naturalwaters that are exposed to sunlight. Tratnyek

Correlation Analysis of Contaminant ReactivityQuantitative Structure-Activity Relationships(QSARs) are of enormous importance inenvironmental chemistry and toxicology because oftheir predictive power, but they also reveal a greatdeal about reaction mechanisms and the nature ofsubstituent effects. We are involved in thedevelopment of QSARs for a wide range of redoxreactions involving organic contaminants. Thiswork involves the use of computational chemistrymethods as well as advanced statistical techniquesin exploratory data analysis. Tratnyek

RESEARCH CENTERSC E N T E R F O R G R O U N D W AT E R R E S E A R C HThe principal mission of the Center forGroundwater Research (CGR) is to conductstate-of-the-art research in areas relating to thetransport and fate of contaminants in thesubsurface. This is accomplished through acombination of research grants and contracts,support from corporate sponsors and collaborationwith other universities, industries and government agencies.

The center coordinates a range of projects relatingto the transport and fate of contaminants in soilsand groundwater. The scope of the center includes,among other things, the development of: 1) newsampling and site characterization techniques;2) new analytical techniques; and 3) improvedgroundwater remediation methods.

The center operates the Large ExperimentalAquifer Program (LEAP) which contains theexperimental cells outlined below. The LEAPfacility provides staff with the capability to conductboth bench-scale experiments and pilot-scaledemonstrations. Current projects include transportthrough fractured clay, air sparging of sourcepetroleum zones containing MTBE, and a pilotscale demonstration of zeolite as an in-situpermeable barrier material.

Students involved in LEAP research graduate witha rare combination of experience in full-scale

remediation engineering and a process-level under-standing of contaminant hydrology and chemistry.

For additional information about CGR, contact:

D R . R I C H A R D J O H N S O N

Phone: 503 748-1193E-mail: rjohnson@ese.ogi.eduCGR Web site: cgr.ese.ogi.edu.

C E N T E R FA C U LT YRichard Johnson, Associate Professor James F. Pankow, ProfessorPatricia L. Toccalino, Assistant ProfessorPaul Tratnyek, Associate Professor

L E A P E Q U I P M E N T• Five tanks: one 10m x 10m x 3m, two 10m x 10m x 5m,

one 10m x 2.5m x 0.5m, and one 8m x 2.5m x 0.5m • In-situ instrumentation, including: automated temperature,

pressure and water level monitoring; multilevel samplers;down hole video camera; and automated vapor and productsensing equipment

• Remediation equipment, including soil vapor extraction andair sparging capabilities

• Automated on-site analytical equipment, including capillaryGC-MS instrumentation

C E N T E R F O R C O A S TA L A N D L A N D - M A R G I NR E S E A R C H ( C C A L M R )The Center for Coastal and Land-Margin Research(CCALMR) is an interdisciplinary research centeraffiliated with the Department of EnvironmentalScience and Engineering. CCALMR conductsresearch, graduate education and advancedtechnology development that directly address theneed for better scientific understanding of coasts,land margins and estuaries. Improved knowledge ofthese complex systems is necessary to preserveand enhance their environmental integrity,maintain the economic viability of communitiesdependent on them and protect human populationsfrom natural and manmade hazards.

Real-world natural resource management issuesmotivate CCALMR research and educationactivities. Insights drawn from the experience ofscience and engineering professionals in the publicand private sectors influence the identification ofemerging research challenges, the design ofresearch projects, the development of supportingtools and applications and the transfer ofknowledge and technology.

Additional information about CCALMR may beobtained from:

A N T Ó N I O M . B A P T I S TA

Phone: 503 748-1193E-mail: baptista@ese.ogi.eduCCALMR Web site: www.ccalmr.ogi.edu/

C C A L M R R E S E A R C H FA C I L I T I E S

CCALMR is well equipped to conduct state-of-the-art scientific research. The following is a list offacilities and instruments available in addition tothose available through the Department ofEnvironmental Science and Engineering.

R E A L - T I M E D ATA A C Q U I S I T I O N N E T W O R K

The pilot nowcast-forecast system CORIE includesa real-time data acquisition network with 12multisensor oceanographic stations in theColumbia River estuary. Field operations areconducted from the Marine EnvironmentalResearch and Training Station (MERTS). MERTS isa facility developed in partnership with andoperated by the Clatsop Community College (CCC).CCC operates two training and research vessels:the 50-foot M/V Forerunner and the 21-foot R/VTansy Point. CCALMR operates a 21-foot researchvessel, the R/V CORIE.

O C E A N O G R A P H I C E Q U I P M E N T• 300, 600 and 1200 kHz Acoustic Doppler current profilers (RD) • 500 and 1500 kHz Acoustic Doppler profilers (Sontek) • Conductivity and temperature pairs (Seabird) • Conductivity, temperature and pressure sensors

(Coastal Leasing and Ocean Sensors) • Optical backscatter sensors (Downing Associates) • Wind gauges (Coastal Leasing) • High-density thermistor chains (CCALMR) • Differential GPS (Trimble) • Spread spectrum radio data modems (FreeWave)

B I O G E O C H E M I C A L R O TAT I N G A N N U L A RF L U M E ( R A L F )RALF, a 2-meter biogeochemical rotating annularflume, supports research on coupled physical andbiogeochemical processes at sediment-waterinterfaces. Instrumentation providing real-time orpseudo real-time data include:

• Three-dimensional Acoustic Doppler Velocimeter (Sontek) • DO (Orion) and pH/ISE (Orion) • DLK-100 Potentiostat (AIS) • Solid State Au/Hg amalgam microelectrodes • Bipotentiostat equipped with rotating disk electrode (Pine)

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A N T Ó N I O M . B A P T I S TAProfessor and Department HeadDirector, Center for Coastal and Land-Margin ResearchPh.D., Civil EngineeringMassachusetts Institute of Technology, 1987baptista@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Integrated understanding andprediction of hydrodynamic andenvironmental processes. Inestuaries and coasts. Develop-ment of associated conceptsand technologies: environmentalobservation and forecastingsystems, numerical methodsand models, physically basedecological indicators.

R E P R E S E N TAT I V E P U B L I C AT I O N SA.M. Baptista, “Environmental

Observation and Forecasting Systems,”Encyclopedia of Physical Science andTechnology, 3rd Edition, Vol. 5,Academic Press, 2002.

E.P. Myers and A.M. Baptista,“Inversion for Tides in the EasternNorth Pacific Ocean,” Advances inWater Resources, Vol. 24 (5), pp. 505-519, 2001.

E.P. Myers and A.M. Baptista,“Analysis of Factors InfluencingSimulations of the 1993 HokkaidoNansei-Oki and 1964 Alaska Tsunamis,”Natural Hazards, 23 (1), pp. 1-28, 2001.

D.C. Steere, A.M. Baptista,D. McNamee, C. Pu and J. Walpole,“Research Challenges in EnvironmentalObservation and Forecasting Systems,”in Proceedings of the 6th AnnualInternational Conference on MobileComputing and Networking (Mobicom2000), Boston, pp. 292-299, 2000.

A. Oliveira, A.B. Fortunato and A.M.Baptista “Mass Balance in Eulerian-Lagrangian Transport Simulations inEstuaries,” ASCE Journal of HydraulicEngineering, 126 (8), pp. 605-614, 2000.

Z. Yang, A.M. Baptista and J. Darland,“Numerical Modeling of FlowCharacteristics in a Rotating AnnularFlume,” Dynamics of Atmospheres andOceans, 31, pp. 271-294, 2000.

A.M. Baptista, M. Wilkin, P. Pearson,P. Turner, C. McCandlish and P. Barrett,“Coastal and Estuarine Forecast Systems:A Multi-Purpose Infrastructure for theColumbia River,” Earth System Monitor,9 (3). NOAA, Washington D.C., 1999.

R O B E R T L . D O N E K E R , P. E .Assistant ProfessorPh.D., Environmental EngineeringCornell University, 1989doneker@ese.ogi.edu

R E S E A R C H I N T E R E S T S

Development of decision supportsystems for environmentalsimulation modeling, engineeringdesign optimization and naturalresource management. Currentresearch focuses on developmentof technology transfer systems withemphasis on water-quality model-ing and control of point and non-point source pollutant transport.

R E P R E S E N TAT I V E P U B L I C AT I O N SR.L. Doneker and G.H. Jirka,

“Schematization in Regulatory MixingZone Analysis,” Journal of WaterResources Planning and Management,ASCE, Vol. 128, No.1, Jan./Feb. 2002.

R.L. Doneker and G.H. Jirka, CORMIX-GI Systems for Mixing Zone Analysis ofBrine Wastewater Disposal,”Desalination, 139, 2001.

R.L. Doneker and G.H. Jirka,Discussion of “Mixing in Inclined DenseJets.” Journal of Hydraulic Engineering,ASCE, Vol. 125, No..3, March 1999.

G.H. Jirka, R.L. Doneker and S.W.Hinton, “User’s Manual for CORMIX: AHydro-Dynamic Mixing Zone Model andDecision Support System for PollutantDischarges into Surface Waters,” EPA#:823/B-97-006.

D.A. Ford, A.P. Kruzic and R.L.Doneker, “Using GLEAMS to Evaluatethe Agricultural Waste ApplicationRule-Based Decision Support System(AWARDS) Computer Program,” WaterScience and Technology, Vol. 28, No. 35,pp. 625-634, 1993.

R.L. Doneker and G.H. Jirka, “ExpertSystems for Mixing Zone Analysis andDesign Aqueous Pollutant Discharges,”Journal of Water Resources Planningand Management, ASCE, Vol. 117, No.6, Nov./Dec. 1991.

G.H. Jirka and R.L. Doneker,“Hydrodynamic Classification ofSubmerged Single Port Discharges,”Journal of Hydraulics Division, ASCE,Vol. 117, No. 9, September 1991.

D A V I D A . J AYAssociate ProfessorPh.D., Physical OceanographyUniversity of Washington, 1987djay@ese.ogi.edu

R E S E A R C H I N T E R E S T S

River basin, estuarine andcontinental shelf processes,turbulent mixing, tides and tidalanalysis. A unifying theme is theinfluence of hydrodynamicprocesses on ecosystems.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. N. Cudaback and D. A. Jay, “Tidal

Asymmetry in an Estuarine Pycnocline,2: Transport,” J. Geophys. Res., 106,pp. 2639-2652, 2001.

C. N. Cudaback and D. A. Jay, “TidalAsymmetry in an Estuarine Pycnocline:Depth and Thickness”, J. Geophys.Res., 105, pp. 26,237-26,252, 2000.

D.A. Jay, W. R. Geyer and D. R.Montgomery, “An EcologicalPerspective on Estuarine Classification:Estuarine Science, A SyntheticApproach to Research and Practice”,J. E. Hobbie, ed., Island Press, pp. 149-175, 2000.

E.P. Flinchem and D. A. Jay, “AnIntroduction to Wavelet Transform TidalAnalysis Methods,” Coast. Estuar. ShelfSci., 51, pp. 177-200, 2000.

D.A. Jay and E.P. Flinchem, “Inter-action of Fluctuating River Flow with aBarotropic Tide: A Test of Wavelet TidalAnalysis Methods”, J. Geophys. Res.,102, pp. 5705-5720, 1997.

B.M. Hickey, L.J. Pietrafesa, D.A. Jayand W.C. Boicourt, “The Columbia RiverPlume Study: Subtidal Variability in theVelocity and Salinity Field,” J. Geophys.Res., 103 (10), pp. 229-368, 1996.

D.A. Jay and J.D. Musiak, “InternalTidal Asymmetry in Channel Flows:Origins and Consequences,”C. Pattiaratchi, ed., “Mixing Processesin Estuaries and Coastal Seas, anAmerican Geophysical Union,”Coastal and Estuarine Sciences, 53,pp. 219-258, 1996.

D.A. Jay and C.A. Simenstad,“Downstream Effects of WaterWithdrawal in a Small, High-gradientBasin: Erosion and Deposition on theSkokomish River Delta,” Estuaries, 19,pp. 501-517, 1996.

R I C H A R D L . J O H N S O NAssociate Professor, Director;Center for Groundwater ResearchPh.D., Environmental ScienceOregon Graduate Center, 1985rjohnson@ese.ogi.edu

R E S E A R C H I N T E R E S T S

Physical and chemical behaviorof organic contaminants in theair, soil and water; analyticalorganic chemistry; groundwatertransport, fate and modeling ofcontaminants in porous andfractured porous media.

R E P R E S E N TAT I V E P U B L I C AT I O N SR.L. Johnson, P.C. Johnson, T.L.

Johnson and A. Leeson, “Helium TracerTests for Assessing Contaminant VaporRecovery and Air Distribution DuringIn-Situ Air Sparging,” BioremediationJournal, 5(4), pp. 321-336, 2001.

R.L. Johnson, P.C. Johnson,T.L. Johnson, Neil R. Thomson andA. Leeson, “Diagnosis of In-Situ AirSparging Performance Using TransientGroundwater Pressure Changes DuringStartup and Shutdown,” BioremediationJournal, 5(4), pp. 299-320, 2001.

R.L. Johnson, P.C. Johnson,I.L. Amerson, T.L. Johnson, C.L. Bruce,A. Leeson and C.M. Vogel, “DiagnosticTools for Integrated In-Situ Air SpargingPilot Tests,” Bioremediation Journal,5(4), pp. 283-298, 2001.

N.R. Thomson and R.L. Johnson,“Air Distribution During In-Situ AirSparging: An Overview of MathematicalModeling”, J. Hazardous Materials 72(2-3), pp. 265-282, 2000.

R.L. Johnson, J.F. Pankow, D. Bender,C. Price and J. Zogorski, “To WhatExtent Will Past MTBE ReleasesContaminate Community Water SupplyWells?” Environ. Science and Technol.,34, 2A-7A, 2000.

L. Slater, A.M. Binley, W. Daily andR.L. Johnson, “Cross-hole ElectricalImaging of a Controlled Saline TracerInjection,” J. Applied Geophysics, 44,pp. 85-102, 2000.

FACULTY

E S E | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G | F A C U L T Y

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J A M E S F. P A N K O WProfessor Ph.D., EnvironmentalEngineering ScienceCalifornia Institute ofTechnology, 1978pankow@ese.ogi.edu

R E S E A R C H I N T E R E S T S

Physical and analytical chemistryof organic compounds and metalsin natural waters and in theatmosphere; the formation andchemistry of atmospheric aerosols;the chemistry of nicotine intobacco smoke.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.F. Pankow, J.H. Seinfeld, W.E. Asher

and G.B. Erdakos, “Modeling theFormation of Secondary OrganicAerosols. 1. Theory and Measurementsfor the (-Pinene-, (-Pinene-, Sabinene-,(3-Carene, and Cyclohexene-OzoneSystems,” Environ. Sci. Technol., 35,pp. 1164-1172, 2001. See also Errata,Environ. Sci. Technol., 35, p. 3272, 2001

J.H. Seinfeld, W.E. Asher,G.B. Erdakos and J. F. Pankow,“Modeling the Formation of SecondaryOrganic Aerosols. 2. The PredictedEffects of Relative Humidity on AerosolFormation in the (-Pinene-, (-Pinene-,Sabinene-, (3-Carene, and Cyclohexene-Ozone Systems,” Environ. Sci. Technol.,35, pp. 1806-1817, 2001.

R.L. Johnson, J. Pankow, D. Bender,C. Price and J. Zogorski, “MTBE,To What Extent Will Past ReleasesContaminate Community Water SupplyWells?” Environ. Sci. Technol., pp.210A-217A, 2000.

J.F. Pankow, B.T. Mader,L.M. Isabelle, W. Luo, A. Pavlick andC. Liang, “Conversion of Nicotine inTobacco Smoke to Its Volatile andAvailable Free-Base Form through theAction of Gaseous Ammonia,” Environ.Sci. Technol., 31, pp. 2428-2433, 1997.

C. Liang and J.F. Pankow,“Gas/Particle Partitioning of OrganicCompounds to Environmental TobaccoSmoke: Partition Coefficient Measure-ments by Desorption,” Environ. Sci.Technol., 30 (9), pp. 2800-2805, 1996.

J.F. Pankow, “An Absorption Modelof Gas/Particle Partitioning in theAtmosphere,” Atmos. Environ., 28,p. 189, 1994.

R E I N H O L D A . R A S M U S S E NProfessorPh.D., Botany Plant PhysiologyWashington University,St. Louis, 1964rrasmus@ese.ogi.edu

R E S E A R C H I N T E R E S T S

Atmospheric chemistry of tracegases; biogenic and anthropogenicemissions of trace gases and theirroles in stratospheric ozonedestruction and troposphericozone formation; measurements oftrace gases at parts per trillion toparts per quadrillion levels;sources and sinks of isoprene andother hydrocarbons.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. Geron, R.A. Rasmussen, R.R. Arnts

and A. Guenther, “A review andSynthesis of Monoterpene Speciationfrom Forests in the United States,”Atmos. Environ, 34 (11), pp. 1761-1781, 2000.

J. Zhang, K.R. Smith, R. Uma, Y. Ma,V.V.N. Kishore, K. Lata, M.A.K. Khalil,R.A. Rasmussen and S.T. Thorneloe,“Carbon monoxide from cookstoves indeveloping countries: 2. Exposurepotentials,” Chemosphere: GlobalChange Sci., 1 (1-3), pp. 367-375, 1999.

J. Zhang, K.R. Smith, R. Uma, Y. Ma,V.V.N. Kishore, K. Lata, M.A.K. Khalil,R.A. Rasmussen and S.T. Thorneloe,“Carbon monoxide from cookstoves indeveloping countries: 1. Emissionfactors,” Chemosphere: Global ChangeSci., 1 (1-3), pp. 353-366, 1999.

E. Grosjean, R.A. Rasmussen andD. Grosjean, “Toxic air contaminants inPorto Alegre, Brazil,” Environ. Sci.Technol., 33 (12), pp. 1970-1978, 1999.

R.A. Rasmussen, M.A.K. Khalil andF. Moraes, “Permafrost MethaneContent: 1. Experimental Data fromSites in Northern Alaska,”Chemosphere, 26, p. 591, 1993.

M.A.K. Khalil, R.A. Rasmussen,J.R. French and J. Holt, “The Influenceof Termites on Atmospheric TraceGases: CH4, CO2, CHCl3, N2O, CO, H2and Light Hydrocarbons,” J. Geophys.Res., 95, p. 3619, 1990.

D.A. Hegg, L.F. Radke, P.V. Hobbs,R.A. Rasmussen and P.J. Riggan,“Emissions of Some Trace Gases fromBiomass Fires,” J. Geophys. Res., 95,p. 5669, 1990.

P AT R I C I A L . T O C C A L I N OAssistant Professor Ph.D., Environmental Science andEngineeringOregon Graduate Institute, 1992toccalino@ese.ogi.edu

R E S E A R C H I N T E R E S T S

Human and ecological riskassessments, water-qualityassessments, contaminant fateand transport in variousenvironmental media.

R E P R E S E N TAT I V E P U B L I C AT I O N SA N D T E C H N I C A L R E P O R T S

P.L. Toccalino, J. Zogorski, L. Nowell,J. Donohue, C. Eiden, S. Krietzman andG. Post, “Health-based Screening LevelMethodology for State-level Analyses,”technical report to U.S. GeologicalSurvey, U.S. Environmental ProtectionAgency and N.J. Department ofEnvironmental Protection, 2002.

R. Johnson, D. Grady and P. Toccalino,“Impact of Remediation on Long-termLeaching Due to Recharge in aContaminated Fractured Till,” technicalreport to the American PetroleumInstitute, 2001.

P.L. Toccalino and R. Binder,“Methodologies for PresentingContaminant concentration Data fromthe Glassboro, New Jersey, Study Areain a Human-Health Risk Context,”technical report to U.S. GeologicalSurvey, U.S. Environmental ProtectionAgency and N.J. Department ofEnvironmental Protection, 2000.

P.L. Toccalino, K. M. Auer, D. A.Mervyn and B. Stirling, “Phase IIRemedial Investigation/Risk AssessmentReport for Westside Light Rail Transit;Construction Spoils at the Port ofPortland’s Portland InternationalCenter,” Portland, Oregon, 1997.

P.L. Toccalino, “Evaluation of theContained Burn of Two M88 NIKERocket Motors for Environmental Safety& Health Implications,” Nevada TestSite X-Tunnel Facility (U25X), LasVegas, 1997.

P.L. Toccalino, R. L. Johnson andD. R. Boone, “Nitrogen Limitation andNitrogen Fixation During AlkaneBiodegradation in a Sandy Soil,” Appl.Environ. Microbiol., 59, pp. 2977-2983,1993.

P A U L G . T R AT N Y E KAssociate ProfessorPh.D., ChemistryColorado School of Mines, 1987tratnyek@ese.ogi.edu

R E S E A R C H I N T E R E S T S

Mechanistic and kinetic aspects ofthe fate of organic pollutants inthe environment; degradationreactions involving pesticides,phenols, munitions, dyestuffs andchlorinated hydrocarbon solvents;chemical and microbiologicalprocesses in sediments, soils andgroundwaters as well asphotochemical processes insurface waters; natural andengineered remediation systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.T. Nurmi and P.G. Tratnyek,

“Electrochemical Properties of NaturalOrganic Matter (NOM), Fractions ofNOM, and Model BiogeochemicalElectron shuttles.” Environ. Sci.Technol., 36 (4), pp. 617-624, 2002.

P.G. Tratnyek, M.M. Scherer, B. Dengand S. Hu, “Effects of Natural OrganicMatter, Anthropogenic Surfactants andModel Quinones on the Reduction ofContaminants by Zero-valent Iron.” Wat.Res., 35 (19), pp. 4435-4443, 2001.

M.M. Scherer, K. Johnson, J.C.Westall and P.G. Tratnyek, “MassTransport Effects on the Kinetics ofNitrobenzene Reduction by Iron Metal.”Environ. Sci. Technol., 35 (13), pp.2804-2811, 2001.

P.G. Tratnyek, T.E. Reilkoff, A. Lemon,M.M. Scherer, B.A. Balko, L.M. Feikand B. Henegar, “Visualizing RedoxChemistry: Probing EnvironmentalOxidation-Reduction Reactions withIndicator Dyes,” The ChemicalEducator, 6 (3), pp. 172-179, 2001.

S. Nam and P.G. Tratnyek, “Reductionof Azo Dyes with Zero-valent Iron.” Wat.Res., 34 (6), pp. 1837-1845, 2000.

P.G. Tratnyek and D.L. Macalady,“Oxidation-Reduction Reactions in theAquatic Environment,” in Handbook ofProperty Estimation Methods forChemicals: Environmental and HealthSciences; ed. D. Mackay and R.S.Boethling, Lewis: Boca Raton, Florida,pp. 383-415, 2000.

F A C U L T Y | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G | E S E

E S E | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G | F A C U L T Y

JOINT FACULTY

D R . J A M E S H U N T Z I C K E R

Center for ProfessionalDevelopmentOGI School of Science& Engineering

ADJUNCT FACULTY

D R . M A R Y A B R A M S

DEQ Laboratory DivisionOregon Department ofEnvironmental Quality

D R . D A V I D B O O N E

Department ofEnvironmental Biology Portland State University

D R . N O R M A N E D E R

Conkling Fiskum &McCormick, Inc.

D R . W I L L I A M F I S H

Department of EnvironmentalSciences and ResourcesPortland State University

D R . B R U C E H O P E

Environmental ToxicologistOregon Department ofEnvironmental Quality

D R . A S L A M K H A L I L

Department of PhysicsPortland State University

K E N N E T H R O S E N B A U M , J . D .

Environmental Law Institute(Visiting Scholar)Washington, D.C.

D R . J O H N C . W E S TA L L

Department of ChemistryOregon State University

RESEARCH SCIENTISTS

W I L L A M A S H E R

Senior Research ScientistPh.D., Environmental Scienceand EngineeringOregon Graduate Center

A R U N C H A W L A

Associate Research ScientistPh.D., Civil EngineeringUniversity of Delaware

T O M C H I S H O L M

Research AssociatePh.D., Marine ScienceCollege of William and Mary

W E N TA I L U O

Associate Research ScientistPh.D., Environmental Scienceand EngineeringOregon Graduate Institute

R O S E M A R I E M I E H R

Research AssociatePh.D., ChemistryTechnical University,Munich, Germany

T O D D S A N D E R S

Associate Research ScientistPh.D., Physical OceanographyUniversity of Delaware

D O U G W I L S O N

Associate Research ScientistPh.D., Physical OceanographyMemorial University ofNewfoundland

Y I N G L O N G ( J O S E P H ) Z H A N G

Associate Research ScientistPh.D., Applied Mathematicsand Fluid MechanicsUniversity of Wollongong,Australia

M I C H A E L Z U L A U F

Associate Research ScientistPh.D., MeteorologyUniversity of Utah

SENIOR STAFF

B O B D A L L U G E

Research AssociateB.S., Psychology Washington State University

L O R N E M . I S A B E L L E

Senior Research AssociateM.S., ChemistrySan Francisco State University

C O L E M C C A N D L I S H

Scientific ProgrammerM.S., Atmospheric SciencesOregon State University

J I M M O H A N

Systems ManagerM.S., Management inScience and TechnologyOregon Graduate Institute

J U L I A N O R M A N

Research AssociateM.S., Environmental Scienceand EngineeringOregon Health &Science University

P H I L I P O R T O N

Research AssociateB.S., Physical OceanographyUniversity of Michigan

R O B Y N P H I L L I P S

Research AssociateM.S., EnvironmentalManagement/ToxicologyDuke University

B O B W AT K I N S

Research TechnicianB.S., Chemical EngineeringWashington State University

M I C H A E L W I L K I N

Research AssociateB.S., Oceanography and GeologyUniversity of Southampton, U.K.

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THE DEPARTMENT OF MANAGEMENT IN

SCIENCE AND TECHNOLOGY provides therigorous educational preparationnecessary for highly effectivemanagerial- and professional-level work in industries,organizations and departments that have a strong technical,engineering, manufacturingor scientific orientation.Our courses, certificate and master’sdegree programs focus on managingpeople and processes and buildingeffective and competitive organizationsin the specific contexts of technology andscience. Managing change and competingin the global marketplace are prominentthemes in the MST program.

LEARN ONLINE, ANYTIME, ANYWHEREMST delivers challenging and engagingversions of its courses over the Internet. Thisis an excellent option for students facing timepressures or working in locations wheretravel to the OGI School campus is notfeasible. Course delivery is based oninteractive Web pages, multimedia lecturesand lessons, faculty-managed chat, andonline discussions, all in a seamless,browser-centric environment. Students maytake individual courses, enroll in theCertificate in Management in Science andTechnology program, or apply for the fullMaster of Science degree (currently only theManaging the Technology Company degreeoption is offered online). Courses offeredonline are identified with a “D” following thecourse number. For further information, visitthe MST Web site at www.ogi.edu/MST/. Linkslead directly to our online educationaladministration partner, Cenquest.

INDIVIDUAL COURSESEach MST course is designed as a valuableprofessional development experience forworking professionals. Project Management,Quality Management, and Building EffectiveOrganizations in Science and Technology,for example, may be taken as stand-alonecourses. We encourage nonmatriculatedstudents to join our courses for careerdevelopment in specific areas.

FOR-CREDIT CERTIF ICATEM A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G Y

The MST department offers a six-coursecertificate in Management in Science andTechnology. The following five courses,plus an additional MST elective coursechosen in consultation with a faculty advisor,are required:

MST 501/ Managerial and Financial Accounting501D/501W for Science and Technology 4 credits

MST 503/503D Marketing in Science and Technology 4 credits

MST 510/510D Principles and Trends in Technology Management 3 credits

MST 512/512D Project Management 4 credits

MST 520/ Managing in Science and Technology520D/520W 4 credits

Elective to be chosen after consultation with faculty advisor 3-4 credits

Additional topical certificate programs are inthe University approval process; please seethe Web site www.ogi.edu/MST/ for updates.

NON-CREDIT CERTIF ICATESThe MST department also offers certificateprograms that do not award academic credit.

E X E C U T I V E E D U C AT I O N F O R H I G H - T E C HFA S T- T R A C K E R S

A P A R T N E R S H I P B E T W E E N O G I , P S U A N D A E A

The OGI School of Science & Engineering atOHSU, the Portland State University Schoolof Business Administration and the OregonCouncil of the American ElectronicsAssociation (AeA) will launch an executiveeducation program for the high-technologyindustry in early 2003.

Designed for the next generation of high-technology executives, the program providesknowledge, skills and tools essential forexecutive development. The program featuresthree value drivers:

• Nationally known high-technology executivesand academics as primary instructors.

• Content directly relevant to people about toenter the executive ranks.

• A local cohort program offering ampleopportunity for participants to build a networkof others with executive aspirations.

The program is presented in workshopformat, with four one-day sessions inFebruary, March, April and May on finance,leadership and management, strategy andmarketing. Each day features two workshopsessions, lunch with the instructors, and

Department ofManagement in Science

and Technologywww.ogi.edu/MST/

D E P A R T M E N T H E A D

Fred Ph i l l ips

503 748-1353E-mail: fphillip@admin.ogi.edu

D E P A R T M E N T A D M I N I S T R A T O R

Victor ia Ty ler

503 748-1335E-mail: vtyler@admin.ogi.edu

A D M I N I S T R A T I V E A S S I S T A N T

Stac i Sutton

503 748-7804E-mail: ssutton@admin.ogi.edu

P R O G R A M A D M I N I S T R A T O R

Maryann Burn ingham

503 748-1794E-mail: maryannb@admin.ogi.edu

G E N E R A L I N Q U I R I E S

503 748-7804E-mail: ssutton@admin.ogi.edu

MST’s academic year cu lminates in a bus inessp lan compet i t ion before fe l low students andjudges f rom the bus iness community.

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M S T | M A N AG E M E N T I N S C I E N C E A N D T E C H N O L O G Y

dinner and social hour with a special guest,usually a prominent local executive.To promote building the cohort communitybetween sessions, an online discussiongroup will be moderated by the PSU or OGIfaculty member.

This program does not award academic credit.

I N D U S T R I A L D E S I G N

This custom certificate program introducesparticipants to the full scope of productdesign for industry and the marketplace.The role of the ID process within theorganization is addressed, as are the keyelements of an effective design project fromconceptualization to product manufacturing,product launch and marketing.

Topics include new product development anddesign management strategy, application ofCAD in product development (includingCAD/CAE/CAM integration), and an overviewof future development in technology for IDand manufacturing. During the previous year,certificate requirements included 40 contact-hours in Industrial Design, 40 contact-hoursin Modeling Computer Aided Development, 20contact-hours in management seminars, plusa number of site visits. This program doesnot award academic credits. Interestedgroups should contact the department headat fphillip@admin.ogi.edu.

REMOTE CLASSROOM SITESAND ALLIANCESTo reach a wider student population and toprovide easier access to MST on-site courses,we have a remote classroom location at theWilsonville Training Center. Currently, one ortwo MST courses per term are offered at theWTC. Please refer to the MST department’sWeb site at www.ogi.edu/MST/ for updatedcourse schedules.

Wilsonville Training Center29353 Town Center Loop EastWilsonville, OR 97070

The Management in Science and Technologydepartment has established an alliance withthe Engineering Technology Managementgraduate program at Portland StateUniversity. Students from either degreeprogram may cross-register and receive fullcourse credit transferable to his or hermatriculated degree program. ETM studentsneed prior approval from their faculty advisors.

ADMISSION REQUIREMENTSAdmission requirements for degree programsare the same as the general requirementsfor the institution. In addition, the MSTdepartment requires:

• A bachelor’s, master’s or doctoral degree froman accredited institution.

• A recommended cumulative undergraduategrade point average of 3.0.

• A minimum of two years of full-time workexperience — preferably at the professional,supervisory or managerial level — in atechnical, scientific, business or related area.

• Three letters of recommendation, one of whichshould come from an employer or supervisor.

• Recommended TOEFL score of 625 if Englishis not the applicant’s first language. Scoresare not required for students who earned anundergraduate degree in the United States, orwho have worked for a business for at least twoyears and where the primary business languageis English.

• GMAT or GRE scores are not required, exceptunder certain circumstances.

Part-time students may apply for admissionto the M.S. program during any quarter. Full-time students are strongly urged to begin inthe fall quarter.

DEGREE REQUIREMENTSMST offers a non-thesis M.S. in Managementin Science and Technology. Students elect oneof three areas of concentration within thedegree program: Managing the TechnologyCompany, Computational Finance orManaging in the Software Industries.Students must complete a minimum of 52credits with an average of B or better; up tofour courses or 16 credits taken in thedepartment before matriculation may be usedtoward the degree requirements. Moststudents will complete the degree programwith between 52 and 55 credit hours.

MST CORE SEQUENCE

All M.S. students must take the MST coresequence, consisting of the following courses ortheir equivalent (35 credits). The courses listedbelow are offered both on campus and online.Either is acceptable for the M.S. in Management inScience and Technology degree. If you intend totake only online courses, please see the DistanceDegree Requirements after this section.

MST 501/ Managerial and Financial Accounting501D/501W for Science & Technology 4 credits

MST 502/502D Financial Management 4 credits

MST 503/503D Marketing: Planning for Market 4 credits

MST 510/510D Principles and Trends in Technology Management 3 credits

MST 512/512D Project Management 4 credits

MST 513/513D Manufacturing Practices and Management 3 credits

MST 520/520D/520W Managing in Science and Technology 4 credits

MST 530/530D Strategic Management and Planning 4 credits

MST 550/550D Capstone Project: Business Plan 4 credits

MST 590/590D Effective Business Writingfor Management 1 credit

OR

MST 591/591D Professional Writing for Non-native Speakers 1 credit

A R E A S O F E M P H A S I SAll emphasis areas require the completion of the35-credit M.S. core sequence. Specific coursesrequired for each emphasis area are:

MANAGING THE TECHNOLOGY COMPANY SEQUENCE

MST Core Sequence plus three of the following sixcourses are required (9-10 credits):

MST 504 Marketing: Going to Market 4 credits(online version unavailable)

MST 511/511D Quality Management 3 credits

MST 514/514D Issues in R&D Management 3 credits

MST 522/ Building Effective Organizations in522D/522W Science and Technology 3 credits

MST 540/ International Management in Science540D/540W and Technology 3 credits

MST 541/541D Seminar in Leadershipand Negotiation 3 credits

ELECTIVES: Any course in the above list not alreadytaken and/or any of the following (6-8 credits):

ECE 555 Engineering Optimization 4 credits

ECE 577 Principles for Technology Developmentand Introduction to Manufacturing 3 credits

ESE 504 Uncertainty Analysis 4 credits

ESE 586 Environmental Law and Regulation 3 credits

CSE 503 Software Engineering Processes 3 credits

CSE 549 Applied Business Forecasting 3 credits

CSE 568 Empirical Research Methods 3 credits

FIN 541 Principles of Modern Finance 4 credits

FIN 544 Investment and Portfolio Management 4 credits

FIN 547 Global Markets and Foreign Exchange 2 credits

FIN 551 Options and Futures I 4 credits

FIN 552 Options and Futures II 4 credits

FIN 558 Advanced Numerical Computingin Finance 2 credits

FIN 561 Risk Management 4 credits

FIN 573 Financial Time-Series Analysis 4 credits

FIN 576 Financial Markets and Trading 2 credits

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MST 515 Supply Chain Management:Advanced Modeling 3 credits

MST 516 Global Logistics andFinancial Management 3 credits

MST 517 Supply Chain Management:Advanced Modeling 3 credits

MST 521/521D Human Resource Management inScience and Technology 3 credits

MST 523 New Products Development 4 credits

MST 524 eBusiness Strategy and Roadmap 4 credits

MST 531 Software Commercialization 3 credits

MST 542 Seminar in Social Issuesin Management 3 credits

MST 543 Commercialization Practicum 3 credits

MST 544/544D Strategic Alliances 3 credits

MST 58X Special Topics(special electives offered on a one-time basis)

Students may petition the MST department forelective credit for other OGI School academiccourses relevant to the theory or practiceof management.

COMPUTATIONAL FINANCE SEQUENCE

MST Core Sequence plus the following threecourses are required (12 credits):

FIN 541 Principles of Modern Finance 4 credits

FIN 551 Options and Futures I 4 credits

FIN 561 Risk Management 4 credits

Electives: three of the following courses arerequired (9 credits)

FIN 544 Investment and Portfolio Management 4 credits

FIN 547 Global Markets and Foreign Exchange 2 credits

FIN 552 Options and Futures II 4 credits

FIN 558 Advanced Numerical Computingin Finance 2 credits

FIN 573 Financial Time-Series Analysis 4 credits

FIN 576 Financial Markets and Trading 2 credits

MANAGING IN THE SOFTWARE INDUSTRIES SEQUENCE

MST Core Sequence plus the following two coursesare required (6 credits):

MST 531 Software Commercialization 3 credits

CSE 500 Introduction to Software Engineering 3 credits

Electives: Four of the following courses arerequired (12-13 credits):

CSE 503 Software Engineering Processes 3 credits

CSE 504 Object-Oriented Analysis and Design 3 credits

CSE 514 Introduction to Database Systems 3 credits

CSE 518 Software Design and Development 3 credits

CSE 560 Artificial Intelligence 3 credits

CSE 564 * Human-Computer Interaction 3 credits

CSE 567 * Developing User-Oriented Systems 3 credits

MST 504 Marketing: Going to Market 3 credits

MST 511/511D Quality Management 3 credits

MST 522/ Building Effective Organizations in522D/522W Science and Technology 3 credits

MST 540/ International Management in Science540D/540W and Technology 3 credits

MST 541 Leadership and Negotiation 3 credits

*Credit will be given for no more than one of theindicated courses.

Students may petition the MST department headfor elective credits for other OGI academic coursesrelevant to the theory or practice of management.

YOU CAN COMPLETE YOUR ENTIREDEGREE ONLINE!

MST ONLINE DEGREE REQUIREMENTSThe Department of Management in Scienceand Technology recommends that studentstake at least two on-campus courses. Aproctored comprehensive exam may berequired at or near the completion of theMST Online degree requirements. Studentsmust complete a minimum of 52 credits withan average of B or better.

MST ONLINE CORE SEQUENCE

All M.S. students must take the MST coresequence, consisting of the following courses ortheir equivalent (35 credits):

MST 501D Managerial and Financial Accountingfor Science and Technology 4 credits

MST 502D Financial Management 4 credits

MST 503D Marketing in Science and Technology 4 credits

MST 510D Principles and Trends inTechnology Management 3 credits

MST 512D Project Management 4 credits

MST 513D Manufacturing Practicesand Management 3 credits

MST 520D Managing in Science and Technology 4 credits

MST 530D Strategic Management and Planning 4 credits

MST 550D Capstone Project: Business Plan 4 credits

MST 590D Effective Business Writing 1 credit

OR

MST 591D Professional Writing forNon-native Speakers 1 credit

AREA OF EMPHASIS —ONLINE DEGREEMST currently offers only one area ofemphasis, Managing the Technology Company,to students who take only online classes.

MANAGING THE TECHNOLOGY COMPANY ONLINE SEQUENCE

MST Online Core Sequence plus three of thefollowing four courses are required (9 credits)

MST 511D Quality Management 3 credits

MST 514D Issues in R&D Management 3 credits

MST 522D Building Effective Organizations inScience and Technology 3 credits

MST 540D International Management in Scienceand Technology 3 credits

Electives: any course in the above list not alreadytaken and/or any of the following (9 credits)

MST 521D Human Resource Management in Science and Technology 3 credits

MST 544D Strategic Alliances 3 credits

Students may petition the MST department headfor elective credits for other OGI School academiccourses relevant to the theory or practiceof management.

COURSE DESCRIPTIONSMST 501, MST 501D, MST 501W Managerial andFinancial Accounting for Science and TechnologyThe course focuses on understanding and evaluatingfinancial reports and information for use in makingdecisions, particularly as they pertain to managing inscience, technology, engineering and manufacturing.

4 credits

MST 502, MST 502D Financial Management for Scienceand TechnologyThe course combines a survey of the relevantaspects of micro- and macroeconomics with in-depth study of key concepts in financialmanagement of a firm, the financial structure andfinancial analysis of the firm, working capital man-agement and short- and long-term financing.Particular attention is paid to valuation of invest-ment alternatives through study of risk and rates ofreturn, bond and stock valuation, and capital budg-eting. The course is designed to achieve a balancebetween understanding theoretical foundations andtechniques of practical application. Prerequisite:MST 501. 4 credits

MST 503, MST 503D Technology Marketing:Planning for MarketThe course introduces the student to the full rangeof issues and activities involved in the marketing oftechnology-based products. The role of marketingwithin the organization is addressed, as are the keyelements of an effective marketing program. Thecourse is organized to cover the full product-introduction process, from market identification toproduct conception and definition, to marketresearch, to competitive analysis, and ultimately toproduct launch. Topics include pricing, sales anddistribution alternatives, and marketing communi-cations. To the extent possible, assignments utilizeand draw from students’ work experiences in tech-nology, engineering, manufacturing and science.

4 credits

MST 504 Going to Market: Delivering Value toCustomers and ShareholdersThe course complements and completes the market-ing knowledge and expertise gained through MST

M S T | M A N AG E M E N T I N S C I E N C E A N D T E C H N O L O G Y

503. Integrating lectures, class discussions, casestudies, videos and individual papers and team proj-ects, the course emphasizes developing the detailedimplementation plan to bring products or services tomarket. The course drills down into the operationalspecifics of pricing, promotion, sales, advertisingand customer relationship management, e-businessand web marketing, supply chain and distributionlogistics, channel alliance building and implementa-tion standards, metrics and controls. The course isessentially practical and interactive. It will not turnstudents into marketing geniuses but will provide anunderstanding of the tools, mechanics and manage-ment of operational marketing implementationprocesses in high-technology environments. It isaimed at both high technology firms and those thatare heavy users of high technology. The goal is toshow how to turn strategy into practice by imple-menting the marketing plan begun in MST 503,developing the specifics of a product or service’sbusiness model and persuasively outlining the blue-print of the business case. 3 credits

MST 510, MST 510D Principles and Trends inTechnology ManagementThis course is about how companies choose, acquireand develop the technologies that they use to devel-op, manufacture, deliver and support their products.We look at these practices from both the vendor andbuyer points of view, and also consider internaltechnology development for internal use. Other top-ics include profitably managing technology cycles;standards; technology forecasting; and the technol-ogy startup company. Related topics such ascompetitive analysis, managing researchers andmaintaining an innovative organizational atmos-phere are covered in MST 503 and MST 514. Theformat includes lectures, discussions, guest speak-ers, and team and homework projects. 3 credits

MST 511, MST 511D Quality ManagementThe course covers total quality management (TQM)from the managerial vantage point — that is, behav-ioral and operational management aspects,excluding sophisticated statistical analysis, of TQM.Classroom discussion, based on the participants’experiences and assigned readings from the text-book and cases, is primary. Lectures generally serveas a basis for a facilitated discussion led by theinstructor. The limitations of TQM also are dis-cussed, given the inherent risks of excessiveoptimism associated with any social trend or per-ceived panacea. 3 credits

MST 512, MST 512D Project ManagementThis introductory course addresses the field of proj-ect management from a management perspectiverather than an engineering or mathematical per-spective. Accordingly, we adopt the life cycle of aproject and structure this course in three segments:Project Initiation, Project Implementation andProject Conclusion. The class is conducted in a sem-inar/workshop environment, with guest speakers onreal-life project experiences. One of the 4 credits isdedicated to Effective Presentation Skills.

MST 513, MST 513D Manufacturing Practicesand ManagementThis course introduces key practices in manufactur-ing management. We will address issues faced by atypical vice president of operations, from strategicdirection through tactics to daily control. Key topicsinclude supply chain management and various tech-niques in planning and execution. 3 credits

MST 514, MST 514D Issues in R & D ManagementParticipants examine issues in managing R&D andtechnological innovation in an environment ofincreasing time- and competence-based competi-tion, a competition that is simultaneously global andlocal in both markets and technology, where com-petitors draw on an existing technology base thatsupports incremental innovation through radicalinnovation, and where quality is a given. Particularattention is given to R&D management issues inintegrating technology into business strategy andoperations, managing internal development andexternal sourcing of technology, seeking competitiveadvantage through collab-orative advantage, andbuilding new technical competence as a part ofevery project. Key trends, new conceptual frame-works, management tools and techniques, and bestpractices in R&D management are examinedthrough presentation, interactive class discussions,selected readings, case studies and invited speakersfrom both small and large companies. 3 credits

MST 515 Supply Chain ManagementSupply Chain Management (SCM) denotes a totalsystem approach to the management of all of thoseactivities involved in physically moving raw materi-als, inventory and finished goods inventory frompoint of origin to point of consumption. SCM is a sys-tem approach to managing the entire flow ofinformation, materials, products and funds to andfrom suppliers and end-customers. 3 credits

MST 516 Global Logistics and Financial ManagementToday’s global business environment points out theimportance of developing strategies that go beyondthe geographical boundaries of one country.Nowadays it is not uncommon to see a companydevelop a new product in the United States, manu-facture it in Asia and sell it in Europe. Wage-ratedifferentials, expanding foreign markets andimproved transportation are breaking down barriersof time and space between countries, forcing thelogistics function to take a global dimension.The course emphasizes operations and logistics infirms that source, produce, distribute and market inmultiple nations. The management of logistics insuch firms differs from its domestic counterpartalong several key dimensions. First, the companymust be able to identify and analyze factors that dif-fer across nations and that influence theeffectiveness of the logistics function. In addition,because of the distances involved, transportationand distribution are of greater significance. Finally,these geographically dispersed facilities and mar-kets must be integrated and managed to enhance thestrategy of the business unit. Therefore, some ses-sions will focus on cross-national decisions andothers on managing across nations. 3 credits

MST 517 Supply Chain Management: Advanced ModelingThis course introduces the use of mathematical pro-gramming in supply chain modeling. The primaryemphasis is on large-scale optimization of real-world supply chain distribution networks. The majorskills taught are problem definition, model formula-tion and solution analysis. We will teach the use ofcommercial software, including the MAPLE algebra-ic modeling system for planning problems, What’sBEST for decision-making and GSCM for largemixed-integer programming network design.

3 credits

MST 520, MST 520D, MST 520W Managing in Scienceand TechnologyThis course develops participants’ ability to under-stand and influence human behavior withintechnology-intensive organizations. By studying andapplying four theory-based frames (structural,human resource, political and symbolic), studentslearn to identify and fill gaps in their current under-standing of challenging organizational situations.The course also analyzes the influence processesand network of relationships required for managingresearch scientists, engineers and other profession-als, both as individuals and in teams, in afast-changing environment. Self-assessment, network-ing and developmental relationships are explored asmeans of developing influence and impact. 4 credits

MST 521, MST 521D Human Resource Management inScience and TechnologyThis course focuses on how managers can work withand use the human resource (HR) managementfunction to create value and deliver results.Specifically, we focus on how managers can improveproductivity in three areas: 1) policies and practicesfor managing people, 2) hiring and motivating work-ers, and 3) rewarding and appraising workers.Students in this course will have the opportunity todevelop and practice skills and abilities in thesethree areas. 3 credits

MST 522, 522D, 522W Building Effective Organizationsin Science and TechnologyThis course focuses on designing effective organiza-tions and managing change in organizations in whichengineering, manufacturing and/or scientific tech-nologies are critical. Tools for assessing the need forreorganization and implementing structural changesare emphasized. The course pays special attentionto organizing for lateral coordination and integra-tion, a required capability in technology-intensiveorganizations. Students are invited to consider therelationship between organizational theory andpractice. A range of theoretical perspectives isreviewed, and students are encouraged to compiletheir own approach from those presented. Casesand actual examples are drawn from the readingsand from course participants’ experiences. TakingMST 520 first is recommended. 3 credits

MST 523 New Product DevelopmentSuccessful product development has been key tosurvival in today’s competitive markets. This coursewas designed to address professionals in productdevelopment organizations or those who support

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such organizations. Technology integration and inno-vative environments are critical to developingprofitable products in today’s technology-orientedcompanies. The course will review cases and articlesaddressing key issues in new product development.Topics such as Disruptive Technologies, TechnologyIntegration, Concurrent Engineering and ManagingTechnological Innovation will be covered. Studentswill form teams and develop a plan for a new prod-uct. The plan will include risk assessments in areassuch as manufacturing, design, test and so on. Theteam will make several presentations throughoutthe course. 4 credits

MST 524 eBusiness: Strategy and RoadmapInformation and technology are changing the busi-ness world. To succeed in this new environment, allcompanies, from established industry leaders tostartups, must understand the new level of threatsand develop strategies that take full advantage ofthe opportunities technology offers. Successful com-panies are pursuing focused e-business strategiesthat build new kinds of enterprises. These enter-prises are (re)designed to attract, serve and retaincustomers, manage suppliers, and inform andempower employees better than ever before. Thecourse offers a practical understanding of what ittakes to develop the “digital enterprise.” The firstpart addresses the issue of developing a robust busi-ness model that capitalizes on the newopportunities. The second covers the e-businessarchitecture and applications (such as customerrelationship management, supply chain manage-ment, selling chain management) and how todevelop and implement the e-business strategy.Cases and articles will illustrate the successfulstrategies and techniques used by leading compa-nies. Previous courses highly recommended:MST 503, MST 530. 4 credits

MST 530, MST 530D Strategic Managementand PlanningThis course focuses on the analysis of fast-changing(“hyper-velocity”) competitive environments and onthe decision-making process leading to the formula-tion and implementation of strategy. The classexplores using time, knowledge and technologies ascompetitive advantages, managing strategic change,and developing strategic plans for a future that can-not be known with certainty. Several models forstrategy formulation, such as Game Theory,Portfolio Analysis, the Five-Forces and Competingon the Edge will be examined. Because the ultimatetest of strategy in the business world is running acompany, class teams will play a computer simula-tion of operating a business in a dynamic,competitive environment. Prerequisites: MST 502/502D, MST 503/503D, MST 520/520D. 4 credits

MST 531 Software CommercializationThis course examines the structure of the softwareindustry, problems of marketing privately developedsoftware, and commercializing software from thegovernment and nonprofit sectors. Because thebusiness models for hardware and software compa-nies differ, the course focuses on the specialproblems of marketing, entrepreneurship, globaliza-

tion and alliances experienced by software firms.Relationships between marketing strategy anddevelopment strategy also are examined. 3 credits

MST 540, 540D, 540W International Management inScience and TechnologyTopics in this course include trends in the conduct ofinternational business, the international businessenvironment, the operation of multinational enter-prises, international technology transfer and thespecial considerations associated with managing onthe international level. 3 credits

MST 541 Leadership and NegotiationThis course focuses on the negotiation and interper-sonal communication skills required to exerciseeffective leadership. Topics include creating clarityabout one’s own values and mission, exercisinginfluence through both formal and informal authoritychannels and being a catalyst for change. 3 credits

MST 542 Seminar in Social Issues in ManagementThis course focuses on ethical dilemmas, socialissues and responsibilities, and government regula-tions and influences. First, the course examinesdifferent frameworks for individual decision makingin an organizational setting. Next, it examines theimpact of organizational policies and practices, andthe words and actions of managers on the behaviorof individuals within those organizations. Finally,the course focuses on the relationship betweenorganizations and the societies in which they oper-ate. We consider the perspectives of keystakeholders, including government regulators,community representatives, customers, employees,managers and stockholders, and examine differentviews on corporate social responsibility. 3 credits

MST 543 Commercialization PracticumStudents work in teams with real technologies.Student teams produce assessments and plans forbringing new technologies to market using VijayJolly’s Mind to Market Technology Commercial-iztion and other frameworks, such as a Total LifeCycle Planning approach. Wherever possible, indus-try advisors will mentor students in their area ofexpertise within the design, management and prod-uct manufacturing process. Each team adopts a realtechnology held by Batelle-Pacific NorthwestLaboratories, OHSU, OGI, Oregon Medical LaserCenter or others. Students make one or more fieldtrips to these institutions. The technologies may bein the areas of environment, health, genetics, multi-media, computers or other fields. Each team’s finalpaper, which may include market research, a designfor a manufacturable product, profiles of desiredmanagement teams, licensing plans, tech-marketingfeasibility and/or preliminary startup business plan,will be submitted to the institution that originatedthe technology. MST students may choose to usetheir 543 project as a preliminary exercise for theCapstone project. 3 credits

MST 544, MST 544D Strategic AlliancesThis course explores a model of implementingstrategic alliances, business partnering and jointventures originally outlined by Robert Lynch, seniorpartner of The Warren Company, in his book

Business Alliances Guide (John Wiley and Sons,1993). The book compiles best practices in strategicalliance formation and implementation distilledfrom approximately 40 high-performance inter-national and domestic strategic alliances. It offers awell articulated framework applicable across abroad range of alliance types. The objective is toprovide each student with an opportunity to learnpractical, effective methods for forming, implement-ing and executing high-performance strategicalliances. 3 credits

MST 550 Capstone Project: Business PlanThe objective of the Capstone course is to provide anopportunity to demonstrate, through an integrativeproject, knowledge gained from other course worktaken in the MST program. Students, in teams ofthree to five, will plan, research, prepare and pres-ent a business plan in both written and oral form.Prerequisites: MST501, 502, 503, 512, 520, 530and instructor approval. 4 credits

MST 58X, MST 58XD - Special TopicsUnder this number, courses of particular relevanceand interest to students and faculty are offered.

Variable credits

MST 590, MST 590D Effective Business Writingfor ManagementThis course reviews several aspects of conventionalpunctuation and grammar that address the needs ofthe participants. In addition, attention is given tostyle for clear, concise communication necessary inbusiness writing. Class size is limited to 10 students.

1 credit

MST 591, MST 591D Professional Writing forNon-native SpeakersThis course is an intensive review of English gram-mar and sentence structure with a focus on formalEnglish for professional purposes. Some attention ispaid to the academic essay as well as business writ-ing. Class size is limited to 10 students. Noprerequisite. 1 credit

Note: descriptions for Computational Finance cours-es, designated FINxxx, are found in the catalogunder the Department of Computer Science andEngineering Course Description section.

M S T | M A N AG E M E N T I N S C I E N C E A N D T E C H N O L O G Y | F A C U L T Y

F R E D Y O U N G P H I L L I P SProfessor and Department HeadPh.D., Management Science/Business AdministrationUniversity of Texasat Austin, 1978fphillip@admin.ogi.edu

R E S E A R C H I N T E R E S T S

Market research, marketinginnovation and high-technologyproducts, managing the newproduct development process,incubation and commercializationof new technologies, strategic andinnovative use of computers

R E P R E S E N TAT I V E P U B L I C AT I O N SEric Landis, Balbinder Banga, Tim

Tolle, Lois Delcambre and FredPhillips, “User Needs Assessment forthe Adaptive Management Portal.”Presented at DGO 2002, the DigitalGovernment Conference, Los Angeles,May 2002.

F. Phillips, Market-OrientedTechnology Management: Innovating forProfit in Entrepreneurial Times.Springer-Verlag, Heidelberg, 2001.

F. Phillips and M. Burningham,“WTO vs. WTA? Exploring the WorldTrade Organization’s Impact onTechnopolis.” Presented at 4thInternational Conference on TechnologyPolicy & Innovation, Curitiba, Brazil,August 2000.

F. Phillips and S. Tuladhar, “Measuresof Organizational Flexibility.”Technological Forecasting & SocialChange 64/1, May 2000.

F. Phillips, L. Ochs and M. Schrock,“The Product is Dead; Long Live theProduct-Service.” Research TechnologyManagement, vol. 42, no. 4, pp. 51-56,July-August 1999.

F. Phillips, A. Donoho, W. Keep, W.Mayberry, J.M. McCann, K. Shapiro andD. Smith, “Electronically ConnectingRetailers and Customers: Summary ofan Expert Roundtable.” Journal ofShopping Center Research, 4:2, pp.63-94, 1997.

P. Brockett, A. Charnes, W.W. Cooper,D.B. Learner and F. Phillips,“Marketing Research Unification byInformation Theoretic Methods,”European Journal of OperationsResearch, 84, pp. 310-329, 1995.

S. Thore, G. Kozmetsky and F. Phillips,“DEA of Financial Statements Data:The U.S. Computer Industry,”Journal ofProductivity Analysis, 5(3), p. 229, 1994.

C . N E I L B E R G L U N DProfessor/Joint Appointmentwith Department of Electricaland Computer EngineeringPh.D., Electrical EngineeringStanford University, 1964berglund@ece.ogi.edu

R E S E A R C H I N T E R E S T S

Management of technology, andadvanced lithography forsemiconductor fabrication.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Ye, M. Takac, C.N. Berglund,

G. Owen and R.F.W. Pease, “An ExactAlgorithm for the Self-Calibration ofPrecision X-Y Stages,” Conference onElectron, Ion and Photon BeamTechnology and Nanofabrication,May 1996.

M.T. Takac, J. Ye, M.R. Raugh,R.F.W. Pease, C.N. Berglund andG. Owen, “Self-Calibration in TwoDimensions: The Experiment.” 1996SPIE International Symposium onMicrolithography, March 1996.

W. Wang, J. Ye, A.B. Owen, C.N.Berglund and R.F.W. Pease, “AdaptiveMetrology: An Economical Strategy forJudging the Acceptability of a MaskPattern,” J. Vac. Sci. Technol., B13(6),November-December 1995.

J. Ye, C.N. Berglund and R.F.W. Pease,“Field Distortion Characterization UsingLinewidth or Pitch Measurement,”J. Vac. Sci. Technol. B13(6),November-December 1995.

J. Ye, C.N. Berglund, J. Robinson andR.F.W. Pease, “A Review of Mask Errorson a Variety of Pattern Generators,”IEEE Transactions on SemiconductorManufacturing, 8(3), pp. 319-325,August 1995.

J. Ingino, G. Owen, C.N. Berglund,R. Browning and R.F.W. Pease,“Workpiece Charging in ElectronBeam Lithography,” J. Vac. Sci.Technol., B12(3), pp. 1367-1371,May-June 1994.

M A R I A N N E K O C HVisiting Associate ProfessorPh.D., Human ResourceManagement andIndustrial RelationsColumbia University, 1989 koch@admin.ogi.edu

R E S E A R C H I N T E R E S T S

The human side of technologytransfer; work/family policies andpractices; coaching faculty in thedevelopment and teaching of e-learning courses.

R E P R E S E N TAT I V E P U B L I C AT I O N S :M. Koch and D Moshavi, “The

Adoption of Family-Friendly Policiesin Family-Owned Firms: Paragon orParadox.” Proceedings of the 2001Southern Management AssociationAnnual Meeting, New Orleans,Louisiana, 2001.

M. Koch, L. Long and A. Meyer,“Adoption of Innovations in Hospitals:Exploring the Validity of a Multi-StageModel,” forthcoming, InternationalJournal of Technology Management;also in Academy of Management BestPapers Proceedings, August 1996.

M. Koch and G. Hundley, “The Effectsof Unionism on Recruitment andSelection Practices,” IndustrialRelations, vol.36, no.3, pp. 349-370,1997.

M. Koch and R. McGrath, “ImprovingLabor Productivity: Human ResourceManagement Policies Do Matter,”Strategic Management Journal, vol.17,pp. 335-354, 1996. Awarded an AnbarElectronic Intelligence Citation ofExcellence Award for 1997.

M. Koch. Hiring Practices and LaborProductivity, Garland Publishing, Inc.,New York, 1995.

J A C K R A I T O NSenior FellowMBA, Finance and StatisticsUniversity of Washington, 1967raiton@admin.ogi.edu

Jack Raiton has been VP and CFOat Planar Systems for the last fouryears, and also served as VP andCFO at Smith’s Home Furnishings.His prior experience includesworking at Tektronix for about 22years, the last 12 as the corporatecontroller, and serving as plantcontroller for Fairchild Cameraand Instruments. Jack earned hisB.S. in mathematics from OregonState University in 1966 and hisM.B.A. in finance and statisticsfrom the University of Washingtonin 1967. He attended HarvardUniversity’s three-month AdvancedManagement Program, and passedthe CPA exam in 1979.

A R E A S O F E X P E R T I S E

Performance measurement,capital structure, stockoptions and incentive plans,forensic accounting.

FACULTY

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A D R I A N R O B E R T SSenior AdvisorPh.D., MetallurgyUniversity of Manchester,England

Adrian Roberts is a consultanton technology management,specializing in R&D managementand technology commercialization.Acting as advisor to BattelleMemorial Institute and otherclients on technology projectsand new business creation, Adrianwas recently appointed interimdirector of Battelle-PacificNorthwest National Laboratories.This past year, he has contributedto the Center for EntrepreneurialGrowth and has taught theMST course on TechnologyManagement, as well as workingwith Brookhaven, Oak Ridge andPacific Northwest NationalLaboratories on programs for theU.S. Department of Energy.

A R E A S O F E X P E R T I S E

Technology management,commercialization oftechnologies, R&D management,strategic planning.

N I C O L E S T E C K L E RAssociate ProfessorPh.D., Organizational BehaviorHarvard University, 1990steckler@admin.ogi.edu

R E S E A R C H I N T E R E S T S

Information sharing acrossorganizational boundaries;leading organizational change;interpersonal communication andinfluence in organizations; andtools for diagnosing and improvingleadership effectiveness.

R E P R E S E N TAT I V E P U B L I C AT I O N SN.A. Steckler and N. Fondas,

“Building Team Leader Effectiveness:A Diagnostic Tool,” OrganizationalDynamics, vol. 23, pp. 20-35,Winter/Spring 1995.

J. White, S. Jacobson, R. Jacques,N. Fondas and N.A. Steckler, “YouJust Don’t Understand: GenderedInteraction and the Process of‘Doing’ Organizational Scholarship,”Journal of Management Inquiry, 4(4),pp. 370-379, December 1995.

N.A. Steckler and A. Donnellon,“Review of Peter K. Manning’s‘Organizational Communication,’”Academy of Management Review,vol. 18, pp. 374-377, 1993.

N.A. Steckler and R. Rosenthal,“Sex Differences in Nonverbal andVerbal Communication with Bosses,Peers, and Subordinates,” Journal ofApplied Psychology, vol. 70, pp. 157-163, 1985.

N.C. Ware, N.A. Steckler and J.Leserman, “Undergraduate Women:Who Chooses a Science Major?”Journal of Higher Education, vol. 56,pp. 73-84, 1985.

A LV I N H . T O N GProfessor Ph.D., Electrical EngineeringUniversity of Minnesota, 1967tong@admin.ogi.edu

Alvin Tong teaches ProjectManagement and the CapstoneProject (Business Plan) course,and has been with MST since1996. Alvin served as a mentorfor the 1999 student team,ArtCentral, that won first place inthe New Venture Championship2000, a national/internationalbusiness plan competition held inBeaverton, Oregon. Alvin has 30years of working experience in thecomputer and related industries,which includes serving as chiefoperating officer of Acer, Inc., aTaiwan-based manufacturer ofpersonal computers. While withAcer, he also served as presidentof their venture capital arm. Priorto Acer, he worked for 14 years atIBM. In addition, he also had asignificant role as the first deputydirector-general of the Hsin-chuScience-Based Industrial Park(SBIP) in Taiwan. Alvin hasconducted numerous management-training seminars and isfrequently invited to speak andlecture on the subject ofglobalization and high-techscience-based industrial parks.

R E P R E S E N TAT I V E P U B L I C AT I O N SP. Schumann, D. Prestwood, A. Tong,

and J. Vanston, Innovate!, McGraw-Hill,Inc., 1994.

F A C U L T Y | M A N AG E M E N T I N S C I E N C E A N D T E C H N O L O G Y | M S T

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M S T | M A N AG E M E N T I N S C I E N C E A N D T E C H N O L O G Y | F A C U L T Y

ADJUNCT FACULTY

K E N A N T H O N YRapid Innovations

J E A N C L A U D E B A L L A N DJCB Associates

M A R K C H E NSoftech Innovation LLC

T U G R U L D A I MIntel Corporation

D E A N D E R R A HInFocus Systems

R I C H A R D D O R FUniversity of California at Davis

D A V I D D R A K ECatalyst Communications, Inc.

W I L L I A M D R E S S E L H A U SDresselhaus Design Group

T O M F L O R AStockamp & Associates

R I C H A R D F O U R N I E RKaiser FoundationHealthplans Northwest

R I C H A R D G O L D G A RTexas Education Agency

S T E P H E N G O M E SCEO2, Inc.

J U L I A N G R E S S E RLogosNet

J I L L B . K E L LYJK Editing

K E I T H L A R S O NIntel Corporation

R I TA L A X T O N - B E N Z A NIMMEDIAD’s ChildRomProductions

K AT H Y M A N G E L - D A V I SProfessionally Speaking

M I C H A E L M C L E A NAC Transit

D E I R D R E M E N D E ZForeign BusinessManagement Consultants

M I G U E L M E N D E ZIndustry Consultant

R A J M E R C H A N TStrategy@work

P A U L N E W M A NCooper Mountain Research, Inc.

R I C H A R D P R I N SGroup 3

J E S S E R E E D E RLeadership Dynamics

Y O N G - I N S H I NIntel Corporation

J AY S H U T T E RMomentum Research Group

L E S L I E S M I DIBM

T H O I T R U O N GEmery Worldwide

H A R V E Y U T E C HNike

J O H N W A L L N E RTektronix, Inc.

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OHSU is an equal opportunity, affirmative action institution.

OHSU includes four schools, two hospitals, numerous primary care and specialty clinics,multiple research institutes, and several public service and outreach units.

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