CHPC REPORT 2010

2/3/11 CHPC Report of Activities Calendar year 2010

Cover photo by CHPC staff member Sam Liston

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CHPC REPORT 2010 C H P C R E P O R T O F A C T I V I T I E S

MISSION AND GOALS The University of Utah's Center for High Performance Computing provides large-scale computer systems, networking, and the expertise to optimize the use of these high-end computer technologies. CHPC facilitates advance research in academic disciplines whose computational requirements exceed the resources available in individual colleges or departments. Since 1996 these collaborations have resulted in more than 651 technical publications acknowledging CHPC support. CHPC's purview is to support faculty and research groups whose main focus requires computing and advanced networking as core instruments central to their research. CHPC’s mission aligns with the University of Utah’s Research mission.

CHPC Goals CHPC’s goals include continuing our commitment to provide excellent support to computational researchers. We expect large data and database support to continue its growth and have recently hired a database support specialist to meet this growth. The volume of data continues to be a challenge but so far we are keeping pace with researcher needs by a combination of centrally funded /scratch space for our general constituency and adding disk capacity for individual departmental needs leveraging the centralized support.

ORGANIZATION STRUCTURE CHPC currently reports to the University Chief Information Officer, Stephen Hess, and also has an indirect reporting line to the Vice President of Research, Thomas Parks. The Director of the Center is Julio Facelli. Other key officers are Julia D. Harrison, Associate Director, Guy Adams, Assistant Director of Systems and Networking, and Joe Breen, Assistant Director of Advanced Network Initiatives, who works with the Department of Cyberinfrastructure and others on advanced network initiatives. CHPC is governed by the Faculty Advisory Board/Allocation Committee whose members are appointed by the center director in consultation with the Vice President of Research. In addition to Julia Harrison and Julio Facelli, the current faculty members are:

• Kyle Dawson, Physics and Astronomy • James Herron, Pharmacology • Jack Simons, Chemistry • James Sutherland, Chemical and Fuels Engineering

Members of this governing board must be faculty members in good standing who are familiar with the use of computers as a primary research instrument.

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Organization Chart

Internal Regulations

Allocation of High Performance Computing Resources

Accounts on CHPC systems are sponsored by a University of Utah faculty member. In a few cases, the associate director may approve accounts for new CHPC staff or when vendors need access to assist with troubleshooting. Priority time, measured in Service Units (SUs) on the HPC clusters, is separated into three types: PI-Owned, Block Grants and General Allocations. The PI-Owned resources managed by CHPC are dedicated to research group members. Block Grants are awarded when a particular research group contributes a large amount toward the purchase of nodes and is willing to share the resources when they are not in use. General Allocations are governed by the Allocation Committee (above), which meets on a quarterly basis to review allocation requests. A service unit is a unit of wall clock time based on 1 hour of computation based on a 2.0 Ghz core metric.

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Allocation requests may be submitted for up to 4 quarters at a time so faculty need only be reviewed one time per year. Users who do not have an allocation, or who are out of allocation for any given quarter, may still submit jobs for processing. These jobs, labeled “free cycle,” only run when there is no work to be done by jobs with existing allocations.

Allocation of Desktop Support

Any tenants of the INSCC building may use CHPC staff for their desktop support, if desired. In addition, research groups who use computers as their main research instrument may request and negotiate desktop support from CHPC. On a case-by-case basis, the director negotiates with the dean or department chair for how the funding of these additional desktop support services will be managed and supported.

OPERATIONS CHPC operates during regular university hours, but our systems are available to researches most of the time. Critical resources are monitored and on a best effort basis our staff members can and often do respond off hours. There is no guarantee of 24x7 support.

HPC Clusters CHPC’s core competency lies in the operation and support of computation clusters. In 2010 we retired some older clusters (delicatearch, tunnelarch, landscapearch.) We also retired a cluster that Greg Voth’s research group took when they left the University of Utah (makena cluster). In the fall of 2010 we added a large cluster that will be largely used by the Institute for Clean and Secure Energy, with some cycles allocated to the general CHPC constituency. As of December 31st, 2010, the computation clusters at CHPC consist of:

Cluster Name Floating Point Operations per Second (in GigaFLOPS)

Apexarch (HIPAA compliant environment) 474

Telluride (Voth Group cluster) 7,324

Turretarch (Statistical interactive) 357

Sanddunearch (General Constituency) 2,995

Sanddunearch (Research group owned nodes) 8,183

Meteo Cluster (Atmospheric Sciences owned) 2,013

Updraft (75% ICSE, 25% General) 22,938

Ember (78% ICSE, 22% General) 32,256

Ember (Research group owned nodes) 3,008

TOTAL 79,548

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Service Desk and User Support CHPC provides a service desk for our users to submit questions or problems. During 2010, CHPC received and responded to 2,326 issues. As of January 10th, all but 7 of those 2,326 issues had been addressed and resolved and the remaining issues are being held for users action, such as confirmation of result. Following is a breakdown by broad category:

User Training

During the Fall and Spring academic semesters CHPC presents a series of hour long lectures to train users to improve their utilization of our services. Lectures include topics in parallel programming, tools, natural language programming and statistics. New courses are introduced and obsolete topics dropped as systems and the needs of users change. The current offerings are:

o Overview of CHPC o Introduction to Parallel Computing o Introduction to IO in the HPC Environment o HIPAA Environment, AI and NLP Services at CHPC o Introduction to programming with MPI o Introduction to programming with OpenMP o Chemistry Packages at CHPC o Mathematical Libraries at CHPC o Statistical Resources at CHPC o Using Python for Scientific Computing o Using Gaussian09 and Gaussview o High-Performance networks and Long-Distance Data Transfers (NEW) o Hybrid MPI-OpenMP Programming o Application support

Software Support

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In addition to a suite of compilers, libraries, profilers and debuggers, CHPC maintains and supports a number of software packages, with various licensing schemes. Some software is only available to the research group that purchased the software. Supported packages include ABAQUS, Amber, Ansys, Gamess, Gaussian, GaussView, HLM3, IDL, Matlab, SAS, S-PLUS and Star-CCM+.

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HPC Usage by Research Group – Calendar Year 2010

PI   Total  Armentrout,  Peter  B.    405,729    Barrows,  Louis  R.    379    Bartl,  Michael    48,493    Bedrov,  Dmitry    35    Belz,  John  W.    119,859    Berzins,  Mar,n    522    Boldyrev,  Alexander    7,315    Brannon,  Rebecca    142,026    Cairns,  Brad    37,438    Camp,  Nicki    22,421    Cannon-­‐Albright,  Lisa    9,183    Cheatham,  Thomas    1,656,740    Cherkaev,  Elena    108    Coats,  Bri+any    5,397    Courdy,  Samir    231    Davis,  Al    112    DeTar,  Carleton    689,463    Ernst,  Richard  D.      5,235    Facelli,  Julio  C.    1,698,453    Frey,  Lewis    652    Garre%,  Tim    4,459    Goldenberg,  David  P.    216    Goldgar,  David    21,110    Gondolo,  Paolo    48    Grant,  David  M.      71,819    Grissom,  Charles      72,224    Hagedorn,  Curt    7    Hall,  Mary    3    Horel,  John    328,109    Huff,  Stanley    493    Hurdle,  John*    5,100    Jenkins,  Mary  Ann    96,639    Jevremovic,  Tatjanta    7    Johnson,  William  P.    13,025    Jorde,  Lynn    170,155    Jui,  Charles    1,926,180    Kaplan,  Jerry    193,522    Krueger,  Steven    96,168    Lemmon,  Mike    554    Liu,  Feng    3,087,538    Ma#hews,  John    19,955    

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Ma#s,  Daniel    78    McLennan,  John    94,463    Miller,  J.D.    2,038    Miller,  Joel  S.    12,240    Molinero,  Valeria    1,591,888    Monson,  Ken    13,390    Parker,  Dennis    27,802    Poulter,  Dale    13,748    Pu,  Zhaoxia    348,963    Rainier,  Rainier    12,863    Reichler,  Thomas    2,459,053    Roemer,  Robert    18    Samore,  Ma*hew    2,004    Schuster,  Jerry    382,861    Simons,  Jack    296,137    Smith,  Grant    219,140    Smith,  Philip  J.    11,607,181    Stang,  Peter    1,046    Starykh,  Oleg    2,927    Steenburgh,  James*    12,096    Stoll,  James  R.    121,694    Strong,  Courtenay    163,160    Sutherland,  James    420    Tav$gian,  Sean    826    Thomas,  Alun  W.    19,843    Thomson,  Gordon    151,019    Thorne,  Michael      447,080    Truong,  Thanh  N.    153,989    Voth,  Gregory  Alan    9,432,967    Whiteman,  Dave    179,432    Wight,  Charles  A.    334    Yandell,  Mark    242,805    Zhdanov,  Michael    379,190    

 

 39,349,817      

*Time  not  tracked  in  Gold  alloca1on  system  –  not  under  batch  control.  

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HPC Usage by Department (in Service Units) – Calendar Year 2010

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HPC Usage by College – Calendar Year 2010

Virtual Machine Support The use of virtual machine support is another area of growth at CHPC. Increasingly we are finding that many applications and computational research needs can be met better and with less staff overhead by utilizing virtualization. Our current VM farm consists of 45 gigahertz of CPU (16 CPU cores @2.83 GHz each), 90,000 megabytes of RAM and 4000 gigabytes of disk. We have plans to add additional capacity and to also build a VM farm within the HIPAA environment. This farm currently supports 68 virtual machines:

• 38 CHPC Service machines (running DNS, NIS, DHCP, webservers, license management, account maintenance, system and network monitoring etc.)

• 14 BMI research machines o bmi-ct-conv.bmi.utah.edu (webserver) o bmi-ct-index.bmi.utah.edu (webserver) o bmi-ct-web.bmi.utah.edu (webserver) o elearn.bmi.utah.edu (BMI) o mpivm2.chpc.utah.edu (John Harris, BMI) o mpivm3.chpc.utah.edu (John Harris, BMI) o mpivm4.chpc.utah.edu (John Harris, BMI) o bmiph1.chpc.utah.edu (Julio Facelli, CHPC/BMI) o dbmi1.chpc.utah.edu (Columbia Collaboration, BMI) o umed-dev.chpc.utah.edu o umedux.chpc.utah.edu o williams-syndrome.chpc.utah.edu o consumerhealtvocab.chpc.utah.edu (Kristina Doing-Harris/BMI) o bmidev.chpc.utah.edu (Randy Madsen – Web Hosting)

• 14 for Ron Price’s Grid Research (Sponsored by ARHQ) o cagrid14 o cigrid-dev1 o cigrid-dev2

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o cigrid-dev3 o cigrid32 o cigrid32-pro o cigrid32-pro1 o cigrid32-pro2 o cigrid32-pro3 o cigridvi o juliens-grid-node o juliens-grid-node2 o kailah-gn o ugrid.chpc.utah.edu

• 1 for the Astronomy group o astromysql.chpc.utah.edu

• 1 for Phil Smith’s research group o software.crsim.utah.edu

Windows Lab Cluster In CHPC’s training lab a cluster of 12 workstations was built with one head node running Microsoft Server 2008R2 HPC pack to test cluster functionality on the workstations. Each workstation is a quad core with 2 gigs of ram with gigabit Ethernet connectivity. We ran Star CCM+ for weeks at a time without issues on medium sized simulations as our test data. The Institute for Clean and Secure Energy (ICSE) research group was very pleased to have the free cycles but definitely missed the faster interconnects of Infiniband. One of the thoughts behind this project was that a lot of processing time is wasted when the lab’s PCs are turned off at night. They could be running cycles when not otherwise in use. The project went very well and was a success. We are writing a paper to present to Microsoft for additional funding to continue more testing. With the funds we receive, we will move this project forward with better hardware and better interconnects.

HIPAA Environment A growing need at the University of Utah’s School of Medicine is access to computation resources using PHI data. In response, CHPC has built a secure environment for such needs. This environment currently has a file server, a small cluster and some Windows desktops. Users must have a valid CHPC account, be screened for IRB approval for the data used, and be trained on HIPAA compliance.

Desktop Support For some research groups CHPC supports their department’s desktops. For researchers who use CHPC clusters or other environments (VMs and interactive systems), users are able to access their files from wherever they are doing this work, thus eliminating the need to have many copies of data. CHPC staff members know that research is the end goal. We measure our success by the success of ourusers. We care if a researcher has network issues ora problem with a desktop component that is preventing them from getting their papers published. As of December 31, 2010 CHPC supported a total of 353 desktop (see table and graph below.)

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Key Metrics (semi-annual report)

1. Computational Power (Theoretical Peak) June 30, 2010 December 31, 2010 Growth %

CHPC 47.35 Tflops 79.55 Tflops* 68%

TOP 500 Mean 96.94 Tflops 129.31 Tflops 33.39%

CHPC/TOP500 Mean 48.84% 61.52% 12.67%

*includes Ember

2. Service Units (1 SU= 1 hour wallclock hour on 2.0 Ghz core): Jan-Jun 2010 Jul-Dec 2010 % Change

Total Service Units Available (Theoretical)

24,248,305

24,478,020 +.95%

Total Service Units used (all systems)

20,290,914 18,713,077* -7.78%

Utilization* 83.7% 76.4% -7.3%

*includes 15 days of ember usage

3. Desktops Supported

June 30, 2010 December 31, 2010 Growth %

Linux 133 107 -19.55%

Windows 139 140 -0.72 %

Macintosh 93 106 +13.98%

Total 365 353 -3.29%

4. Other Metrics

June 30, 2010 December 31, 2010 Growth %

Total Number of Accounts

1146 1254 +9.42%

Total Publications (from 1988 to present)

615 651 +44

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Disk Space Backed Up 37.3 Tbytes 45.4 Tbytes +8.1 Tbytes

(21.72%)

Total Disk Space for Home directories

444.25 Tbytes 487.9 Tbytes

+43.65 Tbytes

(+9.83%)

Total Archival Backups (new service)

124 Tbytes 95 Tbytes -29 Tbytes

(-23.39%)

0

50

100

150

Computational Power: CHPC vs Mean TOP500

CHPC Computational Power (Tflops)

TOP500 Mean - RPEAK (Tflops)

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-

10,000,000

20,000,000

30,000,000

HPC Service Units: Used vs Available

Total Service Units Used (all systems)

Total Service Units Available(Theoretical)

0 50

100 150 200 250 300 350 400

140 143 152 133

107

111 125 129 131

140

43 50 70 93 106

Desktop Support

Mac Desktops Supported

Windows Desktops Supported

Linux Desktop Supported

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Very few departments or research groups have the ability to support an HPC infrastructure of the caliber provided by CHPC. According to user surveys and informal discussions, the centralization of the HPC support function is cost effective while preserving the responsiveness to researcher’s needs characteristic of decentralized operations. IfCHPC’s approval were to be withdrawn the University would be faced with providing substantial funds to individual units to replicate already existing support at CHPC or greatly diminishing the institutional support for computational scientists. Moreover CHPC provides a central resource for human capital with expertise in advance computing. These experts are available to the entire University and would be difficult to replicate in a decentralized model.

INSTITUTIONAL IMPACT

High Profile Accomplishments

• Thomas E. Cheatham, III is one the biggest users of the CHPC clusters. The research in his lab involves the development and application of molecular dynamics and free energy simulation methodologies (with AMBER, CHARMM, NAMD, and other programs) to biomolecular systems in their native environments. Until recently, this has focused heavily on the reliable representation of a large variety of nucleic acid systems (DNA and RNA) in solution. They also work with various coiled-coils, enzymes and cytochrome P450's with a focus on improving stability or understanding how ligands alter receptor structure upon binding. The primary research foci are to assess and validate the simulation resultsand to expose and overcome limitations in the methods and force fields. In addition to continued development of the ptraj program for analysis of MD trajectories, the research group is exploring methods to mine more information from the simulation data and to more broadly disseminate the MD results.

• The Geophysics department receives CHPC support at a number of levels. When the the Schuster research group moved into the new Sutton building, CHPC took on desktop and network support for the Geophysics computational researchers. Many of these users are also users of the HPC clusters; one group in particular, Michael Zhdanov’s group, is involved with collaborative research with CHPC stafferMartin Cuma (see below for more detail on this research.)

0

100

200

300

400

500

600

Storage Data

Disk space backed up (Tbytes)

Disk space for Home Directories (Tbytes)

Total Archive Space (Tbytes)

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• Eccles Observatory: In 2009-2010, staff from CHPC, the Utah Education Network, the University NOC, and University Cyberinfrastructure collaborated with faculty in the Department of Physics and Astronomy to setup networking to the new Eccles Observatory located on Frisco Peak outside of Milford, Utah. This collaboration was able to setup a 100Mb/s microwave link from the observatory to the Milford UEN network. Within the observatory, its auxiliary command building and the State Department of Transportation tower, CHPC staff helped setup a Gigabit network that provides services to the control equipment of the observatory. CHPC collaborated with the University NOC to provide campus wireless at the remote sites. CHPC desktop staff have collaborated with Physics in securing and configuring devices on site as well. CHPC and UEN staff have collaborated to secure the network and make it look like an extension of the University.

• Department of Physics and Astronomy VIRITAS group: CHPC and Cyberinfrastructure staff have collaborated with the Department of Physics and Astronomy’s VERITAS group in reviewing network design and expansion of the remote observatory in Arizona. CHPC staff collaborated with the University Campus Fiber team to train members of the VERITAS group regarding physical fiber installation. The VERITAS team terminated and tested over 100 fiber ends in its expansion that covers several miles of observatory. CHPC loaned high end fiber testing equipment to the VERITAS team to aid in its verification of the network. CHPC staff collaborated with the VERITAS team in specifying and configuring a complete refresh of the network equipment. Ongoing collaboration between CHPC and the VERITAS staff have resulted in troubleshooting and setting up additional monitoring on-site.

• UStar: CHPC, Cyberinfrastructure and the University IT team have collaborated on the UStar building project to assure that the UStar’s data center will meet the needs of the high performance research groups that will house within the building. CHPC staff, University IT staff and Cyberinfrastructure met with research groups and building engineers to specify flooring, electrical, rack layout, etc.

• Paperless account creation system developed and deployed: during 2010 CHPC was able to deploy its paperless account creation. Principle Investigators (PIs) of CHPC supported research projects may now request and approve account creation online. This has simplified the process for our Users and has also made the provisioning of accounts less resource intensive for CHPC staff.

• Hardware donations: CHPC has supported the Comic Ray Delta project with donations of cabling, gear, etc. When CHPC had equipment that it no longer needed, CHPC staff worked with the Cosmic Ray group (and other research groups) to determine if these groups could utilize the equipment before sending to Surplus Property. Often, research groups can utilize equipment longer than normal production cycles allow for support. CHPC staff purposely reaches out to different groups who may be able to utilize hardware that is retiring. Recently, CHPC was able to donate retiring cluster gear to the Department of Mathematics. In the future, more retiring cluster hardware may be of use in several other key research projects, such as the Emulab/FLUX research.

• Supercomputing (SC10) o The Utah exhibit this year was again a successful showcase of selected computation research

accomplished at the University of Utah withCHPC resources. This year we shared our exhibit with the HPC group at Utah State University. Highlighted research included:

§ Kyle Dawson — Astronomy § C. Staes et al, Biomedical Informatics – Collaboration with Columbia § The HIPAA environment § Michael Zhdanov, Geology and Geophysics § Valeria Molinero et al, Chemistry § Thomas Reichler, Atmospheric Sciences

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o CHPC staff member Guy Adams was asked to speak at Dell’s exhibition hall booth on a topic of his choice. After asking for suggestions, it was decided that speaking about CHPC’s recent deployment of Apex-arch, a HIPAA secure cluster, would probably be a unique topic. The full presentation area included various conference attendees, including Intel, Microsoft, other national labs, and various individuals. The talk focused on the unique aspects of running codes against secure data and the many unique challenges that accompany that design. As well as discussing the problems related to the use of public health data in research, Guy Adams also took a look into the future by highlighting gene re-sequencing and DNA research,.

• CHPC staff and the UIT NOC have collaborated in performance troubleshooting and optimization of the network. The collaboration has helped reduce large data transfers significantly, from the order of days to hours.

• HCI Gene Sequencing – During 2010 CHPC has been supporting researchers doing gene sequencing in the Huntsman Cancer Institute. Technological advances in this field are making breakthroughs in the speed at which sequences may be read. CHPC is now running a set of nodes dedicated to this research group who purchased the nodes, leveraging the infrastructure and expertise available at CHPC.

• BMI migration to CHPC support – During 2010 CHPC took on the support of the Biomedical Informatics desktops, adding an additional 31 desktops to CHPC’s responsiblities. We have also begun supporting their continuous development environment using the Atlassian software, Greenhopper and Bamboo. The support of this software is expected to be leveraged by other groups doing significant code development.

• The Utah Academy of Sciences, Arts and Letters awarded “InterPlay: Performing on a High Tech Wire”, written by CHPC staffers Elizabeth and Jimmy Miklavcic, the 2010 "Best Paper in the Arts."

• Anita Orendt: o Taught chemistry section of Math 5900 - Science in Mathematics for the Master of Science for

Secondary School Teachers (MSSST) Program, Summer 2010. o Acted as faculty advisor for the University of Utah American Chemical Society (ACS) Student

Chapter. The Chapter received an Honorable Mention Award from the National ACS. o Participated in the 5th Crystal Structure Prediction blind test (with Julio C Facelli and Marta B

Ferraro) and presented results at a workshop of blind test participants at the Cambridge Crystallographic Data Centre at Cambridge University in England.

o Continued collaborations with Professors Rainier, Pugmire and Grant in the Chemistry Department

o Committee member for student Heather Reese in the Master of Science and Technology Program

• Martin Cuma: o Research with Consortium for Electromagnetic Modeling and Inversion (CEMI) and

collaboration with Technoimaging, LLC. § I provide high performance computing and parallelization support for CEMI and

perform research in the forward modeling and inversion theory. Over the past year, I have continued improving CEMI's parallel electromagnetic inversion codes. This made our programs better performing and numerically more stable.

§ Through collaboration with Technoimaging LLC, a commercial spinoff of the CEMI research, we have successfully ran several inversions of commercial geological survey data and proved that our inversion method is robust and our parallel code performs on par or better than other commercial offers.

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§ I have presented a case study using our inversion code as tool for discovery of a large natural gas deposit at the annual CEMI conference in March 2010. Subsequently, modified results from this study were presented by prof. Zhdanov at two conferences in Europe in the summer 2010, one in Australia and one in Brazil in the fall 2010. I have presented the summary of this research at the annual meeting of the Society of Explorational Geophysicists (SEG) in October 2010. We also made several publications based on this research.

§ We have also used the parallel EM inversion code for other studies, including inversion of magnetotelluric data obtained by the national Earthscope project over the western US. In this study we have for the first time correlated location of the Yellowstone magmatic plume obtained from our EM inversion with that obtained with seismic imaging. Results of this work were presented at the AGU annual meeting in December 2010 and resulted in several publications.

§ Finally, recently, I have been working on parallelizing gravity and magnetic fields inversion code, with the goal of having a robust inversion code able to invert very large surveys, a feature that is lacking with most of the currently available offerings.

o Several particular projects that I worked with over the past year include: § Phillip Smith's group computational fluid dynamics (CFD) commercial codes, Star-

CCM+ and Ansys § Brittany Coats supporting finite element analysis program ABAQUS § Dennis Parker's student Joshua Coon with running his medical imaging optimization

programs on CHPC machines using Matlab o Benchmarking and testing

§ In the spring 2010 I performed a comprehensive benchmark and testing of latest AMD and Intel based server platforms that formed the basis of recommendation for purchase of the latest CHPC parallel cluster.

§ In late fall 2010, in response to research done at the SC10 conference, I have tested four different MPI implementations on CHPC clusters with the conclusion that the open source free MPIs that we have been using perform on par with expensive commercial products. This gave us a good confidence in staying with the open source, saving us an additional expense.

• Sean Igo: o Consultations with various staff from many areas of campus including the School of Medicine,

the Departments of Computer Science, Nutrition and the Linguistics. A few of the consultations were:

§ Ellen Riloff, Computer Science § Catherine Staes, Biomedical Informatics – Death Certificate Surveillance project § Bruce Bray, Biomedical Informatics -- Cardiology Decision Support § Steve Piccolo, Biomedical Informatics § Marta Heilbrun, Radiology – HIPAA cluster usage § Anusha Muthukutty – Poison Control § Katherine Matsumoto-Gray, Linguistics – Shoshoni Dictionary

• Wim Cardoen: o Currently working on a code that will allow calculation properties from condensed phase

based on classical and quantum statistical mechanics. This project has two important objectives:

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§ It will contribute to the CHPC expertise in the domain of parallel computing. The use of the Graphical Processing Units to speed up the calculations is a cornerstone in the development of this code.

§ This code will allow us to develop new algorithms in the simulation of condensed matter problems.

• Ron Price: o SAFTINet Grant: The Scalable Architecture for Federated Translational Inquiries Network

(SAFTINet) will federate geographically-dispersed safety net entities who collectively serve diverse underserved populations. Leveraging the technical, governance, and policy infrastructure of the Distributed Ambulatory Research Therapeutics Network (DARTNet), this project will create a novel federated research network for safety net stakeholder. Where available, linkage will permit aggregation of data from ambulatory electronic health records (EHR), inpatient EHR, and Medicaid administrative data sources. Learning communities will work together to improve data collection and documentation at the point-of-care and ensure a focus on relevant practice-driven research. Overall Project Goal: Enhance the capacity and capability of a safety net focused distributed research network to conduct prospective comparative effectiveness research via a multi-setting, multi-state organization.

o DARTNet Project: The Distributed Ambulatory Research in Therapeutics Network (DARTNet) is a federated network. A collection of databases that reside in multiple member practices and that are linked through a secure Web-based system so they can be searched and queried as one large database while maintaining privacy and confidentiality of patient data.

Bibliography CHPC continues to be cited in publications. Our bibliography contains 641 entries, including 51 entries for 2011 alone. See attached bibliography.

CHPC Bibliography (as of January 11, 2011)

2010 (51) Abbasi, R. U., et al. (2010). "Analysis of large-scale Anisotropy of Ultra-High Energy Cosmic Rays in HiRes

Data." Alcott, T. I., Steenburgh, W. J. (2010). "Snow-to-liquid ratio variability and prediction at a high elevation

site in Utah's Wasatch Mountains." Wea. Forecasting in press. Ci, L., Son, L., Jin, C., Jariwala, D., Wu, D., Li, Y., Srivastava, A., Wang, Z.F., Storr, K., Balicas, L., Liu, F.,

Ajayan, P. M. (2010). "Atomic layers of hybridized boron nitride and graphene domains." Nature Materials 9: 430.

Coon, J. (2010). Dose Delivery Time Reduction Through Optimization of Focal Zone Path, Power, and Size. International Symposium on Therapeutic Ultrasound. Poster.

Coon, J. (2010). "HIFU Treatment Time Reduction through Focal Zone Path Selection." International Journal of Hyperthermia submitted.

Crowl, L., Fogelson, A. (2010). "Analysis of Mechanisms for Lateral Platelet Motion under Arterial Flow Conditions." to be submitted.

Cuma, M., Wilson, G.A., Zhdanov, M.S., Velikhov, E.P., Black, N., and Gribenko, A.V. (2010). Multiple inversion scenarios for enhanced interpretation of CSEM data using iterative migration: A case study for the Shtokman gas field, Barents Sea. SEG Exhibition and 80th Annual Meeting, Denver, CO.

De la Llave, E., Molinero, V., Scherlis, A. (2010). "Water filling of a hydrophilic nanopore." J Chem Physics 133: 034513.

DeMille, T., Cheatham, T, Molinero, V. (2010). "A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions." J. Phys. Chem. B. in press.

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Garcia-Hernandez, A., Facelli, J.C., Colom, L.C. (2010). "Understanding synchronization and hyper-synchronization in the septo-hippocampal system." Neuroscience 11 (Suppl 1): 124.

Gregg, K. L., Fogelson, A. (2010). "Grow with the flow: A spatial-temporal model of platelet deposition and blood coagulation under flow." under review.

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Masiker, M. C., Mayne, M.C., Boone, B. J., Orendt A., Eyring, E.M. (2010). "7Li NMR chemical shift titration and theoretical DFT calculation studies: solvent and anion effects on second-order complexation of 12-crown-4 and 1-aza-12-crown-4 with Lithium cation in several aprotic solvents." Magnetic Resonance in Chemistry 48: 94 - 100.

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Lui, Q. B., O.; Smith, G. D. (2007). The Hydration and Proton Dissociation in the Interaction Between Fluorocarbon-Based Phosphonic Acid and Water Clusters. AIChE Meeting, Salt Lake City, UT.

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Ma, Z., Facelli, J.C., Pugmire, R.J., Dunn, B.C., Turpin, G.C., Eyring, E.M., Ernst, R.D. (2007). "Solid State 13C NMR and Quantum Chemical Investigation of Metal Diene Complexes." Magn Reson Chem 45: 393-400.

McDermott, R. (2007). Building Models to Transition From Dimension to Dimension. Bridges Donostia -- Mathematical Connections in Art, Music and Science, San Sebastian (Donostia), Spain, Tarquin Publications.

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Pu, Z., X. Li, C., Velden, W. T. Liu (2007). "Impact of aircraft dropsonde and satellite wind data on the numerical simulation of two landfalling tropical storms during TCSP." Weather and Forecasting (accepted).

Reichler, T. (2007). Widening of the Tropics During the 20th Century: Observations vs. Simulations. American Geophysical Union Fall Meeting, San Francisco, CA.

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Zhdanov, M. S. U., T. (2007). "Joint iterative migration of electric and magnetic-field data." SEG Expanded Abstracts 26: 599.

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Cardoen, W., Gdanitz, R. J., Simons, J. (2006). "Barrier height, exothermicity, and van der Waals wells on the F + H2 F Ground-State Surface Calculated at the r12=ACPF-2 level." J. Phys. Chem. A 110: 564-571.

Cardoen, W., Simons, J., Gdanitz, R. J. (2006). "F + H2 FH + H Potential Energy Surface: Construction of the Reference Configuration State Function Space and MR-ACPF-2 Results." International Journal of Quantum Chemistry 106: 1516 - 1527.

Cardoen, W., Gdanitz, R. J., Simons, J. (2006). "Transition-State Energy and Geometry, Exothermicity, and van der Waals Wells on the F + H2 FH + H Ground-State Surface Calculated at the r12-ACPF-2 Level." Journal of Phys. Chem. A 110: 564 - 571.

Cheatham, I., T.E., and Case, D.A. (2006). Applying AMBER biomolecular simulation methods to DNA and RNA: Insight into the dynamics, interactions and energetics of varied nucleic acid structures. Computational Studies of DNA and RNA. J. a. L. Sponer, F.: 45 - 72.

Chevallier, C., Bugni, T. S., Feng, X., Harper, M. K., Orendt, A. M., Ireland, C. M. (2006). "Tedanolide C: A Potent New 18-Membered-Ring Cytotoxic Macrolide Isolated from the Papua New Guinea Marine Sponge Ircinia sp." Journal of Organic Chemistry 71: 2510 - 2513.

Difley, S., Simons, J. (2006). "The Role of Angular Electron Pair Correlation in Stablilizing C602-." Inter. J.

Quantum Chem: 507-513. Ehlers, J. R., N.G.; Huynh, L.K.; Pham H.; Marks, M.; Truong, T. N. (2006). "Theoretical study on

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Intermolecular Ring Current Effects." Magnetic Resonance in Chemistry 44: 401-408. Florez, E., Mondragon, F., Truong, T. N., Fuentealba, P. (2006). "Transition-metal atom adsorption on an

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Harper, J. K., Grant, D. M., Zhang, Y., Lee, P. L., Von Dreele, R. (2006). "Characterizing Challenging Microcrystalline Solids with Solid-State NMR Shift Tensor and Synchrotron X-ray Powder Diffraction Data: Structural analysis of Ambuic Acid." J American Chem Society 128: 1547 - 1552.

Huynh, L. K., Ratkiewicz, S., Truong, T. N. (2006). "Kinetics of the Hydrogen Abstraction OH + Alkane --> H2O + Alkyl Reaction Class: An Application of the REaction Class Transition State Theory." Journal of Phys. Chem. A 110(2): 473-484.

Kick, E., Davis, B., and Kentor, J. (2006). "A Cross-National Analysis of Militarization and Inequality." Journal of Political and Military Sociology 34(2 (Winter)): 319-337.

Kick, E. L., Fraser, J.C., and Davis, B. L. (2006). "Performance Management, Managerial Citizenship, and Worker Commitment: A Study of the United States Postal Service with Some Global Implications." Economic and Industrial Democracy 27: 137-172.

Li, X., Zhaoxia P. (2006). Sensitivity of numerical simulations of Hurrican Emily (2005) to cumulus and microphysical parameterizations. AMS 27th Conference on Hurricane and Tropical Meteorology.

Massoth, F. W., Politzer, P., Concha, M.C., Murray, J.S., Jakowski, J., Simons, J. (2006). "Catalytic Hydrodeoxygenation of Methyl-Substituted Phenols: Correlations of Kinetic Parameters with Molecular Properties." J. Phys. Chem. B 110: 14283 - 14291.

Massoth, F. W., Politzer, P., Concha, M.C., Murray, J.S., Jakowski, J., Simons, J. (2006). "Kinetics of catalytic hydrodeoxygenation of methyl-substituted phenols: Correlations with molecular properties." J. Phys. Chem 110: 14280-14291.

McDermott, R. (2006). Building Simple and Not So Simple Stick Models. Bridges London -- Mathematical Connections in Art, Music, and Science, London, England, Tarquin Publications.

McDermott, R. (2006). Transformations of Vertices, Edges and Faces to Derive Polyhedra. Bridges London -- Mathematical Connections in Art, Music, and Science, London England.

Mell, W., and Jenkins, M.A., Gould, J., and Cheney, P. (2006). "A Physics Based Approach to Medeling Grassland Fires." International Journal of Wildland Fire (accepted for publication).

Nichols, C., Deal, S., Rogers, TJ, Miklavcic, J., Miklavcic, B., Ayromlou, M., Wachtel, R., Mercer, P.,

Humbert, J., King, R. (2006). Musical Performance over Internet2 using the AccessGrid. International Computer Music Conference, Tulane University, New Orleans, LA.

Ona, O., Bazterra, V., Caputo, M., Facelli, J., and Ferraro, M. (2006). Global Optimization of Atomic cluster Structures Using Parallel Genetic Algorithms. Material Res. Soc. Symposium Proceedings, Materials Research Society.

Ona, O., Bazterra, V., Caputo, M., Facelli, J., Fuentealba, P., and Ferraro, M. (2006). "Modified genetic algorithms to model cluster structures in medium-sized silicon clusters: Si18-Si60." Physical Review A 73: 053203-053201 - 053203-053211.

Orendt, A., Roberts, SW, and Rainier, JD (2006). "The Role of Asynchronous Bond Formation in the Diastereoselective Epoxidation of Cyclic Enol Ethers: A Density Functional Theory Study." Journal of Organic Chemistry 71: 5565-5573.

Orendt, A. M. (2006). "Revisiting the calculation of 13C chemical shift tensors in cadmium acetate dihydrate with EIM and EIM/cluster methods." Magnetic Resonance in Chemistry 44: 385 - 389.

Orendt, A. M., Roberts, Rainier, J. (2006). "The Role of Asynchronous Bond Formation on the Diastereoselective Epoxidation of Cyclic Enol thers: A Density Functional Theory Study." J. Org. Chem,. 71: 5565 - 5573.

Paesani, F., Zhang, W., Case, D.A., Cheatham, T.E., and Voth, G.A. (2006). "An accurate and simple quantum model for liquid water." J. Chem. Phys. 125: 184507.

Pu, Z., Li, X., Velden, C., Aberson, S., Liu, W T. (2006). "Impact of aircraft dropsonde and satellite wind data on the WRF numerical simulation of two landfalling tropical storms during TCSP." (submitted) Monthly Weather Review.

Pu, Z., Li, X. (2006). Numerical simulations of tropical cyclones during TCSP: The impact of data assimulation and sensitivity to cumulus and microphysical schemes in the WRF model. 7th Annual WRF User's workshop, Boulder, CO.

Pu, Z. a. X. L. (2006). Assimilation of satellite and in situ observations during TCSP for understanding tropical cyclone intensification. AMS 27th Conference on Hurricane and Tropical Meteorology.

Sefzik, T. H., Fidler, J. M., Iulicci, R., Facelli, J. C. (2006). "Modeling the 13C Chemical-shift Tensor in Organic Single-crystals by Quantum Mechanical Methods: Finite Basis Set Effects." Magnetic Resonance in Chemistry 44: 390-400.

Shafer, J. c., Steenburgh, J.A., Cox, J.A. W., Monteverdi, J. P. (2006). "Terrain influences on synoptic storm structure and mesoscale precipitation distribution during IPEX IOP3." Monthly Weather Review 134: 478 - 497.

Simons, J. (2006). "How Do Low-Energy (0.1 - 2 eV) Electrons Cause DNA-Strand Breaks?" Accounts of Chemical Research (submitted).

Simons, J. (2006). "How very low-energy (0.1 - 2 eV) electrons cause DNA strand breaks." Quantum Chemistry in press.

Sobczyk, M., Simons, J. (2006). "Distance dependence of through-bond electron transfer rates in electron-capture and electron-transfer dissociation." International Journal of Mass Spectrometry 253: 274 - 280.

Sobczyk, M., Simons, J. (2006). "The Role of Excited Rydberg States in Electron Transfer Dissociation." J. Phys. Chem. B 110: 7519 - 7527.

Spackova, N., Cheatham, T.E., and Sponer, J. (2006). Molecular dynamics simulations of nucleic acids. Computational Studies of DNA and RNA. F. L. J. Sponer: 301-326.

Stoll, R. P.-A. (2006). "Dynamic subgrid-scale models for momentum and scalar fluzes in large-eddy simulations of neutrally stratified atmospheric boundary layers over heterogeneous terrain." Water Resources Res 42: W01409.

Strohmeier, M., Barich, D. H., Grant, D. M., Miller, J. S., Pugmire, R. J., Simons, J. (2006). "Solid-state NMR of the [TCM? dimer

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7962 - 7969. Sun, R., Jenkins, M.A., Krueger, S., and Charney, J. (2006). "An evaluation of fire plume properties

simulated with the FDS and Clark coupled wildfire model." Canadian Journal of Forest Research (accepted for publication).

Sun, R., Jenkins, M.A., Krueger, S., and Charney, J. (2006). Wildfire evolution in the convective boundary layer. 17th Symposium on Boundary Layers and Turpulence, San Diego, CA

Sun, R. J., M.A.; Krueger, S.; Charney, J. (2006). "An Evaluation of Fire Plume Properties Simulated with the FDS and Clark Coupled Wildfire Model." Can. J. For. Res. 36: 2894 - 2908.

Theodore, M., Sobczyk, M., Simons, J. (2006). "Cleavage of thymine N3-H bonds by low-energy electrons attached to base * orbitals." Chemical Physics In press.

Truong, T. N., Nayak, M., Huynh, H., Cook, T., Mahajan, P., Tran, L., Bharath, J., Jain, S., Pham, H., Boonyasiriwat, C., Nguyen, N., Andersen, E., Kim, Y., Choe, S., Choi, J., Cheatham, T.E., Facelli, J. (2006). "Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing." Journal of Chem. Inf. Model. 46: 971- 984.

Violi, A. a. V., A. (2006). "Combustion-generated nanoparticles produced in a bensene flame: A multiscale approach." Journal of Chemical Physics 125(054302).

Wang, Y., Florez, E., Mondragon, F., Truong, T.N. (2006). "Effects of metal-support interactions on the electronic structures of metal atoms adsorbed on the perfect and defective (100) surfaces." Surface Science 600(9): 1703-1713.

Wijitkosoom, A., Tonmunphean, S., Truong, T.N., Hannongbua, S. (2006). "Structural and dynamical properties of a full-length HIV-1 integrase: molecular dynamics simulation." Journal of Biomolecular Structure and Dynamics 23(6): 613-624.

Zhang, H. R., Pham, M., Truong, T. N., Eddings, E.G., Sarofim, A.F. (2006). "Polymerization reactions of aromatics in a fuel-rich 20 torr naphthalene premixed flame enhanced by ring closure steps." Preprints of Symposia, American Chemical Society, Division of Fuel Chemistry 51(2): 733-735.

Zhdanov, M. S. L., S. K.; Yoshioka, K. (2006). "Integral equation method for 3D modeling of electromagnetic fields in complex structures with inhomogeneous background of conductivity." Geophysics 71: G333 - G345.

2005 (104) Abbasi, R. U., et al. (2005). "Observation of the Ankle and Evidence for a High-Energy Break in the

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Electron Detachment Dissociation (EDD)." J. Phys. Chem. A 109: 11332 - 11337. Anusiewicz, I., Berdys-Kochanska, Joanna, Czaplewiski, Cezary, Sobcyk, Monika, Daranowski, Emma,

Skurski, Piotr, Simons, Jack. (2005). "Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides." J. Phys. Chem. A. 109: 240-249.

Anusiewicz, I., Berdys., J.; Sobczyk, M.; Sawicka, A.; Skurski, P.; Simons, J. (2005). "Coulomb-Assisted Dissociative Electron Attachment: application to a Model Peptide." J. Phys. Chem A109: 250 - 258.

Anusiewicz, I., Berdys-Kochanska, Joanna, Simons, Jack (2005). "Electron Attachment Step in Electron Capture Dissociation (ECD) and Electron Transfer Dissociation (ETD)." J. Phys. Chem. A. 109( ): 5801-5813.

Anusiewicz, M. S., Berdys-Kochanska, J., Skurski, P., and Simons, J. (2005). "A theoretical model for

indirect dissociative electron attachment." Journal of Physical Chemistry A 109: 484-492. Ayton, G., Tepper, H.L., Miriganian, D. T., and Voth, G.A. (2005). "A New Perspective on Coarse-grained

Dynamics of Fluids." Journal of Chemical Physics 120: 4074-4088. Ayton, G. S., McWhirter, J. L. McMurtry, P. and Voth, G.A. (2005). "Coupling field theory with continuum

mechanics: a simulation of domain formation in giant unilammellar vesicles." Biophys J 88: 3855-3869.

Bakulin, A., R. Calvert, and G.T. Schuster (2005). "Relating Interferometric Imaging and Virtual Source Imaging." Geophysics Submitted for Publication( ).

Bazterra, V. E., Cuma, M., Ferraro, M. B., Facelli, J. C. (2005). "A General Framework to Understand Parallel Performance in Heterogeneous Clusters: Analysis of a New Adaptive Parallel Genetic Algorithm." J. of Parallel and Distributed Computing 65: 48-57.

Bazterra, V. E. (2005). "Modified Genetic Algorithm to Model Crystal Structures: III. Determination of Crystal Structure Allowing Simultaneous Molecular Geometry Relaxation." International Journal of Quantum Chemistry 96: 312-320.

Blood, P. R., G.S. Ayton, and G.A. Voth (2005). "Probing the Molecular-Scale Lipid Bilayer Response to Shear Flow using Nonequilibrium Molecular Dynamics." J. Phys. Chem. B. 109: 18673-18679.

Borges, C. R., Taccogno, J., Crouch, D. J., Le, L. Truong, T. N. (2005). "Structure and mechanism of formation of an important ion in doping control." International Journal of Mass Spectrometry 247(1-3): 48-54.

Burns, T. J., Kick, Edward L., Davis, Byron L. (2005 ). Theorization and a Cross-National Analysis of Deforestation. Globalization and the Environment. A.

Jorgensen and E. L. Kick. Leiden, England, Brill Academic Publishers. Case, D. A., Cheatham, T. E., III, Darden, Gohlke, H., Luo, R., Merz, K. M., Jr., Onufrieve, A., Simmerling,

C., Wang, B., Woods, R. (2005). "The AMBER Biomolecular Simulation Programs." J. Comp. Chem. 26: 1668 - 1688.

Chang, R., G.S. Ayton, and G.A. Voth (2005). "Multi-Scale Coupling of Mesoscopic and Atomistic-Level Lipid Bilayer Simulations." J. Chem. Phys. 122: 244716.

Cheatham, T. E., III., Case, D. A. (2005). "Applying AMBER Biomolecular Simulation Methods to DAN and RNA: Insight into the Dynamics, Interactions and Energetics of Varied Nucleic Acid Structures." Comp. Studies of DNA and RNA In Press.

Cheatham, T. E., III (2005). "Molecular Modeling and Atomistic Simulation of Nucleic Acids." Ann. Reports Comp. Chem 1: 75-89.

Chu, J.-W., and G.A. Voth (2005). "Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations." Biophys. J. Submitted for Publication.

Chu, J. W. a. V., G.A. (2005). "Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-Grained Analyses." Proc. Natl Academy of Science 102(13111-13116).

Day, G. M., Motherwell, W. D. S., Ammon, H. Boerrigter, S. X. M., Della Valle, R. G., Venuti, E., Dzyabchenko, A., Dunitz, J., van Eijck, B. P., Erk, P., Facelli, J. C., Bazterra, V. E., Ferraro, M. B., Hofmann, D. W. M., Leusen, F. J. J. Liang, C., Pantelides, C., Karamertzanis, P. G., Price, S. L., Lewis, T. C. Torrissi, A., Nowell, H., Scheraga, H., Arnautova, Y., Schmidt, M. U. Schweizer, B., Verwer, P. (2005). "A Third Blind Test of Crystal Structure Prediction." Acta Crystall B61: 511-527.

Difley, S., Simons, J. (2005). "Role of Angular Electron Pair Correlation in Stabilizing C2-60." International Journal of Quantum Chemistry 106: 507 - 513.

Dixit, S. B., Beveridge, D. L., Case, D. A., Cheatham, T. E., III., Giudice, S., Lankas, F., Lavery, R., Maddocks, J., Osman, R., Sklenar, H., Thayer, K. M., Varnai, P. (2005). "Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Obligonucleotides. II. Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps. ." Biophys J. 89: 3721-3740.

Espinal, J. F., Truong, T.N., Mondragon, F. (2005). "Mechanisms for methane and ethane formation in the reaction of hydrogen with carbonaceous materials." Carbon 43(9): 1820-1827.

Facelli, J. C., Sefzik, T.H., Turco, D., and Iuliucci, R.J. (2005). "Modeling NMR Chemical Shift: A Survey of Density Functional Theory Approaches for Calculating Tensor Properties." Journal of Physical

Chemistry 109: 1180-1187. Facelli, J. C. (2005). "Modeling NMR Chemical Shifts." Invited Article in Handbook of NMR In Press: . Freedman, H., Truong, T.H. (2005). "An Application of Coupled Referenced Interaction Site Model

(RISM)/Molecular Dynamics (MD) Method to the Conformational Analysis of the Alanine Dipeptide." J. Phys. Chem. B. In Press.

Freedman, H., Truong, T. N. (2005). "A coupled reference interaction site model/molecular dynamics study of the potential of mean force curve of the SN2 Cl-+CH3Cl reaction in water." Journal of Physical Chemistry B 109(10): 4726-4730.

Geva, E., S. Jang, and G.A. Voth (2005). "Quantum Rate Theory: A Path Integral Centroid Perspective." Encyclopedia of Materials Modeling; Fundamental Models and Methods In Press.

Hone, T. D., Izvekob, S., and Voth, G.A. (2005). "Fast Centroid Molecular Dynamics: A Force-Matching Approach for the Predetermination of the Effective Centroid Forces." J . Chem. Phys. 122: 054105(054101-054107).

Huynh, L. K., Truong, T. N. (2005). "First-priciples kinetics for combustion systems using reaction class transition state theory." Preprints of Symposia - American Chemical Society, Division of Fuel Chemistry 50(1): 82 - 85.

Ilan, B., Wu, Y., Burnham, C. J., Zhu, F., Tajkhorshid, E., Schulten, K., and Voth, G.A. (2005). "Electrostatics and Charge Delocalization in Proton Channels. I. The Aquaporin Channels and Proton Exclusion." J. Mol. Biol. (submitted).

Iyengar, S. S., Day, T. J. F., and Voth, G.A. (2005). "On the Amphiphilic Behavior of the Hydrated Proton: An Ab Initio Molecular Dynamics Study." Int. J. Mass Spec. 241: 197-204.

Iyengar, S. S., M.K. Petersen, T.J.F. Day, C.J. Burnham, V.E. Tiege, and G.A. Voth (2005). "The Properties of Ion-Water Clusters. I. The Protonated 21-Water Cluster." J. Chem. Phys. 123: 084309.

Izvekov, S., and Voth, G.A. (2005). "Ab Initio Molecular Dynamics Simullation of Aqueous Proton Solvation and Transport Revisited." J. Chem. Phys. 123: 044505 (044501-044509).

Izvekov, S., and G.A. Voth (2005). "Effective Force Field for Liquid Hydrogen Fluoride from Ab Initio Molecular Dynamics Simulation Using the Force-Matching Method." J. Phys. Chem. B. 109: 6573-6586.

Izvekov, S., Voth, G. A. (2005). "Effective Interactions in Liquid State Systems as Revealed by Force-Matching." J. Chem. Phys. Submitted for Publication

Izvekov, S., and G.A. Voth (2005). "Multi-Scale Coarse-Graining of Liquid State Systems." J. Phys. Chem. 123(134105).

Izvekov, S., A. Violi, and G.A. Voth (2005). "Systematic Coarse-Graining of Nanoparticle Interactions in Molecular Dynamics Simulation." J. Phys. Chem. B. 109: 17019-17024

Jenkins, M. A. (2005). "Investigating the Haines Index Using Parallel Model Theory." International Journal of Wildland Fire Submitted for Publication.

Jenkins, M. A., Mell, W., Sun, R., Krueger, S., Zuluaf, M., and Charney, J. (2005). Numerical modeling of wildfires. Workshop on Firest Fires and Point Processes., University of Toronto.

Jeon, J., and G.A. Voth (2005). "The Dynamic Stress Responses to Area Change in Planar Lipid Bilayer Membranes." Biophys. J. 88: 1104-1119

Jiang, Z., J. Yu, B. Hornby, and G.T. Schuster (2005). "Migration of Multiples." The Leading Edge 24: 315-318.

Jui, C. H., et. al. (2005). "Observation of the Ankle and Evidence for a High-Energy Break in the Cosmic Ray Spectrum." Phys. Letters B (in press).

Jui, C. H., et. al. (2005). "Search for Point Sources of Ultra-High Energy Cosmic Rays above 4.0 1019 eV Using a Maximum Likelihood Ratio Test." Astrophys. J. 623: 164-170.

Jui, C. H., et. al. (2005). "A Study of the Composition of Ultra-High Energy Cosmic Rays Using the High Resolution Fly's Eye." Astrophys. J. 622: 910-926.

Jungsuttiwong, S., Limtrakul, J., Truong, T.H. (2005). "Theoretical study of modes of adsorption of water dinner on H-ZSM-5 and H-Faujasite Zeolites." Journal of Physical Chemistry B 109(27): 13342-13351.

Ka, B. J., and G.A. Voth (2005). "An Efficient and Accurate Implementation of Centroid Molecular

Dynamics Using a Gaussian Approximation." J. Phys. Chem. A. Submitted for Publication ( ). Kim, W. S., J. Kim, J.K. Park, S.Mukamel, S.K. Rhee, Y.K. Choi, and J.Y. Lee (2005). "Stacking Effect of

Polyfluorene on the Chemical Shift and Electron Transport." J. Phys. Chem. B. 109: 2686-2626

Kungwan, N., Truong, T. N. (2005). "Kinetics of the Hydrogen Abstraction .bul.CH3 + Alkane -->CH4 + Alkyl Reaction Class: An Application of the Reaction Class Transition State Theory." Journal of Physical Chemistry A 109(34): 7742-7750.

Lloyd, R. D., F.W. Bruenger, G.N. Taylor, and S.C. Miller (2005). "Search for a Genetic Link for Mammary Cancer in a Beagle Colony." In Vivo 19: 723-728.

Lu, G., Huang, Feng L. (2005). "Towards Quantitative Understanding of Formation and Stability of Ge Hut Island on Si(001)." Phys. Rev. Lett. 94: 176103.

Lu, G.-H., Cuma, M., Feng Liu (2005). "First-prinicples Study of Strain Stabilization of Ge(105) Facet on Si(001)." Phys. Rev. Lett. B. 72: 125415.

Lu, G.-H., M. Huang, M. Cuma, and F. Liu (2005). "Relative Stability of Si Surfaces: a First Principles Study." Surface Science 588: 61-70.

Lu, G. H., Cuma, M., and Liu, F. (2005). "Quantitative understanding of strain stabilization of Ge/Si(105) hut on Si(001) surface: a first[principles study." Physical Review B (accepted).

Maupin, C. M., K.F. Wong, A.V. Soudakov, S. Kim, and G.A. Voth (2005). "A Multi-State Empirical Valence Bond Description of Protonatable Amino Acids." J. Phys. Chem. A. In Press( ).

McDermott, R. (2005). A Physical Proof for Five and Only Five Regular Solids. Renaissance Banff -- Bridges: Mathematical Connections in Art, Music and Science.

McDermott, R. (2005). Polyhedral Transformation: Explosion-Implosion. Renaissance Banff -- Bridges: Mathematical Connections in Art, Music and Science, Banff, Alberta,

Canada. McDermott, R. (2005). A Ukrainian Easter Egg Monument Stands for Thirty Years.

Renaissance Banff -- Bridges: Mathematical Connections in Art, Music and Science, Banff, Alberta, Canada.

Mell, W., and M.A. Jenkins (2005). "Simulation of Grass Fire Using WFDS." Int. J. of Wildland Fire. Submitted for Publication.

Moision, R. M., and P. B. Armentrout (2005). "The Special Five-Membered Ring of Proline: An Experimental and Theoretical Investigation of Alkali Metal Cation Interactions with Proline and Its Four- and Six-Membered Ring Anaglogs." J. Phys. Chem. Submitted for Publication ( ).

Oku, K., M. Kurose, M. Kubota, S. Fukuda, M. Kurimoto, Y. Tujisaka, A. Okabe, and M. Sakurai (2005). "Combined NMR and Quantum Chemical Studies on the Interaction between Trehalose and Dienes Relevant to the Antioxidant Function of Trehalose." J. Phys. Chem. B. 109: 3032-3040.

Ona, O., Bazterra, V. E., Caputo, M. C., Ferraro, M. B., Facelli, J. C. (2005). "ab Initio Global Optimization of the Structures of Si_n H, n = 4-10, Using Parallel Genetic Algorithms." Phys. Rev. A. 72.

Orendt, A., Haymore, B., Richardson, D., Robb, S., Sanchez Alvarado, A., Facelli, J. C. (2005). "Design, Implementation and Deployment of a Commodity Cluster for Periodic Comparisons of Gene Sequences." High Performance Computing Paradigm and Infrastruture: 733-744.

Paramore, S., G.S. Ayton, and G.A. Voth (2005). "Extending a Spectrin Repeat Unit I. Linear Force-Extension Response." Biophys J (submitted).

Paramore, S., G.S. Ayton, and G.A. Voth (2005). "Extending a Spectrin Repeat Unit II. Rupture Behavior." Biophys. J. In Press( ).

Petersen, M. K., Wang, F., Blake, N.P., Metiu, H., and Voth, G.A. (2005). "Excess Proton Solvation and Delocalization in a Hydrophilic Pocket of the Proton Conducting Polymer Membrane Nafion." J. Phys. Chem. B 109: 3727-3730.

Pratt, L. M., Le, L. T., Truong, T. N. (2005). "A Computaional Study of Mixed Aggregates of Chloremethyllithium with Lithium Dialkylamides." Journal of Organic Chemistry 70(21): 8298-8302.

Ratkiewicz, A., Truong, T.N. (2005). "Automated mechanism generation: From symbolic calculation to complex chemistry." Internal Journal of Quantum Chemistry 106(1): 244-255.

Reichler, T., Kushner, P.J., and Polvani, L.M. (2005 ). "Response of the Troposphere-stratosphere System to Impulsive Tropospheric Forcing." J. of the

Atmospheric Sciences, In Press. Sawicka, A., Skurski, Piotr, Simons, Jack (2005). "Inverse Potassium Hydride: A Theoretical Study." J.

Phys. Chem. A. 109: 922-927. Sawicka, A., Berdys-Kochanska, J., Skurski, P., and Simons, J. (2005). "Low-Energy (0.1 eV) Electron

Attachment S-S Bond Cleavage Assisted by Coulomb Stablization." International Journal of Quantum Chemistry 102: 838-846.

Schuster, G. T. (2005). "Fermat's interferometric principle for target-oriented tomography." Geophysics (August).

Schuster, G. T. (2005). "Fermet's interferometric principle for multiple migration." GRL (submitted). Sefzik, T., Turco, D., Iuliucci, R., Facelli, J. C. (2005). "Modeling NMR Chemical Shift: A Survey of Density

Functional Theory Approaches for Calculating Tensor Properties." J. Phys. Chem. A. 109: 1180-1187.

Shi, Q., and Voth, G. A. (2005). "Multi-Scale Modeling of Phase Separation in Mixed Lipid Bilayers." Biophys. J. (in press).

Sirigaraensre, J., Truong, T. N., Limtrakul, J. (2005). "Density Functional Study of the Mechanism of the Beckmann Rearrangement Catalyzed by H-ZSM-5: A Cluster and Embedded Cluster Study." Journal of Physical Chemistry B 109(24): 12099-12106.

Sobczyk, M., I. Anusiewicz, J. Berdys-Kochanska, A. Sawicka, P. Skurski, and J. Simons (2005). "Coulomb-Assisted Dissociative Electron Attachment: Application to a Model Peptide." J. Phys. Chem. A. 109: 250-258.

Sobczyk, M., Skurski, Piotr, Simons, Jack (2005). "Dissociative Low-Energy Electron Attachment to the C-S Bond of H3CSCH3 Influenced by Coulomb Stailization." Advances in Quantum Chemistry 48: 239-251.

Sun, R., S.K. Krueger, M.A. Jenkins, W. Mell, and J. Charney (2005). "An Evaluation of FDS and Clark Coupled Wildfire Model." Accepted by 6th Symposium on Fire and Meteorology and the 19th Interior West Fire Council Meeting, Conmore, AB, Canada(Accepted by 6th Symposium on fire and meteorology and the 19th Interior west fire council meeting, Conmore, AB, Canada).

Sun, R., Krueger, S., Jenkins, M.A., Mell, W., and Charney, J. (2005). An evaluation of the Fire Dynamics Simulator and the coupled Clark wildfire model using plume observations. 6th Symposium on Fire and Forest Meteorology, Canmore, B.C., Canada.

Tepper, H. L., and G.A. Voth (2005). "A Coarse-Grained Model for Double-Helix Molecules in Solution: Spontaneous Helix Formation and Equilibrium Properties." J. Chem. Phys. 122: 124906.

Tepper, H. l., and Voth, G. A. (2005). "Protons May Leak Through Pure Lipid Bilayers via a Concerted Mechanism." Biophys. J. 88: 3095-3108.

Tiznado, W., Ona, O., Bazterra, V. E., Caputo, M. C., Ferraro, M. B., Facelli, J. C., Fuentealba, P. (2005). "Theoretical Study of the Adsorption of H and Si_n Clusters (n = 3-10)." J. Chem. Phys. 123: 214302.

Treesukol, P. S., K., Limtrakul, J., Truong, T. N. (2005). "Nature of the Metal-Support Interaction in Bifunctional Catalytic Pt/H-ZSM-5 Zeolite." Journal of Physical Chemistry B 109(24): 11940-11945.

Venkatnathan, A., and G.A. Voth (2005). "Superposition State Molecular Dynamics." J. Chem. Theory Comp. 1: 36-40.

Wang, F., Voth, G. A. (2005). "Computer Simulation of Excess Proton Solvation and Transport in Hydrocholoric Acid Solutions at Intermediate to High Concentrations." J. Phys. Chem. B. Submitted for Publication

Wang, F., and Voth, G. A. (2005). "A Linear-Scaling Self-Consistent Generalization of the Multi-State Empirical Valence Bond Model for Multiple Excess Protons in Aqueous Systems." J. Chem. Phys. 122: 144105(144101-144109).

Wang, Y., Truong, T. N. (2005). "Correlation between electronic structures of metal-intercalated single

wall carbon nanotubes with their field emission properties." Journal of Theoretical & Computational Chemistry 4(Special Issue): 657-668.

Wang, Y., S. Izvekov, T. Yan, and G.A. Voth (2005). "Multi-Scale Coarse-Graining of Ionic Liquids." J. Phys. Chem. B. Submitted for Publication( ).

Wang, Y., and G.A. Voth (2005). "Unique Spatial Heterogeneity in Ionic Liquids." J. Am. Chem. Soc. 127: 12192-12193

Wu, Y., and G.A. Voth (2005). "A Computational Study of the Open and Closed States of the Influenza A M2 Proton Channel." Biophys. J. 89( ): 2402-2411.

Wu, Y., B. Ilan, and G.A. Voth (2005). "Electrostatics and Charge Delocalization in Proton Channels. II. The Minimalist LS2 Channel and Proton Selectivity." J. Mol. Biol. Submitted for Publication ( ).

Wu, Y., H.L. Tepper, and G.A. Voth (2005). "A Flexible Simple Point Charge Water Model with Improved Liquid State Properties." J. Chem. Phys. Submitted for Publication( ).

Xu, J., and Voth, G. A. (2005). "Computer Simulation of Explicit Proton Translocation in Cytochrome c Oxidase: The D-Pathway." Proc. Nat. Academy of Science 102: 6795-6800.

Yan, B., Zhang, P., Legally, M. G., Lu, G. H., and Lui, F. (2005). "A novel mechanism for self-organization of semiconductor nanocrystals by selective surface faceting process." Natural Materials (submitted)

Ye, S. J., R. M. Moision, and P. B. Armentrout (2005). "Sequential Bond Energies of Water to Sodium Clycine Cation." Int. J. Mass. Spec. 240: 233-248.

Yu, J., G.T. Schuster, and R. Estill (2005). "Prestack Migration Deconvolution." Geophysics. In Press( ). Yu, J. a. S., G. T. (2005). "Crosscorrelation migration of VSP data." Geophysics (in press) 2004 (50) Abbasi, R. U., et al. (2004). "Measurement of the Flux of Ultrahigh Energy Cosmic Rays from Monocular

Observations by the High Resolution Fly's Eye Experiment." Phys. Rev. Lett. 92: 151101. Abbasi, R. U., et. al. (2004). "Monocular Measurement of the Spectrum of UHE Cosmic Rays by the FADC

Detector of the HiRes Experiment." Anusiewicz, I., J. Berdys, M. Sobczyk, P. Skurski, and J. Simons (2004). "Effects of Base Pi-Stacking on

Damage to DNA by Low-Energy Electrons." J. Phys. Chem. A. 108: 11381-11387. Ayton, G. S., and G.A. Voth (2004). "Mesoscopic Lateral Diffusion in Lipid Bilayers." Biophys. J. 87:

3299-3311 Ayton, G. S., and G.A. Voth (2004). "The Simulation of Biomolecular Systems at Multiple Length and Time

Scales." Int. J. for Multiscale Comp. Eng. (IJMCE) (Special Issue: Invited Article) 2: 291-311 Bazterra, V. E., Cuma, M., Ferraro, M. B., Facelli, J. C. (2004). "A general framework to understand

parallel performance in heterogeneous clusters: analysis of a new adaptive parallel genetic algorithm." Journal of Parallel and Distributed Computing 65: 48-57.

Bazterra, V. E., Ona, Ofelia, Caputo, Maria C., Ferraro, Marta B., Fuentealba, Patricio, Facelli, J. C. (2004). "Modified Genetic Algorithms to Model Cluster Structures in Medium-size Silicon Clusters." Phys. Rev. A. 69: 053202.

Berdys, J. A., Iwona, Skurski, Piotr, Simons, J. (2004). "Damage to Model DNA Fragments from Very Low-Energy (<1 eV) Electrons." J. Am. Chem. Soc. 126(20): 6441-6447.

Cheng, W. Y. Y., and W. J. Steenburgh (2004 ). "Evaluation of Surface Sensible Weather Forecasts by the WRF and Eta Models Over the Western

United States." Wea. Forecasting 20: 812-821. Clawson, J., Anderson, K., Pugmire, R., Grant D. (2004). "15N NMR Chemical Shift Tensors of Substituted

Hexaazaioswurtzitanes: The Intermediates in the Synthesis of CL-20." J. Phys. Chem. A. 108: 2638-2644.

Davis, B. L., E.L. Kick, and T.J. Burns (2004). "Change Scores, Composites and Reliability Issues in Cross-National Development Research." International J. of Comparative Sociology 45: 299-314.

Del Popolo, M. G., and Voth, G. A. (2004). "On the structure and dynamics of ionic liquids." Journal of Physical Chemistry B 108: 1744-1752.

Di Fiori, N., Orendt, A.M., Caputo, M.C., Ferraro, M.B., and Facelli, J.C. (2004). "Modeling Solid-state

Effects on NMR Chemical Shifts Using Electrostatic Models." Magnetic Resonance in Chemistry 42: 41-47.

Espinal, J., Montaya, A., Mondragon, F., Truong, T.N. (2004). "A DFT Study of Interaction of Carbon Monoxide with Carbonaceous Materials." J. Phys. Chem. B. 108: 1003-1008.

Espinal, J. F., Mondragon, Fanor, Truong, T.N. (2004). "Density Functional Theory Study of Carbon-H2O Reactions during Gasification with Steam." Am. Chem. Soc. 49: 822.

Facelli, J. C. (2004). "Calculations of Chemical Shielding: Theory and Applications." Concepts in Mag. Res. Part A 20A: 42-69.

Freedman, H., Truong, T.H. (2004). "A Coupled Reference Interaction Site Model (RISM)/Molecular Dynamics (MD) Study of Potential Mean Force of the SN2CI + CH3CI Reaction." J. Phys. Chem. A. 109: 4726-4730.

Freedman, H., Truong, T.N. (2004). "Coupled Reference Interaction Site Model/Simulation Approach for Thermochemistry of Solvation: Theory and Prospects." J. Chem. Phys. 121( ): 2187.

Freedman, H., Nguyen, H, Truong, T.H. (2004). "A Study of the Tautomic Equilibria of 2-hydroxypyridine/2-oxopyridine and of Cystosine in Water Using the Coupled Reference Interaction Site Model (RISM)/Molecular Dynamics (MD) Approach." J. Phys. Chem. B. 108: 19043.

Gregory, E., Cheatham, III T.E., J. C. Facelli (2004). "Data Mining Atomic Motions from Computer Siimulations of Nucleic Acids: A Wavelet Study of the Differential Bending of d[GA_4 T_4 C]_n and d[GT_4 A_4 C]_m. ." Currents in Computational Mol. Bio, A. Gramada, P. E. Bourne, Eds.: 528.

Hart, K., Steenburgh, W. J., Onton, D., Siffert, A. (2004). "An Evaluation of Mesoscale-Model-Based Model Output Statistics (MOS) during the 2002 Olympic and Paralympic Winter Games." Wea. Forecasting 19: 200-218.

Hart, K. A. (2004). An evaluation of high-resolution modeling and statistical forecast techniques over complex terrain. Salt Lake City, University of Utah. Ph.D.: 105.

Hart, K. A., W. J. Steenburgh, and D. J. Onton (2004 ). "Model Forecast Improvements with Decreased Horizontal Grid Spacing Over Fine-scale Intermountain

Orography During the 2002 Olympic Winter Games." Wea. Forecasting 20: 558-576. Hone, T. D., and Voth, G.A. (2004). "A centroid moelcular dynamics study of liquid para-Hydrogen and

ortho-Deuterium." J. Chem. Phys. 121: 6412-6422. Huang, M. H., Cuma, M., Lagally, M.G., Feng Lui (2004). "Bending of Nanoscale Thin Si Film Induced by

Growth of Ge Islands: Hut vs. Dome." MRS Procedding 791(Q6.4): 1-6. Ilan, B., E. Tajkhorshid, K. Schulten, and G. A. Voth (2004). "The Mechanism of Proton Exclusion in

Aquaporin Channels." Proteins: Structure, Function, and Bioinformatics 55: 223-228 Izvekov, S., Parrinello, M., Burnham, C. J., Voth, G. A. (2004). "Effective Force Fields for Condensed

Phase Systems From Ab Initio Molecular Dynamics Simulation: A New Method for Force-matching." J. Chem. Phys. 120(23): 10896-10913.

Jenkins, M. A. (2004). "Investigating the Haines Index Using Parcel Model Theory." Int. J. of Wildland Fire 13: 1 - 13.

Jui, C. H., et. al. (2004). "Study of small-scale anisotrphy of ultra-high energy cosmic rays observed in stereo by HiRes." Astrophysics Journal 610: L73-76.

Ka, B. J., Voth, G. A. (2004). "Combining the Semiclassical Initial Value Representation with Centroid Dynamics." J. Phys. Chem B. 108(21): 6883-6892.

Krongpracha, P., Treesukol, P., Limtrakul, J., Truong, T.H. (2004). "A theoretical study of adsoption of carbon monoxide and nitrogen oxide on Ag-ZSM-5 Zeolite." Journal of Physical Chemistry (submitted).

Lapid, H., Agmon, N., Petersen, M.K. and Voth, G.A. (2004). "A bond-0rder analysis of the mechanism for hydrated proton mobility in liquid water." Journal of Chemical Physics 122: 1 - 11.

Limtrakul, J., Inntam, Chan, Truong, T.N. (2004). "Density Functional Theory Study of the Ethylene Epoxidation over Ti-substituted Silicalite (TS-1): An Application of Cluster and Embedded Cluster Methods." J. of Molecular Catalysis A: Chemical 207(139).

McWhirter, J. L., Ayton, G.S., and Voth, G.A. (2004). "Coupling Field Theory with Mesoscopic Dynamical

Simulations of Multi-component Lipid Bilayers." Biophysical Journal 87. Nguyen, H. N., Zhang, S., Peeters, J., Truong, T.N., Nguyen, M.T. (2004). "Direct ab initio Dynamics

Studies of the Reactions of HNO with H and OH radicals." Chem. Phys. Lett. 388(94). Ona, O., V. E. Bazterra, M. C. Caputo, M. B. Ferraro, P. Fuentealba, J. C. Facelli (2004). "Modified Genetic

Algorithms to Model Atomic Cluster Structures: CuSi Clusters." J. Mol. Struct. 681: 149-155. Pala, R., Feng Liu (2004). "Determining the Adsorptive and Catalytic Properties of Strained Metal Surfaces

using Adsortion-induced Stress." J. Chem. Phys. 120(7720). Petersen, M. K., S.S. Iyengar, T.J.F. Day, and G.A. Voth (2004). "The Hydrated Proton at the Water

Liquid/Vapor Interface." J. Phys. Chem. B. 108: 14804-14806 Rega, N., S. S. Iyengar, G. A. Voth, H. B. Schlegel, T. Vreven, and M. J. Frisch (2004). "Hybrid Ab Initio

Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach." J. Phys. Chem. B. 108: 4210 - 4220

Schuster, G. T., J. Yu, J. Sheng, and J. Rickett (2004). "Interferometric/daylight Seismic Imaging." GJI 157: 838-852.

Stokes, B. T., Jui, C.C. H., and Matthews, J.N. (2004). "Using fractal dimensionality in the search for source models of ultra-high energy cosmic rays." Astroparticle Phys. 21: 95.

Strohmeier, M., Grant D. M. (2004). "Experiemental and Theoretical Investigation of the 13C and 15N Chemical Shift Tensors in Melanostatin - Exploring the Chemical Shift Tensor as a Structural Probe." J. Am. Chem Soc. 126: 966-977.

Sun, R., Jenkins, M. A., Krueger, S. K. (2004). "Effects of atmospheric stability, moisture, and wind speed on wildfire behavior and indications of Haines Index. ." Internal Journal of Wildland Fire.

Truong, T. N. (2004). "Computational Science and Engineering Online: An Integrated Web-based Environment for Multi-scale Modeling of Complex Reaction Systems. (Proceedings of the 2nd International Conference on Foundations of Molecular Modeling and Simulations)." Molecular Phys. 102: 353.

Violi, A., A.F. Sarofim, and G.A. Voth (2004). "Kinetic Monte Carlo-Molecular Dynamics Approach To Model Soot Inception." Combust. Sci. and Tech. 176: 991-1005

Violi, A., Truong, T.N., Sarofim, A.F. (2004). "Kinetics of Hydrogen Abstraction Reactions From Polycyclic Aromatic Hydrocarbons by H atoms." J Phys. Chem. A. 108(4846).

Wang, Y., Truong, T.N. (2004). "Theoretical Study of Adsorption of Water Dimer on the Perfect MgO (100) Surface: Molecular Adsorption versus Dissociative Chemisorption." J. Phys. Chem. B. 108: 3289-3294.

Yan, B., Liu, F., Lagally, M.G. (2004). "Local Strain-mediated Chemical Potential Control of Quantum Dot Self-organization in Heteroepitaxy." Phys. Rev. Lett. 92( ): 025502.

Yan, t., Burnham, C. J., Del Popola, M.D., and Voth, G.A. (2004). "Molecular dynamics simulation of ionic liquids: The effect of electronic polarizability." Journal of Physical Chemistry B 108: 11777-11881.

Zang, J., Treibergs, Andrejs, Han, Y., Feng Liu. (2004). "Geometry Constant Defining Shape Transitions of Carbon Nanotubes under Pressure." Phys. Rev. Lett. 92: 105501.

2003 (28) Ahn, E., Hari, P., Whitaker, J., Williams, G.A., Taylor, P.C., and Facelli, J. (2003). "Evidence of indirect

spin -- spin coupling in srystalline and glassy As-chalcogen compounds." Journal of Non-Crystalline Solids 326 & 327: 64 - 67.

Bazterra, V. E., Ferraro, M. B., Facelli, J. C. (2003). "Modified Genetic Algorithm to Model Crystal Structures. III. Determination of Crystal Structures Allowing Simultaneous Molecular Geometry Relaxation." International J. of Quantum Chemistry 96: 312-320.

Blair, S. (2003). "Self-focusing of Narrow 1-D Beams in Photoni Microcavity Arrays." J. of the Optical Society of America B 20: 1520-1526.

Burns, T. J., Kick, E.L., and David, B.L. (2003). "Theorizing and Rethinking Linkages between the Natural Environment and the Modern World-System: Deforestation in the Late 20th Century." Journal of World-Systems Research 9: 357-392.

Cummings, M. P., Handley, S. A., Myers, D. S., Reed, D. L., Rokas, A., Winka, K (2003). "Comparing Bootstrap and Posterior Probability Values in the Four-taxon Case." Systematic Biology 52: 477-487.

Erkoc, S., Leblebicioglu, Kemal, Halici, Ugur (2003). "Application of Genetic Algoritms to Geometry Optimization of Microclusters: A Comparative Study of Empirical Potential Energy Functions for Silicon." Materials and Manufacturing Processing 18: 329-339.

Fogelson, A., and R. Guy (2003). "Platelet-Wall Interactions in Continuum Models of Platelet Aggregation." Biophys. J. 80( ): 1050-1074.

Freedman, H., Truong, T.N. (2003). "A Coupled RISM/MD or MC Simulation Methodology for Solvation Free Energies." Chem. Phys. Lett. 381: 362.

Jenkins, M. A., Krueger, S. K., Sun, R. (2003). Using a Simple Parallel Model to Investigate the Haines Index. 5th Symposium on Fire and Forest Meteorology, Orlando, FL.

Lee, L., and LeVeque, R.J. (2003). "An immersed interface method for incompressible Navier-Stokes equations." SIAM J Sci. Comp 25: 832-856.

Lewis, J. P., Cheatham, T. E., III, Starikov, E.B., Wang, H., Sankey, O.F. (2003). "Dynamically Amorphous Character of Electronic States in Poly(dA)-Poly(dT) DNA." J. Phys. Chem. B. 107: 2581-2587.

Montoya, A., Mondragon, F., Truong, T.N. (2003). "CO2 Adsorption on Carbonaceous Surface: A Combined Experimental and Theoretical Study." Carbon 41: 29.

Myers, D. S., Cummings, M. P. (2003). "Necessity is the Mother of Invention: a Simple Grid Computing System using Commodity Tools." J. of Parallel and Distributed Computing 63: 578-589.

Oklejas, V., and Harris, J. M. (2003). "In-Situ Investigation of Binary Component Self-Assembled Monolayrs: A SERS-Based Spectroelectrochemical Study of the Effects of Monolayer Composition on Interfacial Structure." Langmuir 19: 5794-5801.

Oklejas, V., Sjostrom, C., and Harris, J. M. (2003). "Surface Enhanced Raman Scattering Based Vibrational Stark Effect as a Spatial Probe of Interfacial Electric Fields in the Diffuse Double Layer." J. Phys. Chem. B. 107: 7788-7794.

Ratkiewicz, A., Truong, T.N. (2003). "Application of Chemical Graph Theory for Automated Mechanism Generation." J. of Chemical Information and Computer Sciences 43: 36.

Schuster, G. T., Katz, L., Followill, F., and Yu, J. (2003). "Autocorrelogram migration theory." Geophysics 68: 1685-1694.

Shapolav, V., Yan Wang, Truong, T.N. (2003). "Theoretical Analysis of the Electronic Spectra of Water Adsorbed on the Rutile TiO2 (110) and MgO (100) Surfaces." Chem. Phys. Lett. 381: 362.

Sheley, D., Crosby, T., Zhou, M., Giacoma, J., Yu, J., He, R., and Schuster, G. (2003). "2-D seismic trenching of colluvial wedges and faults in contributions to Neotectonics and seismic hazard from shallow geophysical imaging." Tectonophysics 368: 51-69.

Sheley, D., and G. Schuster (2003). "Reduced-time Migration of Transmission P-S Waves." Geophysics 68: 1695-1707.

Sheng, J., and Schuster, G.T. (2003). "Finite-frequency resolution limits of wave path traveltime tomography for smoothly varying models." Geophysical J. Int 152: 669-676.

Solum, M. S., Veranth, J. M., Jiang, Y. J., Orendt, A. M., Sarofim, A. F., Pugmire, R J. (2003). "The Study of Anthracene Aerosols by Solid-State NMR and ESR." Energy & Fuels 17(3): 738 - 743.

Sun, H., and G.T. Schuster (2003). "3D wavepath migration." Geophysical Prospecting 51: 421-430. Sun, R. (2003). Effect of low-level atmospheric stablity and moisture on wildfire behavior. Meteorology.

Salt Lake City, UT, University of Utah. Master of Science. Sun, R., and M.A. Jenkins (2003). Effects of Near-Surface Atmospheric Stability and Moisture on Wildfire

Behavior and Consequences for Haines Index. 5th Symposium on Fire and Meteorology and the 2nd International Wildland Fire Ecology and Fire Management Congress, Orlando, FL.

Whitaker, J., Ahn, E., Hari, P., Williams, G. A., Taylor, P. C., Facelli, J. C. (2003). "Indirect (J) coupling of inequivalent 75As nuclei in crystalline and glassy As2Se3 and As2S3." J. Chem. Phys. 119: 8519-8525.

Zhang, S., Truong, T.N. (2003). "Kinetics of Hydrogen Abstraction Reaction Class H + H-C(sp3): First-Principle Predictions Using the Reaction Class Transition State Theory." J. Phys. Chem. A. 107.

Zhang, S., Nguyen, H.N., Truong, T.N. (2003). "Theoretical study of Mechanism, Thermodynamics and Kinetics of the Decomposition of Gas phase HMX (Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine." J. Phys. Chem. B. 107: 2981.

2002 (28) Anderson, K. L., Merwin, L.H., Wilson, Facelli, J.C. (2002). "15N Chemical Shifts in Energetic Materials:

CP/MAS and ab Initio Studies of Aminonitropyridines, Aminonitropyrimidines, and Their N-Oxides." Int. J. Mol. Sci. 3: 858-872.

Anusiewicz, I. a. P. S. (2002). "An Ab Initio Study on BeX3 Superhalogen Anions (X=F, C1, Br)." Chem.l Phys. Lett. 358: 426-434.

Ayton, G., Voth, G. A. (2002). "Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers." Biophys J. 83: 3357-3370.

Bazterra, V. E., Ferraro, M. B., Facelli, J. C. (2002). "Modified Genetic Algorithm to Model Crystal Structures. I. Benzene, Naphthalene and Anthracene." J. Chem. Phys. 116: 5984-5991.

Bazterra, V. E., Ferraro, M. B., Facelli, J. C. (2002). "Modified genetic algortithm to model crystal structures. II. Determination of a polymorphic structure of benzene using enthalpy minimization." Journal of Chemical Physics 116: 5992-5995.

Clawson, J. S., Strohmeier, M., Stueber, D., Orendt, A. M., Barich, D. H., Asay, B., Hiskey, M. A., Pugmire, R. J., Grant, D. M. (2002). "15N Chemical shift Tensors of -HMX." J Physical Chem A 106(26): 6352 - 6357.

Day, T. J. F., Soudackov, M., Cuma, M., Schmitt, U. W., Voth, G. A. (2002). "A Second Generation Multi-State Empirical Valence Bond Model for Proton Transport in Aqueous Systems." J. Chem. Phys. 117: 5839-5849.

Fogelson, A., H. Yu, A. Kuharsky (2002). "Computational Modeling of Blood Clotting: Coagulation and Three-dimensional Platelet Aggregation. Polymer and Cell Dynamics: Multiscarel Modeling and Numerical Simulations."

Harper, J. K., J.C. Facelli, D.H. Barich, G. McGeorge, A.E. Mulgrew, D.M. Grant (2002). "13C NMR Investigation of Solid-State Polymorphism in 10-Deacetyl Baccatin III." J. Am. Chem. Soc. 124: 10595.

Horel, J., Potter, T., Dunn, L., Steenburgh, W. J., Eubank, M., Splitt, M., Onton, D. J. (2002). "Weather support for the 2002 Winter Olympic and Paralympic Games." Bulletin of American Meteorolgic Society 83: 227-240.

Izvekov, S., Voth, G. A. (2002). "Carr-Parrinello Molecular Dynamics Simulation of Liquid Water: New Results." J. Chem. Phys. 116: 10372-10376.

Jenkins, M. A. (2002). "A Examination of the Sensitivity of Numerically Simulated Wildfires to Low-level Atmospheric Stability and Moisture, and the Consequences for the Haines Index." International Journal of Wildland Fire 11: 213-223.

Jenkins, M. A., Sun, R. (2002). What Coupled Wildfire-atmosphere Numerical Models Can Do. 4th International Workshop on Disturbance Dynamics in Boreal Forest, Prince George, British Columbia.

Lankas, F., T. E. Cheatham, III, P. Hobza, J. Langowski, N. Spackova, and J. Sponer (2002). "Critical Effect of the N2 Amino Group on Structure, Dynamics and Elasticity of DNA Polypurine Tracts." Biophys. J. 82: 2592-2609.

Reil, K. (2002). "The Energy Spectrum of Ultra High Energy Cosmic Rays Measured by the High Resolution Fly's Eye Detectors."

Rienstra, C. M., Kellogg, L. T., Jaroniec, C. P., Hohwy, M., Reif, B., McMahon, M. T., Tidor, B. Perez, T. L., Griffin, R. G. (2002). "De Novo Determination of Peptide Structure with Solid-state Magic-angle Spinning NMR Spectroscopy." PNAS 19: 10260-10265.

Schlegel, H. B., Iyengar, S. S., Li, X., Milliam, J. M., Voth, G. A., Scuseria, G. E., Frisch, M. J. (2002). "Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born Oppenheimer Dynamics." J. Chem. Phys. 117: 8694-8704.

Schultz, D. M., Steenburgh, W. J., Trapp, R.J., Horel, J., Kingsmill, D.E., Dunn, L.B., Rust, W.D., Cheng,

L., Bansemer, A., Cox, J., Daugherty, J., Jorgensen, D.P., Meitin, J., Showell, L., Smull, B.F., Karp, K., Trainor, M. (2002). "The Intermountain Precipitation Experiment." Bulletin of American Meteorolgic Society 83: 189-210.

Schuster, G. T. (2002). "Geophysics is Kid's Play." The Leading Edge 24( ): 315-318. Skurski, P., I. Dabkowska, A. Sawicka, J. Rak. (2002). "Dipole-bound and Dispersion-bound Anions

Supported by the Asymmetric Tautomers of Aminophosphine: H3NPH and HNPH3." Chemical Physics 279: 101-111.

Smondyrev, A. M. a. G. A. V. (2002). "Molecular Dynamics Simulation of Proton Transport Near the Surface of a Phospholipid Membrane." Biophysical Journal 82: 1460.

Spackova, N., T. E. Cheatham, III, F. Ryjcek, F. Lankas, L. van Meervelt, P. Hobza and J. Sponer (2002). "Molecular Dynamics Simulations and Thermodynamics Analysis of DNA - Drug Complexes. I. Minor groove binding between 4',6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution." Journal of American Chemical Society.

Steenburgh, W. J. (2002). "Using Real-time Mesoscale Modeling in Undergraduate Education." Bulletin of American Meteorolgic Society 10: 1147-1451.

Stefl, R., T.E. Cheatham III, N. Spackova, E. Fadrna, I. Berger, J. Koca and J. Sponer (2002). "Formation Pathways of a Guanine-quadruplex DNA revealed by Molecular Dynamics and Thermodynamical Analysis of the Substates." Journal of American Chemical Society.

Stewart, J., Whiteman, D., Steenburgh, W. J., Bian, X. (2002). "A Climatological Study of Thermally Driven Wind Systems of the U.S. Intermountain West." Bulletin of American Meteorological Society 83: 699-708.

Stueber, D., Orendt, A. M., Facelli, J. C., Parry, R. W., Grant, D. M. (2002). "Carbonates, Thiocarbonates, and the Corresponding Monoalkyl Derivatives: III. The 13C Chemical Shift Tensors in Potassium Carbonate, Bicarbonate and Related Monomethyl Derivatives." Solid State Nuclear Magnetic Resonance 22: 29 - 49.

Violi, A., Kubota, A., Truong, T., Pitz, W., Westbrook, C., Sarfofim, A. (2002). "A Fully-Integrated Kinetci Monte Carlo / Molecular Dynamics Approach for the Simluation of Soot Precursor Growth." Proceedings of the 29th International Symposium on Combustion, Sapporo, Japan

Violi, A., A. Sarofim, T. Truong (2002). "Mechanistic Pathways to Explain H/C Ratio of Soot Precursos." Second Mediterranean Combustion Symposium, Sharm el Sheik, Egypt.

2001 (32) Archbold., G. (2001). "A Fiber-optic Based Calibration Systems for the HiRes Experiment." Proceedings of

ICRC 1. Bellido, J., Belz, J., Dawson, B., Schindel, M., Stokes, B. (2001). "Anisotropy Studies of Ultra-High Energy

Cosmic Rays as Observed by the High Resolution Fly's Eye (HiRes)." Proceedings of ICRC 1. Bergman, D. R. (2001). "Determining the Alignment of HiRes Optics Using a CCD Camera." Proceedings

of ICRC 1. Bergman, D. R. (2001). "A Monocular Spectrum Analysis Using FADC Timing at HiRes." Proceedings of

ICRC 2001 1. Cao, Z. (2001). "A Measurement of the Average Longitudinal Development Profile of Cosmic Ray Air

Showers Between from 1017 eV and 1018.3 eV." Proceedings of ICRC 2001 1. Cao, Z. (2001). "Measurement of the Cosmic Ray Energy Spectrum from 1017 to 1018.3 eV Using a Hybrid

Technique." Proceedings of ICRC 2001 1. Cao, Z. (2001). "Monte Carlo Simluation of the HiRes Experiment." Proceedings of ICRC 1. Cheatham, I., T. E., Young, M. A. (2001). "Molecular Dynamics Simulations of Nucleic Acids: Successes,

limitations and promise." Biopolymers 56: 232-256. Clay, R. W., B.R. Dawson, R.T. Pace, D.S. Riordan, A.G.K. Smith, N.R. Wild. (2001). "Cloud Detection at

the High Resolution Fly's Eye." Proceedings of ICRC 1. Facelli, J. C., Nakagawa, B. K., Orendt, A. M., Pugmire, R. J. (2001). "Cluster analysis of 13C Chemical

Shift Tensor Principal Values in Polycyclic Aromatic Hydrocarbons." J Physical Chem A 105(31): 7468 - 7472.

Izvekov, S., and G. A. Voth (2001). "Ab Initio Molecular Dynamics Simulation of the Ag(111)-Water Interface." J. Chem. Phys. 115: 15.

Jones, B. F., J.N. Matthews, S. A. Moore, S. B. Thomas. (2001). "Calibration and Stability of the High Resolution Fly's Eye Detector." Proceedings of ICRC 2001 1.

Jui, C. H. (2001). "Measurement of the Ultrahigh Energy Cosmic Ray Spectrum Using Monocular Data From the High-Resolution Fly's Eye Experiment." Proceedings of ICRC 1.

Kerber, R., Boucher, K. (2001). "Pseudolikelihood Estimation of Genetic Parameters for Arbitrarily Complex Pedigrees." Poster presented at the Tenth Conference of the International Genetic Epidemiology Society, Garmisch, Germany.

Kick, E. L., Davis, B.L., and Parker, C.R. (2001). "Macrosocial Causes of Suicide and Homicide: A Research-In-Progress Report." International Journal of Comparative Criminology 1: 120-126.

Kick, E. L., and Davis, B.L. (2001). "World-System Structure and Change: An Analysis of Global Networks and Economic Growth Across Two Time Periods." American Behavioral Scientist 44: 1561-1578.

Kuharsky, A., and A. Fogelson (2001). "Surface-mediated Control of Blood Coagulation: The Role of Binding Site Densities and Platelet Deposition." Biophys. J. 80: 1050-1074.

Lefohn, A. E., Ovchinnikov, M., Voth, G. A. (2001). "A Multistate Empirical Valence Bond Approach to Polarizable and Flexible Water Model." J. Phys. Chem B. 105: 6628.

Mathews, J. N. (2001). "Description of the High Resolution Fly's Eye Detector." Proceedings of ICRC 1. Menashe, D., Bihma, O., Laikhtman, B. D. (2001). "Thermodynamic Fluctuations of Site Energies and

Occupation Numbers in the Two-dimensional Coulomb Glass." Physical Review B. 64: 115209. Morrison, P. a. L. W. (2001). "Measuring Air Shower Speeds with the HiRes Fluorescence Detectors."

Proceedings of ICRC 1. Reil, K. A., R. W. Springer. (2001). "Preliminary Stereo Results from the High Resolution Fly's Eye Cosmic

Ray Observatory." Proceedings of ICRC 1. Roberts, M. D. (2001). "Atmospheric Analysis Techniques at HiRes." Proceedings of ICRC 1. Roberts, M. D. (2001). "Atmospheric Monitoring at HiRes - Hardware Systems 1." Proceedings of ICRC 1. Schmitt, U. W., and G. A. Voth. (2001). "The Isotope Substitution Effect on the Hydrated Proton." Chem.

Phys. Lett. 329: 36. Smith, J. D., S.B. Thomas, L.R. Wiencke (2001). "Absolute GPS Time Event Generation and Capture for

Remote Locations." Proceedings of ICRC 1. Song., C. (2001). "Study of the Longitudinal Development of Air Showers with CORSIKA." Proceedings of

ICRC 1. Strohmeier, M., Orendt, A. M., Alderman, D. W., Grant, D. M. (2001). "Investigatioin of the Polymorphs of

dimethyl-3, 6-Dichloro-2, 5-Dihydroxyterephthalate by 13C Solid-State NMR Spectroscopy." J American Chem Society 123(8): 1713 - 1722.

Violi, A., Truong, T., D'Anna, A. D'Alessio, A., Sarofim, A. (2001). "Quantum Mechanic Study of High Molecular Mass Compounds in Combustion Conditions." Proceedings of the 2nd Joint Meeting of the US Sections of the Combustion Institute. Oakland, CA.

Wiencke, L. R. (2001). "Atmospheric Monitoring at HiRes - Hardware Systems 2." Proceedings of ICRC 1. Wiencke, L. R. (2001). "Atmospheric Monitoring at HiRes - The Atmosphere at Dugway." Proceedings of

ICRC 1. Zech, A. (2001). "Comparisons of CORSIKA-generated Showers with HiRes Data." Proceedings of ICRC 1. 2000 (19) Amicangelo, J., Armentrout, P. (2000). "Absolute Binding Energies of Alkali-Metal Cation Complexes with

Benzene Determined by Threshold Collision-Induced Dissociation Experiements and ab Initio Theory." J. Phys. Chem. B. 104: 11420-11432.

Barich, D. H., Orendt, A. M., Pugmire, R. J., Grant, D. M. (2000). "Carbon-13 Chemical-Shift Tensors in Polycyclic Aromatic Compounds. 9. Biphenylene." J Physical Chem A 104(35): 8290 - 8295.

Cuma, M., U. W. Schmitt and G. A. Voth. (2000). "The Multi-Scale Empirical Valence Bond Model for Acid-Base Chemistry in Aqueous Solution." Chem. Phys. Lett. 258: 187.

Davis, B. L., and E.L. Kick (2000). Human Capital Issues and Information Technology in Education in the

New Millennium. Social Dimensions of Information Technology: Issues for the New Millennium. G. D. Garson. Hershey, PA, Idea Group Publishing.

Facelli, J. C. (2000). "Nitrogen-15 chemical shift in the pyridine-methanol complex." Chem. Phys. Lett. 322: 91-96.

Fogelson, A., and J. Keener (2000). "Immersed Interface Methods for Neumann and Related Problems." SIAM J. Sci Comput. 22: 1630-1654.

Green, R. J., Qian, Jun, Kim, Ho-Tae, Anderson, Scott L. (2000). "Hydride Abstraction by NO+ from Ethanol: Effects of Collision Energy and Ion Rotation State." J. Chem. Phys. 113: 3002.

Gutowski, M., Skurski, P., Li, X., Wang, L.S. (2000). " (MgO) n (n = 1-5) Clusters: Multipole-Bound Anions and Photodetachment Spectroscopy." Phys. Rev. Lett. 85: 3145.

Kick, E., Davis, B.L., Lehtinen, M., Wang, L. (2000). "Family and Ecnomic Growth: A World-System Approach and a Cross-National Analysis." International Journal of Comparative Sociology 41: 225-244.

Kick, E. L., Davis, B.L., Lehtinen, M., and Burns, T.J. (2000). "A Cross-National Analysis of Democracy, Political Instability, and National Development Outcomes." Journal for Political and Military Sociology 28: 131-155.

Koizumi, H., . Zhang, Armentrout, P. (2000). "Collision-Induced Dissociation and Theoretcial Studies of Cu+-Dimethyl Ether Complexes." J. Phys. Chem. A. 105: 2444-2452.

Mass, C. F., Steenburgh, W. J. (2000). "An Observational and Numerical Study of an Orographically Trapped Wind Reversal Along the West Coast of the U. S." Mon. Wea. Rev. 129: 1318-1338.

Montoya, A., Truong, T, Sarofim, A. (2000). "Spin Contamination in Hartree-Fock and Density Functional Theory Wavefuntions in Modeling of Adsorption on Graphite." J. Phys. Chem. A. 104: 6108-6110.

Orendt, A. M., Facelli, J. C., Bai, S., Rai, A., Gossett, M., Scott, L. T., Boerio-Goates, J., Pugmire, R. J., Grant, D. M. (2000). "Carbon-13 Shift Tensors in Polycyclic Aromatic Compounds. 8. A Low-Temperature NMR Study of Coronene and Corannulene." J Physical Chem A 104(1): 149 - 155.

Pernice, M. (2000). "A Hybrid Multigrid Method for the Steady-State Incompressible Navier-Stokes Equations." Electronic Transactions on Numerical Analysis 10: 74.

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1999 (31) Bell, R., Simons, J. (1999). "Unusual Thresholds and Isotope Effects in AI+ + H2/D2/HD Reactions." J.

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Johnson, M. A., Truong, T. N. (1999). "Importance of Polarization in Simluations of Condensed Phase Energetic Materials." J. Phys. Chem B. 102: 9392-9393.

Maity, D., Bell, R., Truong, T. (1999). "Mechanism and Quantum Mechanical Tunneling Effects on Inner Hydrogen Atom Transfer in Free Base Porphyrin: A Direct ab Initio Dynamics Study." J. Am. Chem. Soc. 63: 861.

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Orendt, A. M., Facelli, J. C., Grant, D. M. (1999). "A theoretical study of the acetate 13C chemical shift tensor in cadmium acetate dihydrate." Chemical Physics Letters 302: 499 - 504.

Pak, Y., Voth, G. A. (1999). "Reactive Flux Calculations of Methyl Vinyl Ketone Reacting with Cyclopentadiene in Water." J. Phys. Chem. A. 103: 925.

Pavese, M., Berard, D. R., Voth, G. A. (1999). "Ab initio Centroid Molecular Dynamics: A Fully Quantum Method for Condensed Phase Dynamics Simulations." Chem. Phys. Lett. 300: 93.

Pernice, M., Bockelie, J., Swensen, D., Smith, P. (1999). "Progress, Results, and Experiences in Developing an Adaptive Solver for Steady State Turbulent Reacting Flows in Industrial Boilers and Furnaces, Structured Adaptive Mesh Refinement (SAMR) Grid Methods." IMA Volumes in Mathematics and its Applications 117.

Rabbitt, R. D. (1999). "Directional Coding of Three Dimensional Movements by Vestibular Semicircular Canals." Biological Cybernetics 80: 417.

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Skurski, P., M. Gutowski and J. Simons. (1999). "Dipole-Bound Anion of the HNNH3 Isomer of Hydrazine. An Ab Initio Study." J. Phys. Chem. A. 103: 625.

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Tinniswood, A., Lazzi, G., Gandhi, O.P. (1999). "The Use of the Expanding Grid FDTD Method for Simulation of CAD-derived Personal Wireless Telephones." Technical Report, University of Utah.

Truong, T. N., Truong, T. T. (1999). "A Reaction Class Approach with the Integrated Molecular Orbital + Molecular Orbital Methodology." Chem. Phys. Lett. 314: 529.

Truong, T. N. (1999). "Thermal Rates of Hydrogen Exchange of Methane with Zeolite: A Direct ab Initio Dynamics Study on the Importance of Quantum Tunneling Effects." J Phys. Chem. B. 101: 2750.

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Wang, L. L., Boldyrev, A. I., Simons, J. (1999). "Tetracoordinated Planar Carbon in the Al4C- Anion. A Combined Photoelectron Spectroscopy and ab Initio Study X." J. Phys. Chem. A. 103: 503.

Yu, H. (1999). "Three Dimensional Computational Modeling of Platelet Aggregation on Parallel Computers."

1998 (27) Bowden, A. E., Rabbitt, R. D., Weiss, J. A. (1998). "Anatomical Registration and Segmentation by

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Eskicioglu, M. R., and T. Marsland (1998). "Evaluation of JIAJIA Software DSM System on High Performance Architecture." Proceedings of the 32nd Hawaii International Conference on System Sciences and the Proceedings of the 1998 IBM Center for Advanced Studies Conference.

Eskicioglu, M. R., Marsland, T. (1998). "Shared Memory Computing on SP2: JIAJIA Approach." IBM Center for Advanced Studies Conference (CASCON'98).

Fogelson, A., and A. Kuharsky (1998). "Membrane Binding-site Density Can Modulate Activation Thresholds in Enzyme Systems." J. Theor. Biol. 193: 1-18.

Gardiner, J., Weiss, J. (1998). "Experimental Testing and Computational Modeling to Determine the Stress-Strain Distribution in the Human Medical Collateral Ligament." 44th Annual Meeting, Orthopedic Research Society.

Grunbaum, D., D. Eyre, and A. Fogelson (1998). "Functional geometry of ciliated tentacular arrays in active suspension feeders." J. Exp. Biol. 201: 2575-2589.

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Kick, E. L., Davis, B.L., Kiefer, D., and Burns, T.J. (1998). "A Cross-National Analysis of Militarization and Well-Being Relationships in Developing Countries." Social Science Research 27: 351-370.

Maity, D., W. Duncan and T. Truong (1998). "Direct ab Initio Dynamics Studies of the Hydrogen Abstraction Reactions of Hydrogen Atom with Fluormethanes." Journal of Physical Chemistry A 103: 3152.

Michael, J., Barton, R., Saffle, J., Mone, M., Markewitz, B., Hillier, K., Elstad, M., Campbell, E., Troyer, B., Whatley, R., Liou, T., Samuelson, W., Carveth, H., Hinson, D., Morris, S., Davis, B. L., and Day, R. (1998). "Inhaled Nitric Oxide Versus Conventional Therapy: Effects on Oxygenation in ARDS." American Journal of Respiratory Critical Care Medicine 157: 1372-1380.

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of Chemical Physics 108: 6303. Taccardi, B. a. S. V. (1998). "Multiple Components in the Unipolar Electrogram: A Simulation Study in a

Three-Dimensional Model of Ventricular Myocardium." Journal of Cardiovascular Electrophysiology 9: 1062.

Tinniswood, A., Gandhi, O. P. (1998). "Head and Neck Resonance in a Rhesus Monkey - A Comparison with Results from a Human Model." Technical Report, University of Utah.

Tinniswood, A. D., Furse, C. M., Gandhi, O. P. (1998). "Computations of SAR Distributions for Two Anatomically Based Models of the Human Head Using CAD Files of Commercial Telephones and the Paralleled FDTD Code." IEEE Transactions on Antennas and Propagation 46: 829.

Tinniswood, A. D., Furse, C.M., Gandhi, O.P. (1998). "Power Deposition in the Head and Neck of an Anatomically Based Human Body Model for Plane Wave Exposures." Phys. Med. Biol. 43: 2361.

Truong, T., Duncan, W., Tirtowidjojo, M. (1998). "A Reaction Class Approach for Modeling Gas Phase Reaction Rates." Faraday Transactions 1: 1061.

Weiss, J., P. Moulis, H. Ayliffe, T. Rosenberg and V. Cooley. (1998). "Finite Element Simulation of Stresses in Healing Cartilage Defects." ASME Winter Annual Meeting.

Weiss, J., Rabbitt, R., Bowden, A., Maker, B. (1998). "Incorporation of Medical Image in Data in Finite Element Models to Track Strain in Soft Tissues." SPIE 3254: 277.

Weiss, J. A. (1998). "Stresses in the Human Medial Collateral Ligament During Valgus Loading." 5th Japan-USA-Singapore-China Conference on Biomechanics.

1997 (29) Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A.

Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "Atmospheric Monitoring At the High Resolution Fly's Eye: Monitoring Data via the HiRes Laser/LIDAR System." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., Al-Seady, M., Belov, K., Bird, D., Boyer, J. Chen, G., Clay, R., Dai, H., Dawon, B., Ho, Y., Huang, A., Jui, C.C.H., Kidd, M., Kieda, D., Knapp, B., Lee, W. Loh, E, Mannel, E. Mathews, J., O'Halloran, T. Salman, A.Simpson, K., Smith, P., Sokolsky, P., Sommers, P., Taylor, S., Thomas, S., Wiencke, L., Wilkinson, C. (1997). "Atmospheric Monitoring at the High Resolution Fly's Eye: Atmospheric Scattering." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "Atmospheric Monitoring at the High Resolution Fly's Eye: Data from the HiRes2 Flasher Array." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "Calibration and Stability Measurements of a FADC Based Data Acquisition System for the HiRes Fly's Eye Experiement." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "The Capabilities of the High Resolution Fly's Eye Detector." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., Al-Seady, M., Belov, K., Bird, D., Boyer, J., Chen, G., Clay, R., Dai, H., Dawon, B., Ho, Y., Huang, A., Jui, C. C. H., Kidd, M., Kieda, Knapp, B., Lee, W., Loh, E., Mannel, E., Mathews, J., O'Halloran, T., Salman, A., Simpson, K., Smith, J., Sokolsky, P., Sommers, P., Taylor, S., Thomas, S., Wiencke, L., Wilkinson, C. (1997). "Cosmic Ray Composition Measured by HiRes in Coincidence with FE2." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L.

Wiencke and C. Wilkinson (1997). "The HiRes Detector: Absolute Calibration and Alignment." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "A Monte Carlo Study of Reconstruction of Monocular Events Having Limited Track Lengths for the High Resolution Fly's Eye." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "Multi-Component Observations of 1017 eV East with a Hybrid Fluorescence and Surface Detector." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke, C. Wilkinson (1997). "Physics with HiRes Stage 0.5 and Stage 2." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, G. Chen, H. Dai, P. Denholm, J. Gloyn, D. He, M. Huang, C. Jui, D. Kieda, S. Ko, K. Larsen, E. Loh, J. Matthews, J. Meyer, A. Salman, J. Smith, P. Sokolsky, P. Sommers, J. Tang, S. Taylor, S. Thomas, L. Wiencke, D. Bird, R. Clay, B. Dawson, K. Simpson, C. Wilkinson, J. Boyer, Y. Ho, W. Lee, E. Mannel, M. Kidd and T. O'Halloran. (1997). "Radio Controlled Light sources ofr Atmospheric Monitoring at HiRED. Nuclear Instruments and Methods." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. G. Chen, H. Dai, P. Denholm, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson (1997). "Radio Controlled Zenon Flashers for Atmospheric Monitoring at the HiRes Cosmic Ray Observatory." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "Status of the High Resolution Fly's Eye Detector: Operation and Installation." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "Stereo Reconstruction of Eas With the HiRes Detector." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "Testing the High Resolution Fly's Eye Using Laserscope." Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., M. Al-Seady, K. Belov, D. Bird, J. Boyer, G. Chen, R. Clay, H. Dai, B. Dawon, Y. Ho, A. Huang, C. C. H. Jui, M. Kidd, D. Kieda, B. Knapp, W. Lee, E. Loh, E. Mannel, J. Mathews, T. O'Halloran, A. Salman, K. Simpson, J. Smith, P. Sokolsky, P. Sommers, S. Taylor, S. Thomas, L. Wiencke and C. Wilkinson. (1997). "Trigger Sensitivity of the FADC Instrumented HiRes Fly's Eye." Presented at the 25th ICRC, Durban, South Africa.

Bowden, A. E., R. D. Rabbitt, J. A. Weiss and B. N. Maker. (1997). "Use of Medical Image Data to Compute Strain Fields in Biological Tissue." ASME BED 34: 191.

Burns, T. J., Davis, B. L., and Kick, E. L. (1997). "Position in the World-System and National Emissions of Greenhouse Gases." Journal of World-Systems Research 3: 432-466.

Dai, H. Y., Loh, E. C., Sokolsky, P. (1997). "The OWL Detector: Simulation and Reconstruction." Internal Report, University of Utah-UUHEP 97: 4.

Dai, Y., Loh, E. C., Sokolsky, P. (1997). "The OWL Detector: Neutrino Aperture, Detector Spacing and Track Reconstruction." Internal Report, University of Utah, UUHEP 97: 5.

Fain, H., Kick, E.L., Davis, B.L. and Burns, T.J. (1997). "World-System Position, Tropical Climate, National Development and Infant Mortality: A Cross-National Analysis of 86 Countries." Human Ecological Review 3(2): 197-202.

Gardiner, J. C., and J. A. Weiss. (1997). "Representation of Anisotropy in constitutive Models of Biological Soft Tissues." J. of Biomech. Eng. 120: 233.

Liu, F., Orendt, A. M., Alderman, D. W., Grant, D. M. (1997). "Carbon-13 Chemical Shift Tensors in Pentaerythritol." J American Chem Society 119(38): 8981 - 8984.

Orendt, A., Hu, J., Jiang, Y., Facelli, J.C., Wang, W, Pugmire, R. Ye, C., Grant, D. M. (1997). "Solid State 15N and 13C NMR Study of Several Metal 5,10,15,20-Tetraphyenylporphyrin Complexes, Journal of the American Chemical Society." J. Phys. Chem. A. 119: 7114.

Puso, M., Weiss, J. (1997). "Finite Element Implementation of Anisotropic Quasilinear Viscoelasticity Using a Discrete Spectrum Approximation." ASME J. of Biomechanical Engineering 33: 347.

Sellers, B. J., Davis, B. L., Larkin, P. W., Morris, S. E., and Saffle, J. R. (1997). "Early Prediction of Prolonged Ventilator Dependence in Thermally Injured Patients." Journal of Trauma 43(6): 899-903.

Strohmeier, M., Orendt, A. M., Facelli, J. C., solum, M. S., Pugmire, R. J., Parry, R. W., Grant, D. M. (1997). "Solid State 15N and 13C NMR Study of Several Metal 5, 10, 15, 20-Tetraphenylporphyrin Complexes." J American Chem Society 119(30): 7114 - 7120.

Truong, T. (1997). "Thermal Rates of Hydrogen Exchange of Methane with Ziolite: A Direct ab Initio Dynamics Study on the Importance of Quantum Tunneling Effects." J. Phys. Chem. B. 101.

Weiss, J. A., Gardiner, J.C., Quapp, M. (1997). "Material Models for the Study of Soft Tissue Mechanics." ASME BED 249.

1996 (8) Davis, B. L., and E.L. Kick (1996). "Human Capital Issues in the Use of Information Technology in

Education." Social Science Computer Review 14: 169-180. Dillon, R., L. Fauci, A. Fogelson, and D. Gaver (1996). "Modeling Biofilm Processes Using the Immersed

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Population Dynamics and Foreign Wood Trade on Deforestation: A World-System Perspective." Journal of Developing Societies 12(1): 68-87.

Kick, E. L., Davis, B. L., Burns, T. J., and Li, L. (1996). "World System and National Institutional Effects on Infant Mortality in Third World Countries." International Third World Studies Journal and Review 7: 61-67.

Orendt, A., Facelli, J. C., Radziszewski, J. G., Horton, W. J., Grant, D. M., Michl, J. (1996). "C dipolar NMR Spectrum of Matrix-Isolated 0-Benzyne-1, 2-13 C2." Am Chem Society 118: 846 - 852.

Weiss, J. A., B. N. Maker and S. Govindjee (1996). "Finite Element Implementation of Incompressible, Transversely Isotropic Hyperelasticity." Computer Methods In Applied Mechanics and Engineering 135: 107.

Weiss, J. A., D. A. Schauer and J. C. Gardiner (1996). "Modeling Contact in Biological Joints Using Penalty and Augmented Lagrangian Methods." Advances in Bioengineering ASME 34: 347.

1995 (3) Kick, E. L., Davis, B. L., and Burns, T. J. (1995). "International Multiple Networks in World-System

Approaches." International Conference on Social Networks 3: 237-248.

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Women and Men." International Third World Studies Journal and Review 5: 9-23. Davis, B. L. (1994). Economic and Human Development Assessment by Cross National Comparison:

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Elastic Structures." Pure Applied Math 46: 787-818. Saffle, J. R., Davis, B. L., Kagan, R., et. al. (1993). "Development of a Computerized Registry for the

Patient With Burns: Part I." Journal of Burn Care & Rehabilitation 14: 199-206. Saffle, J. R., Davis, B. L., Kagan, R., et. al. (1993). "Development of a Computerized Registry for the

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