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  • Laboratory of Computational Engineeringand

    Research Centre for Computational Science andEngineering

    Annual Report1.1.2002 - 31.12.2002

    Eeva LampinenEditor

    Internal Reports A5July 2003

    Laboratory of Computational EngineeringHelsinki University of Technology

    Tekniikantie 14P.O. Box 9203

    FIN-02015 HUTFINLAND

    ISSN 1455-0466ISBN 951-22-6523-0

    Picaset Oy

  • Contents

    1 Introduction 1

    2 Personnel 2

    3 List of Courses 5

    4 Theses 6

    5 Research Projects 75.1 Computational Information Technology . . . . . . . . . . . . . . . . . . . . 7

    5.1.1 Modelling and Data-Analysis . . . . . . . . . . . . . . . . . . . . . 75.1.2 Complex Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

    5.2 Computational Materials Research . . . . . . . . . . . . . . . . . . . . . . . 195.2.1 Atomic Level Modelling of Structure and Growth of Materials . . . . 195.2.2 Research in Biophysics, Soft Materials and Pattern Formation . . . . 275.2.3 Research on Semiconductor Quantum Structures and Physics of New

    Information Technologies . . . . . . . . . . . . . . . . . . . . . . . 315.2.4 Medical physics: Radiation Dosimetry at Cellular Level . . . . . . . 39

    5.3 Cognitive Science and Technology . . . . . . . . . . . . . . . . . . . . . . . 405.3.1 Psychophysical Research . . . . . . . . . . . . . . . . . . . . . . . . 405.3.2 Cognitive Neuroscience . . . . . . . . . . . . . . . . . . . . . . . . 41

    5.4 Intel computing cluster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

    6 Research Activities 436.1 Visits to the Laboratory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 436.2 Visits by Laboratory Personnel . . . . . . . . . . . . . . . . . . . . . . . . . 436.3 Participation in Conferences and Seminars . . . . . . . . . . . . . . . . . . . 446.4 Other Activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

    7 Publications 50

  • 1 Introduction

    In 2002 the Laboratory of Computational Engineering (LCE) & Research Centre for Com-putational Science and Engineering (CCSE) steadied its staff to about 70 members. Thisyear marks the third year of our Centre as the national Centre of Excellence with truely in-ternational team of researchers of 10 different nationalities. As an extension to the Centreof Excellence activities a joint affiliate centre between CCSE and Wolfson College of OxfordUniversity was set up in Oxford with the state of the art cluster-computing facilities and startedits activities with two full time researcher concentrating on Advanced Computational Scienceand Engineering.

    LCEs and CCSEs research is multidiciplinary in nature and has till recently been carriedout in three mutually supportive fields: Computational Information Technology, Computa-tional materials research, and Cognitive science and technology. In Computational informa-tion technology the areas of interest are Modelling and Data-Analysis, Machine Vision, Com-plex Systems, and Cognitive and Interactive Robot. In Computational materials research theareas of interest are Biophysics and Statistical Mechanics, Modelling of Structure and Growthof Materials, and Nanotechnology and Coherent Quantum Systems. In Cognitive science andtechnology the areas of interest are Psychophysical Research, Neurophysiological Research,Artificial Person, and Brain Computer Interface. In 2002 the fourth field of research wasadded to our repertoire, namely Computational Systems Biology which combines appropriateparts of Computational Information Technology research like Modelling and Data-Analysis,and Complex Systems, and of Computational Materials Research like Biophysics and Statis-tical Mechanics. This new addition marks also an educational extension to our curriculumsuch that we now offer three majors: Computational Engineering, Cognitive Technology andComputational Systems Biology. All of them are part of the new Bioinformation Technologystudy programme, which LCE has played a key role in developing and establishing.

    Year 2002 was in many ways extremely successful year for us: 1) The joint appointmentof Dr. Adrian Sutton, FRS and Professor of Materials Science at Oxford University to a pro-fessorship of Computational Engineering in LCE at Helsinki University of Technology, and2) The appointment of Dr. Christina Krause as a Professor of Cognitive Science at Universityof Helsinki. It should also be mentioned that in 2002 Sami Brandt, Markus Varsta and Ju-uso Tyli were granted Ph.D.s, and eight M.Sc. degrees were finished by research associatesworking in the laboratory. It is worth mentioning that Juuso Tyli became the youngest (28years) double doctor in Finland, with degrees in Economy and in Technology.

    Kimmo KaskiAcademy professor

    1

  • 2 Personnel

    All the laboratory personnel can be reached by e-mail with addressfirst_name.last_name@hut.fi. More complete contact information can be foundfrom the laboratory web page http://www.lce.hut.fi/.List of the personnel in the laboratory:

    ProfessorsKaski Kimmo Academy ProfessorLampinen Jouko ProfessorSams Mikko Academy ProfessorTiippana Kaisa Professor (1.8.-31.12.2002)Tulkki Jukka Professor

    Adjunct Professors (Docents/Visiting Professors)Alexandrov Yurii Prof. (Russian Academy on Sciences, Russia)Barrio Rafael Prof. (Universidad Nacional Autonoma de Mexico, Mexico)Kertsz Jans Prof. (Technical University of Budapest, Hungary)Landau David Prof. (University of Georgia, USA)Lehtokangas Mikko Docent(Tampere University of Technology)Mouritsen Ole Prof. (Technical University of Denmark, Denmark)Parkkinen Jussi Prof. (University of Joensuu)Rissanen Jorma Prof. (IBM Research Center, Almadena, USA)Rih Kari-Jouko Prof. (University of Tampere)Sutton Adrian Prof. (University of Oxford, UK)Tirri Henry Prof. (University of Helsinki)

    SecretariesJrvenp AinoLampinen Eeva

    Senior ResearchersChakraborti Anirban Ph.D.Fingelkurts Alexander Ph.D.Fingelkurts Andrey Ph.D.Frydrych Michael Ph.D.Heikkonen Jukka Academy Fellow, Dr.Tech.Jskelinen Iiro Ph.D.Karttunen Mikko Ph.D.Klucharev Vasily Ph.D.Krause Christina Ph.D.Kuronen Antti Academy Fellow, Ph.D.Patra Michael Marie Curie Fellow.Patriarca Marco Ph.D.Tiippana Kaisa Ph.D.Tuomainen Jyrki Ph.D.Tyli Juuso Ph.D.Varsta Markus Dr. TechVehtari Aki Dr. Tech.

    2

  • Researchersvon Alfthan Sebastian M.Sc.Andersen Tobias M.Sc.Auranen Toni M.Sc.Boxberg Fredrik M.Sc.Brandt Sami M.Sc.Dobsik Martin M.Sc.Huhtala Maria M.Sc.Huttunen Anu M.Sc.Junttila Virpi M.Sc.Juujrvi Jouni M.Sc.Kalliomki Ilkka M.Sc.Koskela Timo M.Sc.Kostiainen Timo M.Sc.Krylov Andrey M.Sc.Ktsyri Jari M.Sc.Lahtinen Jani M.Sc.Lehtonen Janne M.Sc.Leppnen Teemu M.Sc.Litkey Paula M.Sc.Mttnen Riikka M.Sc.Nikunen Petri M.Sc.Nummenmaa Aapo M.Sc.Nurminen Laura M.Sc.Nykopp, Tommi M.Sc.Ojanen Ville M.Sc.Oksanen Jani M.Sc.Onnela Jukka-Pekka M.Sc.Riederer Klaus M.Sc.Rodriquez Mirta M.Sc.Selonen Arto M.Sc.Sysi-Aho Marko M.Sc.Szelestey Peter M.Sc.Srkk Simo M.Sc.Tamminen Toni M.Sc.Terechonkov Roman M.Sc.Zhao Wei M.Sc.

    Researchers in Oxford UniversitySchenk Veit Ph.D.Mustonen Ville M.Sc.

    Research StudentsHyttinen JuhaHyrynen TeppoJuvonen JuhaKettunen JuhoLaitinen Laura

    3

  • Merilinen VeeraMiettinen MarkusMogami KotaMkinen JariMkinen Ville-PetteriOjanen JannePalo PerttiRitaluoto PasiRuokola TomiSaari JukkaSalminen Mikko

    TraineesKaapro AatuKannala JuhoKorhonen ReettaLamminen AnttiLi JingyuanNieminen TapioParviainen MikkoRiihimki JaakkoViinikainen Mikko

    4

  • 3 List of Courses

    Courses in the Laboratory of Computational Engineering S-114.100 Computational Science (3 cr) S-114.200 Special Course on Computational Engineering (4 cr) P S-114.202 Special Course on Computational Engineering II (2-5 cr) P

    Topic: On-line and sequential learning S-114.204 Modelling of Perception (3 cr) P S-114.210 Individual Project in Computational Engineering (2 cr) S-114.215 Special Project in Computational Engineering (2-5 cr) S-114.220 Research Seminar on Computational Science (2-4 cr) P S-114.230 Individual Studies on Computational Engineering (1-6 cr) P S-114.240 Seminar on Computational Engineering (2 cr)

    Topic: Mathematical modeling and methods in natural sciences & engineering S-114.245 Laboratory Seminar on Computational Engineering (2 cr) P S-114.250 Special Course in Computational Science (4 cr) S-114.300 Topical Lectures on Information Theory and Modeling (2 cr) P S-114-310 Basic Course on Modeling and Information Theory (2 cr) S-114.325 Physics III (S) (2 cr) S-114.326 Physics IV (S) (3 cr) S-114.401 Semiconductor Quantum Structures (4 cr) S-114.425 Physics III (Sf) (4 cr) S-114.426 Physics IV (Sf) (4 cr) S-114.500 Basic Course for Biosystems on the Cell (3 cr) S-114.520 Introduction to Bioinformatics (2 cr) S-114.600 Introduction to Bayesian Modelling (2 cr) S-114.710 Perception and Production of Speech (4 cr) Research Seminar on Communication and Cogntion:- The Philosophy of Mind (2 cr)- Audiovisual Speech Perception (2 cr) S-114.740 Special course on Communication and Cognition (2 credits)

    Topic: Biological Human-Machine Interfaces S-114.750 Individual studies in Communication and Cognition (1 - 6 credits) S-114.780 Perception and action (4 cr) S-114.790 Communication and cognition (4 credits)

    For more information see publication: Study Programme, Helsinki University of Technology,or the www-page http://www.lce.hut.fi/teaching/.

    5

  • 4 Theses

    Doctor of Technology Sami Brandt Theorems and Algorithms for Multiple view Geometry with Applications to

    Electron Tomography Juuso Tyli Essays on Asset Return Distributions Markus Varsta Self-Organizing Maps in Sequence Processing

    M.Sc. - Diplomas Sebastian von Alfthan, Computational Study of Amorphous Silicon and Silica Toni Auranen, Nonparamet

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