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IMA Annual Program Year Workshop

Design Principles in Biological Systems

April 21-25, 2008
Organizers:
Bud Mishra Computer Science, Mathematics, Cell Biology, New York University
Partha Mitra Cold Spring Harbor Laboratory

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Abstracts and Talk Materials Dining Guide
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Workshop Background and Goals:

Evolution and Engineering Principles: Evolution is a process of retaining accidentally found solutions to problems that living organisms have to solve in order to survive. Even though the solutions or designs are found accidentally through the process of evolution, the premise of the workshop is that they may be studied in their current form by understanding engineering solutions to the problems being solved. Therefore, a primary goal of this workshop is pedagogy in existing engineering disciplines in relation to biological function.

In addition to studying current engineering theories, it is also important to study the origin of design principles in the evolutionary process, a subject that is currently in its infancy. This connection will be explored in one or more workshop sessions. Also central to the premise of the workshop is the notion of convergent evolution, the extent of which will also be examined.

Physico-chemical and Engineering theories: There are two classes of theoretical explanations in biology:
    (a) Physico-chemical mechanisms ("analysis")
    (b) Engineering theories, or function-solution pairs ("synthesis")
In the past, theoretical biology has largely focused on (a). While (b) has also been studied in a relatively ad hoc manner, it has not been approached from a disciplinary perspective.

A new generation of theoretical biology is currently taking shape with more formal emphasis on design or engineering principles. As part of this workshop we hope to help refine the taxonomy of such principles and emphasize the roots in existing engineering disciplines.

Same principles across scales: While the initial development in this field has largely been in the area of cellular biochemical networks, our premise is that the same design principle may apply to disparate scales and systems. In particular, it is of interest to examine the theoretical parallels between cellular level systems (e.g. biochemical networks in bacteria), and organism level systems (e.g. neural systems) or systems comprising multiple organisms. Therefore, speakers at the workshop will be drawn from investigators working at these different scales of organization.

Schedule
Monday | Tuesday | Wednesday | Thursday | Friday
  Monday, April 21
8:45am-9:30am Registration and coffee   EE/CS 3-176
9:30am-9:40am Welcome to the IMA Douglas N. Arnold (University of Minnesota) EE/CS 3-180
9:40am-10:00am Introduction to the workshop Bud Mishra (New York University), Partha P. Mitra (Cold Spring Harbor Laboratory) EE/CS 3-180
10:00am-10:50am Tutorial on feedback control theory Richard M. Murray (California Institute of Technology) EE/CS 3-180
10:50am-11:20am Coffee   EE/CS 3-176
11:20am-12:00pm Architecture: Human engineered systems Richard M. Murray (California Institute of Technology) EE/CS 3-180
12:00pm-2:00pm Lunch    
2:00pm-2:40pm Architecture: Bacteria John C. Doyle (California Institute of Technology) EE/CS 3-180
2:50pm-3:30pm Architecture: Brains Partha P. Mitra (Cold Spring Harbor Laboratory) EE/CS 3-180
3:30pm-3:50pm Coffee   EE/CS 3-176
3:50pm-4:20pm Response tuning through specific feedback architectures Hana El-Samad (University of California, San Francisco) EE/CS 3-180
4:30pm-5:00pm Circuitry, psychophysics, and electrophysiology of touch in the rat vibrissa system David Kleinfeld (University of California, San Diego) EE/CS 3-180
5:00pm-6:30pm Reception and Poster Session
Lind Hall 400
Quantitative systems analysis of multicellular morphodynamics Anand R. Asthagiri (California Institute of Technology)
A design principle in biochemical reaction networks based on realization theory Bassam Bamieh (University of California, Santa Barbara)
A transcriptional regulatory switch underlying B-cell terminal differentiation and its disruption by dioxin Sudin Bhattacharya (The Hamner Institutes for Health Sciences)
Recurrent and robust patterns underlying human relative preference, and associations with brain circuitry plus genetics Hans C. Breiter MD (Massachusetts General Hospital)
Architecture and inherent robustness of a bacterial cell cycle control system David L. Dill (Stanford University)
Computational hemodynamics analysis in large blood vessels: Effects of hematocrit variation on flow stability Oluwole Daniel Makinde (University of Limpopo)
The advantage of two step transport problem Ezio Marchi (Instituto de Matemática Aplicada)
Biological project: The construction of the cycle in Lotka-Volterra of n-species Ezio Marchi (Instituto de Matemática Aplicada)
Trajectory measures describing the locomotor behavior of Drosophila melanogaster in a circular arena Dan Valente (Cold Spring Harbor Laboratory)
Evolution of song culture in the zebra finch Haibin Wang (Cold Spring Harbor Laboratory)
  Tuesday, April 22
9:00am-9:30am Coffee   EE/CS 3-176
9:30am-10:10am Generic approach to construction of system design space Michael A. Savageau (University of California, Davis) EE/CS 3-180
10:20am-11:00am Transient stochastic analysis of gene networks Mustafa H. Khammash (University of California, Santa Barbara) EE/CS 3-180
11:00am-11:20am Coffee   EE/CS 3-176
11:20am-12:00pm Modeling epigenetic silencing Anirvan Sengupta (Rutgers University) EE/CS 3-180
12:00pm-2:00pm Lunch    
2:00pm-2:40pm Understanding and using bacterial sensory systems Antonis Papachristodoulou (University of Oxford) EE/CS 3-180
2:50pm-3:30pm Monotone input/output systems as a technique for modular analysis of biomolecular network dynamics Eduardo D. Sontag (Rutgers University) EE/CS 3-180
3:30pm-4:00pm Coffee   EE/CS 3-176
4:00pm-4:30pm Second chances   EE/CS 3-180
4:45pm-5:00pm Workshop photo    
  Wednesday, April 23
9:00am-9:30am Coffee   EE/CS 3-176
9:30am-10:10am Design principles in the evolution of animal communication W. Tecumseh Fitch (University of St. Andrews) EE/CS 3-180
10:20am-11:00am Reverse engineering the lordosis behavior neuronal circuit Donald W. Pfaff (Rockefeller University) EE/CS 3-180
11:00am-2:00pm Lunch    
2:00pm-2:40pm Philosophy of biology: Function/design: I Robert Cummins (University of Illinois at Urbana-Champaign) EE/CS 3-180
2:50pm-3:30pm Pluralism about function Peter H. Schwartz (Indiana University Center for Bioethics and Indiana University School of Medicine) EE/CS 3-180
3:30pm-4:00pm Coffee   EE/CS 3-176
4:00pm-4:30pm Second chances   EE/CS 3-180
6:30pm-8:30pm Workshop Dinner   Caspian Bistro
2418 University Ave SE
Minneapolis, MN 55414
612-623-1133 
  Thursday, April 24
9:00am-9:30am Coffee   EE/CS 3-176
9:30am-10:10am Engineering theory of neuronal shape Dmitri Chklovskii (Cold Spring Harbor Laboratory) EE/CS 3-180
10:20am-11:00am Cellular information processing in the face of promiscuity and sloppiness Christopher R. Myers (Cornell University) EE/CS 3-180
11:00am-11:20am Coffee   EE/CS 3-176
11:20am-12:00pm Design principles in synthetic biology Chris J. Myers (University of Utah) EE/CS 3-180
12:00pm-2:00pm Lunch    
2:00pm-2:40pm Fundamental limitations on noise reduction in the cell Glenn Vinnicombe (University of Cambridge) EE/CS 3-180
2:50pm-3:30pm Putting a round worm in a square hole Craig P. Hunter (Harvard University) EE/CS 3-180
3:30pm-4:00pm Coffee   EE/CS 3-176
4:00pm-4:40pm Spontaneous participants' presentations David L. Dill (Stanford University), Jeffery G. Saven (University of Pennsylvania), Eduardo D. Sontag (Rutgers University), Jin Wang (SUNY) EE/CS 3-180
4:40pm-5:10pm Second chances   EE/CS 3-180
  Friday, April 25
9:00am-9:30am Coffee   EE/CS 3-176
9:30am-10:10am Predicting quantitative diversification of multicellular phenotype Anand R. Asthagiri (California Institute of Technology) EE/CS 3-180
10:20am-11:00am Evo-devo and the syntactic and semantic 'design features' of human language Robert C. Berwick (Massachusetts Institute of Technology) EE/CS 3-180
11:00am-11:20am Coffee   EE/CS 3-176
11:20am-12:00pm Wrap-up discussion Partha P. Mitra (Cold Spring Harbor Laboratory) EE/CS 3-180

LIST OF CONFIRMED PARTICIPANTS

NameDepartmentAffiliation
Pranav AgarwalDepartment of Electrical Engineering University of Minnesota
Tanuj AggarwalDepartment of Electrical Engineering University of Minnesota
Claudio AltafiniDepartment of Functional Analysis and Applications International School for Advanced Studies (SISSA/ISAS)
Douglas N. ArnoldSchool of Mathematics University of Minnesota
Anand R. AsthagiriChemistry and Chemical Engineering Department California Institute of Technology
Bassam BamiehDepartment of Mechanical Engineering University of California, Santa Barbara
Sankar BasuDepartment of Engineering National Science Foundation
Daniel J. BatesInstitute for Mathematics and its Applications University of Minnesota
Banu BaydilDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Robert C. BerwickDepartment of Electrical Engineering and Computer Science Massachusetts Institute of Technology
Prateek BhansaliDepartment of Electrical and Computer Engineering University of Minnesota
Yermal Sujeet BhatInstitute for Mathematics and its Applications University of Minnesota
Sudin BhattacharyaComputational Biology Department The Hamner Institutes for Health Sciences
Victor BloomfieldDepartment of Biochemistry University of Minnesota
Khalid BoushabaDepartment of Mathematics Iowa State University
Hans C. BreiterDepartments of Radiology and Psychiatry Massachusetts General Hospital
Maria-Carme T. CaldererSchool of Mathematics University of Minnesota
Hannah CallenderInstitute for Mathematics and its Applications University of Minnesota
John R. CannonMathematics Department University of Central Florida
James A. Carlson Clay Mathematics Institute
Dmitri Chklovskii Cold Spring Harbor Laboratory
Yung-Sze ChoiDepartment of Mathematics University of Connecticut
Sean P CorumDepartment of Physics University of Minnesota
Ludovica Cecilia Cotta-RamusinoInstitute for Mathematics and its Applications University of Minnesota
Robert CumminsDepartment of Philosophy University of Illinois at Urbana-Champaign
Debopriya DasLife Sciences Division Lawrence Berkeley National Laboratory
Tim DenisonDepartment of Neuromodulation Medtronic
David L. DillDepartment of Computer Science Stanford University
Kequan DingScience100 Labs Chinese Academy of Sciences
John C. DoyleDepartment of Control and Dynamical Systems California Institute of Technology
Geir DullerudDepartment of Mechanical Science and Engineering University of Illinois at Urbana-Champaign
Hana El-SamadDepartment of Biochemistry and Biophysics University of California, San Francisco
Gurkan ErdoganMechanical Engineering Department University of Minnesota
Haitao FanDepartment of Mathematics Georgetown University
W. Tecumseh FitchSchool of Psychology University of St. Andrews
Christodoulos A. FloudasDepartment of Chemical Engineering Princeton University
Daniel ForgerDepartment of Mathematics University of Michigan
Melissa K. GardnerBiomedical Engineering Department University of Minnesota
Tryphon T. GeorgiouDepartment of Electrical Engineering University of Minnesota
Jason E. GowerInstitute for Mathematics and its Applications University of Minnesota
Chenjie GuDepartment of Electrical and Computer Engineering University of Minnesota
Robert GuyDepartment of Mathematics University of California, Davis
Esfandiar HaghverdiSchool of Informatics Indiana University
Milena HeringInstitute for Mathematics and its Applications University of Minnesota
Franziska Babette HinkelmannDepartment of Mathematics Virginia Polytechnic Institute and State University
Peter HinowInstitute for Mathematics and its Applications University of Minnesota
Craig P. HunterDepartment of Molecular and Cellular Biology Harvard University
Richard D. JamesDepartment of Aerospace Engineering and Mechanics University of Minnesota
Imre M. JánosiDepartment of Physics of Complex Systems Eötvös Loránd University (ELTE)
Tiefeng JiangDepartment of Statistics University of Minnesota
Mihailo JovanovicDepartment of Electrical and Computer Engineering University of Minnesota
Mustafa H. KhammashDepartment of Mechanical Engineering University of California, Santa Barbara
Varunyu Khamviwith University of Minnesota
David KleinfeldDepartment of Physics University of California, San Diego
Debra KnisleyDepartment of Mathematics East Tennessee State University
Peter R. KramerDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Juan C. LatorreDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Reinhard LaubenbacherVirginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Anton LeykinInstitute for Mathematics and its Applications University of Minnesota
Patrick D LincolnComputer Science Laboratory SRI International
Roger LuiDepartment of Mathematical Sciences Worcester Polytechnic Institute
Laura LuratiInstitute for Mathematics and its Applications University of Minnesota
Oluwole Daniel MakindeDepartment of Applied Mathematics University of Limpopo
Yi MaoDepartment of Mathematics Michigan State University
Ezio MarchiDepartment of Mathematics Instituto de Matemática Aplicada
Curt McNamara Logic Product Development
George MichailidisDepartment of Statistics University of Michigan
Ezra MillerSchool of Mathematics University of Minnesota
Partha P. Mitra Cold Spring Harbor Laboratory
Alejandro Morales ValenciaDepartment of Computational Sciences University of Guadalajara
Richard M. MurrayDepartment of Mechanical Engineering California Institute of Technology
Chris J. MyersElectrical and Computer Engineering Department University of Utah
Christopher R. MyersCornell Theory Center Cornell University
Timothy NewmanDepartment of Physics Arizona State University
Duane NykampSchool of Mathematics University of Minnesota
David J. OddeDepartment of Biomedical Engineering University of Minnesota
Isamu OnishiDepartment of Mathematical and Life Sciences Hiroshima University
Hans G. OthmerDepartment of Mathematics University of Minnesota
Antonis PapachristodoulouDepartment of Engineering Science University of Oxford
Donald W. Pfaff Rockefeller University
Bobby PhilipComputer and Computational Sciences Division Los Alamos National Laboratory
Eric J. RawdonDepartment of Mathematics University of St. Thomas
Jenny SantosoDepartment of Mathematics IBM Deutschland GmbH
Vishal SaraswatSchool of Mathematics University of Minnesota
Michael A. SavageauDepartment of Biomedical Engineering, and Microbiology Graduate Group University of California, Davis
Jeffery G. SavenDepartment of Chemistry University of Pennsylvania
Deena SchmidtInstitute for Mathematics and its Applications University of Minnesota
Peter H. Schwartz Indiana University Center for Bioethics and Indiana University School of Medicine
Hullas SehcalDepartment of Electrical Engineering University of Minnesota
Anirvan SenguptaDepartment of Physics and Astronomy Rutgers University
Gaukhar ShaikhovaDepartment of Mathematics and Information Technology  The L.N.Gumilyov Eurasian National University
Chehrzad ShakibanInstitute of Mathematics and its Application University of Minnesota
Lei ShiDepartment of Chemistry University of Minnesota
Eduardo D. SontagDepartment of Mathematics Rutgers University
Andrew M. SteinInstitute for Mathematics and its Applications University of Minnesota
De Witt L. SumnersDepartment of Mathematics Florida State University
Vladimir SverakSchool of Mathematics University of Minnesota
Erkan TüzelInstitute for Mathematics and its Applications University of Minnesota
Dan Valente Cold Spring Harbor Laboratory
Glenn VinnicombeDepartment of Engineering University of Cambridge
Haibin Wang Cold Spring Harbor Laboratory
Haiyan WangDepartment of Mathematical Sciences and Applied Computing Arizona State University
Jin WangDepartment of Chemistry, Physics and Applied Mathematics SUNY
Zhian WangInstitute for Mathematics and its Applications University of Minnesota
Kelly WeiDepartment of Neuromodulation Medtronic
Hans WeinbergerSchool of Mathematics University of Minnesota
Zhijun WuDepartment of Mathematics Iowa State University
Richard YamadaDepartment of Mathematics University of Michigan
Joung-Hahn Yoon Seoul National University
Hongchao ZhangInstitute for Mathematics and its Applications University of Minnesota