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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
8:45a-9:30a Registration and coffee   EE/CS 3-176
9:30a-9:40a Welcome to the IMA Douglas N. Arnold (University of Minnesota) EE/CS 3-180
9:40a-10:00a Introduction to the workshop Bud Mishra (New York University), Partha P. Mitra (Cold Spring Harbor Laboratory) EE/CS 3-180
10:00a-10:50a Tutorial on feedback control theory Richard M. Murray (California Institute of Technology) EE/CS 3-180
10:50a-11:20a Coffee   EE/CS 3-176
11:20a-12:00p Architecture: Human engineered systems Richard M. Murray (California Institute of Technology) EE/CS 3-180
12:00p-2:00p Lunch    
2:00p-2:40p Architecture: Bacteria John C. Doyle (California Institute of Technology) EE/CS 3-180
2:50p-3:30p Architecture: Brains Partha P. Mitra (Cold Spring Harbor Laboratory) EE/CS 3-180
3:30p-3:50p Coffee   EE/CS 3-176
3:50p-4:20p Response tuning through specific feedback architectures Hana El-Samad (University of California) EE/CS 3-180
4:30p-5:00p Circuitry, psychophysics, and electrophysiology of touch in the rat vibrissa system David Kleinfeld (University of California, San Diego) EE/CS 3-180
5:00p-6:30p 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)
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
9:00a-9:30a Coffee   EE/CS 3-176
9:30a-10:10a Generic approach to construction of system design space Michael A. Savageau (University of California) EE/CS 3-180
10:20a-11:00a Transient stochastic analysis of gene networks Mustafa H. Khammash (University of California) EE/CS 3-180
11:00a-11:20a Coffee   EE/CS 3-176
11:20a-12:00p Modeling epigenetic silencing Anirvan Sengupta (Rutgers University) EE/CS 3-180
12:00p-2:00p Lunch    
2:00p-2:40p Understanding and using bacterial sensory systems Antonis Papachristodoulou (University of Oxford) EE/CS 3-180
2:50p-3:30p Monotone input/output systems as a technique for modular analysis of biomolecular network dynamics Eduardo D. Sontag (Rutgers University) EE/CS 3-180
3:30p-4:00p Coffee   EE/CS 3-176
4:00p-4:30p Second chances   EE/CS 3-180
4:45p-5:00p Workshop photo    
  Wednesday, April 23
9:00a-9:30a Coffee   EE/CS 3-176
9:30a-10:10a Design principles in the evolution of animal communication W. Tecumseh Fitch (University of St. Andrews) EE/CS 3-180
10:20a-11:00a Reverse engineering the lordosis behavior neuronal circuit Donald W. Pfaff (Rockefeller University) EE/CS 3-180
11:00a-2:00p Lunch    
2:00p-2:40p Philosophy of biology: Function/design: I Robert Cummins (University of Illinois at Urbana-Champaign) EE/CS 3-180
2:50p-3:30p Pluralism about function Peter H. Schwartz (Indiana University Center for Bioethics and Indiana University School of Medicine) EE/CS 3-180
3:30p-4:00p Coffee   EE/CS 3-176
4:00p-4:30p Second chances   EE/CS 3-180
6:30p-8:30p Workshop Dinner   Caspian Bistro
2418 University Ave SE
Minneapolis, MN 55414
612-623-1133 
  Thursday, April 24
9:00a-9:30a Coffee   EE/CS 3-176
9:30a-10:10a Engineering theory of neuronal shape Dmitri Chklovskii (Cold Spring Harbor Laboratory) EE/CS 3-180
10:20a-11:00a Cellular information processing in the face of promiscuity and sloppiness Christopher R. Myers (Cornell University) EE/CS 3-180
11:00a-11:20a Coffee   EE/CS 3-176
11:20a-12:00p Design principles in synthetic biology Chris J. Myers (University of Utah) EE/CS 3-180
12:00p-2:00p Lunch    
2:00p-2:40p Fundamental limitations on noise reduction in the cell Glenn Vinnicombe (University of Cambridge) EE/CS 3-180
2:50p-3:30p Putting a round worm in a square hole Craig P. Hunter (Harvard University) EE/CS 3-180
3:30p-4:00p Coffee   EE/CS 3-176
4:00p-4:40p 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
4:40p-5:10p Second chances   EE/CS 3-180
  Friday, April 25
9:00a-9:30a Coffee   EE/CS 3-176
9:30a-10:10a Predicting quantitative diversification of multicellular phenotype Anand R. Asthagiri (California Institute of Technology) EE/CS 3-180
10:20a-11:00a Evo-devo and the syntactic and semantic 'design features' of human language Robert C. Berwick (Massachusetts Institute of Technology) EE/CS 3-180
11:00a-11:20a Coffee   EE/CS 3-176
11:20a-12:00p Wrap-up discussion Partha P. Mitra (Cold Spring Harbor Laboratory) EE/CS 3-180

LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Pranav Agarwal Electrical Engeneering University of Minnesota
Tanuj Aggarwal Electrical Engeneering University of Minnesota
Claudio Altafini Department of Functional Analysis and Applications International School for Advanced Studies (SISSA/ISAS)
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
Anand R. Asthagiri Chemistry and Chemical Engineering Department California Institute of Technology
Bassam Bamieh Department of Mechanical Engineering University of California
Sankar Basu Department of Engineering National Science Foundation
Daniel J. Bates Institute for Mathematics and its Applications University of Minnesota
John Baxter Institute for Mathematics and its Applications University of Minnesota
Banu Baydil Department of Mathematical Sciences Rensselaer Polytechnic Institute
Robert C. Berwick Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology
Prateek Bhansali Department of Electrical and Computer Engineering University of Minnesota
Yermal Sujeet Bhat Institute for Mathematics and its Applications University of Minnesota
Sudin Bhattacharya Computational Biology Department The Hamner Institutes for Health Sciences
Victor Bloomfield Department of Biochemistry University of Minnesota
Khalid Boushaba Department of Mathematics Iowa State University
Hans C. Breiter MD Departments of Radiology and Psychiatry Massachusetts General Hospital
Maria-Carme T. Calderer School of Mathematics University of Minnesota
Hannah Callender Institute for Mathematics and its Applications University of Minnesota
John R. Cannon Mathematics Department University of Central Florida
James A. Carlson   Clay Mathematics Institute
Dmitri Chklovskii   Cold Spring Harbor Laboratory
Yung-Sze Choi Department of Mathematics University of Connecticut
Sean P Corum Department of Physics University of Minnesota
Ludovica Cecilia Cotta-Ramusino Institute for Mathematics and its Applications University of Minnesota
Robert Cummins Department of Philosophy University of Illinois at Urbana-Champaign
Debopriya Das Life Sciences Division Lawrence Berkeley Laboratory
Tim Denison Department of Neuromodulation Medtronic
David L. Dill Department of Computer Science Stanford University
Kequan Ding   Chinese Academy of Sciences
Marko Djordjevic Mathematical Biosciences Institute Ohio State University
John C. Doyle Control and Dynamical Systems California Institute of Technology
Geir Dullerud Department of Mechanical Science and Engineering University of Illinois at Urbana-Champaign
Hana El-Samad Department of Biochemistry and Biophysics University of California
Gurkan Erdogan Mechanical Engineering University of Minnesota
Haitao Fan Department of Mathematics Georgetown University
W. Tecumseh Fitch School of Psychology University of St. Andrews
Christodoulos A. Floudas Department of Chemical Engineering Princeton University
Daniel Forger Department of Mathematics University of Michigan
Melissa Gardner Biomedical Engineering Department University of Minnesota
Tryphon T. Georgiou Department of Electrical Engineering University of Minnesota
Jason E. Gower Institute for Mathematics and its Applications University of Minnesota
Chenjie Gu Department of Electrical and Computer Engineering University of Minnesota
Robert Guy Department of Mathematics University of California
Esfandiar Haghverdi School of Informatics Indiana University
Milena Hering Institute for Mathematics and its Applications University of Minnesota
Franziska Babette Hinkelmann Department of Mathematics Virginia Polytechnic Institute and State University
Peter Hinow Institute for Mathematics and its Applications University of Minnesota
Craig P. Hunter Department of Molecular and Cellular Biology Harvard University
Richard D. James Department of Aerospace Engineering and Mechanics University of Minnesota
Imre M. Jánosi Department of Physics of Complex Systems Eötvös Loránd University (ELTE)
Tiefeng Jiang Department of Statistics University of Minnesota
Mihailo Jovanovic Department of Electrical and Computer Engineering University of Minnesota
Mustafa H. Khammash Department of Mechanical Engineering University of California
Varunyu Khamviwith   University of Minnesota
David Kleinfeld Department of Physics University of California, San Diego
Debra Knisley Department of Mathematics East Tennessee State University
Peter R. Kramer Department of Mathematical Sciences Rensselaer Polytechnic Institute
Juan Latorre Department of Mathematical Sciences Rensselaer Polytechnic Institute
Reinhard Laubenbacher Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Anton Leykin Institute for Mathematics and its Applications University of Minnesota
Patrick D Lincoln Computer Science Laboratory SRI International
Roger Y. Lui Department of Mathematical Sciences Worcester Polytechnic Institute
Laura Lurati Institute for Mathematics and its Applications University of Minnesota
Oluwole Daniel Makinde Department of Applied Mathematics University of Limpopo
Yi Mao Department of Mathematics Michigan State University
Ezio Marchi Department of Mathematics Instituto de Matemática Aplicada
Curt McNamara   Logic Product Development
George Michailidis Department of Statistics University of Michigan
Ezra Miller School of Mathematics University of Minnesota
Partha P. Mitra   Cold Spring Harbor Laboratory
Alejandro Morales Valencia Department of Computational Sciences University of Guadalajara
Richard M. Murray Department of Control and Dynamical Systems California Institute of Technology
Chris J. Myers Electrical and Computer Engineering Department University of Utah
Christopher R. Myers Cornell Theory Center Cornell University
Timothy Newman Department of Physics Arizona State University
Duane Nykamp School of Mathematics University of Minnesota
David Odde Department of Biomedical Engineering University of Minnesota
Isamu Ohnishi Department of Mathematical and Life Sciences Hiroshima University
Hans G. Othmer Department of Mathematics University of Minnesota
Antonis Papachristodoulou Department of Engineering Science University of Oxford
Donald W. Pfaff   Rockefeller University
Bobby Philip Computer and Computational Sciences Division Los Alamos National Laboratory
Eric J. Rawdon Department of Mathematics University of St. Thomas
Jenny Santoso Department of Mathematics IBM Deutschland GmbH
Vishal Saraswat School of Mathematics University of Minnesota
Michael A. Savageau Department of Biomedical Engineering, and Microbiology Graduate Group University of California
Jeffery G. Saven Department of Chemistry University of Pennsylvania
Deena Schmidt Institute for Mathematics and its Applications University of Minnesota
Peter H. Schwartz   Indiana University Center for Bioethics and Indiana University School of Medicine
Hullas Sehcal Electrical Engeneering University of Minnesota
Anirvan Sengupta Department of Physics and Astronomy Rutgers University
Gaukhar Shaikhova Department of Mathematics and Information Technology The L.N.Gumilyov Eurasian National University
Chehrzad Shakiban Institute of Mathematics and its Application University of Minnesota
Lei Shi Department of Chemistry University of Minnesota
Eduardo D. Sontag Department of Mathematics Rutgers University
Andrew Stein Institute for Mathematics and its Applications University of Minnesota
De Witt L. Sumners Department of Mathematics Florida State University
Vladimir Sverak School of Mathematics University of Minnesota
Erkan Tüzel Institute for Mathematics and its Applications University of Minnesota
Dan Valente   Cold Spring Harbor Laboratory
Glenn Vinnicombe Department of Engineering University of Cambridge
Haibin Wang   Cold Spring Harbor Laboratory
Haiyan Wang Department of Mathematical Sciences and Applied Computing Arizona State University
Jin Wang Department of Chemistry, Physics and Applied Mathematics SUNY
Zhian Wang Institute for Mathematics and its Applications University of Minnesota
Kelly Wei Department of Neuromodulation Medtronic
Hans Weinberger School of Mathematics University of Minnesota
Zhijun Wu Department of Mathematics Iowa State University
Richard Yamada Department of Mathematics University of Michigan
Joung-Hahn Yoon   Seoul National University
Hongchao Zhang Institute for Mathematics and its Applications University of Minnesota