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IMA Tutorial

Network Dynamics and Cell Physiology

April 17-18, 2008
Organizers:
Daniel Forger Mathematics, University of Michigan
John J. Tyson Biology, Virginia Polytechnic Institute & State University

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Description:

Complex networks of interacting proteins control the physiological properties of a cell (metabolism, reproduction, motility, signaling, etc.). Intuitive reasoning about these networks is often sufficient to guide the next experiment, and a cartoon drawing of a network can be useful in codifying the results of hundreds of observations. But what tools are available for understanding the rich dynamical repertoire of such control systems? Why does a control system behave the way it does? What other behaviors are possible? How do these behaviors depend on the genetic and biochemical parameters of the system (gene dosage, enzymatic rate constants, equilibrium binding constants, etc)? Using basic principles of biochemical kinetics, network diagrams can be converted into sets of ordinary differential equations and their properties explored by analytical and computational methods. We will describe the basic ideas and tools required for this type of modeling and illustrate the approach with a variety of examples taken from modern research in cell biology (growth, division, death, signaling, rhythms, and disease).

Schedule
Thursday | Friday | 
  Thursday, April 17
8:15a-8:50a Registration and Coffee   EE/CS 3-176
8:50a-9:00a Welcome to the IMA Douglas N. Arnold (University of Minnesota) EE/CS 3-180
9:00a-10:00a Lecture 1: Cell physiology, molecular biology and mathematical modeling John J. Tyson (Virginia Polytechnic Institute and State University) EE/CS 3-180
10:00a-10:30a Coffee   EE/CS 3-176
10:30a-11:30a Lecture 2: Network motifs: sniffers, buzzers, toggles and blinkers John J. Tyson (Virginia Polytechnic Institute and State University) EE/CS 3-180
11:30a-1:30p Lunch    
1:15p-2:30p Computer Lab 1: Phase planes, vector fields, nullclines, bifurcations Daniel Forger (University of Michigan), John J. Tyson (Virginia Polytechnic Institute and State University) Lind Hall 409
2:30p-3:00p Coffee   EE/CS 3-176
3:00p-4:00p Lecture 3: Cell cycle regulation John J. Tyson (Virginia Polytechnic Institute and State University) EE/CS 3-180
4:00p-5:00p Computer Lab 2: Modeling exercises Daniel Forger (University of Michigan), John J. Tyson (Virginia Polytechnic Institute and State University) Lind Hall 409
  Friday, April 18
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:00a Lecture 4: Stochastic modeling of molecular regulatory networks Daniel Forger (University of Michigan) EE/CS 3-180
10:00a-10:30a Break   EE/CS 3-176
10:30a-11:30a Lecture 5: Models of circadian rhythms Daniel Forger (University of Michigan) EE/CS 3-180
11:30a-12:30p Lunch    
1:15p-2:30p Computer Lab 3: Stochastic Simulation Daniel Forger (University of Michigan), John J. Tyson (Virginia Polytechnic Institute and State University) Lind Hall 409
2:30p-3:00p Break   EE/CS 3-176
3:00p-4:00p Lecture 6: Synchronization and phase resetting Daniel Forger (University of Michigan) EE/CS 3-180

LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
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
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
Yermal Sujeet Bhat Institute for Mathematics and its Applications University of Minnesota
Sudin Bhattacharya Computational Biology Department The Hamner Institutes for Health Sciences
Khalid Boushaba Department of Mathematics Iowa State University
Don Button Marine Science/Biochemistry University of Alaska
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
Ludovica Cecilia Cotta-Ramusino Institute for Mathematics and its Applications University of Minnesota
Kequan Ding   Chinese Academy of Sciences
Peng Feng Department of Mathematics Florida Gulf Coast University
Christodoulos A. Floudas Department of Chemical Engineering Princeton University
Daniel Forger Department of Mathematics University of Michigan
Jason E. Gower Institute for Mathematics and its Applications University of Minnesota
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
Tiefeng Jiang Department of Statistics University of Minnesota
Fumiaki Katagiri Plant Biology University of Minnesota
Varunyu Khamviwith   University of Minnesota
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
Anton Leykin Institute for Mathematics and its Applications University of Minnesota
James Lu Department of Inverse Problems Johann Radon Institute for Computational and Applied Mathematics
Roger Y. Lui Department of Mathematical Sciences Worcester Polytechnic Institute
Laura Lurati Institute for Mathematics and its Applications University of Minnesota
Suping Lyu Materials and Biosciences Center Medtronic
Ezio Marchi Department of Mathematics Instituto de Matemática Aplicada
Ezra Miller School of Mathematics University of Minnesota
Alejandro Morales Valencia Department of Computational Sciences University of Guadalajara
Jeff Morgan Department of Mathematics University of Houston
Theoden Netoff Department of Biomedical Engineering University of Minnesota
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
Bobby Philip Computer and Computational Sciences Division Los Alamos National Laboratory
Mary Porter Department of Genetics, Cell Biology, and Development University of Minnesota
Eric J. Rawdon Department of Mathematics University of St. Thomas
Beatrice M. Riviere Department of Mathematics University of Pittsburgh
Leonid Rubchinsky Department of Mathematical Sciences Indiana University-Purdue University
Deena Schmidt Institute for Mathematics and its Applications University of Minnesota
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
Ali Shojaie Department of Statistics University of Michigan
Andrew Stein Institute for Mathematics and its Applications University of Minnesota
Vladimir Sverak School of Mathematics University of Minnesota
Erkan Tüzel Institute for Mathematics and its Applications University of Minnesota
John J. Tyson Department of Biology Virginia Polytechnic Institute and State University
Haiyan Wang Department of Mathematical Sciences and Applied Computing Arizona State University
Zhian Wang Institute for Mathematics and its Applications University of Minnesota
Chris Warren BME University of Minnesota
Zhijun Wu Department of Mathematics Iowa State University
Richard Yamada Department of Mathematics University of Michigan
Yuncheng You Department of Mathematics University of South Florida
Hongchao Zhang Institute for Mathematics and its Applications University of Minnesota