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Abstracts and Talk Materials
Network Dynamics and Cell Physiology
April 17-18, 2008


Daniel Forger - University of Michigan
http://www.math.lsa.umich.edu/people/facultyDetail.php?uniqname=forger
John Tyson - Virginia Polytechnic Institute and State University
http://mpf.biol.vt.edu/people/tyson/tyson.html

Computer Lab 1: Phase planes, vector fields, nullclines, bifurcations
April 17, 2008 1:15 pm - 2:30 pm

How to use WinPP and XPP. Models of bistability and oscillations. Drawing phase plane portraits. How portraits depend on parameter values. One-parameter bifurcation diagrams.

 

Computer Lab 2: Modeling exercises
April 17, 2008 4:00 pm - 5:00 pm

Building simple models of cell cycle, circadian rhythm, programmed cell death, glycolysis, Ca2+ oscillations, etc.

 

Computer Lab 3: Stochastic Simulation
April 18, 2008 1:15 pm - 2:30 pm

Simulations of simple models of genetic networks using the Gillespie Method. Comparison of behavior for small and large number of chemical events.

Daniel Forger - University of Michigan
http://www.math.lsa.umich.edu/people/facultyDetail.php?uniqname=forger

Lecture 4: Stochastic modeling of molecular regulatory networks
April 18, 2008 9:00 am - 9:00 am

Relation between stochastic and deterministic formalisms. Two discrete simulation methods proposed by Gillespie. 1/N relationship. Noise induced oscillations. Chemical Langevin equations and hybrid methods. Introduction to simulation packages.

 

Lecture 5: Models of circadian rhythms
April 18, 2008 10:30 am - 11:30 am

Basic properties of circadian clocks. Goodwin and early models. More realistic models. Model predictions and their experimental validation. Temperature Compensation. Unanswered questions.

 

Lecture 6: Synchronization and phase resetting
April 18, 2008 3:00 pm - 4:00 pm

Phase Response Curves, Phase Transition Curves and Winfree’s Type 0 vs. Type 1 distinction. Global vs. local coupling. Pulse vs. sustained coupling. Coupling induced rhythmicity. Relationship between phase resetting and coupling.

John Tyson - Virginia Polytechnic Institute and State University
http://mpf.biol.vt.edu/people/tyson/tyson.html

Lecture 1: Cell physiology, molecular biology and mathematical modeling
April 17, 2008 9:00 am - 10:00 am

An introduction to cell growth and division, programmed cell death, cell differentiation, motility, and signaling. Basic molecular mechanisms governing these processes. Modeling molecular mechanisms with ordinary differential equations.

 

Lecture 2: Network motifs: sniffers, buzzers, toggles and blinkers
April 17, 2008 10:30 am - 11:30 am

Simple models of regulatory motifs. Positive and negative feedback. Signal-response curves and bifurcation diagrams. Adaptation. Ultrasensitivity. Bistability and oscillations. Simple bifurcations: saddle-node and Hopf. Homoclinic bifurcations.

 

Lecture 3: Cell cycle regulation
April 17, 2008 3:00 pm - 4:00 pm

Physiological characteristics of the cell division cycle. Molecular biology of cyclin-dependent kinases. Simple model of bistability and oscillations in the CDK control system of frog eggs. More complex models of yeast cell cycles. Mammalian cell cycle and cancer.

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