Biophysical Modeling of Cells and Populations

G23.1131 (cross-listed as G63.2852/G85.2081)

Spring 2009


Course Information

This course develops the biophysical approach to modeling biological systems, applied to classic problems of molecular biology, as well as to systems of recent interest. The course is organized in a bottom-up way, beginning with models of cooperativity in binding, of promoter recognition and activation, proceeding through models of simple and complex networks, and working towards a population-level description of various systems. Diverse biological examples will be presented to illustrate key concepts in biophysical modeling.

Instructor: Edo Kussell

Teaching Assistants: TBA

Lectures: M,W 11:00am - 12:15pm in 194 Mercer, Room 307


Syllabus

Basic elements Jan 21 Introduction and some estimates
Jan 26 A statistical mechanics primer
Jan 28 Cooperativity of binding
Feb 2, 4 Transcriptional regulation
Classic systems Feb 9 DNA Looping
Feb 11 Modeling the lac operon
Feb 16 NO CLASS (President's Day)
Feb 18, 23 Modeling the phage λ switch
Feb 25, 2 Modeling bacterial chemotaxis
Mar 4 Diffusion
Mar 9 Sensing and measurement
Mar 11 Precision in Drosophila development
Mar 16, 18 NO CLASS (Spring break)
Mar 23 Kinetic proofreading
Noise and networks Mar 25 Introduction to networks
Mar 30 Flux-balance analysis of metabolic networks
Apr 1 Oscillations
Apr 6 Modeling the circadian clock of cyanobacteria
Apr 8 Analysis of noise
Apr 13 Noise in genetic networks
Populations Apr 15, 20 Stochastic population models
Apr 22 Growth of structured populations
Apr 27, 29 Optimality in population diversity
May 4 Individuals, strategies, and the replicator dynamic


Grading 40% Problem Sets (~ 5)
Due: Mar 9 20% Midterm Paper (10-15 pages)
Due: May 8 40% Final Project (presentation + paper)

Recitation Weekly - covers mathematical background for the lectures.
Schedule of topics will be provided.

Books

Phillips, R., Kondev, J., Theriot, J., Physical Biology of the Cell, Garland Science, 2008.

Berg, Howard, C., Random Walks in Biology, Princeton University Press, 1993.

Ptashne, M., A Genetic Switch: Phage Lambda Revisited, 3rd edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2004.

Muller-Hill, B., The lac Operon: A Short History of a Genetic Paradigm, Walter de Gruyter & Co., Berlin, 1996.

Papers

Will be available on Blackboard.