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

Phone: (212) 998-7663
Office: 1009 Silver Center
Email: elk2@nyu.edu
Office hours: Mondays, 3pm - 4pm in Brown Building, Room 856

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.