AMATH 531: Mathematical Theory of Cellular Dynamics

SLN 21794, TTh, 12:30-1:50, Parrington Hall 112


Instructor:

Professor Hong Qian
Lewis 319
tel: 543-2584
fax: 685-1440
hqian@u.washington.edu
office hours: Wed. 11-12


Course Description

Develops a coherent mathematical theory for processes inside living cells. Focuses on analyzing dynamics leading to functions of cellular components (gene regulation, signaling biochemistry, metabolic networks, cytoskeletal biomechanics, and epigenetic inheritance) using deterministic and stochastic models. Prerequisite: AMATH 402, AMATH 403; course in probability.

Syllabus

Must Read Materials

McQuarrie (1967) and Gillespie (2007) on Stochastic theory and simulations of chemcial kinetics

Reading Materials

Qian: Cellular biology in terms of stochastic nonlinear biochemical dynamics, Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems, Cooperativity in cellular biochemical processes

Anderson: More is different

Hopfield: Physics, computation, and why biology looks so different?

Laughline et al: The middle way

Ao et al: A theory of mesoscopic phenomena

Qian & Bishop: The chemical master equation approach to nonequilibrium steady-state of open biochemical systems

Wilkinson: Stochastic modelling for quantitative description of heterogeneous biological systems

Delbrück: Statistical fluctuations in autocatalytic reactions

Higham: Modeling and simulating chemical reactions

Qian: Cooperativity and specificity in enzyme kinetics: A single-molecule time-based perspective

Fox: Gaussian stochastic processes in physics

Kwon et al: Structure of stochastic dynamics near fixed points

Homework Problems and Reading Reports

Your weekly homework is either an assigned problem set or to write a single-space two-page report for a paper chosen from this list. Reports containing no equations are highly discouraged.

Week 1: There is no homework/report.

Week 2: Homework #1, Due Th. Oct. 9

Week 3: Homework #2, Due Th. Oct. 16

Week 4: Homework #3, Due Tu. Oct. 23


<qian@amath.washington.edu> Mon Sep 24 16:15:50 PDT 2012