AMATH 531: Mathematical Theory of Cellular Dynamics

SLN 10246, MWF, 10:30-11:20, MEB 235


Instructor:

Professor Hong Qian
Lewis 319
tel: 543-2584
fax: 685-1440
hqian@u.washington.edu
office hours: Wed. 1-2


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

Course Notes, Part 1

Course Notes, Part 2

Course Notes, Part 3

Course Notes, Part 4

Course Notes, Part 5

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,

Qian: Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems,

Qian: Cooperativity in cellular biochemical processes

Anderson: More is different

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

Laughline et al: The middle way

Qian 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

Week 1: There is no homework/report.

Week 2: Homework #1, Due Fri. Oct. 14

Week 3: Homework #2, Due Fri. Oct. 21

Week 4: Homework #3, Due Fri. Oct. 28

Week 5: Homework #4, Due Fri. Nov. 4

Week 7: Homework #5, Due Mon. Nov. 21


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