AMATH 531: Mathematical Theory of Cellular Dynamics
SLN 21794, TTh, 12:301:50, Parrington Hall 112
Instructor:

Professor Hong Qian
Lewis 319
tel: 5432584
fax: 6851440
hqian@u.washington.edu
office hours: Wed. 1112

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.
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 steadystate 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 singlemolecule timebased 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 singlespace twopage 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
Week 6: Homework #4, Due Th. Nov. 6