Date Assigned 
Type 
Assignment 
Date Due 
8/25 
Reading 
 Read NCM Chapter 1 (skip 1.5), from course packet. See
NCMChap1guide.txt. Bring questions about Matlab to class.
 Read for discussion:
Statistical Fluctuations in Autocatalytic Reactions
M. Delbruck
Journal of Chemical Physics 1940 Volume 8 pp 120124 (search for volume 8, page 120)
Or try this link.
 Start Ecoli world contest in matlab  see matlab file ecoliworld2b.m. Simulations due 9/1 but please bring questions about writing your matlab code to class on 8/27.
The challenge is to write an improved "rule" for survival. The contest is to see who lives the longest, on average, over 50 trials.
 For those without a prior course in probability, please begin reading
Stochastic Modeling for Systems Biology (SMSB) Chapter 3. We'll go over basic probability in detail in the third
week.

8/27 
8/27 
Reading 
 Stochastic Modelling for Systems Biology Chapter 1
(Introduction) & Chapter 2 (Petri net formalism).
 Review article: Modeling and Simulating Chemical Reactions,
Desmond J. Higham, SIAM Review 2008 (Society for Industrial and Applied
Mathematics Vol. 50, No. 2, pp. 347Ð368)
 As an example of a signal transduction system, please read:
Spiro PA, Parkinson JS, Othmer HG. A model of excitation and adaptation
in bacterial chemotaxis. Proc Natl Acad Sci U S A. 1997 Jul
8;94(14):72638.

9/3 
9/3 
Reading 
 Spiro et al (above)
 Higham review article (above)
 Keep working on Wilkinson chapter 3.

9/8 
9/3 
Exercises 
Problem set 1 
9/10 due in class 
9/89/15 
Reading 
Finish Wilkinson Chapter 3 (probability review) 
9/89/15 
9/11 
Exercises 
Problem set 2 
9/17 due in class 
9/15 
Reading 
 Background, not required reading: Neher E, Sakmann B.
Singlechannel currents recorded from membrane of denervated frog muscle fibres.
Nature. 1976 Apr 29;260(5554):799802. Unfortunately, this is not available except by paying heavy roylaties to Nature Magazine.
 SingleChannel Recording, Chapter 9.19.3 (course packet)

9/17 
9/17 
First Project Proposal 
Project proposal (one page) due. As a guide to what I expect for the projects, here is a rubric I will use for grading the projects.

9/24 
9/17 
Reading 
 Moler, Numerical Computing with Matlab Chapter 1.7, Floating Point Arithmetic (course packet).
 Moler, Numerical Computing with Matlab Chapter 9, Random Numbers (course packet).

9/22 
9/17 
Reading 
 Wilkinson, Chapter 4, Stochastic Simulation. Read sections 4.14.7 on numerical generation
of pseudorandom samples from different distributions. Also read section 4.8 (optional) if you would like
an introduction to the R programming language.

9/24 
9/25 
Exercises 
Problem set 3 
FRIDAY 10/3 
9/2910/8 
Readings on Markov Chains and Time Series Analysis 
 Wilkinson Chapter 5 "Markov Processes" (required)
 Colquhoun & Hawkes (Stochastic Interpretation of IonChannel Mechanisms, course packet) sections 410 (required)
 Taylor & Karlin, An Introduction to Stochastic Modeling, Chapters IIIIV (optional: supplementary material on Markov Chains).
 Chatfield, The analysis of time series: an introduction, Chapters 3 & 6 (spectral analysis of stochastic time series) (required)
 Chatfield, The analysis of time series: an introduction, Chapters 7 & 8 (more on spectral analysis of stochastic time series) (optional)
 Austin et al, Nature 2006 Vol 439 No 2, Gene network shaping of inherent noise spectra. (for discussion)
 Pedraza et al, Science 2005 Vol 307, Noise Propagation in Gene Networks. (for discussion)


10/6 
Exercises 
Problem set 4 
10/20 
10/8 
Reading 
Wilkinson Chapter 6 "Chemical and Biochemical Kinetics"
Review Higham article 
10/13 
10/27 
Readings on Diffusion & Brownian Motion 
 Berg, Random Walks in Biology, Chapters 15. This is a treatment of random walks and diffusion
from a biologist's point of view.
 Taylor & Karlin Chapter VIII (Brownian Motion)  on reserve at KSL. This is an introductory treatment of diffusion processes
from a mathematical point of view. Read after finishing the chapters in Berg's book.

11/3 
11/2 
Readings on diffusion models 
 Berg & Purcell, Biophysical Journal 1977, Physics of Chemoreception
 Gerstein & Mandelbrot, Biophysical Journal 1964, RANDOM WALK MODELS FOR THE
SPIKE ACTIVITY OF A SINGLE NEURON

optional for 11/24 

Reading 
 Terman & Ermentrout draft chapter


11/19 
Exercises 
Problem set 5 
12/3 
11/19 
Reading 
 Wilkinson Chapter 7, "Case Studies"
 Finish/review Higham review article.
 optional: further case studies in C. Fall et al, Computational Cell Biology Chapters 1213. See in particular 13.1 on the bacterial flagellar motor.

11/24 
11/19 
Reading 
Wilkinson Chapter 8, "Beyond the Gillespie Algorithm" 
11/26 
11/19 
Reading 
 Vellela & Qian (2007). A Quasistationary Analysis of a Stochastic Chemical Reaction:
Keizer's Paradox, Bull Math Biol. 2007 Jul;69(5):172746. Epub 2007 Feb 23
 Kurtz, T.G. (1972). The relationship between stochastic and deterministic models for chemical
reactions. J. Chem. Phys. 57, 2976–2978.

12/1 
Assigned 


Due 