Friday September 27: Math problem set 1: Enzyme kinetics
            Solutions to Math problem set 1

Friday September 27: Mechanics problem set 1

Thursday October 5: Math problem set 2: Phase planes and bifurcation diagrams
            Solutions to Math problem set 2

Tuesday October 10: Diffusion and energy states problem set

Tuesday October 24: Math problem set 3: PDEs and Spatial Pattern Formation
            Solutions to Math problem set 3

Guidelines and general tips for presentations on Saturday, September 30

Possible Java mini-projects, Wednesday October 18

Tuesday September 26: Fusing theoretical and experimental approaches

Pollard TD
The cytoskeleton, cellular motility and the reductionist agenda.
Nature. 2003 Apr 17;422(6933):741-5

Cohen JE
Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better.
PLoS Biol. 2004 Dec;2(12):e439.

Lazebnik Y.
Can a biologist fix a radio? -- Or, what I learned while studying apoptosis,
Cancer Cell. 2002 Sep;2(3):179-82

Thursday September 28: The microscopic world

Purcell EM
Life at low Reynolds number
American Journal of Physics. 1977; 45(1):3-11

Monday October 2: Diffusion and Brownian motion

Einstein A.
On the motion of small particles suspended in liquids at rest required by the molecular-kinetic theory of heat
Annalen der Physik. 1905; 17:549-560.

Thursday October 5: Segment polarity network

von Dassow G, Meir E, Munro EM, Odell GM.
The segment polarity network is a robust developmental module.
Nature. 2000 Jul 13;406(6792):188-92.

Monday October 9: No Journal Club!

Thursday October 12: Actomyosin-based delivery of Cdc42

Wedlich-Soldner R, Altschuler S, Wu L, Li R.
Spontaneous cell polarization through actomyosin-based delivery of the Cdc42 GTPase.
Science. 2003 Feb 21;299(5610):1231-5. Epub 2003 Jan 30.

Monday October 16: Howard/Howard-related paper to be decided

Thursday October 19: Turing patterns in biological systems
12754941

Meinhardt H
Complex pattern formation by a self-destabilization of established patterns: chemotactic orientation and phyllotaxis as examples.
C R Biol. 2003 Feb;326(2):223-37.

The following text books have been reserved from the UW library and will be available to students during the course. If you have your own copies, you may (but are not required to) bring them with you.

J.D. Murray (2002) Mathematical biology
QH323.5 M88 2002 v.1 and v.2

Leah Edelstein-Keshet (2005) Mathematical models in biology
QH323.5 E34 2005

Phillip Charles Nelson (2004) Biological physics: energy, information, life
QH505 N37 2004

Howard Berg (1993) Random walks in biology
QH323.5 B45 1993

Steven H Strogatz (1994) Nonlinear dynamics and chaos
Q172.5.C45 S767 1994

Daniel Kaplan and Leon Glass (1995) Understanding nonlinear dynamics
QA845.K36 1995b

Paul R Wellen (2005) An Introduction to programming with Mathematica
QA76.73.M29 W45 2005

Press et al (1997) Numerical recipes in C (free online version)
QA297.N8655 1997

Alberts et al (2002) Molecular biology of the cell (free online version)
QH581.2 .M64 2002

Voet and Voet (2006) Fundamentals of Biochemistry: Life at the molecular level
QU4 V876f 2006

The following are some research papers that explore topics in mathematical modelling or present experimental results that would be suitable for exploring using mathematical techniques.

Barkai N, Leibler S.
Robustness in simple biochemical networks.
Nature. 1997 Jun 26;387(6636):913-7.

Chance B.
The kinetics of the enzyme-substrate compound of peroxidase. 1943.
J. Biol. Chem. 1943 151: 553-577.

Cytrynbaum EN, Sommi P, Brust-Mascher I, Scholey JM, Mogilner A
Early spindle assembly in Drosophila embryos: role of a force balance involving cytoskeletal dynamics and nuclear mechanics.
Mol Biol Cell. 2005 Oct;16(10):4967-81. Epub 2005 Aug 3.

von Dassow G, Meir E, Munro EM, Odell GM.
The segment polarity network is a robust developmental module.
Nature. 2000 Jul 13;406(6792):188-92.

Yuh CH, Bolouri H, Davidson EH.
Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene.
Science. 1998 Mar 20;279(5358):1896-902.

Elowitz MB, Levine AJ, Siggia ED, Swain PS.
Stochastic gene expression in a single cell.
Science. 2002 Aug 16;297(5584):1183-6.

Elowitz MB, Leibler S
A synthetic oscillatory network of transcriptional regulators.
Nature. 2000 Jan 20;403(6767):335-8.

Goldbeter A, Koshland DE Jr
An amplified sensitivity arising from covalent modification in biological systems.
Proc Natl Acad Sci U S A. 1981 Nov;78(11):6840-4.

Hartwell LH, Hopfield JJ, Leibler S, Murray AW.
From molecular to modular cell biology.
Nature. 1999 Dec 2;402(6761 Suppl):C47-52.

Hodgkin AL.
Ionic movements and electrical activity in giant nerve fibres.
Proc R Soc Lond B Biol Sci. 1958 Jan 1;148(930):1-37.

Hodgkin AL, Huxley AF.
A quantitative description of membrane current and its application to conduction and excitation in nerve.
J Physiol. 1952 Aug;117(4):500-44.

Howard J
Elastic and damping forces generated by confined arrays of dynamic microtubules.
Phys Biol. 2006 Feb 28;3(1):54-66.

Kim KJ, Rieke F
Slow Na+ inactivation and variance adaptation in salamander retinal ganglion cells.
J Neurosci. 2003 Feb 15;23(4):1506-16.

Lipkow K, Andrews SS, Bray D.
Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli.
J Bacteriol. 2005 Jan;187(1):45-53.

Novak B, Csikasz-Nagy A, Gyorffy B, Chen K, Tyson JJ.
Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions.
Biophys Chem. 1998 May 5;72(1-2):185-200.

Lazebnik Y.
Can a biologist fix a radio? -- Or, what I learned while studying apoptosis,
Cancer Cell. 2002 Sep;2(3):179-82

Rieke F, Baylor DA.
Single-photon detection by rod cells of the retina.
Reviews of Modern Physics 70 (3): 1027-1036 JUL 1998

Wedlich-Soldner R, Altschuler S, Wu L, Li R.
Spontaneous cell polarization through actomyosin-based delivery of the Cdc42 GTPase.
Science. 2003 Feb 21;299(5610):1231-5. Epub 2003 Jan 30.

Below are some general online resources to help you with this course. Please keep in mind that these resources may not cover all topics covered in the course and may approach topics from a different angle.

Thinking in Java (good free/online book on Java programming)

KickJava, online Javadoc to the standard library, with examples

Java examples (shows how to use various library components)

Java library for science

Java tips (tips on how to do important/common things)

Mathematica Resources

Tips on using Mathematica

A glossary of useful mathematical terms & functions, written by and for Mathematica

Tips on mathematica and some useful GUI tools