The course is a "hands-on" laboratory style course consisting of 6 x 2 hour lab sessions worth a total of 100%.

*The purpose of computing is insight, not numbers* — Richard Hamming

The broad categories of computational biophysics are Simulation, Visualisation and Modelling. At a finer scale, it embraces a wide range of areas including numerical methods, algorithms and data analysis. Simulation and modelling are usually taught by stressing numerical techniques — this course focuses on using symbolic or computer algebra.

- to use computers as an aid to understanding real physical systems;
- learn about methods for the analysis of these systems.

*Mathematica*Basics — provides some of the background necessary for the following sessions:- Course Overview
- References
- Book-keeping
- Getting Help
- Basic Calculations

- Stochastic
Processes — presents applications of random number generators (rngs)
in computer simulation of stochastic processes:
- Random number generation
- One dimensional random walk
- Fitting data in the presence of noise
- Modelling fern growth
- Two dimensional random walk

- Molecular
Conformation — introduces numerical methods for conformational
modelling, and for solving minimisation problems:
- Preliminaries
- Coulomb potential
- Lennard-Jones potential
- Ethane rotational conformation

- Population
Dynamics — appies numerical methods for discrete (iterative) models
and for solving ordinary differential equations (ODEs) to models from
population dynamics:
- Discrete logistic equation for a single species
- Continuous logistic equation for a single species
- Kermack-MacKendrick disease model

- Fourier
Transform — introduces Fourier methods which have application in
convolution or deconvolution of data, correlation and autocorrelation,
filtering, and power spectrum estimation:
- Definition of DFT
- One-dimensional DFT
- Two-dimensional DFT
- Applications

- Action
Potential — models voltage-dependent membrane currents in the squid
giant axon using the Hodgkin-Huxley formalism:
- RC Circuit
- Passive Transmission Line
- Hodgkin-Huxley Model

You can submit your solutions as follows:

- Name your assignment. For example, Joanna Bloggs should name each
assignment
(the`JB.nb`which stands for`.nb`*Mathematica*Notebook, is automatic and hidden under Windows but is visible on Macintosh systems). - Go to the appropriate subfolder of the Solutions
Folder. E.g., for the
*Mathematica*Basics assignment go to theFolder. Under the Netscape File menu you will find the`Basics`command. Use this to submit your solution. Note that this folder is a "drop folder", i.e., its contents are not visible (so that other students cannot copy your solution).`Upload File...`

If you have any problems, please contact rourkt01@student.uwa.edu.au.

Information on 2nd Year Biophysics Courses

Information on the Biophysics Honours Course

To contact us directly, send e-mail to Ralph James (ralph@physics.uwa.edu.au) or Tim St.Pierre (stpierre@physics.uwa.edu.au)