UWA 3rd YEAR BIOPHYSICS COURSES

MODULE A: Quantum Foundations of Biophysics

 
• MATTER AND ENERGY - The Four Forces: Nuclear strong and weak, gravity, and electromagnetism (fields in electrostatics); Matter and Energy: electromagnetic radiation, Planck's constant, speed of light, wave/particle duality, atomic emission & atomic absorption spectra

   

• THE ELECTRONIC STRUCTURE OF ATOMS - The Bohr model, its problems and the Heisenberg Uncertainty Principle, Quantum behaviour of electrons and the wave nature of matter, The Hydrogen atom according to wave mechanics: the Zeeman effect and electronic energy states in multi-electron atoms - the Pauli exclusion principle, Hydrogen bonds and the van der Waals force, The Schroedinger Wave Equation

MODULE B: Protein Physics

 
• INTRODUCTION TO PROTEIN STRUCTURE AND FUNCTION - Biological systems and biomolecules, nucleic acids and proteins, protein structure, fibrous proteins, globular proteins, X-ray diffraction from protein crystals, electron density maps, protein function.

   

• PHYSICAL METHODS FOR DETERMINING SIZE, SHAPE AND MOLAR MASS OF MACROMOLECULES - Monodisperse and polydisperse systems, ultracentrifugation, sedimentation velocity, sedimentation equilibrium, density gradient sedimentation, viscometric measurements, electrophoresis, isoelectric focussing, dynamic light scattering.

   

• STEREOCHEMISTRY OF PROTEINS Linear polymers, random walk model of linear polymers, elasticity of polymers, proteins as polymers, the peptide bond, steric hindrance, side chian properties, van der Waals interactions, Lennard-Jones (6-12 ) potential, electrostatic interactions, hydrogen bonds.

   

• PROTEIN THERMODYNAMICS (HOW DO PROTEINS FOLD?) - Free energy and entropic forces, solvent interactions and solvent entropy, polypeptide chains in water, the folding process, folding pathways, simulations and predictions, experimental studies on folding, rapid laser heating of proteins.

   

• PROTEIN DYNAMICS (HOW DO PROTEINS FUNCTION?) - Excitement and relaxation of protein structure, equilibrium fluctuations, kinetics of proteins, proteins as complex systems, multiple conformational states of native proteins, protein function, functionally important motions.

MODULE C: Biophysical Dynamics

 
• THERMODYNAMICS OF THE LIVING STATE - Coupled processes in living systems; Equilibrium thermodynamics; Laws of thermodynamics; Thermodynamic potentials; Conditions for equilibrium; Non-equilibrium stationary states; Information theory and biology.

   

• MOLECULAR SELF-ORGANISATION - Physical chemistry of bioploymers; Kinetics of self-assembly; Membrane dynamics; Phase transitions

   

• MECHANOCHEMICAL PROCESSES - Muscle structure; Sliding filament theory; Muscle mechanics

MODULE D: Electromagnetism and its Biological Applications

 
• ELECTROMAGNETISM - Electrostatics, Coulomb's Law, Gauss' Law, Ampere's Law, Calculus of Vector Fields, Maxwell's Equations, Magnetic Fields & Magnetism in Matter, Magnetic Materials and their Properties, Electrochemical nature of the Central Nervous System (CNS) - origin of the EEG, Electrical disorders of the CNS: The nature of epilepsy, EEG, MEG

   

• RADIOACTIVITY - Fundamental aspects, Beneficial aspects (diagnostics: x-ray, CT scanning, radioactive dyes), Harmful aspects (exposure to radioactive sources, damage to cells and structures)

MODULE E: Investigative Techniques and Instrumentation

 
• Electrophysiology

   

• Ultrasound

   

• Lasers and Photodynamic Interactions

   

• Moessbauer and EPR Spectroscopy

MODULE F: Computational Biophysics

Course Information

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

Motto

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

What is Computational Biophysics?

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.

Course Objectives:

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

Assignments

1. Introduction to Mathematica — provides some of the background necessary for the following sessions:
   • Notebooks
   • Instructions
   • Basic Navigation
   • Numerical Calculations
   • Algebraic Calculations
   • Plots
2. Stochastic Processes — presents applications of random number generators (rngs) in computer simulation of stochastic processes:
   • Random number generation in Mathematica
   • One dimensional random walk
   • Fitting data in the presence of noise
   • Modelling fern growth
   • Two dimensional random walk
3. Molecular Conformation — introduces numerical methods for conformational modelling, and for solving minimisation problems:
   • Preliminaries
   • Coulomb potential
   • Lennard-Jones potential
   • Ethane rotational conformation
4. 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
5. 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
6. 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

Solutions

You can submit your solutions as follows:

1. Make sure you name and number your assignment. For example, Joanna Bloggs could name her first assignment JB.1.nb (the .nb which stands for Mathematica Notebook, is automatic and hidden under Windows but is visible on Macintosh systems).
2. Go to the appropriate subfolder of the Solutions Folder (e.g., to submit JB.1.nb, Joanna would go into Folder 1). Under the File menu you will find the Upload File... 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).

If you have any problems, please contact paul@physics.uwa.edu.au.

MODULE G: Methods in Experimental Biophysics

 
• This module follows the 3rd year Physics module "Methods in Experimental Physics"

Experimental Research Projects

Students intending to major in Biophysics must undertake three separate experimental projects, one from within the Physics Department and two allocated from amongst the various participating bio-science departments.

Each project involves approximately 50 hours of lab work over a maximum of six weeks, followed by a detailed report. Some projects may also include background reading and a review essay.