UWA 2nd YEAR BIOPHYSICS COURSES


 
Units available in 2006
 
 
Units (6 pts each)
BIOPHYSICAL FOUNDATIONS & PROCESSES BIOP2201
Semester 1
BIOMEASUREMENT BIOP2202
Semester 2
BIOMINERALISATION BIOP2203
 
Semester 1

On-line reference text mirrored here by courtesy of Kenneth R. Koehler

BIOPHYSICAL FOUNDATIONS & PROCESSES BIOP2201 (6 pts)


Topic 1A: BIOMOLECULAR ENSEMBLES (13 lectures)

Basic Fluid Dynamics

Viscosity, continuity, Poiseuilles equation, (Newtonian fluids: parabolic velocity profile) Bernouilli's equation, Navier-Stokes equations, Reynold's number (laminar & turbulent flow)
Examples of turbulence

Application of Poiseuilles equation to the study of bifurcation in an artery

Hemodynamics

Pressure wave transmission through an elastic vessel, models of blood flow: non-viscous (Moens-Korteweg model) & viscous (hydrodynamic model), calculation of impedance

Cardiovascular system

Homeostasis (principle of negative feedback control), measurement techniques, pressure, flow (doppler ultrasound, doppler laser)

Classical equilibrium thermodynamics

Statistical basis, entropy, disorder & information, enthalpy, Gibbs free energy, Hess's law, fluctuations

Linear nonequilibrium thermodynamics

Linear irreversible theory for systems close to equilibrium, Onsager's principle, Prigogine's principle, connection between fluctuations & dissipation

Diffusion

Diffusion potential, Fick's laws, active and passive transport

Nonlinear irreversible thermodynamics for systems far from equilibrium

Nonlinear rate equations, bifurcations & instability, Rayleigh-Benard convection, chemical clocks, unstable systems, circadian rhythms

Structure of biological membranes

Dynamics of membrane lipids, molecular dynamics, measurement techniques, surface organisation of lipid bilayers, membrane surface charge & ion binding10 Membrane proteins, structure & stability, a-helices, b-sheet, 3D examples, energetics, interaction with ions

Membrane excitability

Nernst equation, Goldman-Hodgkin-Katz equation, electroosmosis, facilitated diffusion

Membrane receptors and ion channels

Allosteric models, Hill equation, single ion channel kinetics, mechanosensitive ion channels

Topic 1B: BIOSYSTEMS (13 lectures)


Bioquest 2000

Description of a system

System variables,units, dimensions & dimensionless parameters, conserved quantities, equation of state, continuity, scaling considerations

Atomic & molecular interaction dynamics

Ternary & quaternary structure, rhodopsin dynamics, protein folding

Macromolecular system

Sheet dynamics: membranes & proteins, helical structure: chirality & transfer channels, polypeptides & polymers

Cellular system

Energy & entropy, transport, steady-state & transient behaviour, longterm change, infection (phages vs symbiotes)

Multicellular systems

Corporate behaviour in bacterial cultures, 2D growth patterns; random walks & fractals, 3D structure, avian egg & incubation processes, slime mould mechanics, interneuronal action & brain hard-wiring

Population structure & dynamics

Intra-relationships: social & nurturing requirements, external factors: environment, food, disease, predator-prey dynamics, ethology; multi-generational development: epidemics & plagues, evolution & extinction of species, human civilisation....; ecosystems: nutrients, producers, comsumers, decomposers eutrophication

Topic 1C: BIOPHYSICAL DYNAMICS (13 lectures)


BIOMEASUREMENT BIOP2202 (6 pts)


Topic 2A: SENSING (13 lectures)

Basics of nerve action

Review of electrostatics, RC networks and axon membranes, myelination, action potential

Neural processes

synaptic mechanisms, neural transmission & interactive networks, sensory transduction

Geometric optics

lenses & focal length, reflection, refraction, interference & diffraction, aberrations, focussing (accommodation) & ageing effects

Eye structure

primitive vision, insect vision & polarisation, animal vision & evolutionary design

Photoreception

rhodopsin facilitated receptor potential, sensitivity & spectral response of rods & cones, quantum aspects of photon detection, colour & neural encoding, dark & light adaptation

Signal processing

spatial modulation transfer function, spatial & temporal contrast, optical & neural resolution, visual acuity

Psychovisual aspects

stereopsis & depth perception, optical illusions

Basics of audition

resonance & cilia response, mechanosensitive channels, Boltzmann equation & opening statistics

Frequency Response

spectral analysis, filters & temporal processes, primitive ear & electrical properties (turtles & lizards)

Mammalian ear

structure & function, conduction of sound through bone, movement sensitive cells, surface waves: dispersion & evanescence, echolocation in bats & cetaceans

Middle ear mechanisms

mechanical & acoustic impedance, transfer function, linearity & operating point, positive feedback, transients & masking

Auditory processes

binaural systems, distortion in nonlinear processes, intermodulation

Topic 2B: IMAGING (13 lectures)

Introduction

indirect imaging concepts, radiation scattering, periodic interference

3D transforms

Fourier & reciprocal space, diffraction & crystal lattices

Atomic imaging

crystallographic techniques

Molecular structure

studies of biological interest

NMR

magnetic moment & spin, induction, resonance & relaxation, water in biological systems

MRI

linear magnetic field gradients, spin relaxation times, steady-state free precession, planar & 3D imaging methods, biomagnetic effects

Optical microscopy

lasers optics, fluorescence & polarisation techniques, confocal microscopy

Electron microscopy

principles & techniques, diffraction patterns & imaging

Ultrasonography

reflection, absorption & doppler

Other & overview

PET & future trends, summary & comparison

Topic 2C: TRANSDUCERS (13 lectures)

Introduction

black box characterisation, principles of measurement & back action, response time: steady state & transients

Electrodes

electrode/ electrolyte interface, impedance vs frequency, amplifiers & matching, patch-clamping, enzyme immobilisation techniques, EEG, ECG, EMG

Magnetometers

principles, Hall probe, flux-gate, electrolytic flow measurement, SQUIDs, biomagnetism & detection

Transducers

capacitive, inductive, accelerometers, piezoelectric, ISFET, PdMOS & TMOS devices

Signal Processing

IMPEDANCE CONSIDERATIONS
Buffer Amplifiers Capacitance Effects Inductive Effects Example - Microelectrode for Nerve Impulses

TIME and FREQUENCY DOMAINS
Action Potentials Sound

SIGNAL CONDITIONING
Operational Amplifier Circuits Active Filters Transfer Function

FEEDBACK and CONTROL SYSTEMS
Feedback Control Systems

Principles of Sampling

statistics, distributions - gaussian, log-normal, binomial, poisson; confidence limits

BIOMINERALIZATION BIOP2203 (6 pts)


Topic 3A: BIOMINERALIZATION (13 lectures)

Skeletal Architecture

relationship between form & function in the animal kingdom; Wolff's Law & consequences for bone development; contrast & comparison of species; exoskeleton vs internal skeleton: evolutionary implications

Bone Macrostructure

gross morphology; moments of inertia; stress analysis: stress-strain curves, viscoelasticity, fatigue, compressive & tensile properties

Continuum Properties

composition of mineralised tissue; measurement of mineral abundance Oligo-energetic x-ray methods; neutron activation analysis; Compton & coherent scattering; bulk mechanical properties; transmission of sound & ultrasound; opto-acoustical & piezoelectric properties; calorimetry of bone & unmineralised matrix

Microstructure

imaging & quantification using: high-resolution computed tomography, magnetic resonance imaging, optical & acoustic microscopy; "architectural" vs "material" properties; histomorphometry; Fourier & fractal methods; Euler principle

Ultrastructure

composition of bone & cartilage; nanometer investigation using: x-ray scattering & diffraction analysis, synchrotron radiation, scanning tunneling & electron microscopy, atomic force microscopy, Mossbauer spectroscopy, PIXE; effects of ionising radiation on ultrastructure & strength

Biomineralisation

formation of collgenous matrix; crosslinks; calcium-based and iron-based forms; mineralogenesis: bioenergetics & regulation; "memory effect" on bone in response to strain; role of proteoglycans; polarised light microscopy in quantification of transduction

Calcium Homeostasis in humans

compartment model of calcium kinetics; theory & practice of isotopic tracers; predicting bone fragility in humans; structural effects of aging & disease; osteoporosis

Topic 3B: BIOMECHANICS (13 lectures)

Introduction (pdf) 29kb

ANIMALS as MACHINES   lecture notes (pdf) 2.4Mb

Mechanical Model of the Body Exerting Forces with Muscles Energy Cost of Movement Scaling and Similarity

BIOMECHANICS of TERRESTRIAL LOCOMOTION

Legged Locomotion Walking Running Energetics of Terrestrial Locomotion Human Locomotion Jumping

BIOMECHANICS of LOCOMOTION through FLUIDS

Fluid Statics Fluid Dymanics Buoyancy Swimming by Undulation Rowing Hydrofoils Jet Propulsion

BIOMECHANICS of FLIGHT

Aerodynamics of Wings Gliding Soaring Flapping Flight

Topic 3C: DATA ACQUISITION (13 lectures)

The Measurement Interface

SIGNAL SAMPLING
Sampling Theorem Aliasing

DIGITAL SIGNALS
Number Codes Analog-to-Digital Conversion Digital-to-Analog Conversion Digital Signal Transmission

INTERFACING to COMPUTERS
Microprocessors Structure of Microcomputers Interfacing

MEASUREMENT UNCERTAINTIES
Systematic Uncertainties Random Uncertainties

NOISE

Data Arrangement

scalar, vector, tensor, etc; matrix concepts: transpose, determinant, inverse, data type; basic spreadsheet options: cut & paste, sorting; simple error tests

Data Analysis

basic stats: mean, std. dev., gaussian, median, IQR, random, graphing: type, scale & axes, units; curve fitting: linear regression, polynomial, trigonometric, user functions, chi squared & scaling, hypothesis testing, validity, confidence

Computer Modelling

variables, parameters & constants, accuracy, precision, systematic & stochastic errors, thorough investigation of specific examples:
Laboratories
Laboratory Manual (Semester 1)
Laboratory Manual (Semester 2)
Contact

Shane Chambers - chambers@cyllene.uwa.edu.au

Annual Field Trip to Rottnest Island

Rottnest Island Field Trip Highlights - 1997

Rottnest Island Field Trip Highlights - 1998

Rottnest Island Field Trip Highlights - 1999

Rottnest Island Field Trip Highlights - 2000

Rottnest Island Field Trip Highlights - 2001

Rottnest Island Field Trip Highlights - 2002

Rottnest Island Field Trip Highlights - 2003

3rd Year Biophysics Courses

Biophysics Honours

UWA Biophysics Homepage


Contact Information

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