UWA 2nd YEAR BIOPHYSICS COURSES
Online 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,
NavierStokes 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:
nonviscous (MoensKorteweg 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,
RayleighBenard 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,
ahelices, bsheet,
3D examples,
energetics,
interaction with ions
Membrane excitability
Nernst equation,
GoldmanHodgkinKatz 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,
steadystate & 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 hardwiring
Population structure & dynamics
Intrarelationships: social & nurturing requirements,
external factors:
environment, food, disease,
predatorprey dynamics,
ethology;
multigenerational development:
epidemics & plagues,
evolution & extinction of species,
human civilisation....;
ecosystems: nutrients, producers, comsumers, decomposers
eutrophication
Topic 1C: BIOPHYSICAL DYNAMICS (13 lectures)
 THERMODYNAMICS OF THE LIVING STATE  Coupled processes in
living systems; Thermodynamic potentials; Nonequilibrium stationary states; Information theory
and biology.
 MOLECULAR SELFORGANISATION  Physical chemistry of
bioploymers; Kinetics of selfassembly; Membrane dynamics; Phase
transitions
 MECHANOCHEMICAL PROCESSES  Muscle structure; Sliding filament
theory; Muscle mechanics
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)
indirect imaging concepts,
radiation scattering,
periodic interference
Fourier & reciprocal space,
diffraction & crystal lattices
crystallographic techniques
studies of biological interest
NMR
magnetic moment & spin,
induction, resonance & relaxation,
water in biological systems
MRI
linear magnetic field gradients,
spin relaxation times,
steadystate 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,
patchclamping,
enzyme immobilisation techniques,
EEG, ECG, EMG
Magnetometers
principles,
Hall probe,
fluxgate,
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, lognormal, 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:
stressstrain curves,
viscoelasticity,
fatigue,
compressive & tensile properties
Continuum Properties
composition of mineralised tissue;
measurement of mineral abundance
Oligoenergetic xray methods;
neutron activation analysis;
Compton & coherent scattering;
bulk mechanical properties;
transmission of sound & ultrasound;
optoacoustical & piezoelectric properties;
calorimetry of bone & unmineralised matrix
Microstructure
imaging & quantification using:
highresolution 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:
xray 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;
calciumbased and ironbased 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
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
AnalogtoDigital Conversion
DigitaltoAnalog 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:

Annual Field Trip to Rottnest Island 






Contact Information
To contact us directly, send email to Ralph James (ralph@physics.uwa.edu.au) or Tim StPierre (stpierre@physics.uwa.edu.au)