# UWA 2nd YEAR BIOPHYSICS COURSES

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

## MODULE A: BIOSPHERE 563.201 (4 pts)

### Topic A1: 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 A2: 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

## MODULE B: BIOSENSING 563.202 (4 pts)

### Topic B1: 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 B2: 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,
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

## MODULE C: BIODATA 563.203 (4 pts)

### Topic C1: TRANSDUCERS

#### 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

### Topic C2: DATA ACQUISITION

#### 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

#### Storage Devices

ROM, RAM,
temporary & permanent memory,
tapes, disks, floppies & hard wired
#### 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 biophysical examples:
i) Gomperz (sigmoid) curve,
ii) oscillating membrane:
Bessel functions J,Y,
iii) fractal aspects of growth,
iv) insolation vs season, location & hour,
v) modelling gas exchange:
diffusion,
respiration

## MODULE D: BODY PHYSICS 563.201 (4 pts)

### Topic D1: 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 D2: BIOMECHANICS (13 lectures)

#### ANIMALS as MACHINES

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

## 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)