# 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

#### 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)

• THERMODYNAMICS OF THE LIVING STATE - Coupled processes in living systems; Thermodynamic potentials; 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

## 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

## 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)