PHY3061 2013-2014 - Module Description

PHY3061	The Biophysics of Cells and Tissues	2013-14
	Prof. C.P. Winlove

Delivery Weeks:	T1:01-11
Level:	6 (NQF)
Credits:	15 NICATS / 7.5 ECTS
Enrolment:	15 students (approx)

Description

This module describes the fundamental physical properties of biomolecules, cells and tissues and introduces some of the biophysical and biomechanical challenges in understanding the behaviour of normal tissues and their failures in disease.

Module Aims

The physical properties of tissues and their constituent cells and biomolecules are central to their biological functions. Physical processes are also vital to normal growth and development and diseases, ranging from arthritis to cancer, may be related to failures in these processes.

Intended Learning Outcomes (ILOs)

A student who has passed this module should be able to:

Module Specific Skills and Knowledge:
1. describe the physical consequences of the biochemical structure of extracellular and cytoskeletal macromolecules;
2. apply hydrodynamics and statistical physics to the problems of water and solute transport through polymer matrices;
3. use core physics knowledge to explain, and solve quantitative problems inspired by, the properties of cells and tissues and to construct
4. apply concepts from solid- and fluid-mechanics to membrane properties and processes;
Discipline Specific Skills and Knowledge:
1. use physics techniques in a multi-discplinary context;
Personal and Key Transferable / Employment Skills and Knowledge:
1. undertake co-operative learning though peer-group discussions.

Syllabus Plan

The Biophysics of the Extracellular Matrix
1. Overview: Biological Functions of Extracellular Matrix
2. Biophysics of Matrix Macromolecules
  1. Proteoglycans
    1. Structure
    2. Biophysical Properties and Functions: theory of water and solute transport in polymers; polyelectrolyte theory and osmotic pressure.
  2. The Fibrous Proteins: Collagen and Elastin
    1. Structure and Functions
    2. Molecular Mechanics
    3. Tissue Biomechanics
3. Tissue Biomechanics
  1. Theoretical Models
    1. Lumped Parameter Models
    2. Pore-elasticity
  2. Soft Tissues
    1. Ligaments: structure and functions; mechanics
    2. Cartilage: structure and functions; mechanics; physical aspects of cartilage diseases
    3. Blood Vessels: structure and functions; physical aspects of vascular diseases
  3. Bone
    1. Structure
    2. Bone as an adaptive, fibre-reinforced composite
Cellular Biophysics
1. Overview: the cell as a physical system
2. The Physics of the Cell Membrane
  1. Structure and functions
  2. Phospholipids
    1. The hydrophobic interaction
    2. The Fluid Mosaic Model
  3. Membrane Proteins
    1. Organisation
    2. Functions
3. The Cytoskeleton
  1. The Red Cell (Cortical) Skeleton
    1. Structure
    2. Functions
  2. The Cytoplasmic Skeleton
    1. Structure
    2. Functions: cell growth and motility; molecular motors
4. Cell Mechanics
  1. Experimental Measurement
    1. Atomic Force Microscopy
    2. Optical trapping
    3. Magnetic Bead Rheometry
    4. Micropipette Aspiration
    5. Fluctuation Spectroscopy
  2. Theoretical Models
    1. Lumped Parameter Models
    2. The Tensegrity Model
5. Mechanotransduction
  1. Cellular transduction, reception and response
  2. In Vitro Experiments
    1. Compressive Loading
    2. Cell stretching
    3. Fluid Flow
  3. Physiological and Pathological Implications

Learning and Teaching

Learning Activities and Teaching Methods

Description	Study time	KIS type
20×1-hour lectures	20 hours	SLT
2×1-hour problems/revision classes	2 hours	SLT
5×6-hour self-study packages	30 hours	GIS
4×4-hour problem sets	16 hours	GIS
Reading, private study and revision	82 hours	GIS

Assessment

Weight	Form	Size	When	ILOS assessed	Feedback
0%	Guided self-study	5×6-hour packages	Fortnightly	1-6	Discussion in class
0%	4 × Problems sets	4 hours per set	Fortnightly	1-6	Solutions discussed in problems classes.
100%	Final Examination	2 hours 30 minutes	January	1-6	Mark via MyExeter, collective feedback via ELE and solutions.

Resources

The following list is offered as an indication of the type & level of information that students are expected to consult. Further guidance will be provided by the Module Instructor(s).

Core text:

Not applicable

Supplementary texts:

Aidley D.J. (1978), The Physiology of Excitable Cells (2^nd edition), CUP, ISBN 0-521-29308-1 (UL: 591.188 AID)
Caro C.G., Pedley T.J., Schroter R.C. and Seed W.A. (2012), The Mechanics of the Circulation (2^nd edition), OUP, ISBN 978-0521151771 (UL: 612.1181 MEC)
Cotterill R. (2002), Biophysics: An Introduction, Wiley, ISBN 978-0471485384 (UL: 571.4 COT)
Daune M. (1999), Molecular Biophysics: Structures in Motion, Oxford, ISBN 978-0198577829 (UL: On Order)
Ethier C.R. and Simmons C.A. (2007), Introductory Biomechanics: From Cells to Organisms, Cambridge, ISBN 978-0521841122 (UL: On Order)
Fung Y.C. (1993), Biomechanics: the mechanics of living tissues (2^nd edition), Springer, ISBN 978-0387979472 (UL: On order)
Katz B. (1966), Nerve, Muscle and Synapse, McGraw-Hill (UL: 591.188 KAT)
Miles F.A. (1969), Excitable Cells, Heinemann, ISBN 0-433-21971-8 (UL: 591.188 MIL)
Philips R., Kondev J. and Theriot J. (2008), Physical Biology of the Cell, Garland Science, ISBN 978-0815341635 (UL: On order)
Sneppen K. and Zocchi G. (2005), Physics in Molecular Biology, Cambridge, ISBN 978-0-521-84419-2 (UL: On order)

ELE:

http://newton.ex.ac.uk/redirects/ELE/phy3061

Further Information

Prior Knowledge Requirements

Pre-requisite Modules	Vector Mechanics (PHY1021), Properties of Matter (PHY1024) and Thermal Physics (PHY2023)
Co-requisite Modules	none

Re-assessment

Re-assessment is not available except when required by referral or deferral.

Original form of assessment	Form of re-assessment	ILOs re-assessed	Time scale for re-assessment
Whole module	Written examination (100%)	1-6	August/September assessment period

Notes: See Physics Assessment Conventions.

KIS Data Summary

Learning activities and teaching methods
SLT - scheduled learning & teaching activities	22 hrs
GIS - guided independent study	128 hrs
PLS - placement/study abroad	0 hrs
Total	150 hrs

Summative assessment
Coursework	0%
Written exams	100%
Practical exams	0%
Total	100%

Miscellaneous

IoP Accreditation Checklist	N/A this is an optional module
Availability	unrestricted
Distance learning	NO
Keywords	Physics; Placeholder; Main; Topic placeholder; Specific; Cells; Tissues placeholder; Tissues; Specific skill; Biophysics; .
Created	01-Oct-10
Revised	N/A