PHYM008 2013-2014 - Module Description

PHYM008	Physical Methods in Biology and Medicine	2013-14
	Prof. C. Soeller

Delivery Weeks:	T2:01-11
Level:	7 (NQF)
Credits:	15 NICATS / 7.5 ECTS
Enrolment:	8 students (approx)

Description

This module will discuss principles and current techniques used for the understanding of biology at cellular and molecular level and the particular challenges arising in their application to living systems. In addition it will highlight some of the contributions these approaches can make to medicine and the life sciences.

Module Aims

Advances both in understanding biology at the cellular and molecular level as well as clinical diagnosis are increasingly dependent on the availability of new experimental techniques that are almost always based on physics ideas and principles. This module aims to give students an understanding of the physical basis of these techniques as well as their strengths and weaknesses, potential and limitations while also providing a concise introduction into muscle biophysics.

Intended Learning Outcomes (ILOs)

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

Module Specific Skills and Knowledge:
1. describe and explain the physical consequences of the physical make-up of biological cells especially cardiac and skeletal muscle cells;
2. analyse and explain, by applying the general principles of physics and optics, a wide range of experimental methods used to investigate biological cells and cell systems;
3. give physics-based explanations of, and solve quantitative problems inspired by, the properties of cells and tissues;
4. apply biophysical concepts to muscle cell properties and processes;
Discipline Specific Skills and Knowledge:
1. apply physics-based techniques in a multi-disciplinary context;
2. explain and apply the concepts of convolution and deconvolution to the solution of measurement problems;
3. explain and apply the concepts of complex measurement methods to the design of biophysical experiments;
4. discuss the possibilities offered by complex physical measurement methods, including advanced new microscopy techniques;
Personal and Key Transferable / Employment Skills and Knowledge:
1. retrieve and evaluate information from specialist research literature;
2. undertake co-operative learning though peer-group discussions.

Syllabus Plan

Biophysics of Muscle Cells as a Model System for Experimental Methods
1. Revision of cell biophysics
2. Specific structures and Properties of muscle cells
3. Biophysics of muscular activation
Signal Processing for Microscopy and Related Experimental Methods
1. A-to-D conversion and aliasing
2. Signal-averaging techniques to retrieve signals from noise
3. Impulse responses, convolution and deconvolution in 2D and 3D
Determination of Protein Structure
1. Protein structure and its interaction with radiation
2. Structural analysis of biomolecules
Spectroscopy
1. Molecular spectroscopy of biomolecules
2. Properties of fluorescent dyes and labels for probing biological systems
3. Applications to the study of muscle cells
Microscopy Techniques
1. Fluorescence microscopy
  1. optical microscopy Modalities
  2. wide-field microscopy
  3. confocal microscopy
2. Nonlinear and other microscopies
  1. multi-photon microscopy
  2. TIRF and FRET microscopy
  3. CARS microscopy
3. Modern single molecule techniques
4. Super-resolution microscopy
  1. localisation microscopy
  2. stimulated emission depletion microscopy
  3. structured illumination microscopy
5. Application to investigation of muscle biophysics
Other Techniques
1. Computed tomography
  1. Whole body scanning
  2. Micro CT methods
2. Magnetic resonance spectroscopy and applications in muscle

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	1-10	Discussion in class
0%	4 × Problems sets	4 hours per set	Fortnightly	1-10	Solutions discussed in problems classes.
100%	Final Examination	2 hours 30 minutes	May/June	1-10	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:

Alberts B. et al. (2008), Molecular Biology of the Cell (5^th edition), Garland, ISBN 978-0-815-34105-5 (UL: 571.6 ALB)
Hille B. (2001), Ionic Channels of Excitable Membranes (3^rd edition), Sinauer Associates, ISBN 978-0-878-93321-1 (UL: On order)
Hobbie R.K. (2010), Intermediate Physics for Medicine and Biology, (4^th edition), Springer, ISBN 978-1-441-92167-3 (UL: 574.191 HOB/X)
Leake M.C. (2013), Single Molecule Cellular Biophysics, Cambridge University Press, ISBN 978-1-107-00583-9 (UL: On Order)
Mertz J. (2009), Introduction to Optical Microscopy, Roberts and Co., ISBN 978-0-981-51948-7 (UL: On order)
Paley J. (Ed) (2006), Handbook of Biological Confocal Microscopy (3^rd edition), Springer, ISBN 978-0-387-25921-5 (UL: On order)

ELE:

http://newton.ex.ac.uk/redirects/ELE/phym008

Further Information

Prior Knowledge Requirements

Pre-requisite Modules	Thermal Physics (PHY2023) , Electromagnetism II (PHY3051) and Nuclear and High Energy Physics (PHY3052)
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%)	1-10	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	MPhys and PGRS only
Distance learning	NO
Keywords	Physics; Biomedical Physics; Spectroscopy; Microscopy; Imaging.
Created	01-Oct-10
Revised	13-Sep-13