Undergraduate

modules

Modules

PHY3038 : Biophysics

Semesters
Semester 2 Credit Value: 10
ECTS Credits: 5.0

Aims

To present a range of topics in the physics of biological systems.

Outline Of Syllabus

1) The building blocks of biological systems: Biomolecules, the central dogma, cells as machines, temporal scales, clocks and oscillators, molecular machines.

2) Biological thermodynamics - Deterministic vs thermal forces, biological systems as energy minimizers, equilibrium thermodynamics, configurational energy, functionals, entropy in biological systems, entropy and hydrophobicity, maximum entropy methods, energy vs entropy, Euler-Lagrange equations.

3) Statistical mechanics in biological systems - theory of stat. mech. applied to biology, stat-mech of gene expression, osmosis pressure applied to viruses and cells.

4) Ligand - receptor binding - importance in drug development, thermodynamics and stat-mech models, the Hill function, force dependent behaviour.

5) Biopolymers - Random walks, DNA looping, single molecule mechanics, random walk models for force-extension curves, physics of chromosome folding, persistence length

6) Diffusion - Active vs passive transport, Fick's law, solution and properties of diffusion equations, the Smoluchowski equation, the Einstein relation.

7) Dynamics of molecular motors - Rectified Brownian motion , one-state models, driven-diffusion equation,
two-state models, the polymerization ratchet, the translation ratchet

8) BIological Electricity - electricity in cells, the Nernst equation, two state models of ion channels, voltage relaxation as an RC circuit, the Cable equation, Hodgkin - Huxley and membrane transport

9) The physics of cancer - introduction to cancer, fluid mechanics models of cancer metastasis, soft matter physics of cancer invasion, mathematical models of tumour growth.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Scheduled Learning And Teaching ActivitiesLecture241:0024:00Lectures
Guided Independent StudyAssessment preparation and completion118:0018:00Exam revision
Guided Independent StudyAssessment preparation and completion115:0015:00Completion of assignment
Scheduled Learning And Teaching ActivitiesSmall group teaching121:0012:00Tutorials
Scheduled Learning And Teaching ActivitiesDrop-in/surgery120:102:00Office hours
Guided Independent StudyIndependent study129:0029:00Review lecture material and prepare for tutorials.
Total100:00
Teaching Rationale And Relationship

The predominance of lectures is appropriate for the module which has a theoretical bias. The tutorial sessions provide an opportunity for the students to practise the numerical methods required for calculations. Officer hours (two per week) will provide an opportunity for more direct contact between individual students and the lecturer: a typical student might spend one or two hours over the course of the module, either individually or as part of a group.

Assessment Methods

The format of resits will be determined by the Board of Examiners

Exams
Description Length Semester When Set Percentage Comment
Written Examination1202A80N/A
Other Assessment
Description Semester When Set Percentage Comment
Report2M202,000 words
Assessment Rationale And Relationship

The exam is used to test the development in understanding of the theoretical content of the module.

The coursework will test computational skills relating to biophysics that cannot be assessed in an exam environment

Reading Lists

Timetable