Dr T Savin, Dr T O'Leary
Timing and Structure
Michaelmas term. 16 lectures (including 2 examples classes). Assessment: Coursework 100%
The aims of the course are to:
- introduce to sub cellular processes and the role of thermal fluctuations
- shift from the classical biology approach to a more physical description
- illustrate mathematical/computing approaches to study regulatory networks and biomolecular dynamics
- provide background knowledge on stochastic processes
The course covers topics in stochastic processes and statistical mechanics with application to examples from biology. No background in biology is assumed.
- Cells are a very well organized machinery
- But molecular processes are subject to fluctuations, i.e. stochasticity
- How is it possible?
Mathematical formalism (Savin)
- Probabilities & Random Variables
- Stochastic Processes
- Master Equation, Fokker-Plank Equation
Regulation of gene expression (O'Leary)
- Gene expression analysis
- Stochastic gene expression
- Stochastic simulations
Cell structural organization (Savin)
- Biomolecules (DNA, cytoskeleton)
- Statistical physics for biology
- Polymer mechanics
- Transport processes in cells
Coursework activity #1: Analysis of noise in prokaryotic gene expression
Cells often express genes in low copy numbers, leading to substantial variability in protein. In this coursework you will build a simple model of gene expression, analyse it mathematically and simulate a stochastic version of the model.
Posted Fri week 5
Due Fri week 7
Coursework activity #2: Modelling DNA’s mechanical response
The mechanical properties of DNA and other biological filaments are important factors for cell functions. In this coursework you will simulate a DNA molecule using a bead-spring chain model undergoing thermal fluctuations, and compare your results with the theory and existing experimental data.
Posted Fri week 8
Due Fri two weeks later
Please see the Booklist for Group G Courses for references for this module.
Please refer to Form & conduct of the examinations.
Last modified: 17/05/2018 14:25