Introductory description

N/A.

Module web page

Module aims

Outline syllabus

This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.

1. Force fields for biomolecular simulation.
2. Free energy calculations. Thermodynamic integration and perturbation; potentials of mean force.
3. Advanced sampling. Biased sampling methods, replica exchange molecular dynamics. Coarse-graining for biomolecular simulation.
4. Calculated properties. Energetics, structure and dynamics; relationship to experimentally determined quantities.
5. Example applications. Drug-enzyme binding free energies and computer-aided drug design, protein structure prediction, delivery of pharmaceuticals across lipid membranes, the interface between nanomaterials and biological systems.

Learning outcomes

By the end of the module, students should be able to:

• Students will be able to describe the theoretical background and application of a selection of computational methods (including molecular dynamics, free energy calculations and techniques to study rare events) in biophysical chemistry.
• Students will have an appreciation of the advantages and disadvantages of different computational methods in the context of solving particular biological problems (e.g. protein folding, membrane transport, drug binding).
• Students will be able to evaluate the strengths and weaknesses of biomolecular simulation studies found in the literature.
• Students will be able to perform and analyse computational calculations involving biological molecules and relate them to experimental data.

Indicative reading list

● A.R. Leach, Molecular Modelling: principles and applications, Longman (1996).
● M. Tuckerman, Statistical Mechanics, Oxford Graduate Texts (2010).
● D. Frenkel & B. Smit, Understanding Molecular Simulation, From Algorithms to Applications (2001).
● A selection of papers from the recent research literature, that may change from year to year, will also be provided.

Subject specific skills

Students will be able to describe the theoretical background and application of a selection of computational methods (including molecular dynamics, free energy calculations and techniques to study rare events) in biophysical chemistry.
Students will have an appreciation of the advantages and disadvantages of different computational methods in the context of solving particular biological problems (e.g. protein folding, membrane transport, drug binding).
Students will be able to evaluate the strengths and weaknesses of biomolecular simulation studies found in the literature.
Students will be able to perform and analyse computational calculations involving biological molecules and relate them to experimental data.

Transferable skills

Biochemistry knowledge, programming, data analysis