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Monte-Carlo and molecular dynamics modelling of biopolymers, DNA, proteins and molecular motors

The mechanical properties, deformation behaviour and relaxation of biopolymer chains and proteins have been the subject of much interest in recent years because of their importance in understanding the structure of cells and muscles.

Molecular modelling techniques are generally based on ab initio electronic structure calculations, semi-empirical methods or molecular mechanics. Molecular mechanics approaches do not take account of electron transfer processes, which can be crucially important, but instead rely on the use of parametrised interatomic force fields which are assumed to be transferable. Although electron reorganisation effects are not considered, these methods can be usefully applied to study the conformation and dynamics of large systems over long time scales.

Activities

We have developed and applied such methods to study protein folding, DNA translocation as well as studying molecular motor mechanisms. This is done by constructing minimalist models and determining the potential parameters before carrying out Monte-Carlo (MC) and molecular dynamics (MD) simulations. For example, in modelling DNA translocation through cell membrane pores (alpha-hemolysin) potential profiles are constructed (as in the figures below) and these were used in our MC and MD simulations to extract translocation times and so study their dependences on the DNA sequence and on other external factors.

Publications