Biological Modelling

Quantitative modelling makes it possible to extract the maximum amount of information from experimental data...

Dr Bernard Piette

Within the BSI, we are particularly interested in modelling cellular processes such as the dynamics of microtubules, cell signalling, reaction-diffusion in cells, as well as studying the mechanisms of self-assembly, the structure and dynamics of proteins, protein complexes and viruses.  Our efforts crystallize on a variety of interdisciplinary projects emerging from specific biological questions, mostly raised by our partners in the School of Biological and Biomedical Sciences.

There is scope for developing completely new ways of thinking mathematically about biological questions, utilising mathematical techniques familiar to topologists, group theorists, geometers, field theorists, as well as mechanical engineers, polymer physicists and soft condensed matter physicists.  All of these are areas in which the BSI possesses a wealth of expertise.

Areas of Research

Patterns of Vibration in Icosahedral Viruses

An important area of study within the BSI is the study of viral capsid dynamics.  A top-down approach is employed, inspired by the group-theoretical analysis of a coarse-grained capsid, which is intended to be used in a future perturbative analysis of viral capsid dynamics. 

This work has already shown that at the lowest order in the perturbative series, there is a surprising structure shared by the large class of Caspar-Klug capsids, which had hitherto gone unnoticed in bottom-up simulations. The analysis provides a deeper insight into stability properties of capsids, complementary to that obtained through molecular dynamics.

Contact: admin.bsi@durham.ac.uk for a more specialised research contact.

Elasticity of Biopolymers and other Bio-macromolecules

This research builds on two area of expertise in the BSI; bio-polymer elasticity and bio-polymer collapse and electron transport on such chains.  The large scale all atom simulations, which are typically employed to understand the behaviour of macromolecules, suffer from the drawback of yielding information on time scales (≈ ns) much smaller than those of biological interest.  Hence a coarse-grained description amenable to methods of continuum mechanics and statistical physics is being employed by BSI researchers (including Buddhapriya Chakrabarti, Bernard Piette, Wojtek Zakrzewski).  An important part of this research is to understand the coupled effect of electronic and mechanical degrees of freedom in inducing collapse of bio-polymers.

Contact: admin.bsi@durham.ac.uk for a more specialised research contact

Modelling of the Cytoskeleton and its Function

The study of the structure and function of the cytoskeleton is of particular interest within the BSI.  Microtubules, which are a constituent part of the cytoskeleton, exhibit dynamical instability which is essential for the division of chromosomes and for the formation of the phragmoplast in some plant cells. Most of the biological processes involving microtubules rely on dynamics fuelled by the laws of thermodynamics.  BSI researchers are employing a physical model of microtubule dynamics that been developed based on thermodynamics, and are using Monte Carlo simulations to reproduce two sets of independent experimental data. This model has already confirmed that the tip of microtubules, usually referred to as the cap, made of GTP-tubulin, is several layers deep.

Contact: admin.bsi@durham.ac.uk for a more specialised research contact.