Computer Simulations of the Biological Mesoscale using Fluctuating Finite Element Analysis

Computational models are invaluable for visualisation in molecular biology, as they
employ our best quantitative physical understanding of biomolecules and their
interactions to predict their dynamics, which is often missing from biophysical
experiments. Now that biophysical techniques are revealing highly organised
supermacromolecular architectures at the length-scale directly above that of single
molecules, which was invisible until very recently, there is a need for new computational
tools to interpret these experiments. We are writing modelling software that provides a
continuum mechanics description of proteins, and which uses experimental electron
microscopy data as input to the calculations. The model uses the Finite Element
algorithm that we have generalised to include thermal fluctuations, known as Fluctuating
Finite Element Analysis (FFEA), we are using this program to model the action of
molecular motors, and are improving our physical description of biomolecules and their
interactions by adding more accurate representations of the environment.