Computer Simulations of the Biological Mesoscale using Fluctuating Finite Element Analysis

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Computational models are invaluable for visualisation in molecular biology, as theyemploy our best quantitative physical understanding of biomolecules and theirinteractions to predict their dynamics, which is often missing from biophysicalexperiments. Now that biophysical techniques are revealing highly organisedsupermacromolecular architectures at the length-scale directly above that of singlemolecules, which was invisible until very recently, there is a need for new computationaltools to interpret these experiments. We are writing modelling software that provides acontinuum mechanics description of proteins, and which uses experimental electronmicroscopy data as input to the calculations. The model uses the Finite Elementalgorithm that we have generalised to include thermal fluctuations, known as FluctuatingFinite Element Analysis (FFEA), we are using this program to model the action ofmolecular motors, and are improving our physical description of biomolecules and theirinteractions by adding more accurate representations of the environment.