Computer Simulations of the Biological Mesoscale using Fluctuating Finite Element Analysis

计算模型对于分子生物学的可视化是无价的，因为它们利用我们对生物分子及其相互作用的最好的定量物理理解来预测它们的动力学，这在生物物理实验中经常缺失。现在，生物物理技术正在揭示高度组织化的超大分子结构，其长度尺度直接高于单分子，这是不可见的，直到最近，有必要新的计算工具来解释这些实验。我们正在编写建模软件，提供蛋白质的连续力学描述，并使用实验电子显微镜数据作为计算的输入。该模型使用我们已经推广到包括热波动的有限元算法，称为波动有限元分析（FFEA），我们正在使用该程序来模拟分子马达的动作，并通过添加更准确的环境表示来改进我们对生物分子及其相互作用的物理描述。

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.