Statistical Mechanics and Computer Simulations of Biological Molecules

这项研究的主要重点是计算机模拟， 生物分子 一类新的蒙特卡罗模拟 由主要研究者开发， 放松通常的马尔可夫约束，使大大改善 具有重要非均匀性和局部性的系统的有效性 各向异性 这些新的和相当普遍的方法将被用来 研究生物分子的模型。 这项研究将 研究这些分子的平衡涨落， 蛋白质折叠的问题。 自由能的计算 平均力的差异和潜力将使用 由校长开发的多直方图技术 调查员 另一个重要的应用领域是 用x射线测定生物分子的结构 散射 目前最有效的方法之一， 优化X射线数据结构的拟合包括 模拟退火与分子动力学 的应用 新的蒙特卡罗模拟方法有望改善 这些结构决定的效率。 该奖项是由材料理论计划联合资助， 材料研究与计算生物学系 在生物仪器和 资源 %%% 这项计算研究将集中在算法开发， 蒙特卡罗模拟及其在生物学问题中的应用 重要性 将对生物的行为进行模拟 分子和蛋白质的折叠。 这项研究有很大的 这些新的蒙特卡罗模拟应该被证明是 与传统的分子动力学技术竞争。 的 研究由材料理论计划和 计算生物学活动

The main thrust of this research concerns computer simulations of biological molecules. A new class of Monte Carlo simulations has been developed by the principal investigator which (slightly) relaxes the usual Markovian constraint to enable greatly improved efficiency for systems with important inhomogeneity and local anisotropy. These new and quite general methods will be used to investigate models of biological molecules. The research will study equilibrium fluctuations of such molecules and continue work on the protein folding problem. Calculations of free-energy differences and potentials of mean force will be carried out using multiple histogram techniques developed by the principal investigator. Another important area of application is the determination of the structure of biological molecules from x-ray scattering. One of the most effective current methods of optimizing the fit of the structure of x-ray data involves simulated annealing with molecular dynamics. The application of new Monte Carlo simulation methods has promise of improving the efficiency of some of these structure determinations. The award is funded jointly by the Materials Theory program in the Division of MAterials Research and the Computational Biology Activity in the Division of Biological Instrumentation and Resources. %%% This computational research will focus on algorithm development for Monte Carlo simulation and applications to problems of biological importance. Simulations will be done on the behavior of biological molecules and the folding of proteins. The research has great potential should these new Monte Carlo simulations be shown to be competitive with conventional molecular dynamics techniques. The research is jointly funded by the Materials Theory program and the Computational Biology Activity.