Statistical Mechanics and Computer Simulations of Biological Molecules

这项研究的主要目的是对生物分子进行计算机模拟。主要研究人员开发了一类新的蒙特卡罗模拟，它(略微)放松了通常的马尔可夫约束，使具有重要的非均匀和局部各向异性的系统的效率得到了极大的提高。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波动，并继续研究蛋白质折叠问题。自由能差和平均力势的计算将使用首席研究人员开发的多种直方图技术进行。另一个重要的应用领域是从X射线散射中确定生物分子结构。目前优化X射线数据结构拟合的最有效方法之一是使用分子动力学模拟退火法。新的蒙特卡罗模拟方法的应用有望提高其中一些结构确定的效率。该奖项由材料研究部的材料理论项目和生物仪器与资源部的计算生物学活动共同资助。这项计算研究将集中在蒙特卡罗模拟的算法开发和生物重要性问题的应用上。将对生物分子的行为和蛋白质的折叠进行模拟。如果这些新的蒙特卡罗模拟被证明与传统的分子动力学技术竞争，这项研究将具有巨大的潜力。这项研究由材料理论计划和计算生物学活动共同资助。

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.