Statistical Mechanics and Computer Simulations of Biological Molecules

这项研究的主要内容涉及生物分子的计算机模拟。主要研究者开发了一类新的蒙特卡罗模拟，它（稍微）放宽了通常的马尔可夫约束，从而大大提高了具有重要非均匀性和局部各向异性的系统的效率。这些新的和相当普遍的方法将用于研究生物分子的模型。该研究将研究这类分子的平衡波动，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由首席研究员开发的多重直方图技术进行。另一个重要的应用领域是通过x射线散射确定生物分子的结构。目前优化x射线数据结构拟合的最有效方法之一是分子动力学模拟退火。新的蒙特卡罗模拟方法的应用有望提高某些结构确定的效率。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于蒙特卡罗模拟的算法开发和应用于生物重要性问题。模拟生物分子的行为和蛋白质的折叠。如果这些新的蒙特卡罗模拟显示出与传统分子动力学技术的竞争，该研究将具有巨大的潜力。这项研究是由材料理论项目和计算生物学活动共同资助的。

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.