Mathematical Sciences: Numerical Methods for Molecular Dynamics

9304268斯基尔研究员继续研究分子动力学的数值方法。其目标是找到适合于大型并行计算机的数值算法，这些算法可以更有效地对蛋白质、DNA和脂质等大分子的动力学进行建模。重点是使用积分格式，特别是辛格式，它可以使用大的时间步长来为长期积分产生定性正确的模拟。目标是以最少的计算工作量获得所需的信息，方法是对模型问题进行数学分析和计算实验。开发的技术将在现实的分子模型上进行测试，作为涉及软件开发的不同的、互补的研究项目的一部分。在要考虑的技术中，更著名的是多时间步长、约束动力学和快速库仑解算器。正在设计的数学公式和计算机程序可以预测蛋白质和DNA等大分子的典型运动。其目的是找到在大型计算机上实现非常快速计算的捷径。这些想法的准确性和速度都经过了测试，更有用的想法被放入生物学家和其他科学家用来研究分子行为的软件中。计算机模拟可以帮助科学家了解分子如何执行生物功能，而这可能是很难通过实验观察到的。这类研究对农业和医疗用途的分子设计也很有用。***

9304268 Skeel The investigator continues work on numerical methods for molecular dynamics. The objective is to find numerical algorithms suitable for large parallel computers that can much more efficiently model the dynamics of macromolecules such as proteins, DNA, and lipids. Emphasis is on the use of integration schemes, notably symplectic schemes, that can use large time steps to produce qualitatively correct simulations for long-time integrations. The goal is to obtain the desired information with the least computational effort, and the methodology is to use mathematical analysis and computational experiments on model problems. The techniques developed are to be tested on realistic molecular models as part of a different, complementary research project involving software development. Among the techniques to be considered, the better known ones are multiple time steps, constraint dynamics, and fast Coulomb solvers. Mathematical formulas and computer programs are being devised that can predict typical motions of large molecules such as proteins and DNA. The aim is find shortcuts that enable very fast calculations on large computers. These ideas are tested for accuracy and speed, and the more useful ones are put into the software that biologists and other scientists use to study the action of molecules. Computer simulations can help the scientist to understand how molecules perform biological functions, which can be very difficult to observe experimentally. Such studies are also useful in the design of molecules for agricultural and medical purposes. ***