ITR: Reduced Basis Methodologies for Computation, Analysis and Visualization of Bio-Molecular Simulations

“pi将研究和开发软件和计算方法，以解决分子动力学（MD）模拟中最具挑战性的当前问题之一-大型蛋白质，由数万个原子组成，在生理范围内至少折叠一微秒的时间。”这将使用基于MD轨迹奇异值分解（SVD）的降基方法来完成。这项工作将包括：-开发一个块SVD更新方案，该方案将使新的轨迹信息与当前截断的SVD近似相关联，从而避免必须存储整个轨迹-开发，分析，实现与SVD更新方案协同工作的减基积分器，以更快地计算减基模拟——适应为潜在语义索引开发的快速前进算法，以开发快速图形查询工具，以定位可能匹配感兴趣的局部结构的站点——开发I/O支持和可视化功能，以处理将出现的极大的数据操作和表示问题研究的结果将是一个有效的时间集成方案，可以大大限制存储，但在多个尺度上解决细节。它将在一微秒的时间尺度上在完全溶剂化的蛋白质分子上进行演示，并且高阶，低频运动将被可视化。

`The PIs will investigate and develop software and computational methods to address one of the most challenging current problems in molecular dynamics (MD) simulations - large proteins, consisting of tens of thousands of atoms in solution over the physiological range of at least a microsecond of folding time. This will be accomplished using a reduced basis approach based on singular value decomposition (SVD) of the MD trajectory.The work will entail:- developing a block SVD updating scheme that will enable new trajectory information to be adjoined to a current truncated SVD approximation to a prior trajectory and avoid having to store the entire trajectory - developing, analyzing, and implementing a reduced basis integrator that will work in concert with the SVD updating scheme to compute the reduced basis simulation more rapidly- adapting the fast marching algorithms developed for latent semantic indexing to develop the rapid graphical query tools to locate sites that potentially match local structures of interest- developing the I/O support and visualization capabilities to handle the extremely large data manipulation and representation problems that will be generatedThe result of the research will be an efficient time integration scheme that can drastically limit storage and yet resolve detail on multiple scales. It will be demonstrated on a fully solvated protein molecule over a time scale of a microsecond, and the high order, low frequency motions will be visualized.