ITR: Multiscale Simulation of Biomolecular Assemblies on a Computational Grid

犹他大学的Greg Voth、Gary Ayton和Thomas Cheatham通过信息技术研究计划得到化学系的支持，这是理论化学和计算生物学之间的合作努力。他们将开发和实施一种新的多尺度计算网格模拟方法，旨在研究大型生物分子组装中的空间和时间耦合现象。应用包括DNA、肌动蛋白细丝、微管和淀粉样斑块。目前，在宏观尺度的维度问题上进行原子模拟是很难计算的。此外，传统的连续介质模拟方法随着中尺度区域的到来而瓦解。这项研究有望建立一种可行的微观到宏观模拟方法，在大型生物系统的背景下，将研究远程静电学、水振动、溶剂相互作用、构象采样和外场。

Greg Voth, Gary Ayton, and Thomas Cheatham of the University of Utah are supported by the Division of Chemistry through the Information Technology Research program in a collaborative effort between theoretical chemistry and computational biology. They will develop and implement a novel multi-scale computational grid simulation method designed to examine spatially and temporally coupled phenomena in large biomolecular assemblies. Applications include DNA, actin filaments, microtubes, and amyloid plaques.Currently, it is computationally intractable to perform atomistic simulations on macro-scale dimensional problems. Moreover, traditional continuum simulation methods break down as the meso-scale regime is reached. This research is expected to result in the construction of a viable micro-to-macro simulation methodology which, in the context of large biological systems, will address long-range electrostatics, water vibrations, solvent interactions, conformational sampling, and external fields.