CRC: Connecting Biology with Chemistry through Multiscale Theory and Computer Simulation

Gregory A.Voth、David P.Goldenberg、Valeria P.Molineo(犹他大学)和Hans C.Anderson(斯坦福大学)共同支持开发生物分子组装的新理论和计算能力。他们的方法从分子尺度开始，延伸到与生物系统(肽、蛋白质、RNA)相关的更长的长度和时间尺度。主要项目目标包括：1)开发在多个尺度上描述生物分子系统的理论和计算机模拟能力，包括从原子尺度分子动力学数据开始的粗粒度生物分子系统的系统方法；2)开发在多尺度粗粒度模型中模拟真实动力学行为的新方法；以及3)将这些新工具应用于终点应用，包括核糖体和艾滋病毒衣壳的可变分辨率粗粒度建模。粗粒化方法的开发还将涉及与计算生物物理学家V.Tozzini(意大利比萨Scuola Normer Superiore)和理论化学家Arthur F.Voter(洛斯阿拉莫斯国家实验室)的国际合作。核糖体方面的合作将与斯坦福大学的实验学家乔迪·普格利西和计算生物学家凯文·桑邦马苏(洛斯阿拉莫斯国家实验室)合作，而艾滋病毒衣壳的合作将与犹他州的韦斯利·桑奎斯特合作。21世纪见证了生物科学和物理科学之间的一场新兴科学革命。使用物理概念和方法对生物系统进行计算建模是这场革命的一个关键方面。该项目的特定终点应用将有助于提供对关键生物过程的新见解，并提高我们对疾病机制和治疗的理解。该项目的概念和计算机模拟方法将通过出版的文献、网络基础设施、研讨会以及直接和间接合作广泛传播。随着多尺度生物物理建模的结果和概念将被应用到本科化学课程中，教育影响也将是显著的。与高中科学教师的接触也将是该项目的一个重要组成部分。这个项目是由化学合作研究计划资助的，在一定程度上是由NSF信息技术研究计划资助的过去项目(Voth，PI)的成功延续。

Gregory A. Voth, David P. Goldenberg, Valeria P. Molinero (University of Utah) and Hans C. Anderson (Stanford University) are jointly supported to develop new theoretical and computational capabilities for biomolecular assemblies. Their approach begins at the molecular scale and extends to much larger length and time scales relevant to biological systems (peptides, proteins, RNA). Key project goals include: 1) Development of a theoretical and computer simulation capability to describe biomolecular systems at multiple scales, including a systematic approach for coarse-graining biomolecular systems starting with atomistic-scale molecular dynamics data; 2) development of new approaches to modeling real dynamical behavior in multiscale coarse-grained models; and 3) application of these new tools to end point applications including the variable resolution coarse-grained modeling of the ribosome and the HIV viral capsid. The coarse-graining method development will also involve an international collaboration with computational biophysicist V. Tozzini (Scuola Normale Superiore, Pisa Italy) and theoretical chemist Arthur F. Voter (Los Alamos National Laboratory). Collaborations on the ribosome will be with experimentalist Jody Puglisi (Stanford) and computational biologist Kevin Sanbonmatsu (Los Alamos National Laboratory), while collaborations on the HIV capsid will be with Wesley Sunquist (Utah).The 21st Century is witnessing an emerging scientific revolution at the interface between the biological and physical sciences. Computational modeling of biological systems using physical concepts and methods is a key aspect of this revolution. The specific end point applications of this project will help provide new insight into key biological processes and improve our understanding of disease mechanisms and treatments. The concepts and computer simulation methods from this project will be broadly disseminated through published literature, cyberinfrastructure, a workshop, and direct and indirect collaborations. The educational impacts will also be significant, as the multiscale biophysical modeling results and concepts will implemented into the undergraduate chemistry curriculum. Outreach to high school science teachers will also be an important component of the project. This project is funded by the Collaborative Research in Chemistry Program and is, in part, a successful continuation of a past project (Voth, PI) funded by the NSF Information Technology Research Program.