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

Gregory A. Voth，大卫P. Goldenberg，Valeria P. Molinero（犹他州大学）和Hans C.安德森（斯坦福大学）共同支持开发新的理论和计算能力的生物分子组装。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）相关的更大的长度和时间尺度。主要项目目标包括：1）发展理论和计算机模拟能力，以在多尺度上描述生物分子系统，包括从原子尺度分子动力学数据开始的粗粒化生物分子系统的系统方法; 2）发展在多尺度粗粒化模型中模拟真实的动力学行为的新方法;以及3）将这些新工具应用于端点应用，包括核糖体和HIV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化学家V. Tozzini（意大利比萨的Scuola Normale Bronchiore）和理论化学家亚瑟F。洛斯阿拉莫斯国家实验室（Los Alamos National Laboratory）核糖体的合作将与实验学家乔迪Puglisi（斯坦福大学）和计算生物学家凯文Sanbonmatsu（洛斯阿拉莫斯国家实验室），而艾滋病毒衣壳的合作将与韦斯利Sunquist（犹他州）。21世纪正在见证一个新兴的科学革命之间的接口生物和物理科学。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为关键生物过程提供新的见解，并提高我们对疾病机制和治疗方法的理解。该项目的概念和计算机模拟方法将通过出版文献、网络基础设施、研讨会以及直接和间接合作广泛传播。教育的影响也将是显着的，作为多尺度生物物理建模的结果和概念将实施到本科化学课程。对高中科学教师的宣传也将是该项目的一个重要组成部分。 该项目由化学合作研究计划资助，部分是由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.