Hands-on Workshops on Computational Biophysics

描述(申请人提供)：计算技术以遗传、结构和动态信息的形式提供急需的细胞过程的微观视图。将这些不断增长的信息转化为与健康相关的战略不仅需要适当的工具，而且需要适当的培训。科学家们刚刚接触到一种 “计算显微镜”需要培训分子建模和可视化软件工具的使用，而那些来自计算背景的人需要培训工具在生物问题上的应用。为此，我们提议举办为期五天的计算生物物理学研讨会，介绍大分子建模和生物信息学中心(CMMB)广泛使用的软件。拟议的工作将利用CMMB在生物医学科学家培训方面的经验，从过去一系列广受欢迎的动手讲习班的720多页书面培训材料开始。讲习班的方案将提供关于CMMB软件程序、VMD(视觉分子动力学；204,000注册用户)和NAMD(纳米级分子动力学，49,400注册用户)及其在科学查询中的应用方面的培训。讲习班参与者(通常是生命科学的实验和计算研究生和博士后)将探索用于模拟生物系统的物理模型和计算方法，并在原子水平上调查其功能。将介绍相关的物理概念、数学技术和计算方法，包括用于分子建模、并行计算机上的分子动力学模拟和转向分子动力学模拟的力场和算法。讲习班使用的最新学习材料和评价数据随后将分发给生物医学界。CMMB寻求每年举办三次动手研讨会，一次在其本土机构举办，两次在大都市地区举办。

DESCRIPTION (provided by applicant): Computational technologies provide much needed microscopic views of cellular processes, coming in the form of genetic, structural, and dynamic information. Translating this ever growing amount of information into health relevant strategies requires not only the proper tools, but also the proper training. Scientists new to the notion of a "computational microscope" need training in the use of molecular modeling and visualization software tools, while those from a computational background need training in the application of the tools to biological problems. To this end, we propose five-day computational biophysics workshops introducing the widely used software of the Center for Macromolecular Modeling and Bioinformatics (CMMB). The proposed effort will take advantage of the CMMB's experience in the training of biomedical scientists, starting from over 720 pages of written training material an a past series of popular hands-on workshops. The program of the workshops will provide training in the CMMB's software programs, VMD (visual molecular dynamics; 204,000 registered users) and NAMD (nanoscale molecular dynamics; 49,400 registered users), and their application to scientific inquiries. Workshop participants (typically experimental and computational graduate students and postdoctoral associates in the life sciences) will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. Updated learning materials used in the workshops and evaluation data will be subsequently disseminated to the biomedical community. The CMMB seeks to host three hands-on workshops per year, one local workshop at its home institution, and two extramural workshops in large metropolitan areas.