Complementary Methods for Equilibrium Sampling of Biomolecules

生物分子平衡采样的补充方法

• 批准号: 1119091
• 负责人: Daniel Zuckerman
• 金额: $ 108.39万
• 依托单位: University of Pittsburgh
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-01-01 至 2016-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1119091&HistoricalAwards=false
• 关键词: Complementary; Methods; Equilibrium; Sampling; Biomolecules

Intellectual merit:Proteins and nucleic acids often act like small machines, carrying out functions in the cell such as the synthesis of additional molecules, communication/'signaling' among systems in the cell, and locomotion. Such functions typically involve significant changes to the shapes of the molecules. Computer simulation methodology for studying such molecular motions will be developed in the current project. The new methodology will combine advances in software and hardware. For example, new software is being developed to exploit the 99.9% of computer memory that goes unused in typical current simulations. The importance of this type of research can be understood in terms of biomolecular timescales: although cutting-edge simulations on special computers today can reach the microsecond scale or even beyond for small systems, it is widely appreciated that key biochemical phenomena occur at timescales of even seconds and longer - that is, one million times longer than computational capacity. Until this computing gap is bridged, it will be extremely difficult to systematically study the full range of biomolecular motions which keep cells working.Broader impactsBesides research, the proposal targets science pedagogy in two ways. First, the principal investigator will prepare a significantly expanded second edition of his textbook, Statistical Physics of Biomolecules: An Introduction. This book is written for modern interdisciplinary graduate students (e.g., in biophysics or computational biology) who come from diverse semi-quantitative backgrounds. It explains the physical principles underlying biomolecular behavior. Second, the principal investigator will target a significant deficiency in modern science education: science writing. A new course and auxiliary web materials will be developed, geared toward modern students saturated with "new media". The complexities of today's world demand that science writing should be both informative and appealing.

智力优点：蛋白质和核酸通常像小机器一样，在细胞中执行功能，例如合成额外的分子，细胞中系统之间的通信/“信号”以及运动。 这些功能通常涉及分子形状的显著变化。 本项目将发展研究这种分子运动的计算机模拟方法。 新的方法将结合联合收割机在软件和硬件方面的进步。 例如，正在开发新的软件，以利用在典型的电流模拟中未使用的99.9%的计算机内存。 这类研究的重要性可以从生物分子的时间尺度来理解：尽管今天在特殊计算机上进行的尖端模拟可以达到微秒级，甚至超过小型系统，但人们普遍认为，关键的生化现象发生在甚至数秒甚至更长的时间尺度上-也就是说，比计算能力长100万倍。 在这一计算差距被弥合之前，系统地研究维持细胞工作的生物分子运动的全方位将是极其困难的。更广泛的影响除了研究之外，该提案还以两种方式针对科学教育。 首先，首席研究员将准备一个显着扩大他的教科书，生物分子的统计物理学第二版：介绍。 本书是为现代跨学科研究生（例如，在生物物理学或计算生物学），他们来自不同的半定量背景。 它解释了生物分子行为背后的物理原理。 第二，主要研究者将针对现代科学教育中的一个重大缺陷：科学写作。 一个新的课程和辅助网络材料将开发，面向现代学生与“新媒体”饱和。 当今世界的复杂性要求科学写作既要信息丰富，又要吸引人。