Postdoc: Brownian Dynamics of DNA Slithering

博士后：DNA滑动的布朗动力学

基本信息

批准号：
9704681
负责人：
Tamar Schlick
金额：
$ 4.62万
依托单位：
New York University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
1997
资助国家：
美国
起止时间：
1997-05-15 至 2000-04-30
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=9704681&HistoricalAwards=false
关键词：
Postdoc Brownian Dynamics DNA Slithering

项目摘要

The PI's will develop and apply novel computational modeling techniques on high-performance computers to enhance our understanding of DNA on a global level, i.e., thousands of base pairs. Specifically, the PI's will describe the dynamical features of slithering in supercoiled DNA over microsecond to millisecond time frames. Slithering, which is thought to be important in recombination mechanisms, is a reptilian motion in which individual base pairs slide against each other in a "conveyor-belt" fashion. The PI's will extend a previously developed Langevin dynamics model of supercoiled DNA to incorporate hydrodynamic interactions. The DNA molecule will be represented by a B-spline model that smoothly transforms into a bead model. The singular value decomposition will be used to transform a vector in the space of the independent variables defining the DNA curve ("control" points) to a vector in the space of the actual curve (DNA) points. Because the millisecond simulations are computationally intensive, a 12-processor Power Challenge computer and efficient parallel strategies will be employed. To measure characteristic times related to slithering, the PI's will use three-dimensional graphics tools to analyze interparticle distance and curvature time-evolution, and thus determine the scaling of site juxtaposition times with DNA size. The computational modeling of this project will complement experiments and provide insight into the vital role of supercoiled DNA in replication, recombination, and transcription. The algorithms developed here are general and can be applied to a wide range of other important biomolecular problems.

PI 将在高性能计算机上开发和应用新颖的计算建模技术，以增强我们对全球水平 DNA（即数千个碱基对）的理解。具体来说，PI 将描述超螺旋 DNA 在微秒到毫秒时间范围内滑动的动力学特征。滑动被认为在重组机制中很重要，是一种爬行动物运动，其中各个碱基对以“传送带”方式相互滑动。 PI 将扩展先前开发的超螺旋 DNA 的 Langevin 动力学模型，以纳入流体动力学相互作用。 DNA 分子将由 B 样条模型表示，并平滑地转换为珠子模型。奇异值分解将用于将定义 DNA 曲线（“控制”点）的自变量空间中的向量转换为实际曲线（DNA）点空间中的向量。由于毫秒模拟计算量较大，因此将采用 12 处理器 Power Challenge 计算机和高效的并行策略。为了测量与滑动相关的特征时间，PI 将使用三维图形工具来分析粒子间距离和曲率时间演化，从而确定位点并置时间与 DNA 大小的比例。该项目的计算模型将补充实验，并深入了解超螺旋 DNA 在复制、重组和转录中的重要作用。这里开发的算法是通用的，可以广泛应用于其他重要的生物分子问题。