Postdoc: Brownian Dynamics of DNA Slithering
Postdoc: Brownian Dynamics of DNA Slithering
批准号:
9704681
负责人:
Tamar Schlick
金额:
$4.62万
依托单位:
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
项目状态:
已结题
起止时间:
1997-05-15 至 2000-04-30
中文摘要
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英文摘要
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.
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国内基金
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