COMPUTER MODELLILNG AND OTHER THERORETICAL STUDIES OF BIOPOLYMERS

该项目的目的是执行和进一步发展 分子动力学，随机动力学，蒙特卡罗， 流体力学和计算机图形学来研究解决方案 肽、蛋白质、核酸和脂质双层的结构。 的 因此，项目涉及方法和模型两方面的问题。 这 去年，研究的方法部分主要涉及： (i)序参量精度的统计分析， 从动力学模拟计算的扩散常数;（ii）统计 聚合物中协调二面角转变的分析及其应用 到“扭结”运动在膜链;（iii）一个详尽的比较， 构象搜索的Monte Carlo和动力学算法 （四）系统的分析; 根据短轨迹计算的速率偏差。 模拟相关 更多的建模包括：（i）丁烷系列的MD模拟， 辛烷、十二烷、十六烷和二十烷， 平移和旋转扩散的粘度依赖性，以及 异构化;（ii）流体相二棕榈酰分子动力学模拟 磷脂酰胆碱脂质双层在水中，包括分析表明， 在100 ps的时间尺度上， 膜内部和膜中碳的重新取向动力学 纯十六烷 这一结果强烈暗示， 膜的粘度与分子量关系更密切。 在表面而不是在内部的相互作用。

The purpose of this project is to implement and to further develop the methods of molecular dynamics, stochastic dynamics, Monte Carlo, hydrodynamics and computer graphics to investigate the solution structures of peptides, proteins, nucleic acids and lipid bilayers. The project thus involves questions of both methodology and modeling. This past year the methodological part of the research principally involved: (i) statistical analysis of the accuracy of order parameters and diffusion constants computed from dynamics simulations; (ii) statistical analysis of concerted dihedral transitions in polymers, with application to "kink" motions in membrane chains; (iii) an exhaustive comparison of Monte Carlo and dynamics algorithms for conformational searching using the bistable oscillator as a paradigm; (iv) an analysis of systematic bias in rates calculated from short trajectories. Simulations pertaining more to modeling included: (i) MD simulations of the series butane, octane, dodecane, hexadecane, and eicosane, with extensive analysis of the viscosity dependence of translational and rotational diffusion, and isomerization; (ii) MD simulation of a fluid phase dipalmitoyl phosphatidylcholine lipid bilayer in water, including an analysis showing that on the 100 ps timescale there is effectively no difference in the reorientational dynamics of the carbons in the membrane interior and in pure hexadecane. The result strongly implies that the apparently high viscosity of the membrane is more closely related to molecular interactions on the surface rather than in the interior.