Nonequilibrium Dynamics of Macromolecules

大分子的非平衡动力学

• 批准号: 469830597
• 负责人: Professor Dr. Wolfhard Janke
• 金额: --
• 依托单位: Institut für Theoretische Physik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/469830597?language=en
• 关键词: Nonequilibrium; Dynamics; Macromolecules

The project is designed to explore the nonequilibrium kinetics of conformational transitions in macromolecules. Particular emphasis will be laid on the role of solvent viscosity in the kinetics of the collapse transition of a polymer upon changing the solvent condition from good to poor. We will employ a coarse-grained explicit solvent framework for Molecular Dynamics (MD) simulations using the Lowe-Andersen (LA) thermostat that allows easy tuning of the solvent viscosity and preserves hydrodynamic interactions. To a great extent, this mimics the situation a real polymer experiences in a solution. The nonequilibrium kinetics of the collapse transition will be probed in terms of various scaling laws for the relaxation time, growth of the relevant time-dependent length scale characterizing the local ordering, and aging properties. We will first consider the case of flexible homopolymers followed by a study of semiflexible homopolymers. Motivated by the hydrophobic (H) and hydrophilic (P) classification of amino acid residues of proteins, in the next step we will study HP-heteropolymers for selected sequences. Preliminary results for flexible homopolymers suggest that depending on the solvent viscosity one observes prolonged periods of intermediate sausage-like structures along with the usual pearl-necklace-like local ordering. For semiflexible homopolymers and flexible HP-heteropolymers too, we expect to encounter such novel phenomena. We will design analysis tools for extracting quantitative information relying on our experience with coarsening kinetics of spin and particle systems, and on our expertise in identifying different shape factors (asphericity, prolateness, cylindricity, etc.) of equilibrium polymer conformations. We will compare the results obtained for these three different classes of polymers to identify the presence of any universality in the kinetics. Taking a step ahead, in the final part of the project we will perform MD simulations of a chemically realistic polymer, viz., polyalanine which shows a coil-helix transition. We will use an all-atom description of polyalanine and initially a coarse-grained solvent setup using the LA thermostat. Next we shall use specifically water as a solvent using an all-atom description (TIP3P). In combination with the preceding results, this part will lead to a comprehensive understanding of the kinetics of various conformational transitions of macromolecules. At the same time, this will also make our results amenable to experimental verification.

该项目旨在探索大分子构象转变的非平衡动力学。特别强调的是溶剂粘度的作用，在聚合物的崩溃转变的动力学时，改变溶剂条件从好到差。我们将采用一个粗粒度的明确的溶剂框架分子动力学（MD）模拟使用Lowe-Andersen（LA）恒温器，允许轻松调整溶剂粘度，并保留流体动力学相互作用。在很大程度上，这模拟了溶液中真实的聚合物经历的情况。塌缩过渡的非平衡动力学将探讨在各种尺度律的弛豫时间，增长的相关时间依赖性的长度尺度表征的本地订购，和老化性能。我们将首先考虑柔性均聚物的情况，然后研究半柔性均聚物。受蛋白质氨基酸残基的疏水性（H）和亲水性（P）分类的启发，下一步我们将研究所选序列的HP-杂聚物。灵活的均聚物的初步结果表明，根据溶剂的粘度观察到的中间香肠状结构沿着与通常的珍珠项链般的本地订购延长的时间。对于半柔性的均聚物和柔性的HP-杂聚物，我们也期望遇到这样的新现象。我们将设计分析工具，用于提取定量信息，这依赖于我们在自旋和粒子系统粗化动力学方面的经验，以及我们在识别不同形状因子（非球面度、长轴度、圆柱度等）方面的专业知识。平衡聚合物构象。我们将比较这三种不同类型的聚合物所获得的结果，以确定动力学中是否存在任何普遍性。更进一步，在项目的最后部分，我们将对化学上真实的聚合物进行MD模拟，即，聚丙氨酸，其显示卷曲-螺旋转变。我们将使用聚丙氨酸的全原子描述，最初使用LA恒温器设置粗粒度溶剂。接下来，我们将使用全原子描述（TIP 3 P）专门使用水作为溶剂。结合前面的结果，这一部分将导致对大分子的各种构象转变的动力学的全面理解。同时，这也将使我们的结果易于实验验证。