Nonequilibrium Dynamics of Macromolecules

该项目旨在探索大分子构象转变的非平衡动力学。特别强调溶剂粘度在溶剂条件由好变差时聚合物坍塌转变动力学中的作用。我们将采用一种粗粒度的显式溶剂框架进行分子动力学（MD）模拟，使用low - andersen （LA）恒温器，可以轻松调整溶剂粘度并保持流体动力学相互作用。在很大程度上，这模拟了聚合物在溶液中的真实情况。从松弛时间的各种标度规律、表征局部有序的相关时变长度标度的增长以及老化性能等方面探讨了崩溃转变的非平衡动力学。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。基于蛋白质氨基酸残基的疏水(H)和亲水(P)分类，下一步我们将针对选定的序列研究hp -异聚物。柔性均聚物的初步结果表明，根据溶剂粘度的不同，人们观察到中间长时间的类似香肠的结构以及通常的珍珠项链状的局部有序。对于半柔性均聚物和柔性hp -杂聚物，我们也希望能遇到这样的新现象。我们将根据我们在自旋和粒子系统的粗化动力学方面的经验，以及我们在识别平衡聚合物构象的不同形状因素（非球面、延伸度、圆柱度等）方面的专业知识，设计用于提取定量信息的分析工具。我们将比较这三种不同类型聚合物的结果，以确定动力学中是否存在普遍性。向前迈出一步，在项目的最后一部分，我们将对化学上真实的聚合物进行MD模拟，即聚丙氨酸，它显示了线圈-螺旋过渡。我们将使用聚丙氨酸的全原子描述和最初使用LA恒温器的粗粒度溶剂设置。接下来，我们将使用全原子描述法（TIP3P）具体地使用水作为溶剂。结合前面的结果，这一部分将导致对大分子各种构象转变动力学的全面理解。同时，这也将使我们的结果易于实验验证。

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.