Nonequilibrium dynamics of complex systems: proteins and active matter

复杂系统的非平衡动力学：蛋白质和活性物质

• 批准号: RGPIN-2018-04605
• 负责人: Schofield, Jeremy
• 金额: $ 5.25万
• 依托单位: University of Toronto
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=748364
• 关键词: Nonequilibrium; dynamics; complex; systems; proteins

This proposal outlines the development and application of theoretical tools designed to characterize the long time dynamics of complex systems, with a particular focus on the dynamics of structural transitions in model protein systems and the physics of nanomotor systems that operate out of equilibrium. Both projects involve a combination of coarse-grain simulations, numerical analysis techniques as well as fundamental theoretical work.The first project concerns the construction and validation of a simple model designed to mimic a protein in solution. The goal of these studies is to establish the connection between chemical composition, the populations of different three-dimensional structures as a function of temperature, and the dynamics of proteins. Simulations of the system will be compared with theoretical predictions in order to examine how particular interactions can lead to diseases linked to the misfolding of proteins and how non-desirable intramolecular interactions influence the stability and folding behavior of proteins. A large number of molecular machines have evolved in the natural world that actively harness external environmental conditions to perform essential biological functions at the nanoscale. Such machines can operate both as individual units and cooperatively in large groups. Synthetic nanomotors are of particular interest since their morphology and chemical properties may be tailored to carry out specific tasks. In the second project, we consider the dynamics of a system of nanomotors operating out of equilibrium whose activity arises due to catalytic chemical processes occurring at the surface of the motors. Our studies are based on microscopic models that are able to account for intermolecular interactions, many-body concentration gradients, fluid flows and the effect of random thermal fluctuations. Suspensions of motors exhibit complex collective phenomena, including dynamical clustering, phase separation, and giant-number fluctuations. This behavior can arise from a combination of effects arising from chemical activity and hydrodynamic effects in which fluid flow induced by the motion of a given motor exerts non-uniform pressure forces on others. We plan to study in detail the way in which the collective dynamics is mediated by such interactions and use our simulations to explore the mechanisms through which large density fluctuations and dynamical clustering arise as a function of the catalytic properties of the motors and the environmental conditions. We will use statistical mechanical tools developed for driven multi-phase systems to formulate exact expressions for quantities that characterize the evolution of the nanomotor system operating under conditions that are far from equilibrium.

该提案概述了旨在描述复杂系统的长时间动力学的理论工具的开发和应用，特别侧重于模型蛋白质系统中结构转变的动力学以及非平衡运行的纳米运动系统的物理学。这两个项目都涉及粗粒模拟、数值分析技术和基本理论工作的结合。第一个项目涉及一个简单模型的构建和验证，该模型旨在模拟溶液中的蛋白质。这些研究的目标是建立化学成分、作为温度函数的不同三维结构的群体和蛋白质动力学之间的联系。该系统的模拟将与理论预测进行比较，以检验特定的相互作用如何导致与蛋白质错误折叠有关的疾病，以及不受欢迎的分子内相互作用如何影响蛋白质的稳定性和折叠行为。自然界中已经进化出了大量的分子机器，它们积极地利用外部环境条件在纳米尺度上执行基本的生物功能。这样的机器既可以作为单独的单元运行，也可以以大组的形式协作运行。合成纳米电机特别令人感兴趣，因为它们的形态和化学性质可以被定制来执行特定的任务。在第二个项目中，我们考虑了一个不平衡运行的纳米电机系统的动力学，该系统的活动是由于发动机表面发生的催化化学过程而产生的。我们的研究基于微观模型，这些模型能够解释分子间相互作用、多体浓度梯度、流体流动和随机热涨落的影响。电机的悬浮呈现出复杂的集体现象，包括动态聚集、相分离和巨数波动。这种行为可能是由化学活动和流体动力效应引起的效应的组合产生的，在这种效应中，给定马达的运动引起的流体流动对其他马达施加不均匀的压力。我们计划详细研究这种相互作用调节集体动力学的方式，并利用我们的模拟来探索大密度涨落和动态聚集产生的机制，这些机制是发动机的催化特性和环境条件的函数。我们将使用为驱动多相系统开发的统计机械工具来表达表征在远离平衡的条件下运行的纳米电机系统的演化的精确的量的表达式。