Conformational phase transitions of highly flexible polymers: theory, computer simulation and single molecule experiments

提案编号：CTS-0522564 PRINCIPAL调查员：E.S.G.SHAQFEHINSTUTION：Stanford UNIVERSITY最近在PI的研究小组中的合作工作证明，伸展流动中的线圈-拉伸转变是一个“一阶”转变，这是一个争论了30年的话题。在这个转变中，有一个构象滞后区，在那里，两个动力学分离的构象状态可以存在于无量纲伸缩速率的相同值处。这是链内流体动力相互作用的直接结果。对这种材料的流变性进行建模需要一种新的范式。根据这笔拨款，研究人员将使用大规模计算机模拟、统计力学的投影方法和单分子DNA实验来开发这样一个范例的要素。特别是，布朗动力学模拟将被用来研究理解构象滞后的主要动力学过程：解离(从卷曲-解开的转变)的动力学，崩塌的动力学(从扩展状态到卷曲状态)，以及在滞后区域中涨落诱导在扩展状态和卷曲状态之间的“跳跃”的动力学。将研究不同的流动类型，包括平面混合流动、三维线性流动和非线性流动，这些流动显示了这种构象滞后的新特征。大规模模拟和单分子实验的结合提供了一个强大的工具，使研究人员能够在聚合物溶液流变学中检验这一新范式。溶液流变学中的构象滞后和构象相变的研究还处于起步阶段，因此这些新概念的广泛影响并不是完全明显的。已经很清楚的是，在许多情况下，溶液中的应力状态取决于与这些滞后状态中的分子的时间历史相关的巨大时间尺度，特别是在微流体环境中。这项拟议的工作在培训方面具有更广泛的影响，并向本科生和研究生传授一种关于流动中分子动力学的新方法。通过这个项目，研究生和本科生将在这个涉及流体力学、微制造和材料加工以及数值方法的多学科研究方面进行培训。Shaqfeh教授已经通过CPIMA材料中心参与了外展项目，其中包括在大学为代表不足的群体举办研讨会。将通过开发基于网络的模块来加强教学基础设施，这些模块向高中生介绍DNA动力学、利用流动操纵DNA的方法以及计算大分子上的力。这些将基于实验中DNA的可视化电影和模拟代码，这两个代码都将在互联网上提供。

PROPOSAL NO.: CTS-0522564PRINCIPAL INVESTIGATOR: E.S.G. SHAQFEHINSTITUTION: STANFORD UNIVERSITYRecent collaborative work in the PI's research group has demonstrated, that the coil-stretch transition in an extensional flow is a "first order" transition, a topic that had been debated for 30 years. In this transition there is a region of conformation hysteresis where two kinetically separated conformation states can exist at the same value of the dimensionless stretching rate. This is a direct consequence of intra-chain hydrodynamic interactions. The modeling of the rheology of such a material requires a new paradigm. Under this grant the researchers will use a large-scale computer simulation, projection methods from statistical mechanics, and single molecule DNA experiments to develop the elements of such a paradigm. In particular, Brownian dynamics simulations will be developed to study the kinetic processes that are principle to understanding conformation hysteresis: the kinetics of the unraveling (transition from coiled-unravelled), the kinetics of the collapse (from the extended to the coiled state), and the kinetics of fluctuation induced "hopping" between the extended and coiled-states in the hysteretic regime. Different flow types will be studied, including planar mixed flows, three dimensional linear flows, and nonlinear flows, that demonstrate new characteristics of this conformation hysteresis. The combination of large-scale simulation and single molecule experiments provides a powerful tool that will allow the researchers to examine this new paradigm in polymer solution rheology. The study of conformation hysteresis and conformational phase transitions in solution rheology is in its infancy and thus the full broad impact of these new ideas is not completely apparent. It is already clear that in many instances the state of stress in a solution is dependent on enormous time scales associated with the time history of the molecules in these hysteretic states, especially in microfluidics contexts. The proposed work has broader impacts in terms of training, and teaching undergraduate and graduate students a new way of thinking about the dynamics of molecules in flow. Through this project, graduate students and undergraduate students will be trained in this multidisciplinary research that involves fluid mechanics, microfabrication and materials processing, and numerical methods. Prof. Shaqfeh engages in outreach programs already through the CPIMA materials center, which include giving seminars at colleges for under-represented groups. Teaching infrastructure will be enhanced through the development of web-based modules for introducing high school students to DNA dynamics, methods for manipulating DNA using flow, and for calculating forces on large molecules. These will be based on visualization movies of the DNA from the experiments and the simulation codes, both of which will be made available on the Internet.