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

提案编号： CTS-0522564主要制造商：E.S.G. SHAQFEHINSTITUTION： 斯坦福大学PI的研究小组最近的合作工作已经证明，在拉伸流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。 在这种转变中，存在构象滞后区域，其中两个动力学分离的构象状态可以以相同的无量纲拉伸速率值存在。 这是链内流体动力学相互作用的直接结果。 这种材料的流变学建模需要一种新的范式。在这项资助下，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实验来开发这种范式的元素。 特别是，布朗动力学模拟将被开发来研究的动力学过程，是理解构象滞后的原则：解开的动力学（从卷曲-解开的过渡），崩溃的动力学（从扩展到卷曲状态），和波动的动力学诱导的“跳跃”之间的滞后制度的扩展和卷曲状态。不同的流动类型，包括平面混合流，三维线性流，和非线性流，将被研究，展示这种构象滞后的新特性。 大规模模拟和单分子实验的结合提供了一个强大的工具，使研究人员能够研究聚合物溶液流变学中的这种新范式。 溶液流变学中构象滞后和构象相变的研究尚处于起步阶段，因此这些新思想的全面广泛影响还不完全明显。 已经清楚的是，在许多情况下，溶液中的应力状态取决于与这些滞后状态下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。拟议的工作有更广泛的影响，在培训方面，并教本科生和研究生一种新的方式来思考流动中的分子动力学。 通过这个项目，研究生和本科生将在这个多学科的研究，涉及流体力学，微细加工和材料加工，以及数值方法的培训。 Shaqfeh教授已经通过CPIMA材料中心参与了外展计划，其中包括在大学为代表性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，向高中生介绍DNA动力学、使用流动操纵DNA的方法以及计算大分子上的力。这些将基于实验和模拟代码的DNA的可视化电影，两者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.