POWRE: Issues in Condensed Matter Physics: Phase Separation and Solvated Protein Structure

9870464 Sagui本项目涵盖凝聚态物理的两条理论研究线；弹性场对二元合金与粘弹性流体体系相分离过程的影响以及与在溶剂化环境中进行蛋白质结构分析的x射线数据的改进相关的问题。在相分离过程中发生的生长和排序动力学决定了材料的许多重要微观结构。反过来，材料的许多有趣的机械、电气和磁性能取决于其微观结构。典型地，当一个系统从相图的单相部分迅速淬灭到共存曲线内的一点时，它是动态有序的。长波长的不稳定性创造了一个初始的水滴状或相互连接的结构，随着时间的推移，它增长到宏观大小。人们早就认识到，弹性场的存在对相分离过程有重要的影响。例如，在合金系统中，已经观察到和/或预测了形状转变、畴的有序、动力学减速和可能的反向粗化效应。然而，目前对这些效应的理论认识尚不完整，本项目旨在通过适当的朗格万方程的大规模三维模拟来研究弹性场对二元合金体系的影响。弹性效应在粘弹性流体和泡沫中也起着重要作用。粘弹性流体，如各种聚合物熔体，是非牛顿流体，其特点是在相对短的时间尺度上具有弹性，而在长时间尺度上具有流动性。在相分离过程中，这些体系受到远程相关弹性场的强烈影响，其对生长动力学的影响目前尚不清楚。本文将采用数值模拟的方法研究粘弹性流体的相分离问题。研究的第二部分旨在采用最先进的分子动力学和优化技术，作为改进蛋白质结构计算的x射线数据的辅助过程。蛋白质是复杂的、具有生物活性的大分子，具有多种不同的结构和动态特性。人们早就知道，它们的许多活性生物学功能是由它们的三维结构决定的，它们折叠以产生特定的结合位点和/或催化活性区域。从蛋白质的基本氨基酸序列预测蛋白质结构是该领域的突出问题之一。正是在这种情况下，基于x射线数据的结构预测已被证明是至关重要的。该项目旨在通过引入新开发的优化技术来促进结构预测，从而推动这一领域的发展。PI将特别集中在蛋白质结构模型不健全或定义不清的情况下，如溶剂化环境中的蛋白质环的情况。这是在研究和教育领域的女性专业机会（POWRE）计划下提供的访问教授奖学金，由MPS多学科活动办公室（OMA）共同资助。相分离活动是PI当前工作的自然延伸，而蛋白质结构研究将使PI过渡到一个新的研究领域，即分子生物学。

9870464 Sagui This project covers two lines of theoretical investigations in Condensed Matter Physics; effects of elastic fields on the process of phase separation in binary alloy and viscoelastic fluid systems; and issues related to the refinement of X-ray data for structural analysis of proteins in a solvated environment. The kinetics of growth and ordering that take place during the process of phase separation determines much of the important microstructure of materials. In turn, many of the interesting mechanical, electrical and magnetic properties of materials depend on the microstructure. Typically, when a system is rapidly quenched from the single-phase part of its phase diagram to a point inside its coexistence curve, it orders kinetically. A long-wavelength instability creates an initial droplet-like or interconnected structure, which grows to macroscopic size as time evolves. It has long been realized that the presence of elastic fields influences the process of phase separation in important ways. For example, in alloy systems shape transformations, ordering of domains, a kinetic slowing down, and possibly reverse coarsening effects have either been observed and/or predicted. However, theoretical understanding of these effects is at present incomplete, and this project aims to investigate the effects of elastic field on binary alloy systems through large-scale three-dimensional simulations of appropriate Langevin equations. Elastic effects also play an important role in viscoelastic fluids and foams. Viscoelastic fluids such as various polymer melts, are non-Newtonian fluids that are charac terized by elasticity on relatively short time scales, and fluidity on long time scales. During phase separation, these systems are strongly influenced by the presence of long-range, correlated elastic fields, whose influence on the growth kinetics are presently not understood. The problem of phase separation of viscoelastic fluids will be investigated with numerica l simulations. The second part of the research is aimed at employing state-of-the art molecular dynamics and optimization techniques as aids in the process of refining X-ray data for protein structure calculations. Proteins are complex, biologically active macromolecules exhibiting a large variety of different structural and dynamic properties. It has long been known that much of their active biological functions are determined by their three-dimensional structure, which fold so as to produce specific binding sites and/or catalytically active regions. One of the outstanding problems in the field, is the prediction of protein structure from its basic amino acid se quence. It is in this context that structural predictions based on X-ray data have proven to be of paramount importance. The project aims to move this field forward, through the introduction of newly developed optimization techniques in order to facilitate structural predictions. The PI will concentrate specifically on cases where models for the protein structure are ill or poorly defined, as in the case of protein loops in a solvated environment. %%% This is a Visiting Professorship grant made under the Professional Opportunities for Women in Research and Education (POWRE) program, and is co-funded by the MPS Office of Multidisciplinary Activities(OMA). The phase separation activities are natural extensions of the current work of the PI, while the protein structure research will enable the PI to transition into a new area of research, namely that of molecular biology.