Coarse-Graining of Molecular Liquids in Time and Space

俄勒冈州大学的Marina Guenza获得了化学系化学理论、模型和计算方法项目的奖项。 Guenza博士开发计算和理论方法来研究复杂的分子液体。这种计算机模拟是有用的，因为它们可以解释基于液体分子性质的实验结果。然而，他们在他们可以研究的系统的大小方面有严重的限制。 为了允许模拟更大的系统，Guenza和同事采用了一种粗粒化，即粗粒化积分方程理论（IECG）。 这种方法只使用必要的细节 从而减少计算时间。 这允许研究大型和更复杂的系统。该方法已被证明是非常准确的结构，热力学和动力学性质的预测。该项目的主要目标是进一步优化该方法，将其扩展到许多系统，并使想要使用该方法的科学家能够使用该方法。该项目的第二个方面侧重于进一步发展研究蛋白质、核酸及其复合物的方法。Guenza和她的研究小组从事外展活动，以高中学生从农村俄勒冈州学区。本研究的重点是扩展复杂分子液体模拟的长度尺度和时间尺度范围。 在第一个项目中，Guenza及其同事正在扩展粗粒化积分方程理论（IECG）方法的能力，以处理非均匀分子液体，例如固体界面。在第二个项目中，他们正在努力扩展朗之万蛋白质动力学方程（LE4PD）来处理蛋白质，核酸及其复合物。该方法是基于一个朗之万方程的大分子在溶液中的动力学，这也占局部构象障碍和内部疏水区域的大分子的存在下。发展理论来描述长时间跨越障碍的动态与马尔可夫状态模型的整合是这项工作的一个关键组成部分。

Marina Guenza of the University of Oregon is supported by an award from the Chemical Theory, Models and Computational Methods program in the Division of Chemistry. Dr. Guenza develops computational and theoretical methods to study complex molecular liquid. Such computer simulations are useful because they can explain experimental findings based on the molecular nature of the liquid. However, they have severe limitations in the size of the system that they can study. To allow simulation of larger systems, Guenza and coworkers employ a kind of coarse graining, the Integral Equation theory of Coarse-Graining (IECG). This approach uses only essential details in the description of the molecules thereby reducing computational time. This allows for the study of large and more complex systems. The method has been shown to be very accurate in its predictions of structural, thermodynamic, and dynamical properties. Further optimization of the method, its extension to many systems, and making the method accessible to the scientists that want to use it, are the main goals of this project. A second aspect of the project focuses on the further development of an approach to study proteins, nuclear acids and their complexes. Guenza and her research group engage in outreach activities to high school students from rural Oregon school districts. The focus of this research is to extend the range of length scales and time scales where complex molecular liquids can be simulated. In the first project, Guenza and coworkers are extending the capabilities of the Integral Equation theory of Coarse-Graining (IECG) approach to treat non-uniform molecular liquids, for example, at solid interfaces. In the second project, they are working to extend the Langevin Equation for Protein Dynamics (LE4PD) to treat proteins, nucleic acids, and their complexes. The approach is based on a Langevin equation for the dynamics of macromolecules in solution, which also accounts for the presence of local conformational barriers and the internal hydrophobic region in the macromolecule. Developing the theory to describe the long-time barrier-crossing dynamics by integration with Markov State Models is a key component of this work.