Many-Body Expansion of Direct and Mutual Polarization Models

加州大学伯克利分校的Teresa Head-Gordon获得了化学部化学理论、模型和计算方法项目的支持，以开发可用于对复杂分子系统的行为做出准确预测的计算和理论模型和方法。他们正在开发和测试几个具有成本效益的近似模型的准确性。目标是了解这些近似模型何时是足够的，以及何时需要更昂贵和更准确的模型。Head-Gordon教授和她的同事使用他们的方法研究了几个重要的分子和生物分子系统的性质和行为，包括过冷水、离子液体和蛋白质。离子液体比工业过程中使用的传统溶剂更环保。例如，离子液体能够溶解生物植物材料，从而可以将它们转化为可再生能源产品。Head-Gordon团队还研究了从水中的小肽到蛋白质-蛋白质和蛋白质-核酸相互作用的形成的生物系统。这种相互作用是多种生物学过程所必需的，如信号传递、基因表达调控、细胞分裂和DNA修复。该项目的另一个目标是促进本科生研究的机会，并指导妇女在自然科学方面。Head-Gordon研究小组开发了极化的多体展开(MBE)，以解决具有更精确力场的大型凝聚相系统的表征。原则上，相互极化模型对经典力场的物理学提供了重大改进。然而，相应增加的计算成本使得凝聚相观测值的统计收敛变得更加困难。研究人员正在分析四种不同极化模型对三体截断的MBE的近似质量：IAMOEBA：只考虑直接极化的原子论模型；阿米巴：原子点偶极模型；PB-SAM：一种新的线性化泊松-玻尔兹曼方程(PBE)的半解析解，它考虑了完全相互极化；以及IPB-SAM：只考虑直接极化的原子论模型。新的基于原子论的极化模型和算法为散装水和离子液体以及多肽和蛋白质提供了更复杂的模型物理水平。PBE的新PB-SAM配方允许模拟复杂的形成机制和缔合率，这是理解拥挤的细胞环境中功能所需的，例如，大肠杆菌细胞质中的~1000个蛋白质或其他复杂材料如Nafion。此外，它还为化学软件的使用者提供了正确应用理论模型的实用指南，关于凝聚相化学体系的统计性质和机制实际上需要比经典的成对加性力场有所改进。

Teresa Head-Gordon of the University of California, Berkeley is supported by an award from the Chemical Theory, Models and Computational Methods program in the Chemistry Division to develop computational and theoretical models and methods that can be used to make accurate predictions for the behavior of complex molecular systems. They are developing and testing the accuracy of several cost-effective approximate models. The goal is to understand when these approximate models are adequate and when more costly and accurate models are required. Professor Head-Gordon and her coworkers use their methods to study the properties and behavior of several important molecular and biomolecular systems including supercooled water, ionic liquids and proteins. Ionic liquids are more environmentally benign than traditional solvents used in industrial processes. For example, ionic liquids are able to dissolve biological plant materials so that they may be converted into renewable energy products. The Head-Gordon group also studies biological systems ranging from small peptides in water to the formation of protein-protein and protein-nucleic acid interactions. Such interactions are required for diverse biological processes such as signaling, regulation of gene expression, cell division, and DNA repair. An additional goal of this project is to foster opportunities for undergraduate research and to mentor women in the physical sciences. The Head-Gordon research group has developed the Many-Body Expansion (MBE) of polarization to tackle the characterization of large condensed phase systems with a more accurate force field. In principle, mutually polarizable models offer a significant improvement in the physics of classical force fields. However, the corresponding increased computational cost renders statistical convergence of condensed phase observables more difficult to achieve. The researchers are analyzing the quality of the approximation to the MBE truncated at 3-bodies for four different polarizable models: iAMOEBA: an atomistic model that only accounts for direct polarization; AMOEBA: an atomistic point dipole model that accounts for mutual polarization; PB-SAM: a new semi-analytical solution to the linearized Poisson-Boltzmann equation (PBE) that accounts for complete mutual polarization; and iPB-SAM: devised to account for direct polarization only. The new atomistic-based polarizable models and algorithms provide a more sophisticated level of model physics for bulk water and ionic liquids as well as peptides and proteins. New PB-SAM formulations of the PBE allow simulation of the mechanism of complex formation and rate of association needed for understanding function in the crowded cellular environment, for example ~1000 proteins in E. coli cytoplasm or other complex materials such as Nafion. In addition it provides a practical guide to consumers of chemical software in the proper application of theoretical models, as to which statistical properties and mechanisms of condensed phase chemical systems actually require an advancement over a classical pairwise additive force field.