Many-Body Expansion of Direct and Mutual Polarization Models
直接极化和互极化模型的多体扩展
基本信息
- 批准号:1363320
- 负责人:
- 金额:$ 42万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Continuing Grant
- 财政年份:2014
- 资助国家:美国
- 起止时间:2014-07-01 至 2017-06-30
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
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.
加州大学伯克利分校的Teresa Head-Gordon获得了化学系化学理论、模型和计算方法项目的奖励,以开发可用于准确预测复杂分子系统行为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。 我们的目标是了解这些近似模型何时是足够的,何时需要更昂贵和准确的模型。 教授头戈登和她的同事使用他们的方法来研究几个重要的分子和生物分子系统,包括过冷水,离子液体和蛋白质的性质和行为。 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,使得它们可以转化为可再生能源产品。 海德-戈登小组还研究生物系统,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。 这种相互作用是多种生物过程所必需的,如信号传导、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,并指导物理科学领域的妇女。海德-戈登研究小组开发了偏振的多体展开(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,相互极化模型在经典力场的物理学中提供了一个显着的改进。然而,相应增加的计算成本使得凝聚相观测量的统计收敛更难以实现。研究人员正在分析四种不同极化模型在三体截断的MBE近似的质量:iAMOEBA:一种只考虑直接极化的原子模型; AMOEBA:一种考虑互极化的原子点偶极模型; PB-SAM:一种新的线性化泊松-玻尔兹曼方程(PBE)的半解析解,它考虑了完全的互极化;和iPB-SAM:设计成仅考虑直接极化。新的基于原子的可极化模型和算法为本体水和离子液体以及肽和蛋白质提供了更复杂的模型物理水平。PBE的新PB-SAM制剂允许模拟理解拥挤细胞环境中的功能所需的复合物形成机制和缔合速率,例如大肠杆菌中的约1000种蛋白质。coli细胞质或其他复合材料如Nafion。此外,它提供了一个实用的指导化学软件的消费者在正确应用的理论模型,凝聚相化学系统的统计特性和机制,实际上需要一个进步,在一个经典的成对加性力场。
项目成果
期刊论文数量(6)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Parallel implementation of approximate atomistic models of the AMOEBA polarizable model
AMOEBA极化模型的近似原子模型的并行实现
- DOI:10.1016/j.cplett.2016.10.015
- 发表时间:2016
- 期刊:
- 影响因子:2.8
- 作者:Demerdash, Omar;Head-Gordon, Teresa
- 通讯作者:Head-Gordon, Teresa
An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction
- DOI:10.1063/1.4933375
- 发表时间:2015-11-07
- 期刊:
- 影响因子:4.4
- 作者:Albaugh, Alex;Demerdash, Omar;Head-Gordon, Teresa
- 通讯作者:Head-Gordon, Teresa
TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
- DOI:10.1063/1.4962909
- 发表时间:2016-09-28
- 期刊:
- 影响因子:4.4
- 作者:Dziedzic, Jacek;Mao, Yuezhi;Skylaris, Chris-Kriton
- 通讯作者:Skylaris, Chris-Kriton
Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase
- DOI:10.1021/acs.jctc.6b00335
- 发表时间:2016-08-01
- 期刊:
- 影响因子:5.5
- 作者:Demerdash, Omar;Head-Gordon, Teresa
- 通讯作者:Head-Gordon, Teresa
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Teresa Head-Gordon其他文献
Amyloid-Beta Heterogeneous Conformational Ensembles: Differences Between the 40- and 42-Residue Peptides and Implications for Dimer Polyamorphism
- DOI:
10.1016/j.bpj.2011.11.3437 - 发表时间:
2012-01-31 - 期刊:
- 影响因子:
- 作者:
K. Aurelia Ball;Aaron H. Phillips;Nicolas L. Fawzi;David E. Wemmer;Teresa Head-Gordon - 通讯作者:
Teresa Head-Gordon
The Combined Force Field-Sampling Problem in Simulation of Intrinsically Disordered Peptides
- DOI:
10.1016/j.bpj.2017.11.3641 - 发表时间:
2018-02-02 - 期刊:
- 影响因子:
- 作者:
James Lincoff;Sukanya Sasmal;Teresa Head-Gordon - 通讯作者:
Teresa Head-Gordon
A Coarse Grained Molecular Dynamics Study of Amyloid Beta Transmembrane Pores
- DOI:
10.1016/j.bpj.2011.11.1331 - 发表时间:
2012-01-31 - 期刊:
- 影响因子:
- 作者:
Shachi Katira;Teresa Head-Gordon - 通讯作者:
Teresa Head-Gordon
Biological insights from integrative modeling of intrinsically disordered protein systems
来自内在无序蛋白质系统综合建模的生物学见解
- DOI:
10.1016/j.sbi.2025.103063 - 发表时间:
2025-08-01 - 期刊:
- 影响因子:7.000
- 作者:
Zi Hao Liu;Maria Tsanai;Oufan Zhang;Teresa Head-Gordon;Julie D. Forman-Kay - 通讯作者:
Julie D. Forman-Kay
Evaluation and Improvement of the Amber ff99SB Force Field with an Advanced Water Model
- DOI:
10.1016/j.bpj.2010.12.1900 - 发表时间:
2011-02-02 - 期刊:
- 影响因子:
- 作者:
Paul S. Nerenberg;Clare So;Ajay Tripathy;Teresa Head-Gordon - 通讯作者:
Teresa Head-Gordon
Teresa Head-Gordon的其他文献
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{{ truncateString('Teresa Head-Gordon', 18)}}的其他基金
Reactive Force Field Design Guided by Energy Decomposition Analysis
能量分解分析引导的反作用力场设计
- 批准号:
2313791 - 财政年份:2023
- 资助金额:
$ 42万 - 项目类别:
Continuing Grant
Reactive and Non-Reactive Force Field Design Guided by Advances in Energy Decomposition Analysis
以能量分解分析进展为指导的反应性和非反应性力场设计
- 批准号:
1955643 - 财政年份:2020
- 资助金额:
$ 42万 - 项目类别:
Continuing Grant
From Theory of Energy Decomposition Analysis to Rational Force Field Design
从能量分解分析理论到合理力场设计
- 批准号:
1665315 - 财政年份:2017
- 资助金额:
$ 42万 - 项目类别:
Continuing Grant
Collaborative Research: S2I2: Conceptualization of a Center for Biomolecular Simulation
合作研究:S2I2:生物分子模拟中心的概念化
- 批准号:
1331445 - 财政年份:2014
- 资助金额:
$ 42万 - 项目类别:
Standard Grant
Collaborative Research: SI2-CHE: Development and Deployment of Chemical Software for Advanced Potential Energy Surfaces
合作研究:SI2-CHE:先进势能表面化学软件的开发和部署
- 批准号:
1265731 - 财政年份:2013
- 资助金额:
$ 42万 - 项目类别:
Standard Grant
Conference: Undergraduate Opportunities at the UC System Wide Bioengineering Symposium, June 21 - June 23, 2012, Berkeley, CA
会议:加州大学系统生物工程研讨会本科生机会,2012 年 6 月 21 日至 6 月 23 日,加利福尼亚州伯克利
- 批准号:
1243416 - 财政年份:2012
- 资助金额:
$ 42万 - 项目类别:
Standard Grant
Potential Energy Surfaces of Various Accuracy for Biomolecular Simulations
用于生物分子模拟的各种精度的势能面
- 批准号:
1147444 - 财政年份:2011
- 资助金额:
$ 42万 - 项目类别:
Standard Grant
Collaborative Research: Cyberinfrastructure for Next Generation Biomolecular Modeling
合作研究:下一代生物分子建模的网络基础设施
- 批准号:
0535710 - 财政年份:2005
- 资助金额:
$ 42万 - 项目类别:
Continuing Grant
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