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Reviews in Computational Chemistry, Volume 32 计算化学评论,第32卷
Pub Date : 2022-03-25 DOI: 10.1002/9781119625933
G. Crippen
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引用次数: 0
LATTICE‐BOLTZMANN MODELING OF MULTICOMPONENT SYSTEMS 多组分系统的格子BOLTZMANN建模
Pub Date : 2018-10-19 DOI: 10.1002/9781119518068.CH1
U. Schiller, O. Kuksenok
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引用次数: 0
THE CONSTRUCTION OF AB INITIO‐BASED POTENTIAL ENERGY SURFACES 基于从头算的势能曲面的构造
Pub Date : 2018-10-19 DOI: 10.1002/9781119518068.CH5
R. Dawes, E. Quintas-Sánchez
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引用次数: 15
INDEX 索引
Pub Date : 2018-10-19 DOI: 10.1002/9781119518068.index
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引用次数: 0
Reviews in Computational Chemistry, Volume 31 计算化学评论,第31卷
Pub Date : 2018-10-19 DOI: 10.1002/9781119518068
J. Gauld
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引用次数: 3
THE ROLE OF COMPUTATIONS IN CATALYSIS 计算在催化中的作用
Pub Date : 2018-10-19 DOI: 10.1002/9781119518068.CH4
H. Metiu, V. Agarwal, H. Kristoffersen
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引用次数: 0
MODELING MECHANOCHEMISTRY FROM FIRST PRINCIPLES 从第一性原理建模力学化学
Pub Date : 2018-10-19 DOI: 10.1002/9781119518068.CH6
H. Kulik
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引用次数: 2
MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS 绘制蛋白质中的能量传输网络
Pub Date : 2018-05-09 DOI: 10.1002/9781119518068.CH2
D. Leitner, T. Yamato
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the evolution of protein structural change following ligand photolysis, and time-resolved IR and Raman techniques, e.g., have provided detailed pictures of the nature and rate of energy transport in peptides and proteins, including recent advances in identifying transport through individual amino acids of several heme proteins. Computational tools to locate energy transport pathways in proteins have also been advancing. Energy transport pathways in proteins have since some time been identified by molecular dynamics (MD) simulations, and more recent efforts have focused on the development of coarse graining approaches, some of which have exploited analogies to thermal transport in other molecular materials. With the identification of pathways in proteins and protein complexes, network analysis has been applied to locate residues that control protein dynamics and possibly allostery, where chemical reactions at one binding site mediate reactions at distance sites of the protein. In this chapter we review approaches for locating computationally energy transport networks in proteins. We present background into energy and thermal transport in condensed phase and macromolecules that underlies the approaches we discuss before turning to a description of the approaches themselves. We also illustrate the application of the computational methods for locating energy transport networks and simulating energy dynamics in proteins with several examples.
几十年来,蛋白质对分子内发生的化学反应或脉冲激发的反应一直吸引着化学家。近年来,超快x射线研究提供了关于配体光解后蛋白质结构变化演变的更详细信息,时间分辨红外和拉曼技术,例如,提供了肽和蛋白质中能量传输的性质和速率的详细图片,包括通过几种血红素蛋白的单个氨基酸识别传输的最新进展。用于定位蛋白质中能量传输途径的计算工具也在不断发展。一段时间以来,蛋白质中的能量传递途径已经被分子动力学(MD)模拟识别出来,最近的努力集中在粗粒化方法的发展上,其中一些方法利用了其他分子材料中的热传递的类比。随着蛋白质和蛋白质复合物途径的识别,网络分析已被用于定位控制蛋白质动力学和可能的变构的残基,其中一个结合位点的化学反应介导蛋白质距离位点的反应。在本章中,我们回顾了蛋白质中能量传输网络的计算定位方法。在转向方法本身的描述之前,我们介绍了凝聚相和大分子中的能量和热传输的背景,这些方法是我们讨论的方法的基础。我们还举例说明了计算方法在定位能量传输网络和模拟蛋白质能量动力学中的应用。
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引用次数: 13
UNCERTAINTY QUANTIFICATION FOR MOLECULAR DYNAMICS 分子动力学的不确定度量化
Pub Date : 2018-01-04 DOI: 10.1002/9781119518068.CH3
P. Patrone, A. Dienstfrey
The goals of this chapter are twofold. First, we wish to introduce molecular dynamics (MD) and uncertainty quantification (UQ) in a common setting in order to demonstrate how the latter can increase confidence in the former. In some cases, this discussion culminates in our providing practical, mathematical tools that can be used to answer the question, "is this simulation reliable?" However, many questions remain unanswered. Thus, a second goal of this work is to highlight open problems where progress would aid the larger community.
本章的目标有两个。首先,我们希望在一个共同的环境中引入分子动力学(MD)和不确定性量化(UQ),以证明后者如何增加对前者的信心。在某些情况下,这种讨论在我们提供实用的数学工具时达到高潮,这些工具可用于回答“这个模拟可靠吗?”然而,许多问题仍未得到解答。因此,这项工作的第二个目标是突出开放的问题,其中的进展将有助于更大的社区。
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引用次数: 1
Machine Learning in Materials Science 材料科学中的机器学习
Pub Date : 2016-05-06 DOI: 10.1002/9781119148739.CH4
Tim Mueller, A. Kusne, R. Ramprasad
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引用次数: 200
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