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Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)最新文献

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Efficient Sampling of High-Dimensional Free Energy Landscapes: A Review of Parallel Bias Metadynamics 高维自由能景观的有效采样:平行偏置元动力学综述
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2021-01-01 DOI: 10.1007/978-981-33-6639-8_6
S. Alamdari, J. Sampath, A. Prakash, Luke D. Gibson, J. Pfaendtner
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引用次数: 0
Foundations of Molecular Modeling and Simulation: Select Papers from FOMMS 2018 分子建模与模拟的基础:2018年的论文选集
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2021-01-01 DOI: 10.1007/978-981-33-6639-8
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引用次数: 0
Strain Controlling Catalytic Efficiency of Water Oxidation for Ni1−xFexOOH Alloy 应变控制Ni1−xFexOOH合金水氧化催化效率
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2019-02-13 DOI: 10.1007/978-981-33-6639-8_1
Ester Korkus Hamal, M. C. Toroker
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引用次数: 0
Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion. 通过多态迭代玻尔兹曼反演建立粗粒度水力场。
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2016-01-01 Epub Date: 2016-06-02 DOI: 10.1007/978-981-10-1128-3_3
Timothy C Moore, Christopher R Iacovella, Clare McCabe

A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use of structure-based coarse-graining methods. The model is derived to match the bulk and interfacial properties of liquid water and improves upon previous work that used single state iterative Boltzmann inversion. The model accurately reproduces the density and structural correlations of water at 305 K and 1.0 atm, stability of a liquid droplet at 305 K, and shows little tendency to crystallize at physiological conditions. This work also illustrates several advantages of using multistate iterative Boltzmann inversion for deriving generally applicable coarse-grained forcefields.

利用多态迭代玻尔兹曼反演建立了粗粒度水模型。根据之前的工作，使用 k-means 算法将多个水分子动态映射到单个粗粒度珠子上，从而可以使用基于结构的粗粒度方法。推导出的模型与液态水的体积和界面特性相匹配，并改进了之前使用单态迭代玻尔兹曼反演的工作。该模型准确地再现了水在 305 K 和 1.0 atm 下的密度和结构相关性，以及液滴在 305 K 下的稳定性，并且在生理条件下几乎没有结晶倾向。这项工作还说明了使用多态迭代玻尔兹曼反演来推导普遍适用的粗粒度力场的几个优点。
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引用次数: 0
Molecular Modeling and the Materials Genome: Foundations of Molecular Modeling and Simulation 2015, FOMMS 2015, The Resort at the Mountains, Mt. Hood, OR, USA, July 12-16, 2015 Molecular Modeling and Materials Genome: Foundations of Molecular Modeling and Simulation 2015, formms 2015, the Resort at the Mountains, Mt. Hood, OR, USA, 2015年7月12-16日
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2016-01-01 DOI: 10.1007/978-981-10-1128-3
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引用次数: 0
A Discontinuous Potential Model for Protein-Protein Interactions. 蛋白质-蛋白质相互作用的不连续电位模型。
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2016-01-01 Epub Date: 2016-06-02 DOI: 10.1007/978-981-10-1128-3_1
Qing Shao, Carol K Hall

Protein-protein interactions play an important role in many biologic and industrial processes. In this work, we develop a two-bead-per-residue model that enables us to account for protein-protein interactions in a multi-protein system using discontinuous molecular dynamics simulations. This model deploys discontinuous potentials to describe the non-bonded interactions and virtual bonds to keep proteins in their native state. The geometric and energetic parameters are derived from the potentials of mean force between sidechain-sidechain, sidechain-backbone, and backbone-backbone pairs. The energetic parameters are scaled with the aim of matching the second virial coefficient of lysozyme reported in experiment. We also investigate the performance of several bond-building strategies.

蛋白质之间的相互作用在许多生物和工业过程中起着重要作用。在这项工作中，我们开发了一个每个残基两个头的模型，使我们能够使用不连续的分子动力学模拟来解释多蛋白质系统中的蛋白质-蛋白质相互作用。该模型利用不连续电位来描述非键相互作用和虚拟键，以保持蛋白质的天然状态。几何参数和能量参数由侧链-侧链、侧链-主干和主干-主干对之间的平均力势导出。为了与实验报道的溶菌酶的二次维里系数相匹配，对能量值进行了标定。我们还研究了几种债券建设策略的绩效。
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引用次数: 0
Atomistic Modeling and Simulation for Solving Gas Extraction Problems 求解瓦斯抽取问题的原子建模与仿真
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2015-01-01 DOI: 10.1007/978-981-10-1128-3_9
G. Norman, V. Pisarev, G. Smirnov, V. Stegailov
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引用次数: 4
Homogeneous Nucleation of [dmim+][Cl-] from its Supercooled Liquid Phase: A Molecular Simulation Study [dmim+][Cl-]过冷液相均形核的分子模拟研究
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2015-01-01 DOI: 10.1007/978-981-10-1128-3_7
Xiaoxia He, Yan-Fei Shen, F. Hung, E. Santiso
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引用次数: 0
A Hierarchical, Component Based Approach to Screening Properties of Soft Matter 基于分层、分量的软物质性质筛选方法
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2015-01-01 DOI: 10.1007/978-981-10-1128-3_5
Christoph Klein, J. Sallai, Trevor J. Jones, C. Iacovella, C. McCabe, P. Cummings
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引用次数: 38
Influence of the Precursor Composition and Reaction Conditions on Raney-Nickel Catalytic System 前驱体组成及反应条件对raney -镍催化体系的影响
Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.)
Pub Date : 2015-01-01 DOI: 10.1007/978-981-10-1128-3_8
S. Schweizer, R. Chaudret, T. Spyriouni, J. Low, L. Subramanian
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引用次数: 2
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