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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
{"title":"Efficient Sampling of High-Dimensional Free Energy Landscapes: A Review of Parallel Bias Metadynamics","authors":"S. Alamdari, J. Sampath, A. Prakash, Luke D. Gibson, J. Pfaendtner","doi":"10.1007/978-981-33-6639-8_6","DOIUrl":"https://doi.org/10.1007/978-981-33-6639-8_6","url":null,"abstract":"","PeriodicalId":91866,"journal":{"name":"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.)","volume":"292 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76459811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Foundations of Molecular Modeling and Simulation: Select Papers from FOMMS 2018","authors":"","doi":"10.1007/978-981-33-6639-8","DOIUrl":"https://doi.org/10.1007/978-981-33-6639-8","url":null,"abstract":"","PeriodicalId":91866,"journal":{"name":"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.)","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80961208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Strain Controlling Catalytic Efficiency of Water Oxidation for Ni1−xFexOOH Alloy","authors":"Ester Korkus Hamal, M. C. Toroker","doi":"10.1007/978-981-33-6639-8_1","DOIUrl":"https://doi.org/10.1007/978-981-33-6639-8_1","url":null,"abstract":"","PeriodicalId":91866,"journal":{"name":"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.)","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85357296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion.","authors":"Timothy C Moore, Christopher R Iacovella, Clare McCabe","doi":"10.1007/978-981-10-1128-3_3","DOIUrl":"10.1007/978-981-10-1128-3_3","url":null,"abstract":"<p><p>A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the <i>k</i>-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.</p>","PeriodicalId":91866,"journal":{"name":"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.)","volume":"2016 ","pages":"37-52"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7262820/pdf/nihms-1592656.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37999812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"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","authors":"","doi":"10.1007/978-981-10-1128-3","DOIUrl":"https://doi.org/10.1007/978-981-10-1128-3","url":null,"abstract":"","PeriodicalId":91866,"journal":{"name":"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.)","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77350153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"A Discontinuous Potential Model for Protein-Protein Interactions.","authors":"Qing Shao,&nbsp;Carol K Hall","doi":"10.1007/978-981-10-1128-3_1","DOIUrl":"https://doi.org/10.1007/978-981-10-1128-3_1","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":91866,"journal":{"name":"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.)","volume":"2016 ","pages":"1-20"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-981-10-1128-3_1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35059870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Atomistic Modeling and Simulation for Solving Gas Extraction Problems","authors":"G. Norman, V. Pisarev, G. Smirnov, V. Stegailov","doi":"10.1007/978-981-10-1128-3_9","DOIUrl":"https://doi.org/10.1007/978-981-10-1128-3_9","url":null,"abstract":"","PeriodicalId":91866,"journal":{"name":"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.)","volume":"46 1","pages":"137-151"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75298330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Homogeneous Nucleation of [dmim+][Cl-] from its Supercooled Liquid Phase: A Molecular Simulation Study","authors":"Xiaoxia He, Yan-Fei Shen, F. Hung, E. Santiso","doi":"10.1007/978-981-10-1128-3_7","DOIUrl":"https://doi.org/10.1007/978-981-10-1128-3_7","url":null,"abstract":"","PeriodicalId":91866,"journal":{"name":"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.)","volume":"27 1","pages":"107-123"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85133171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"A Hierarchical, Component Based Approach to Screening Properties of Soft Matter","authors":"Christoph Klein, J. Sallai, Trevor J. Jones, C. Iacovella, C. McCabe, P. Cummings","doi":"10.1007/978-981-10-1128-3_5","DOIUrl":"https://doi.org/10.1007/978-981-10-1128-3_5","url":null,"abstract":"","PeriodicalId":91866,"journal":{"name":"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.)","volume":"25 1","pages":"79-92"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82600569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"Influence of the Precursor Composition and Reaction Conditions on Raney-Nickel Catalytic System","authors":"S. Schweizer, R. Chaudret, T. Spyriouni, J. Low, L. Subramanian","doi":"10.1007/978-981-10-1128-3_8","DOIUrl":"https://doi.org/10.1007/978-981-10-1128-3_8","url":null,"abstract":"","PeriodicalId":91866,"journal":{"name":"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.)","volume":"48 1","pages":"125-135"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88041120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
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