Pub Date : 2010-09-23DOI: 10.1002/9780470890905.CH1
S. Giordano, A. Mattoni, L. Colombo
Understanding the mechanical properties of materials with theory traditionally has been done by using continuum methods, ranging from elastic theory (in both linear and nonlinear regimes), to plastic theory, and to fracture mechanics. The computational counterpart of continuum modeling is represented by finite element analysis. Continuum theories have been extremely successful, as proved by the tremendous achievements reached in structural design of buildings, ships, bridges, air-/space crafts, nuclear reactors, and so on. Overall this represents the core of theoretical and computational solid mechanics. In the last 20 years or so, the technological rush toward nano-sized systems has forced researchers to investigate mechanical phenomena at a length scale in which matter no longer can be considered as a continuum. This is the case, for instance, of investigating the crack-related features in a material displaying elastic or structural complexity (or, equivalently, inhomogeneity or disorder) at the nanoscale. This problem of atomic-scale granularity immediately seems to be prohibitive for (standard) solid mechanics. To better elaborate on this
{"title":"Brittle Fracture: From Elasticity Theory to Atomistic Simulations","authors":"S. Giordano, A. Mattoni, L. Colombo","doi":"10.1002/9780470890905.CH1","DOIUrl":"https://doi.org/10.1002/9780470890905.CH1","url":null,"abstract":"Understanding the mechanical properties of materials with theory traditionally has been done by using continuum methods, ranging from elastic theory (in both linear and nonlinear regimes), to plastic theory, and to fracture mechanics. The computational counterpart of continuum modeling is represented by finite element analysis. Continuum theories have been extremely successful, as proved by the tremendous achievements reached in structural design of buildings, ships, bridges, air-/space crafts, nuclear reactors, and so on. Overall this represents the core of theoretical and computational solid mechanics. In the last 20 years or so, the technological rush toward nano-sized systems has forced researchers to investigate mechanical phenomena at a length scale in which matter no longer can be considered as a continuum. This is the case, for instance, of investigating the crack-related features in a material displaying elastic or structural complexity (or, equivalently, inhomogeneity or disorder) at the nanoscale. This problem of atomic-scale granularity immediately seems to be prohibitive for (standard) solid mechanics. To better elaborate on this","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470890905.CH1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50685433","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}
Pub Date : 2010-09-23DOI: 10.1002/9780470890905.CH6
Sophya Garashchuk, V. Rassolov, O. Prezhdo
{"title":"Semiclassical Bohmian Dynamics","authors":"Sophya Garashchuk, V. Rassolov, O. Prezhdo","doi":"10.1002/9780470890905.CH6","DOIUrl":"https://doi.org/10.1002/9780470890905.CH6","url":null,"abstract":"","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470890905.CH6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50685629","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}
Pub Date : 2010-09-23DOI: 10.1002/9780470890905.CH5
M. Berkowitz, J. Kindt
{"title":"Molecular Detailed Simulations of Lipid Bilayers","authors":"M. Berkowitz, J. Kindt","doi":"10.1002/9780470890905.CH5","DOIUrl":"https://doi.org/10.1002/9780470890905.CH5","url":null,"abstract":"","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50685562","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}
Pub Date : 2007-04-30DOI: 10.1002/9780470189078.CH3
J. Mittal, W. P. Krekelberg, J. Errington, Thomas M Truskett
{"title":"Computing Free Volume, Structural Order, and Entropy of Liquids and Glasses","authors":"J. Mittal, W. P. Krekelberg, J. Errington, Thomas M Truskett","doi":"10.1002/9780470189078.CH3","DOIUrl":"https://doi.org/10.1002/9780470189078.CH3","url":null,"abstract":"","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470189078.CH3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50651534","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}
Pub Date : 2007-04-30DOI: 10.1002/9780470189078.CH6
L. Gagliardi
Ab initio quantum chemistry has advanced so far in the last 40 years that it now allows the study of molecular systems containing any atom in the Periodic Table. Transition metal and actinide compounds can be treated routinely, provided that electron correlation and relativistic effects are properly taken into account. Computational quantum chemical methods can be employed in combination with experiment, to predict a priori, to confirm, or eventually, to refine experimental results. These methods can also predict the existence of new species, which may eventually be made by experimentalists. This latter use of computational quantum chemistry is especially important when one considers experiments that are not easy to handle in a laboratory, as, for example, explosive or radioactive species. It is clear that a good understanding of the chemistry of such species can be useful in several areas of scientific and technological exploration. Quantum chemistry can model molecular properties and transformations, and in
{"title":"Transition metal and actinide containing systems studied with multiconfigurational quantum chemical methods","authors":"L. Gagliardi","doi":"10.1002/9780470189078.CH6","DOIUrl":"https://doi.org/10.1002/9780470189078.CH6","url":null,"abstract":"Ab initio quantum chemistry has advanced so far in the last 40 years that it now allows the study of molecular systems containing any atom in the Periodic Table. Transition metal and actinide compounds can be treated routinely, provided that electron correlation and relativistic effects are properly taken into account. Computational quantum chemical methods can be employed in combination with experiment, to predict a priori, to confirm, or eventually, to refine experimental results. These methods can also predict the existence of new species, which may eventually be made by experimentalists. This latter use of computational quantum chemistry is especially important when one considers experiments that are not easy to handle in a laboratory, as, for example, explosive or radioactive species. It is clear that a good understanding of the chemistry of such species can be useful in several areas of scientific and technological exploration. Quantum chemistry can model molecular properties and transformations, and in","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470189078.CH6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50651589","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}
Pub Date : 2007-02-14DOI: 10.1002/9780470116449.CH3
A. Fernández-Ramos, Benjamin A. Ellingson, B. Garrett, D. Truhlar
This review describes the application of variational transition state theory (VTST) to the calculation of chemical reaction rates. In 1985 two of us, together with Alan D. Isaacson, wrote a book chapter on this subject entitled “Generalized Transition State Theory” for the multi-volume series entitled Theory of Chemical Reaction Dynamics.1 Since that time, variational transition state theory has undergone important improvements due mainly to the ability of this theory to adapt to more challenging problems. For instance, the 1985 chapter mainly describes the application of VTST to bimolecular reactions involving 3–6 atoms, which were the state-of-the-art at that moment. The study of those reactions by VTST dynamics depended on the construction of an analytical potential energy surface (PES). Nowadays, thanks to the development of more efficient algorithms and more powerful computers, the situation is completely different, and most rate calculations are based on “on the fly” electronic structure calculations, which together with hybrid approaches, like combined quantum mechanical molecular mechanical methods (QM/MM), allow researchers to apply VTST to systems with hundreds or even tens of thousands of atoms. Three other major advances since 1985 are that transition state dividing surfaces can now be defined much more realistically, more accurate methodsmore » have been developed to include multidimensional quantum mechanical tunneling into VTST, and the theory has also been extended to reactions in condensed phases.« less
本文综述了变分过渡态理论在化学反应速率计算中的应用。1985年，我们中的两人与艾伦·d·艾萨克森(Alan D. Isaacson)一起，为《化学反应动力学理论》(Theory of Chemical Reaction dynamics)多卷本系列撰写了一本书的章节，题目是“广义过渡态理论”。从那时起，变分过渡态理论经历了重要的改进，主要是由于该理论能够适应更具有挑战性的问题。例如，1985年的章节主要描述了VTST在涉及3-6个原子的双分子反应中的应用，这在当时是最先进的。这些反应的动力学研究依赖于解析势能面(PES)的建立。如今，由于更高效的算法和更强大的计算机的发展，情况完全不同了，大多数速率计算都是基于“动态”电子结构计算，再加上混合方法，如组合量子力学分子力学方法(QM/MM)，使研究人员能够将VTST应用于具有数百甚至数万个原子的系统。自1985年以来的其他三个主要进展是:现在可以更实际地定义过渡态划分面，已经开发出更精确的方法，将多维量子力学隧道效应纳入到VTST中，并且该理论也已扩展到凝聚态反应。«少
{"title":"Variational Transition State Theory with Multidimensional Tunneling","authors":"A. Fernández-Ramos, Benjamin A. Ellingson, B. Garrett, D. Truhlar","doi":"10.1002/9780470116449.CH3","DOIUrl":"https://doi.org/10.1002/9780470116449.CH3","url":null,"abstract":"This review describes the application of variational transition state theory (VTST) to the calculation of chemical reaction rates. In 1985 two of us, together with Alan D. Isaacson, wrote a book chapter on this subject entitled “Generalized Transition State Theory” for the multi-volume series entitled Theory of Chemical Reaction Dynamics.1 Since that time, variational transition state theory has undergone important improvements due mainly to the ability of this theory to adapt to more challenging problems. For instance, the 1985 chapter mainly describes the application of VTST to bimolecular reactions involving 3–6 atoms, which were the state-of-the-art at that moment. The study of those reactions by VTST dynamics depended on the construction of an analytical potential energy surface (PES). Nowadays, thanks to the development of more efficient algorithms and more powerful computers, the situation is completely different, and most rate calculations are based on “on the fly” electronic structure calculations, which together with hybrid approaches, like combined quantum mechanical molecular mechanical methods (QM/MM), allow researchers to apply VTST to systems with hundreds or even tens of thousands of atoms. Three other major advances since 1985 are that transition state dividing surfaces can now be defined much more realistically, more accurate methodsmore » have been developed to include multidimensional quantum mechanical tunneling into VTST, and the theory has also been extended to reactions in condensed phases.« less","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470116449.CH3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51147667","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}
Pub Date : 2007-01-05DOI: 10.1002/9780470125847.CH3
Jiali Gao
{"title":"Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials","authors":"Jiali Gao","doi":"10.1002/9780470125847.CH3","DOIUrl":"https://doi.org/10.1002/9780470125847.CH3","url":null,"abstract":"","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470125847.CH3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51148087","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}
Pub Date : 2007-01-05DOI: 10.1002/9780470125915.CH5
C. Mundy, S. Balasubramanian, K. Bagchi, M. Tuckerman, G. Martyna, M. Klein
{"title":"Nonequilibrium Molecular Dynamics","authors":"C. Mundy, S. Balasubramanian, K. Bagchi, M. Tuckerman, G. Martyna, M. Klein","doi":"10.1002/9780470125915.CH5","DOIUrl":"https://doi.org/10.1002/9780470125915.CH5","url":null,"abstract":"","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470125915.CH5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51147825","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}
Pub Date : 2007-01-05DOI: 10.1002/9780470125892.CH6
Chung F. Wong, Thomas S. Thacher, H. Rabitz
{"title":"Sensitivity Analysis in Biomolecular Simulation","authors":"Chung F. Wong, Thomas S. Thacher, H. Rabitz","doi":"10.1002/9780470125892.CH6","DOIUrl":"https://doi.org/10.1002/9780470125892.CH6","url":null,"abstract":"","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470125892.CH6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51147743","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}
Pub Date : 2007-01-05DOI: 10.1002/9780470125885.CH6
G. Ravishanker, P. Auffinger, David R. Langley, B. Jayaram, Matthew A. Young, David L. Beveridge
{"title":"Treatment of Counterions in Computer Simulations of DNA","authors":"G. Ravishanker, P. Auffinger, David R. Langley, B. Jayaram, Matthew A. Young, David L. Beveridge","doi":"10.1002/9780470125885.CH6","DOIUrl":"https://doi.org/10.1002/9780470125885.CH6","url":null,"abstract":"","PeriodicalId":51148,"journal":{"name":"Reviews in Computational Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/9780470125885.CH6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51148179","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：