Ab Initio Molecular Dynamics Analysis Based on Reduced-Dimensionality Reaction Route Map

Ab Initio Molecular Dynamics Analysis Based on Reduced-Dimensionality Reaction Route Map

Author: Takuro Tsutsumi

Publisher: Springer Nature

Published: 2023-12-05

Total Pages: 123

ISBN-13: 981997321X

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This thesis proposes useful tools, on-the-fly trajectory mapping method and Reaction Space Projector (ReSPer), to analyze chemical reaction mechanisms by combining the reaction route map and the ab initio molecular dynamics. The key concept for the proposed tools is the Cartesian distance between pairwise molecular structures, and a practical procedure to get the optimal distance is introduced. The on-the-fly trajectory mapping method tracks the distance function between reference structures and molecular structures along the trajectory. Although this method provides fruitful insight into dynamic reaction behaviors, the visualization of reaction routes into a low-dimensional space is still challenging because of the multi-dimensionality. ReSPer successfully constructs a low-dimensional reaction space defined by mathematically-selected principal coordinates representing mutual distance relationships in the full-dimensional space. ReSPer also enables us to project trajectories into the reaction space in the reduced dimension. In this thesis, these methods are applied to several reactions, including bifurcating and photochemical reactions, revealing dynamically-allowed reaction mechanisms. This thesis provides robust and versatile tools to elucidate dynamical reaction routes on the basis of the reduced-dimensionality reaction route map and will help control chemical reaction dynamics and select descriptors for machine learning.


Book Synopsis Ab Initio Molecular Dynamics Analysis Based on Reduced-Dimensionality Reaction Route Map by : Takuro Tsutsumi

Download or read book Ab Initio Molecular Dynamics Analysis Based on Reduced-Dimensionality Reaction Route Map written by Takuro Tsutsumi and published by Springer Nature. This book was released on 2023-12-05 with total page 123 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis proposes useful tools, on-the-fly trajectory mapping method and Reaction Space Projector (ReSPer), to analyze chemical reaction mechanisms by combining the reaction route map and the ab initio molecular dynamics. The key concept for the proposed tools is the Cartesian distance between pairwise molecular structures, and a practical procedure to get the optimal distance is introduced. The on-the-fly trajectory mapping method tracks the distance function between reference structures and molecular structures along the trajectory. Although this method provides fruitful insight into dynamic reaction behaviors, the visualization of reaction routes into a low-dimensional space is still challenging because of the multi-dimensionality. ReSPer successfully constructs a low-dimensional reaction space defined by mathematically-selected principal coordinates representing mutual distance relationships in the full-dimensional space. ReSPer also enables us to project trajectories into the reaction space in the reduced dimension. In this thesis, these methods are applied to several reactions, including bifurcating and photochemical reactions, revealing dynamically-allowed reaction mechanisms. This thesis provides robust and versatile tools to elucidate dynamical reaction routes on the basis of the reduced-dimensionality reaction route map and will help control chemical reaction dynamics and select descriptors for machine learning.


New Horizons in Computational Chemistry Software

New Horizons in Computational Chemistry Software

Author: Michael Filatov

Publisher: Springer Nature

Published: 2022-07-30

Total Pages: 316

ISBN-13: 3031076583

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This volume presents the current status of software development in the field of computational and theoretical chemistry and gives an overview of the emerging trends. The challenges of maintaining the legacy codes and their adaptation to the rapidly growing hardware capabilities and the new programming environments are surveyed in a series of topical reviews written by the core developers and maintainers of the popular quantum chemistry and molecular dynamics programs. Special emphasis is given to new computational methodologies and practical aspects of their implementation and application in the computational chemistry codes. Modularity of the computational chemistry software is an emerging concept that enables to bypass the development and maintenance bottleneck of the legacy software and to customize the software using the best available computational procedures implemented in the form of self-contained modules. Perspectives on modular design of the computer programs for modeling molecular electronic structure, non-adiabatic dynamics, kinetics, as well as for data visualization are presented by the researchers actively working in the field of software development and application. This volume is of interest to quantum and computational chemists as well as experimental chemists actively using and developing computational software for their research. Chapters "MLatom 2: An Integrative Platform for Atomistic Machine Learning” and “Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol" are available open access under a CC BY 4.0 License via link.springer.com.


Book Synopsis New Horizons in Computational Chemistry Software by : Michael Filatov

Download or read book New Horizons in Computational Chemistry Software written by Michael Filatov and published by Springer Nature. This book was released on 2022-07-30 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents the current status of software development in the field of computational and theoretical chemistry and gives an overview of the emerging trends. The challenges of maintaining the legacy codes and their adaptation to the rapidly growing hardware capabilities and the new programming environments are surveyed in a series of topical reviews written by the core developers and maintainers of the popular quantum chemistry and molecular dynamics programs. Special emphasis is given to new computational methodologies and practical aspects of their implementation and application in the computational chemistry codes. Modularity of the computational chemistry software is an emerging concept that enables to bypass the development and maintenance bottleneck of the legacy software and to customize the software using the best available computational procedures implemented in the form of self-contained modules. Perspectives on modular design of the computer programs for modeling molecular electronic structure, non-adiabatic dynamics, kinetics, as well as for data visualization are presented by the researchers actively working in the field of software development and application. This volume is of interest to quantum and computational chemists as well as experimental chemists actively using and developing computational software for their research. Chapters "MLatom 2: An Integrative Platform for Atomistic Machine Learning” and “Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol" are available open access under a CC BY 4.0 License via link.springer.com.


Quantum Chemistry in the Age of Machine Learning

Quantum Chemistry in the Age of Machine Learning

Author: Pavlo O. Dral

Publisher: Elsevier

Published: 2022-09-16

Total Pages: 702

ISBN-13: 0323886043

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Quantum chemistry is simulating atomistic systems according to the laws of quantum mechanics, and such simulations are essential for our understanding of the world and for technological progress. Machine learning revolutionizes quantum chemistry by increasing simulation speed and accuracy and obtaining new insights. However, for nonspecialists, learning about this vast field is a formidable challenge. Quantum Chemistry in the Age of Machine Learning covers this exciting field in detail, ranging from basic concepts to comprehensive methodological details to providing detailed codes and hands-on tutorials. Such an approach helps readers get a quick overview of existing techniques and provides an opportunity to learn the intricacies and inner workings of state-of-the-art methods. The book describes the underlying concepts of machine learning and quantum chemistry, machine learning potentials and learning of other quantum chemical properties, machine learning-improved quantum chemical methods, analysis of Big Data from simulations, and materials design with machine learning. Drawing on the expertise of a team of specialist contributors, this book serves as a valuable guide for both aspiring beginners and specialists in this exciting field. Compiles advances of machine learning in quantum chemistry across different areas into a single resource Provides insights into the underlying concepts of machine learning techniques that are relevant to quantum chemistry Describes, in detail, the current state-of-the-art machine learning-based methods in quantum chemistry


Book Synopsis Quantum Chemistry in the Age of Machine Learning by : Pavlo O. Dral

Download or read book Quantum Chemistry in the Age of Machine Learning written by Pavlo O. Dral and published by Elsevier. This book was released on 2022-09-16 with total page 702 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantum chemistry is simulating atomistic systems according to the laws of quantum mechanics, and such simulations are essential for our understanding of the world and for technological progress. Machine learning revolutionizes quantum chemistry by increasing simulation speed and accuracy and obtaining new insights. However, for nonspecialists, learning about this vast field is a formidable challenge. Quantum Chemistry in the Age of Machine Learning covers this exciting field in detail, ranging from basic concepts to comprehensive methodological details to providing detailed codes and hands-on tutorials. Such an approach helps readers get a quick overview of existing techniques and provides an opportunity to learn the intricacies and inner workings of state-of-the-art methods. The book describes the underlying concepts of machine learning and quantum chemistry, machine learning potentials and learning of other quantum chemical properties, machine learning-improved quantum chemical methods, analysis of Big Data from simulations, and materials design with machine learning. Drawing on the expertise of a team of specialist contributors, this book serves as a valuable guide for both aspiring beginners and specialists in this exciting field. Compiles advances of machine learning in quantum chemistry across different areas into a single resource Provides insights into the underlying concepts of machine learning techniques that are relevant to quantum chemistry Describes, in detail, the current state-of-the-art machine learning-based methods in quantum chemistry


Ab Initio Molecular Dynamics

Ab Initio Molecular Dynamics

Author: Dominik Marx

Publisher: Cambridge University Press

Published: 2009-04-30

Total Pages: 503

ISBN-13: 1139477196

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Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.


Book Synopsis Ab Initio Molecular Dynamics by : Dominik Marx

Download or read book Ab Initio Molecular Dynamics written by Dominik Marx and published by Cambridge University Press. This book was released on 2009-04-30 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.


Indian Journal of Chemistry

Indian Journal of Chemistry

Author:

Publisher:

Published: 2000

Total Pages: 784

ISBN-13:

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Book Synopsis Indian Journal of Chemistry by :

Download or read book Indian Journal of Chemistry written by and published by . This book was released on 2000 with total page 784 pages. Available in PDF, EPUB and Kindle. Book excerpt:


Machine Learning in Biomolecular Simulations

Machine Learning in Biomolecular Simulations

Author: Gennady Verkhivker

Publisher:

Published: 2019

Total Pages: 0

ISBN-13:

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This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.


Book Synopsis Machine Learning in Biomolecular Simulations by : Gennady Verkhivker

Download or read book Machine Learning in Biomolecular Simulations written by Gennady Verkhivker and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.


Machine Learning Meets Quantum Physics

Machine Learning Meets Quantum Physics

Author: Kristof T. Schütt

Publisher: Springer Nature

Published: 2020-06-03

Total Pages: 473

ISBN-13: 3030402452

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Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.


Book Synopsis Machine Learning Meets Quantum Physics by : Kristof T. Schütt

Download or read book Machine Learning Meets Quantum Physics written by Kristof T. Schütt and published by Springer Nature. This book was released on 2020-06-03 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.


Physics Briefs

Physics Briefs

Author:

Publisher:

Published: 1994

Total Pages: 934

ISBN-13:

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Book Synopsis Physics Briefs by :

Download or read book Physics Briefs written by and published by . This book was released on 1994 with total page 934 pages. Available in PDF, EPUB and Kindle. Book excerpt:


Cumulated Index Medicus

Cumulated Index Medicus

Author:

Publisher:

Published: 1997

Total Pages: 1828

ISBN-13:

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Book Synopsis Cumulated Index Medicus by :

Download or read book Cumulated Index Medicus written by and published by . This book was released on 1997 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt:


Calculation of NMR and EPR Parameters

Calculation of NMR and EPR Parameters

Author: Martin Kaupp

Publisher: John Wiley & Sons

Published: 2006-03-06

Total Pages: 621

ISBN-13: 3527604960

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This is the first book to present the necessary quantum chemical methods for both resonance types in one handy volume, emphasizing the crucial interrelation between NMR and EPR parameters from a computational and theoretical point of view. Here, readers are given a broad overview of all the pertinent topics, such as basic theory, methodic considerations, benchmark results and applications for both spectroscopy methods in such fields as biochemistry, bioinorganic chemistry as well as with different substance classes, including fullerenes, zeolites and transition metal compounds. The chapters have been written by leading experts in a given area, but with a wider audience in mind. The result is the standard reference on the topic, serving as a guide to the best computational methods for any given problem, and is thus an indispensable tool for scientists using quantum chemical calculations of NMR and EPR parameters. A must-have for all chemists, physicists, biologists and materials scientists who wish to augment their research by quantum chemical calculations of magnetic resonance data, but who are not necessarily specialists in these methods or their applications. Furthermore, specialists in one of the subdomains of this wide field will be grateful to find here an overview of what lies beyond their own area of focus.


Book Synopsis Calculation of NMR and EPR Parameters by : Martin Kaupp

Download or read book Calculation of NMR and EPR Parameters written by Martin Kaupp and published by John Wiley & Sons. This book was released on 2006-03-06 with total page 621 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book to present the necessary quantum chemical methods for both resonance types in one handy volume, emphasizing the crucial interrelation between NMR and EPR parameters from a computational and theoretical point of view. Here, readers are given a broad overview of all the pertinent topics, such as basic theory, methodic considerations, benchmark results and applications for both spectroscopy methods in such fields as biochemistry, bioinorganic chemistry as well as with different substance classes, including fullerenes, zeolites and transition metal compounds. The chapters have been written by leading experts in a given area, but with a wider audience in mind. The result is the standard reference on the topic, serving as a guide to the best computational methods for any given problem, and is thus an indispensable tool for scientists using quantum chemical calculations of NMR and EPR parameters. A must-have for all chemists, physicists, biologists and materials scientists who wish to augment their research by quantum chemical calculations of magnetic resonance data, but who are not necessarily specialists in these methods or their applications. Furthermore, specialists in one of the subdomains of this wide field will be grateful to find here an overview of what lies beyond their own area of focus.