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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.

New Horizons of Computational Science

Author: Toshikazu Ebisuzaki

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 317

ISBN-13: 9401008647

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Proceedings of the International Symposium on Supercomputing held in Tokyo, Japan, September 1-3, 1997

Book Synopsis New Horizons of Computational Science by : Toshikazu Ebisuzaki

Download or read book New Horizons of Computational Science written by Toshikazu Ebisuzaki and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proceedings of the International Symposium on Supercomputing held in Tokyo, Japan, September 1-3, 1997

Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology

Author: National Research Council

Publisher: National Academies Press

Published: 2008-04-20

Total Pages: 183

ISBN-13: 0309114187

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Life on Earth would be impossible without plants. Humans rely on plants for most clothing, furniture, food, as well as for many pharmaceuticals and other products. Plant genome sciences are essential to understanding how plants function and how to develop desirable plant characteristics. For example, plant genomic science can contribute to the development of plants that are drought-resistant, those that require less fertilizer, and those that are optimized for conversion to fuels such as ethanol and biodiesel. The National Plant Genome Initiative (NPGI) is a unique, cross-agency funding enterprise that has been funding and coordinating plant genome research successfully for nine years. Research breakthroughs from NPGI and the National Science Foundation (NSF) Arabidopsis 2010 Project, such as how the plant immune system controls pathogen defense, demonstrate that the plant genome science community is vibrant and capable of driving technological advancement. This book from the National Research Council concludes that these programs should continue so that applied programs on agriculture, bioenergy, and others will always be built on a strong foundation of fundamental plant biology research.

Book Synopsis Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology by : National Research Council

Download or read book Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology written by National Research Council and published by National Academies Press. This book was released on 2008-04-20 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Life on Earth would be impossible without plants. Humans rely on plants for most clothing, furniture, food, as well as for many pharmaceuticals and other products. Plant genome sciences are essential to understanding how plants function and how to develop desirable plant characteristics. For example, plant genomic science can contribute to the development of plants that are drought-resistant, those that require less fertilizer, and those that are optimized for conversion to fuels such as ethanol and biodiesel. The National Plant Genome Initiative (NPGI) is a unique, cross-agency funding enterprise that has been funding and coordinating plant genome research successfully for nine years. Research breakthroughs from NPGI and the National Science Foundation (NSF) Arabidopsis 2010 Project, such as how the plant immune system controls pathogen defense, demonstrate that the plant genome science community is vibrant and capable of driving technological advancement. This book from the National Research Council concludes that these programs should continue so that applied programs on agriculture, bioenergy, and others will always be built on a strong foundation of fundamental plant biology research.

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.

Recent Advances in Computational Chemistry Software

Author: Roger Amos

Publisher: World Scientific Publishing Company

Published: 2010-10

Total Pages: 400

ISBN-13: 9789814289320

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There are many chemistry software packages in existence today encompassing a variety of theoretical methods and computational techniques. Many of the programs currently used are well established but evolving constantly and it is believed the time is right to revisit the state of the software in light of major developments in functionality and computer hardware. This book is a reference for computational software, not as a series of user manuals, but as an update on new developments in the major program packages highlighting what is unique to these packages and also fundamental techniques that are common to all.

Book Synopsis Recent Advances in Computational Chemistry Software by : Roger Amos

Download or read book Recent Advances in Computational Chemistry Software written by Roger Amos and published by World Scientific Publishing Company. This book was released on 2010-10 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are many chemistry software packages in existence today encompassing a variety of theoretical methods and computational techniques. Many of the programs currently used are well established but evolving constantly and it is believed the time is right to revisit the state of the software in light of major developments in functionality and computer hardware. This book is a reference for computational software, not as a series of user manuals, but as an update on new developments in the major program packages highlighting what is unique to these packages and also fundamental techniques that are common to all.

Computational Chemistry

Author: David Young

Publisher: John Wiley & Sons

Published: 2004-04-07

Total Pages: 408

ISBN-13: 0471458430

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A practical, easily accessible guide for bench-top chemists, thisbook focuses on accurately applying computational chemistrytechniques to everyday chemistry problems. Provides nonmathematical explanations of advanced topics incomputational chemistry. Focuses on when and how to apply different computationaltechniques. Addresses computational chemistry connections to biochemicalsystems and polymers. Provides a prioritized list of methods for attacking difficultcomputational chemistry problems, and compares advantages anddisadvantages of various approximation techniques. Describes how the choice of methods of software affectsrequirements for computer memory and processing time.

Book Synopsis Computational Chemistry by : David Young

Download or read book Computational Chemistry written by David Young and published by John Wiley & Sons. This book was released on 2004-04-07 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: A practical, easily accessible guide for bench-top chemists, thisbook focuses on accurately applying computational chemistrytechniques to everyday chemistry problems. Provides nonmathematical explanations of advanced topics incomputational chemistry. Focuses on when and how to apply different computationaltechniques. Addresses computational chemistry connections to biochemicalsystems and polymers. Provides a prioritized list of methods for attacking difficultcomputational chemistry problems, and compares advantages anddisadvantages of various approximation techniques. Describes how the choice of methods of software affectsrequirements for computer memory and processing time.

Computational Chemistry Methods

Author: Ponnadurai Ramasami

Publisher: Walter de Gruyter GmbH & Co KG

Published: 2020-08-10

Total Pages: 227

ISBN-13: 3110629925

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This book reviews a variety of methods in computational chemistry and their applications in different fields of current research. Ab initio methods and regression analyses are discussed with special focus on their application to investigate chemical structures as for example dyes or drug compounds. Further topics are the use of computational methods in the modeling of spectroscopic data or to study reaction mechanisms.

Book Synopsis Computational Chemistry Methods by : Ponnadurai Ramasami

Download or read book Computational Chemistry Methods written by Ponnadurai Ramasami and published by Walter de Gruyter GmbH & Co KG. This book was released on 2020-08-10 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews a variety of methods in computational chemistry and their applications in different fields of current research. Ab initio methods and regression analyses are discussed with special focus on their application to investigate chemical structures as for example dyes or drug compounds. Further topics are the use of computational methods in the modeling of spectroscopic data or to study reaction mechanisms.

Reviews in Computational Chemistry, Volume 1

Author: Kenny B. Lipkowitz

Publisher: John Wiley & Sons

Published: 2009-09-22

Total Pages: 443

ISBN-13: 0470126051

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This book is an account of current developments in computational chemistry, a new multidisciplinary area of research. Experts in computational chemistry, the editors use and develop techniques for computer-assisted molecular design. The core of the text itself deals with techniques for computer-assisted molecular design. The book is suitable for both beginners and experts. In addition, protocols and software for molecular recognition and the relationship between structure and biological activity of drug molecules are discussed in detail. Each chapter includes a mini-tutorial, as well as discussion of advanced topics. Special Feature: The appendix to this book contains an extensive list of available software for molecular modeling.

Book Synopsis Reviews in Computational Chemistry, Volume 1 by : Kenny B. Lipkowitz

Download or read book Reviews in Computational Chemistry, Volume 1 written by Kenny B. Lipkowitz and published by John Wiley & Sons. This book was released on 2009-09-22 with total page 443 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is an account of current developments in computational chemistry, a new multidisciplinary area of research. Experts in computational chemistry, the editors use and develop techniques for computer-assisted molecular design. The core of the text itself deals with techniques for computer-assisted molecular design. The book is suitable for both beginners and experts. In addition, protocols and software for molecular recognition and the relationship between structure and biological activity of drug molecules are discussed in detail. Each chapter includes a mini-tutorial, as well as discussion of advanced topics. Special Feature: The appendix to this book contains an extensive list of available software for molecular modeling.

Reviews in Computational Chemistry, Volume 5

Author: Kenny B. Lipkowitz

Publisher: John Wiley & Sons

Published: 2009-09-22

Total Pages: 482

ISBN-13: 0470126094

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Führende Experten auf dem Gebiet der Computer-Chemie präsentieren in dem fünften Band der erfolgreichen Reihe 'Reviews in Computational Chemistry' die neuesten Entwicklungen. Um den interessierten Chemiker auf dem aktuellen Stand zu halten, ist der Reihe im Anhang eine Liste mit der Software zum Thema beigefügt

Book Synopsis Reviews in Computational Chemistry, Volume 5 by : Kenny B. Lipkowitz

Download or read book Reviews in Computational Chemistry, Volume 5 written by Kenny B. Lipkowitz and published by John Wiley & Sons. This book was released on 2009-09-22 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Führende Experten auf dem Gebiet der Computer-Chemie präsentieren in dem fünften Band der erfolgreichen Reihe 'Reviews in Computational Chemistry' die neuesten Entwicklungen. Um den interessierten Chemiker auf dem aktuellen Stand zu halten, ist der Reihe im Anhang eine Liste mit der Software zum Thema beigefügt

New Horizons in Predictive Drug Metabolism and Pharmacokinetics

Author: Alan G. E. Wilson

Publisher: Royal Society of Chemistry

Published: 2015-11-20

Total Pages: 444

ISBN-13: 1849738289

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This book thoroughly explores the predictive role of drug metabolism and pharmacokinetics in drug discovery and in improving success rates and safety assessments of chemicals.

Book Synopsis New Horizons in Predictive Drug Metabolism and Pharmacokinetics by : Alan G. E. Wilson

Download or read book New Horizons in Predictive Drug Metabolism and Pharmacokinetics written by Alan G. E. Wilson and published by Royal Society of Chemistry. This book was released on 2015-11-20 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book thoroughly explores the predictive role of drug metabolism and pharmacokinetics in drug discovery and in improving success rates and safety assessments of chemicals.