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
Total Pages: 123
Release: 2023-12-05
Genre: Science
ISBN: 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.

New Horizons in Computational Chemistry Software

New Horizons in Computational Chemistry Software
Author: Michael Filatov
Publisher: Springer Nature
Total Pages: 316
Release: 2022-07-30
Genre: Science
ISBN: 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.

Quantum Chemistry in the Age of Machine Learning

Quantum Chemistry in the Age of Machine Learning
Author: Pavlo O. Dral
Publisher: Elsevier
Total Pages: 702
Release: 2022-09-16
Genre: Science
ISBN: 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

Ab Initio Molecular Dynamics

Ab Initio Molecular Dynamics
Author: Dominik Marx
Publisher: Cambridge University Press
Total Pages: 578
Release: 2010-01-29
Genre:
ISBN:

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Focusing on a breakthrough combination methodology, this handbook and ready reference is the first book to collect and present all facets of the important Car-Parrinello approach. Clearly divided into three sections, the text covers basic and advanced techniques, before finishing with applications. A must-have for all computational researchers and producers of pharmaceuticals and other complex molecules.

Ab Initio Molecular Dynamics

Ab Initio Molecular Dynamics
Author: Dominik Marx
Publisher: Cambridge University Press
Total Pages: 503
Release: 2009-04-30
Genre: Science
ISBN: 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.

Indian Journal of Chemistry

Indian Journal of Chemistry
Author:
Publisher:
Total Pages: 784
Release: 2000
Genre: Analytical chemistry
ISBN:

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Introduction to Quantum Mechanics

Introduction to Quantum Mechanics
Author: David J. Tannor
Publisher: University Science Books
Total Pages: 600
Release: 2018-02-01
Genre: Science
ISBN: 9781891389993

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Introduction to Quantum Mechanics covers quantum mechanics from a time-dependent perspective in a unified way from beginning to end. Intended for upper-level undergraduate and graduate courses this text will change the way people think about and teach quantum mechanics in chemistry and physics departments.

Machine Learning in Chemistry

Machine Learning in Chemistry
Author: Edward O. Pyzer-Knapp
Publisher:
Total Pages: 140
Release: 2020-10-22
Genre: Science
ISBN: 9780841235052

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Atomic-scale representation and statistical learning of tensorial properties -- Prediction of Mohs hardness with machine learning methods using compositional features -- High-dimensional neural network potentials for atomistic simulations -- Data-driven learning systems for chemical reaction prediction: an analysis of recent approaches -- Using machine learning to inform decisions in drug discovery : an industry perspective -- Cognitive materials discovery and onset of the 5th discovery paradigm.

Physics Briefs

Physics Briefs
Author:
Publisher:
Total Pages: 934
Release: 1994
Genre: Physics
ISBN:

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Cumulated Index Medicus

Cumulated Index Medicus
Author:
Publisher:
Total Pages: 1140
Release: 1984
Genre: Medicine
ISBN:

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