Neural Networks in Chemical Reaction Dynamics

Neural Networks in Chemical Reaction Dynamics

Author: Lionel Raff

Publisher: Oxford University Press

Published: 2012-01-18

Total Pages: 303

ISBN-13: 0199909881

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This monograph presents recent advances in neural network (NN) approaches and applications to chemical reaction dynamics. Topics covered include: (i) the development of ab initio potential-energy surfaces (PES) for complex multichannel systems using modified novelty sampling and feedforward NNs; (ii) methods for sampling the configuration space of critical importance, such as trajectory and novelty sampling methods and gradient fitting methods; (iii) parametrization of interatomic potential functions using a genetic algorithm accelerated with a NN; (iv) parametrization of analytic interatomic potential functions using NNs; (v) self-starting methods for obtaining analytic PES from ab inito electronic structure calculations using direct dynamics; (vi) development of a novel method, namely, combined function derivative approximation (CFDA) for simultaneous fitting of a PES and its corresponding force fields using feedforward neural networks; (vii) development of generalized PES using many-body expansions, NNs, and moiety energy approximations; (viii) NN methods for data analysis, reaction probabilities, and statistical error reduction in chemical reaction dynamics; (ix) accurate prediction of higher-level electronic structure energies (e.g. MP4 or higher) for large databases using NNs, lower-level (Hartree-Fock) energies, and small subsets of the higher-energy database; and finally (x) illustrative examples of NN applications to chemical reaction dynamics of increasing complexity starting from simple near equilibrium structures (vibrational state studies) to more complex non-adiabatic reactions. The monograph is prepared by an interdisciplinary group of researchers working as a team for nearly two decades at Oklahoma State University, Stillwater, OK with expertise in gas phase reaction dynamics; neural networks; various aspects of MD and Monte Carlo (MC) simulations of nanometric cutting, tribology, and material properties at nanoscale; scaling laws from atomistic to continuum; and neural networks applications to chemical reaction dynamics. It is anticipated that this emerging field of NN in chemical reaction dynamics will play an increasingly important role in MD, MC, and quantum mechanical studies in the years to come.


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


Stochastic Local Search

Stochastic Local Search

Author: Holger H. Hoos

Publisher: Morgan Kaufmann

Published: 2005

Total Pages: 678

ISBN-13: 1558608729

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Stochastic local search (SLS) algorithms are among the most prominent and successful techniques for solving computationally difficult problems. Offering a systematic treatment of SLS algorithms, this book examines the general concepts and specific instances of SLS algorithms and considers their development, analysis and application.


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.


Wavelets in Chemistry

Wavelets in Chemistry

Author: Beata Walczak

Publisher: Elsevier

Published: 2000-05-10

Total Pages: 571

ISBN-13: 008054374X

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Wavelets seem to be the most efficient tool in signal denoising and compression. They can be used in an unlimited number of applications in all fields of chemistry where the instrumental signals are the source of information about the studied chemical systems or phenomena, and in all cases where these signals have to be archived. The quality of the instrumental signals determines the quality of answer to the basic analytical questions: how many components are in the studied systems, what are these components like and what are their concentrations? Efficient compression of the signal sets can drastically speed up further processing such as data visualization, modelling (calibration and pattern recognition) and library search. Exploration of the possible applications of wavelets in analytical chemistry has just started and this book will significantly speed up the process. The first part, concentrating on theoretical aspects, is written in a tutorial-like manner, with simple numerical examples. For the reader's convenience, all basic terms are explained in detail and all unique properties of wavelets are pinpointed and compared with the other types of basis function. The second part presents applications of wavelets from many branches of chemistry which will stimulate chemists to further exploration of this exciting subject.


Chemical Master Equation for Large Biological Networks

Chemical Master Equation for Large Biological Networks

Author: Don Kulasiri

Publisher: Springer Nature

Published: 2021-09-12

Total Pages: 231

ISBN-13: 9811653518

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This book highlights the theory and practical applications of the chemical master equation (CME) approach for very large biochemical networks, which provides a powerful general framework for model building in a variety of biological networks. The aim of the book is to not only highlight advanced numerical solution methods for the CME, but also reveal their potential by means of practical examples. The case studies presented are mainly from biology; however, the applications from novel methods are discussed comprehensively, underlining the interdisciplinary approach in simulation and the potential of the chemical master equation approach for modelling bionetworks. The book is a valuable guide for researchers, graduate students, and professionals alike.


Robust Intelligence and Trust in Autonomous Systems

Robust Intelligence and Trust in Autonomous Systems

Author: Ranjeev Mittu

Publisher: Springer

Published: 2016-04-07

Total Pages: 277

ISBN-13: 148997668X

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This volume explores the intersection of robust intelligence (RI) and trust in autonomous systems across multiple contexts among autonomous hybrid systems, where hybrids are arbitrary combinations of humans, machines and robots. To better understand the relationships between artificial intelligence (AI) and RI in a way that promotes trust between autonomous systems and human users, this book explores the underlying theory, mathematics, computational models, and field applications. It uniquely unifies the fields of RI and trust and frames it in a broader context, namely the effective integration of human-autonomous systems. A description of the current state of the art in RI and trust introduces the research work in this area. With this foundation, the chapters further elaborate on key research areas and gaps that are at the heart of effective human-systems integration, including workload management, human computer interfaces, team integration and performance, advanced analytics, behavior modeling, training, and, lastly, test and evaluation. Written by international leading researchers from across the field of autonomous systems research, Robust Intelligence and Trust in Autonomous Systems dedicates itself to thoroughly examining the challenges and trends of systems that exhibit RI, the fundamental implications of RI in developing trusted relationships with present and future autonomous systems, and the effective human systems integration that must result for trust to be sustained. Contributing authors: David W. Aha, Jenny Burke, Joseph Coyne, M.L. Cummings, Munjal Desai, Michael Drinkwater, Jill L. Drury, Michael W. Floyd, Fei Gao, Vladimir Gontar, Ayanna M. Howard, Mo Jamshidi, W.F. Lawless, Kapil Madathil, Ranjeev Mittu, Arezou Moussavi, Gari Palmer, Paul Robinette, Behzad Sadrfaridpour, Hamed Saeidi, Kristin E. Schaefer, Anne Selwyn, Ciara Sibley, Donald A. Sofge, Erin Solovey, Aaron Steinfeld, Barney Tannahill, Gavin Taylor, Alan R. Wagner, Yue Wang, Holly A. Yanco, Dan Zwillinger.


Reviews in Computational Chemistry, Volume 31

Reviews in Computational Chemistry, Volume 31

Author: Abby L. Parrill

Publisher: John Wiley & Sons

Published: 2018-10-25

Total Pages: 368

ISBN-13: 1119518075

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The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered on molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 31 include: Lattice-Boltzmann Modeling of Multicomponent Systems: An Introduction Modeling Mechanochemistry from First Principles Mapping Energy Transport Networks in Proteins The Role of Computations in Catalysis The Construction of Ab Initio Based Potential Energy Surfaces Uncertainty Quantification for Molecular Dynamics


Analysis of Kinetic Reaction Mechanisms

Analysis of Kinetic Reaction Mechanisms

Author: Tamás Turányi

Publisher: Springer

Published: 2014-12-29

Total Pages: 369

ISBN-13: 366244562X

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Chemical processes in many fields of science and technology, including combustion, atmospheric chemistry, environmental modelling, process engineering, and systems biology, can be described by detailed reaction mechanisms consisting of numerous reaction steps. This book describes methods for the analysis of reaction mechanisms that are applicable in all these fields. Topics addressed include: how sensitivity and uncertainty analyses allow the calculation of the overall uncertainty of simulation results and the identification of the most important input parameters, the ways in which mechanisms can be reduced without losing important kinetic and dynamic detail, and the application of reduced models for more accurate engineering optimizations. This monograph is invaluable for researchers and engineers dealing with detailed reaction mechanisms, but is also useful for graduate students of related courses in chemistry, mechanical engineering, energy and environmental science and biology.