Crystal Structure Prediction Using Neural Network Potential And Age Fitness Pareto Genetic Algorithm
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Crystal Structure Prediction Using Neural Network Potential And Age Fitness Pareto Genetic Algorithm
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Author : Sadman Sadeed Omee
language : en
Publisher: OAE Publishing Inc.
Release Date : 2024-03-02
Crystal Structure Prediction Using Neural Network Potential And Age Fitness Pareto Genetic Algorithm written by Sadman Sadeed Omee and has been published by OAE Publishing Inc. this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-03-02 with Technology & Engineering categories.
While crystal structure prediction (CSP) remains a longstanding challenge, we introduce ParetoCSP, a novel algorithm for CSP, which combines a multi-objective genetic algorithm (GA) with a neural network inter-atomic potential model to find energetically optimal crystal structures given chemical compositions. We enhance the updated multi-objective GA (NSGA-III) by incorporating the genotypic age as an independent optimization criterion and employ the M3GNet universal inter-atomic potential to guide the GA search. Compared to GN-OA, a state-of-the-art neural potential-based CSP algorithm, ParetoCSP demonstrated significantly better predictive capabilities, outperforming by a factor of 2.562 across 55 diverse benchmark structures, as evaluated by seven performance metrics. Trajectory analysis of the traversed structures of all algorithms shows that ParetoCSP generated more valid structures than other algorithms, which helped guide the GA to search more effectively for the optimal structures. Our implementation code is available at https://github.com/sadmanomee/ParetoCSP.
An Introduction To Genetic Algorithms For Scientists And Engineers
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Author : David Alexander Coley
language : en
Publisher: World Scientific Publishing Company
Release Date : 1999-01-29
An Introduction To Genetic Algorithms For Scientists And Engineers written by David Alexander Coley and has been published by World Scientific Publishing Company this book supported file pdf, txt, epub, kindle and other format this book has been release on 1999-01-29 with Computers categories.
This invaluable book has been designed to be useful to most practising scientists and engineers, whatever their field and however rusty their mathematics and programming might be. The approach taken is largely practical, with algorithms being presented in full and working code (in BASIC, FORTRAN, PASCAL AND C) included on a floppy disk to help the reader get up and running as quickly as possible. The text could also be used as part of an undergraduate course on search and optimisation. Student exercises are included at the end of several of the chapters, many of which are computer-based and designed to encourage exploration of the method.
Introduction To Genetic Algorithms
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Author : S.N. Sivanandam
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-10-24
Introduction To Genetic Algorithms written by S.N. Sivanandam and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-10-24 with Technology & Engineering categories.
Theoriginofevolutionaryalgorithmswasanattempttomimicsomeoftheprocesses taking place in natural evolution. Although the details of biological evolution are not completely understood (even nowadays), there exist some points supported by strong experimental evidence: • Evolution is a process operating over chromosomes rather than over organisms. The former are organic tools encoding the structure of a living being, i.e., a cr- ture is “built” decoding a set of chromosomes. • Natural selection is the mechanism that relates chromosomes with the ef ciency of the entity they represent, thus allowing that ef cient organism which is we- adapted to the environment to reproduce more often than those which are not. • The evolutionary process takes place during the reproduction stage. There exists a large number of reproductive mechanisms in Nature. Most common ones are mutation (that causes the chromosomes of offspring to be different to those of the parents) and recombination (that combines the chromosomes of the parents to produce the offspring). Based upon the features above, the three mentioned models of evolutionary c- puting were independently (and almost simultaneously) developed.
Protein Structure
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Author : Harold A. Scheraga
language : en
Publisher: Academic Press
Release Date : 2014-07-01
Protein Structure written by Harold A. Scheraga and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-07-01 with Technology & Engineering categories.
Protein Structure deals with the chemistry and physics of biologically important molecules—the proteins—particularly the determination of the structure of various proteins, their thermodynamics, their kinetics, and the mechanisms of different reactions of individual proteins. The book approaches the study of protein structure in two ways: firstly, by determining the general features of protein structure, the overall size, and shape of the molecule; and secondly, by investigating the molecule internally along with the various aspects of the internal configuration of protein molecules. It describes in detail experimental methods for determining protein structure in solution, such as the hydrodynamic method, the thermodynamic optical method, and the electrochemical method. The book then explains the results of experiments carried out on insulin, lysozyme, and ribonuclease. The text notes that the experiments, carried out on native and denatured proteins as well as on derivatives prepared by chemical modification (e.g., by methylation, iodination, acetylation, etc.), can lead to greater understanding of secondary and tertiary structures of proteins of known sequence. The book is suitable for biochemists, micro-biologists, cellular researchers, or investigators involved in protein structure and other biological sciences related to muscle physiologists, geneticists, enzymologists, or immunologists.
Evolutionary Optimization Algorithms
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Author : Dan Simon
language : en
Publisher: John Wiley & Sons
Release Date : 2013-06-13
Evolutionary Optimization Algorithms written by Dan Simon and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-06-13 with Mathematics categories.
A clear and lucid bottom-up approach to the basic principles of evolutionary algorithms Evolutionary algorithms (EAs) are a type of artificial intelligence. EAs are motivated by optimization processes that we observe in nature, such as natural selection, species migration, bird swarms, human culture, and ant colonies. This book discusses the theory, history, mathematics, and programming of evolutionary optimization algorithms. Featured algorithms include genetic algorithms, genetic programming, ant colony optimization, particle swarm optimization, differential evolution, biogeography-based optimization, and many others. Evolutionary Optimization Algorithms: Provides a straightforward, bottom-up approach that assists the reader in obtaining a clear but theoretically rigorous understanding of evolutionary algorithms, with an emphasis on implementation Gives a careful treatment of recently developed EAs including opposition-based learning, artificial fish swarms, bacterial foraging, and many others and discusses their similarities and differences from more well-established EAs Includes chapter-end problems plus a solutions manual available online for instructors Offers simple examples that provide the reader with an intuitive understanding of the theory Features source code for the examples available on the author's website Provides advanced mathematical techniques for analyzing EAs, including Markov modeling and dynamic system modeling Evolutionary Optimization Algorithms: Biologically Inspired and Population-Based Approaches to Computer Intelligence is an ideal text for advanced undergraduate students, graduate students, and professionals involved in engineering and computer science.
Computational Intelligence In Multimedia Processing Recent Advances
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Author : Aboul-Ella Hassanien
language : en
Publisher: Springer
Release Date : 2008-04-23
Computational Intelligence In Multimedia Processing Recent Advances written by Aboul-Ella Hassanien and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-04-23 with Computers categories.
For the last decades Multimedia processing has emerged as an important technology to generate content based on images, video, audio, graphics, and text. Furthermore, the recent new development represented by High Definition Multimedia content and Interactive television will generate a huge volume of data and important computing problems connected with the creation, processing and management of Multimedia content. "Computational Intelligence in Multimedia Processing: Recent Advances" is a compilation of the latest trends and developments in the field of computational intelligence in multimedia processing. This edited book presents a large number of interesting applications to intelligent multimedia processing of various Computational Intelligence techniques, such as rough sets, Neural Networks; Fuzzy Logic; Evolutionary Computing; Artificial Immune Systems; Swarm Intelligence; Reinforcement Learning and evolutionary computation.
Chemical Biology
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Author : Jonathan E. Hempel
language : en
Publisher: Humana
Release Date : 2016-09-24
Chemical Biology written by Jonathan E. Hempel and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-09-24 with Science categories.
This volume seeks to enable the discovery of tools in chemical biology by providing readers with various techniques ranging from initial chemical genetic screening to target identification. To successfully highlight the essential components of the chemical biology tool discovery process, the book is organizes into four parts that focus on platforms for molecular discovery in in vitro cellular systems, in vivo chemical genetic screening protocols, and methods used to discover functional protein targets. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Practical and informative, Chemical Biology: Methods and Protocols seeks to improve the success rate of the chemical biology field through the dissemination of detailed and experiential knowledge.
Good Thinking
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Author : Denise D. Cummins
language : en
Publisher: Cambridge University Press
Release Date : 2012-04-16
Good Thinking written by Denise D. Cummins and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-04-16 with History categories.
Do you know what economists mean when they refer to you as a "rational agent"? Or why a psychologist might label your idea a "creative insight"? After reading this book, you will know how the best and brightest thinkers judge the ways we decide, argue, solve problems, and tell right from wrong.
Stochastic Optimization
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Author : Stanislav Uryasev
language : en
Publisher: Springer Science & Business Media
Release Date : 2001-05-31
Stochastic Optimization written by Stanislav Uryasev and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2001-05-31 with Technology & Engineering categories.
Stochastic programming is the study of procedures for decision making under the presence of uncertainties and risks. Stochastic programming approaches have been successfully used in a number of areas such as energy and production planning, telecommunications, and transportation. Recently, the practical experience gained in stochastic programming has been expanded to a much larger spectrum of applications including financial modeling, risk management, and probabilistic risk analysis. Major topics in this volume include: (1) advances in theory and implementation of stochastic programming algorithms; (2) sensitivity analysis of stochastic systems; (3) stochastic programming applications and other related topics. Audience: Researchers and academies working in optimization, computer modeling, operations research and financial engineering. The book is appropriate as supplementary reading in courses on optimization and financial engineering.
Galileo Unbound
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Author : David D. Nolte
language : en
Publisher: Oxford University Press
Release Date : 2018-07-12
Galileo Unbound written by David D. Nolte and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-07-12 with Science categories.
Galileo Unbound traces the journey that brought us from Galileo's law of free fall to today's geneticists measuring evolutionary drift, entangled quantum particles moving among many worlds, and our lives as trajectories traversing a health space with thousands of dimensions. Remarkably, common themes persist that predict the evolution of species as readily as the orbits of planets or the collapse of stars into black holes. This book tells the history of spaces of expanding dimension and increasing abstraction and how they continue today to give new insight into the physics of complex systems. Galileo published the first modern law of motion, the Law of Fall, that was ideal and simple, laying the foundation upon which Newton built the first theory of dynamics. Early in the twentieth century, geometry became the cause of motion rather than the result when Einstein envisioned the fabric of space-time warped by mass and energy, forcing light rays to bend past the Sun. Possibly more radical was Feynman's dilemma of quantum particles taking all paths at once -- setting the stage for the modern fields of quantum field theory and quantum computing. Yet as concepts of motion have evolved, one thing has remained constant, the need to track ever more complex changes and to capture their essence, to find patterns in the chaos as we try to predict and control our world.