Download or read book Sequential Monte Carlo and Applications in Molecular Dynamics written by Qiming Du and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis consists in three parts, all connecting to the Sequential Monte Carlo (SMC) framework. The primary motivation is to understand the generalized Adaptive Multilevel Splitting, an algorithm that aims at estimating the rare-event transition probability between metastable states in the context of Molecular Dynamics. In the first part, we deal with the Adaptive SMC framework. We prove that the variance estimator proposed by Lee and Whiteley in the non-adaptive setting, is still consistent in this adaptive setting, under a slightly weaker assumption than the one to establish central limit theorem. In the theoretical perspective, We propose a new strategy that deals with the adaptiveness and genealogy of the particle system separately, based on coalescent tree-based expansions. In the second part, we propose Asymmetric SMC framework, a generalization of the classical SMC framework. The motivation is to reduce the computational burden brought by the mutation kernels. We provide central limite theorem for the assoticated Feynman-Kac measures, along with consistent asymptotic variance estimators. We remark that in some specific setting, the gAMS algorithm enters into the Asymmetric SMC framework, which leads to a consistent variance estimator and asymptotic normality for the gAMS algorithm. However, this result does not cover the general setting of gAMS algorithm. Our analysis is based on generalized coalescent tree-based expansions, which may provide an universal strategy that can be used to derive consistent variance estimators in the general SMC context. In the third part, we propose some strategies that combine the gAMS algorithm and modern statistical/machine learning. We investigate the coupling of gAMS algorithm and a nonparametric regressor--Mondrian Forests (MF), to improve the performance of gAMS algorithm. The proposed iterative updating strategy may be helpful in developing automated and efficient rare-event estimation strategy in a high-dimensional and low temperature setting.
Download or read book An Introduction to Sequential Monte Carlo written by Nicolas Chopin and published by Springer Nature. This book was released on 2020-10-01 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a general introduction to Sequential Monte Carlo (SMC) methods, also known as particle filters. These methods have become a staple for the sequential analysis of data in such diverse fields as signal processing, epidemiology, machine learning, population ecology, quantitative finance, and robotics. The coverage is comprehensive, ranging from the underlying theory to computational implementation, methodology, and diverse applications in various areas of science. This is achieved by describing SMC algorithms as particular cases of a general framework, which involves concepts such as Feynman-Kac distributions, and tools such as importance sampling and resampling. This general framework is used consistently throughout the book. Extensive coverage is provided on sequential learning (filtering, smoothing) of state-space (hidden Markov) models, as this remains an important application of SMC methods. More recent applications, such as parameter estimation of these models (through e.g. particle Markov chain Monte Carlo techniques) and the simulation of challenging probability distributions (in e.g. Bayesian inference or rare-event problems), are also discussed. The book may be used either as a graduate text on Sequential Monte Carlo methods and state-space modeling, or as a general reference work on the area. Each chapter includes a set of exercises for self-study, a comprehensive bibliography, and a “Python corner,” which discusses the practical implementation of the methods covered. In addition, the book comes with an open source Python library, which implements all the algorithms described in the book, and contains all the programs that were used to perform the numerical experiments.
Download or read book Sequential Monte Carlo Methods in Practice written by Arnaud Doucet and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 590 pages. Available in PDF, EPUB and Kindle. Book excerpt: Monte Carlo methods are revolutionizing the on-line analysis of data in many fileds. They have made it possible to solve numerically many complex, non-standard problems that were previously intractable. This book presents the first comprehensive treatment of these techniques.
Download or read book A Guide to Monte Carlo Simulations in Statistical Physics written by David P. Landau and published by Cambridge University Press. This book was released on 2009-09-10 with total page 489 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dealing with all aspects of Monte Carlo simulation of complex physical systems encountered in condensed-matter physics and statistical mechanics, this book provides an introduction to computer simulations in physics. This edition now contains material describing powerful new algorithms that have appeared since the previous edition was published, and highlights recent technical advances and key applications that these algorithms now make possible. Updates also include several new sections and a chapter on the use of Monte Carlo simulations of biological molecules. Throughout the book there are many applications, examples, recipes, case studies, and exercises to help the reader understand the material. It is ideal for graduate students and researchers, both in academia and industry, who want to learn techniques that have become a third tool of physical science, complementing experiment and analytical theory.
Download or read book A Guide to Monte Carlo Simulations in Statistical Physics written by David P. Landau and published by Cambridge University Press. This book was released on 2000-08-17 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes all aspects of Monte Carlo simulation of complex physical systems encountered in condensed-matter physics and statistical mechanics, as well as in related fields, such as polymer science and lattice gauge theory. The authors give a succinct overview of simple sampling methods and develop the importance sampling method. In addition they introduce quantum Monte Carlo methods, aspects of simulations of growth phenomena and other systems far from equilibrium, and the Monte Carlo Renormalization Group approach to critical phenomena. The book includes many applications, examples, and current references, and exercises to help the reader.
Download or read book Applications of the Monte Carlo Method in Statistical Physics written by Kurt Binder and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deals with the computer simulation of complex physical sys- tems encounteredin condensed-matter physics and statistical mechanics as well as in related fields such as metallurgy, polymer research, lattice gauge theory and quantummechanics.
Download or read book Fast Sequential Monte Carlo Methods for Counting and Optimization written by Reuven Y. Rubinstein and published by John Wiley & Sons. This book was released on 2013-11-13 with total page 177 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive account of the theory and application of Monte Carlo methods Based on years of research in efficient Monte Carlo methods for estimation of rare-event probabilities, counting problems, and combinatorial optimization, Fast Sequential Monte Carlo Methods for Counting and Optimization is a complete illustration of fast sequential Monte Carlo techniques. The book provides an accessible overview of current work in the field of Monte Carlo methods, specifically sequential Monte Carlo techniques, for solving abstract counting and optimization problems. Written by authorities in the field, the book places emphasis on cross-entropy, minimum cross-entropy, splitting, and stochastic enumeration. Focusing on the concepts and application of Monte Carlo techniques, Fast Sequential Monte Carlo Methods for Counting and Optimization includes: Detailed algorithms needed to practice solving real-world problems Numerous examples with Monte Carlo method produced solutions within the 1-2% limit of relative error A new generic sequential importance sampling algorithm alongside extensive numerical results An appendix focused on review material to provide additional background information Fast Sequential Monte Carlo Methods for Counting and Optimization is an excellent resource for engineers, computer scientists, mathematicians, statisticians, and readers interested in efficient simulation techniques. The book is also useful for upper-undergraduate and graduate-level courses on Monte Carlo methods.
Download or read book An Event Driven Hybrid Molecular Dynamics and Direct Simulation Monte Carlo Algorithm written by and published by . This book was released on 2007 with total page 43 pages. Available in PDF, EPUB and Kindle. Book excerpt: A novel algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with the solvent particles with hard core potentials. The algorithm uses event-driven molecular dynamics (MD) for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in event-driven algorithms, rather, the momentum and energy exchange in the solvent is determined stochastically using the Direct Simulation Monte Carlo (DSMC) method. The coupling between the solvent and the solute is consistently represented at the particle level, however, unlike full MD simulations of both the solvent and the solute, the spatial structure of the solvent is ignored. The algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard wall subjected to uniform shear. The algorithm closely reproduces full MD simulations with two orders of magnitude greater efficiency. Results do not confirm the existence of periodic (cycling) motion of the polymer chain.
Download or read book Applications of the Monte Carlo Method in Statistical Physics written by K. Binder and published by Springer. This book was released on 1984-03-01 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: Monte Carlo computer simulations are now a standard tool in scientific fields such as condensed-matter physics, including surface-physics and applied-physics problems (metallurgy, diffusion, and segregation, etc. ), chemical physics, including studies of solutions, chemical reactions, polymer statistics, etc. , and field theory. With the increasing ability of this method to deal with quantum-mechanical problems such as quantum spin systems or many-fermion problems, it will become useful for other questions in the fields of elementary-particle and nuclear physics as well. The large number of recent publications dealing either with applications or further development of some aspects of this method is a clear indication that the scientific community has realized the power and versatility of Monte Carlo simula tions, as well as of related simulation techniques such as "molecular dynamics" and "Langevin dynamics," which are only briefly mentioned in the present book. With the increasing availability of recent very-high-speed general-purpose computers, many problems become tractable which have so far escaped satisfactory treatment due to prac tical limitations (too small systems had to be chosen, or too short averaging times had to be used). While this approach is admittedly rather expensive, two cheaper alternatives have become available, too: (i) array or vector processors specifical ly suited for wide classes of simulation purposes; (ii) special purpose processors, which are built for a more specific class of problems or, in the extreme case, for the simulation of one single model system.
Download or read book Simulation and the Monte Carlo Method written by Reuven Y. Rubinstein and published by John Wiley & Sons. This book was released on 2016-10-21 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: This accessible new edition explores the major topics in Monte Carlo simulation that have arisen over the past 30 years and presents a sound foundation for problem solving Simulation and the Monte Carlo Method, Third Edition reflects the latest developments in the field and presents a fully updated and comprehensive account of the state-of-the-art theory, methods and applications that have emerged in Monte Carlo simulation since the publication of the classic First Edition over more than a quarter of a century ago. While maintaining its accessible and intuitive approach, this revised edition features a wealth of up-to-date information that facilitates a deeper understanding of problem solving across a wide array of subject areas, such as engineering, statistics, computer science, mathematics, and the physical and life sciences. The book begins with a modernized introduction that addresses the basic concepts of probability, Markov processes, and convex optimization. Subsequent chapters discuss the dramatic changes that have occurred in the field of the Monte Carlo method, with coverage of many modern topics including: Markov Chain Monte Carlo, variance reduction techniques such as importance (re-)sampling, and the transform likelihood ratio method, the score function method for sensitivity analysis, the stochastic approximation method and the stochastic counter-part method for Monte Carlo optimization, the cross-entropy method for rare events estimation and combinatorial optimization, and application of Monte Carlo techniques for counting problems. An extensive range of exercises is provided at the end of each chapter, as well as a generous sampling of applied examples. The Third Edition features a new chapter on the highly versatile splitting method, with applications to rare-event estimation, counting, sampling, and optimization. A second new chapter introduces the stochastic enumeration method, which is a new fast sequential Monte Carlo method for tree search. In addition, the Third Edition features new material on: • Random number generation, including multiple-recursive generators and the Mersenne Twister • Simulation of Gaussian processes, Brownian motion, and diffusion processes • Multilevel Monte Carlo method • New enhancements of the cross-entropy (CE) method, including the “improved” CE method, which uses sampling from the zero-variance distribution to find the optimal importance sampling parameters • Over 100 algorithms in modern pseudo code with flow control • Over 25 new exercises Simulation and the Monte Carlo Method, Third Edition is an excellent text for upper-undergraduate and beginning graduate courses in stochastic simulation and Monte Carlo techniques. The book also serves as a valuable reference for professionals who would like to achieve a more formal understanding of the Monte Carlo method. Reuven Y. Rubinstein, DSc, was Professor Emeritus in the Faculty of Industrial Engineering and Management at Technion-Israel Institute of Technology. He served as a consultant at numerous large-scale organizations, such as IBM, Motorola, and NEC. The author of over 100 articles and six books, Dr. Rubinstein was also the inventor of the popular score-function method in simulation analysis and generic cross-entropy methods for combinatorial optimization and counting. Dirk P. Kroese, PhD, is a Professor of Mathematics and Statistics in the School of Mathematics and Physics of The University of Queensland, Australia. He has published over 100 articles and four books in a wide range of areas in applied probability and statistics, including Monte Carlo methods, cross-entropy, randomized algorithms, tele-traffic c theory, reliability, computational statistics, applied probability, and stochastic modeling.
Download or read book A Practical Guide to Kinetic Monte Carlo Simulations and Classical Molecular Dynamics Simulations written by Uwe Burghaus and published by . This book was released on 2006 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The guidelines of this textbook are numerous example programs, flux diagrams, schemes, and figures presenting the obtained results. Step by step, the authors explain how steady state Monte Carlo Simulation (MCS) and time resolved, so-called kinetic or dynamic Monte Carlo Simulation (KMCS), schemes, respectively, can be set up. Furthermore, examples of classical Molecular Dynamics Simulations (MDS) are included. In addressing the same type of problem by way off all these methods, the different schemes can directly be compared. For the example programs, they have chosen problems related to the adsorption of gas-phase species on surfaces (i.e. mainly lattice models related to gas-surface adsorption dynamics). Furthermore, the growth of deposits on grid surfaces has been address including fractal growth phenomena.
Download or read book Quantum Monte Carlo Methods in Physics and Chemistry written by M.P. Nightingale and published by Springer Science & Business Media. This book was released on 1998-12-31 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years there has been a considerable growth in interest in Monte Carlo methods, and quantum Monte Carlo methods in particlular. Clearly, the ever-increasing computational power available to researchers, has stimulated the development of improved algorithms, and almost all fields in computational physics and chemistry are affected by their applications. Here we just mention some fields that are covered in the lecture notes contained in this volume, viz. electronic structure studies of atoms, molecules and solids, nuclear structure, and low- or zero-temperature studies of strongly-correlated quantum systems, both of the continuum and lattice variety, and cooperative phenomena in classical systems. Although each area of application may have its own peculiarities, requiring specialized solutions, all share the same basic methodology. It was with the intention of bringing together researchers and students from these various areas that the NATO Advanced Study Institute on Quantum Monte Carlo Methods in Physics and Chemistry was held at Cornell University from 12 to 24 July, 1998. This book contains material presented at the Institute in a series of mini courses in quantum Monte Carlo methods. The program consisted of lectures predominantly of a pedagogical nature, and of more specialized seminars. The levels varied from introductory to advanced, and from basic methods to applications; the program was intended for an audience working towards the Ph.D. level and above. Despite the essentially pedagogic nature of the Institute, several of the lectures and seminars contained in this volume present recent developments not previously published.
Download or read book Monte Carlo Methods in Statistical Physics written by Kurt Binder and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the seven years since this volume first appeared. there has been an enormous expansion of the range of problems to which Monte Carlo computer simulation methods have been applied. This fact has already led to the addition of a companion volume ("Applications of the Monte Carlo Method in Statistical Physics", Topics in Current Physics. Vol . 36), edited in 1984, to this book. But the field continues to develop further; rapid progress is being made with respect to the implementation of Monte Carlo algorithms, the construction of special-purpose computers dedicated to exe cute Monte Carlo programs, and new methods to analyze the "data" generated by these programs. Brief descriptions of these and other developments, together with numerous addi tional references, are included in a new chapter , "Recent Trends in Monte Carlo Simulations" , which has been written for this second edition. Typographical correc tions have been made and fuller references given where appropriate, but otherwise the layout and contents of the other chapters are left unchanged. Thus this book, together with its companion volume mentioned above, gives a fairly complete and up to-date review of the field. It is hoped that the reduced price of this paperback edition will make it accessible to a wide range of scientists and students in the fields to which it is relevant: theoretical phYSics and physical chemistry , con densed-matter physics and materials science, computational physics and applied mathematics, etc.
Download or read book Monte Carlo Methods in Statistical Physics written by K. Murthy and published by Universities Press. This book was released on 2004 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: Monte Carlo simulations comprise a substantial part of the new and third major arm of investigation in the physical sciences that has emerged in recent times, to augment the traditional ones of experiment and theory. With the advent of high-speed digital computing, numerical simulations techniques like Monte Carlo have been very successful in extracting real world observations out of seemingly intractable theoretical models.
Download or read book The Monte Carlo Method in Condensed Matter Physics written by Kurt Binder and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Monte Carlo method is now widely used and commonly accepted as an important and useful tool in solid state physics and related fields. It is broadly recognized that the technique of "computer simulation" is complementary to both analytical theory and experiment, and can significantly contribute to ad vancing the understanding of various scientific problems. Widespread applications of the Monte Carlo method to various fields of the statistical mechanics of condensed matter physics have already been reviewed in two previously published books, namely Monte Carlo Methods in Statistical Physics (Topics Curro Phys. , Vol. 7, 1st edn. 1979, 2ndedn. 1986) and Applications of the Monte Carlo Method in Statistical Physics (Topics Curro Phys. , Vol. 36, 1st edn. 1984, 2nd edn. 1987). Meanwhile the field has continued its rapid growth and expansion, and applications to new fields have appeared that were not treated at all in the above two books (e. g. studies of irreversible growth phenomena, cellular automata, interfaces, and quantum problems on lattices). Also, new methodic aspects have emerged, such as aspects of efficient use of vector com puters or parallel computers, more efficient analysis of simulated systems con figurations, and methods to reduce critical slowing down at i>hase transitions. Taken together with the extensive activity in certain traditional areas of research (simulation of classical and quantum fluids, of macromolecular materials, of spin glasses and quadrupolar glasses, etc.
Download or read book Theory Application and Implementation of Monte Carlo Method in Science and Technology written by Pooneh Saidi Bidokhti and published by BoD – Books on Demand. This book was released on 2019-12-18 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Monte Carlo method is a numerical technique to model the probability of all possible outcomes in a process that cannot easily be predicted due to the interference of random variables. It is a technique used to understand the impact of risk, uncertainty, and ambiguity in forecasting models. However, this technique is complicated by the amount of computer time required to achieve sufficient precision in the simulations and evaluate their accuracy. This book discusses the general principles of the Monte Carlo method with an emphasis on techniques to decrease simulation time and increase accuracy.
Download or read book Markov Chain Monte Carlo Innovations And Applications written by Wilfrid S Kendall and published by World Scientific. This book was released on 2005-11-08 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Markov Chain Monte Carlo (MCMC) originated in statistical physics, but has spilled over into various application areas, leading to a corresponding variety of techniques and methods. That variety stimulates new ideas and developments from many different places, and there is much to be gained from cross-fertilization. This book presents five expository essays by leaders in the field, drawing from perspectives in physics, statistics and genetics, and showing how different aspects of MCMC come to the fore in different contexts. The essays derive from tutorial lectures at an interdisciplinary program at the Institute for Mathematical Sciences, Singapore, which exploited the exciting ways in which MCMC spreads across different disciplines.
