Download or read book Chapter 4 Applications of Monte Carlo Simulation in Modelling of Biochemical Processes written by Kiril Ivanov Tenekedjiev and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The biochemical models describing complex and dynamic metabolic systems are typically multi-parametric and non-linear, thus the identification of their parameters requires nonlinear regression analysis of the experimental data. The stochastic nature of the experimental samples poses the necessity to estimate not only the values fitting best to the model, but also the distribution of the parameters, and to test statistical hypotheses about the values of these parameters. In such situations the application of analytical models for parameter distributions is totally inappropriate because their assumptions are not applicable for intrinsically non-linear regressions. That is why, Monte Carlo simulations are a powerful tool to model biochemical processes.
Download or read book Applications of Monte Carlo Methods in Biology Medicine and Other Fields of Science written by Charles J. Mode and published by BoD – Books on Demand. This book was released on 2011-02-28 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is an eclectic mix of applications of Monte Carlo methods in many fields of research should not be surprising, because of the ubiquitous use of these methods in many fields of human endeavor. In an attempt to focus attention on a manageable set of applications, the main thrust of this book is to emphasize applications of Monte Carlo simulation methods in biology and medicine.
Download or read book Annual Reports in Computational Chemistry written by Ralph A. Wheeler and published by Elsevier. This book was released on 2014-12-03 with total page 237 pages. Available in PDF, EPUB and Kindle. Book excerpt: Annual Reports in Computational Chemistry provides timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. - Quantum chemistry - Molecular mechanics - Force fields - Chemical education and applications in academic and industrial settings
Download or read book Applications of Monte Carlo Methods in Biology Medicine and Other Fields of Science written by Charles J. Mode and published by IntechOpen. This book was released on 2011-02-28 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is an eclectic mix of applications of Monte Carlo methods in many fields of research should not be surprising, because of the ubiquitous use of these methods in many fields of human endeavor. In an attempt to focus attention on a manageable set of applications, the main thrust of this book is to emphasize applications of Monte Carlo simulation methods in biology and medicine.
Download or read book Value of Information and Flexibility written by Martin J. Vilela and published by Springer Nature. This book was released on 2021-10-21 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a consistent methodology for making decisions under uncertain conditions, as is almost always the case. Tools such as value of information and value of flexibility are explored as a means to make more complex and nuanced decisions. The book develops the complete formalism for assessing the value of acquiring information with two novel approaches. Firstly, it integrates the fuzzy characteristics of data, and secondly develops a methodology for assessing data acquisition actions that optimize the value of projects from a holistic perspective. The book also discusses the formalism for including flexibility in the project decision assessment. Practical examples of oil- and gas-related decision problems are included and discussed to facilitate the learning process. This book provides valuable advice and case studies applicable to engineers, researchers, and graduate students, particularly in the oil and gas industry and pharmaceutic industry.
Download or read book Handbook in Monte Carlo Simulation written by Paolo Brandimarte and published by John Wiley & Sons. This book was released on 2014-06-17 with total page 688 pages. Available in PDF, EPUB and Kindle. Book excerpt: An accessible treatment of Monte Carlo methods, techniques, and applications in the field of finance and economics Providing readers with an in-depth and comprehensive guide, the Handbook in Monte Carlo Simulation: Applications in Financial Engineering, Risk Management, and Economics presents a timely account of the applicationsof Monte Carlo methods in financial engineering and economics. Written by an international leading expert in thefield, the handbook illustrates the challenges confronting present-day financial practitioners and provides various applicationsof Monte Carlo techniques to answer these issues. The book is organized into five parts: introduction andmotivation; input analysis, modeling, and estimation; random variate and sample path generation; output analysisand variance reduction; and applications ranging from option pricing and risk management to optimization. The Handbook in Monte Carlo Simulation features: An introductory section for basic material on stochastic modeling and estimation aimed at readers who may need a summary or review of the essentials Carefully crafted examples in order to spot potential pitfalls and drawbacks of each approach An accessible treatment of advanced topics such as low-discrepancy sequences, stochastic optimization, dynamic programming, risk measures, and Markov chain Monte Carlo methods Numerous pieces of R code used to illustrate fundamental ideas in concrete terms and encourage experimentation The Handbook in Monte Carlo Simulation: Applications in Financial Engineering, Risk Management, and Economics is a complete reference for practitioners in the fields of finance, business, applied statistics, econometrics, and engineering, as well as a supplement for MBA and graduate-level courses on Monte Carlo methods and simulation.
Download or read book Modeling and Simulation in Ecotoxicology with Applications in MATLAB and Simulink written by Kenneth R. Dixon and published by CRC Press. This book was released on 2016-04-19 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring roles critical to environmental toxicology, Modeling and Simulation in Ecotoxicology with Applications in MATLAB and Simulink covers the steps in modeling and simulation from problem conception to validation and simulation analysis. Using the MATLAB and Simulink programming languages, the book presents examples of mathematical functions a
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 Stochastic Biomathematical Models written by Mostafa Bachar and published by Springer. This book was released on 2012-10-19 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stochastic biomathematical models are becoming increasingly important as new light is shed on the role of noise in living systems. In certain biological systems, stochastic effects may even enhance a signal, thus providing a biological motivation for the noise observed in living systems. Recent advances in stochastic analysis and increasing computing power facilitate the analysis of more biophysically realistic models, and this book provides researchers in computational neuroscience and stochastic systems with an overview of recent developments. Key concepts are developed in chapters written by experts in their respective fields. Topics include: one-dimensional homogeneous diffusions and their boundary behavior, large deviation theory and its application in stochastic neurobiological models, a review of mathematical methods for stochastic neuronal integrate-and-fire models, stochastic partial differential equation models in neurobiology, and stochastic modeling of spreading cortical depression.
Download or read book Simulation Algorithms for Computational Systems Biology written by Luca Marchetti and published by Springer. This book was released on 2017-09-27 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explains the state-of-the-art algorithms used to simulate biological dynamics. Each technique is theoretically introduced and applied to a set of modeling cases. Starting from basic simulation algorithms, the book also introduces more advanced techniques that support delays, diffusion in space, or that are based on hybrid simulation strategies. This is a valuable self-contained resource for graduate students and practitioners in computer science, biology and bioinformatics. An appendix covers the mathematical background, and the authors include further reading sections in each chapter.
Download or read book Theory and Applications of Monte Carlo Simulations written by Wai Kin (Victor) Chan and published by BoD – Books on Demand. This book was released on 2013-03-06 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of this book is to introduce researchers and practitioners to recent advances and applications of Monte Carlo Simulation (MCS). Random sampling is the key of the MCS technique. The 11 chapters of this book collectively illustrates how such a sampling technique is exploited to solve difficult problems or analyze complex systems in various engineering and science domains. Issues related to the use of MCS including goodness-of-fit, uncertainty evaluation, variance reduction, optimization, and statistical estimation are discussed and examples of solutions are given. Novel applications of MCS are demonstrated in financial systems modeling, estimation of transition behavior of organic molecules, chemical reaction, particle diffusion, kinetic simulation of biophysics and biological data, and healthcare practices. To enlarge the accessibility of this book, both field-specific background materials and field-specific usages of MCS are introduced in most chapters. The aim of this book is to unify knowledge of MCS from different fields to facilitate research and new applications of MCS.
Download or read book Advanced Dynamic System Simulation written by Granino A. Korn and published by John Wiley & Sons. This book was released on 2013-02-22 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: A unique, hands-on guide to interactive modeling and simulation of engineering systems This book describes advanced, cutting-edge techniques for dynamic system simulation using the DESIRE modeling/simulation software package. It offers detailed guidance on how to implement the software, providing scientists and engineers with powerful tools for creating simulation scenarios and experiments for such dynamic systems as aerospace vehicles, control systems, or biological systems. Along with two new chapters on neural networks, Advanced Dynamic-System Simulation, Second Edition revamps and updates all the material, clarifying explanations and adding many new examples. A bundled CD contains an industrial-strength version of OPEN DESIRE as well as hundreds of program examples that readers can use in their own experiments. The only book on the market to demonstrate model replication and Monte Carlo simulation of real-world engineering systems, this volume: Presents a newly revised systematic procedure for difference-equation modeling Covers runtime vector compilation for fast model replication on a personal computer Discusses parameter-influence studies, introducing very fast vectorized statistics computation Highlights Monte Carlo studies of the effects of noise and manufacturing tolerances for control-system modeling Demonstrates fast, compact vector models of neural networks for control engineering Features vectorized programs for fuzzy-set controllers, partial differential equations, and agro-ecological modeling Advanced Dynamic-System Simulation, Second Edition is a truly useful resource for researchers and design engineers in control and aerospace engineering, ecology, and agricultural planning. It is also an excellent guide for students using DESIRE.
Download or read book Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes written by Miguel Cerrolaza and published by Academic Press. This book was released on 2017-12-28 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes covers new and exciting modeling methods to help bioengineers tackle problems for which the Finite Element Method is not appropriate. The book covers a wide range of important subjects in the field of numerical methods applied to biomechanics, including bone biomechanics, tissue and cell mechanics, 3D printing, computer assisted surgery and fluid dynamics. Modeling strategies, technology and approaches are continuously evolving as the knowledge of biological processes increases. Both theory and applications are covered, making this an ideal book for researchers, students and R&D professionals. - Provides non-conventional analysis methods for modeling - Covers the Discrete Element Method (DEM), Particle Methods (PM), MessLess and MeshFree Methods (MLMF), Agent-Based Methods (ABM), Lattice-Boltzmann Methods (LBM) and Boundary Integral Methods (BIM) - Includes contributions from several world renowned experts in their fields - Compares pros and cons of each method to help you decide which method is most applicable to solving specific problems
Download or read book Monte Carlo Simulation in Systems Biology written by Jan Schellenberger and published by . This book was released on 2010 with total page 176 pages. Available in PDF, EPUB and Kindle. Book excerpt: Constraint Based Reconstruction and Analysis (COBRA) is a framework within the field of Systems Biology which aims to understand cellular metabolism through the analysis of large scale metabolic models. These models are based on meticulously curated reconstructions of all chemical reactions in an organism. Instead of attempting to predict the exact state of the biological system, COBRA describes the physiological constraints that the system must satisfy and studies the range of solutions satisfying these constraints. Monte Carlo Sampling is one of the COBRA methods used to study how biological properties are distributed over the entire solution space. A set of randomly distributed solutions is generated and serves as a proxy for the entire space. Various aspects of Monte Carlo Sampling in Systems Biology are illustrated : 1) Monte Carlo Sampling has been used historically (Chapter 1), 2) A faster and more efficient procedure for generating Monte Carlo Samples is developed (Chapter 2); 3) Carbon 13 tracing experiments are an important tool for measuring reaction rates through a network. Monte Carlo Sampling was used to optimize the choice of label and explain and measure the dimensionality of output data (Chapter 3); 4) It is possible to incorporate the thermodynamic "loop-law'' into many COBRA methods including sampling (Chapter 4). Additionally two software projects are presented which assist in analyzing COBRA models : 1) the BiGG knowledgebase of reconstructions (Chapter 5) and 2) the COBRA Matlab toolbox v. 2.0 (Chapter 6). These two projects make COBRA methods available to the scientific community.
Download or read book Biological Modeling and Simulation written by Russell Schwartz and published by MIT Press. This book was released on 2008-07-25 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
Download or read book Machine Learning and Hybrid Modelling for Reaction Engineering written by Dongda Zhang and published by Royal Society of Chemistry. This book was released on 2023-12-20 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last decade, there has been a significant shift from traditional mechanistic and empirical modelling into statistical and data-driven modelling for applications in reaction engineering. In particular, the integration of machine learning and first-principle models has demonstrated significant potential and success in the discovery of (bio)chemical kinetics, prediction and optimisation of complex reactions, and scale-up of industrial reactors. Summarising the latest research and illustrating the current frontiers in applications of hybrid modelling for chemical and biochemical reaction engineering, Machine Learning and Hybrid Modelling for Reaction Engineering fills a gap in the methodology development of hybrid models. With a systematic explanation of the fundamental theory of hybrid model construction, time-varying parameter estimation, model structure identification and uncertainty analysis, this book is a great resource for both chemical engineers looking to use the latest computational techniques in their research and computational chemists interested in new applications for their work.
Download or read book Biophysics written by Mark C. Leake and published by CRC Press. This book was released on 2016-09-15 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: An Up-to-Date Toolbox for Probing Biology Biophysics: Tools and Techniques covers the experimental and theoretical tools and techniques of biophysics. It addresses the purpose, science, and application of all physical science instrumentation and analysis methods used in current research labs. The book first presents the historical background, concepts, and motivation for using a physical science toolbox to understand biology. It then familiarizes undergraduate students from the physical sciences with essential biological knowledge. The text subsequently focuses on experimental biophysical techniques that primarily detect biological components or measure/control biological forces. The author describes the science and application of key tools used in imaging, detection, general quantitation, and biomolecular interaction studies, which span multiple length and time scales of biological processes both in the test tube and in the living organism. Moving on to theoretical biophysics tools, the book presents computational and analytical mathematical methods for tackling challenging biological questions including exam-style questions at the end of each chapter as well as step-by-step solved exercises. It concludes with a discussion of the future of this exciting field. Future innovators will need to be trained in multidisciplinary science to be successful in industry, academia, and government support agencies. Addressing this challenge, this textbook educates future leaders on the development and application of novel physical science approaches to solve complex problems linked to biological questions. Features: Provides the full, modern physical science toolbox of experimental and analytical techniques, such as bulk ensemble methods, single-molecule tools, and live-cell and test tube methods Incorporates worked examples for the most popular physical science tools, including full diagrams and a summary of the science involved in the application of the tool Reinforces the understanding of key concepts and biological questions A solutions manual is available upon qualifying course adoption.
