Parallel Continuation Based Global Optimization For Molecular Conformation And Protein Folding
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Parallel Continuation Based Global Optimization For Molecular Conformation And Protein Folding
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Author : Thomas Frederick Coleman
language : en
Publisher:
Release Date : 1994
Parallel Continuation Based Global Optimization For Molecular Conformation And Protein Folding written by Thomas Frederick Coleman and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1994 with Conformational analysis categories.
Parallel Continuation Based Global Optimization For Molecular Conformation And Protein Folding
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Author :
language : en
Publisher:
Release Date : 1994
Parallel Continuation Based Global Optimization For Molecular Conformation And Protein Folding written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1994 with categories.
This paper presents the authors' recent work on developing parallel algorithms and software for solving the global minimization problem for molecular conformation, especially protein folding. Global minimization problems are difficult to solve when the objective functions have many local minimizers, such as the energy functions for protein folding. In their approach, to avoid directly minimizing a ''difficult'' function, a special integral transformation is introduced to transform the function into a class of gradually deformed, but ''smoother'' or ''easier'' functions. An optimization procedure is then applied to the new functions successively, to trace their solutions back to the original function. The method can be applied to a large class of nonlinear partially separable functions including energy functions for molecular conformation and protein folding. Mathematical theory for the method, as a special continuation approach to global optimization, is established. Algorithms with different solution tracing strategies are developed. Different levels of parallelism are exploited for the implementation of the algorithms on massively parallel architectures.
Optimization In Computational Chemistry And Molecular Biology
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Author : Christodoulos A. Floudas
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-06-29
Optimization In Computational Chemistry And Molecular Biology written by Christodoulos A. Floudas 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 2013-06-29 with Computers categories.
Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches covers recent developments in optimization techniques for addressing several computational chemistry and biology problems. A tantalizing problem that cuts across the fields of computational chemistry, biology, medicine, engineering and applied mathematics is how proteins fold. Global and local optimization provide a systematic framework of conformational searches for the prediction of three-dimensional protein structures that represent the global minimum free energy, as well as low-energy biomolecular conformations. Each contribution in the book is essentially expository in nature, but of scholarly treatment. The topics covered include advances in local and global optimization approaches for molecular dynamics and modeling, distance geometry, protein folding, molecular structure refinement, protein and drug design, and molecular and peptide docking. Audience: The book is addressed not only to researchers in mathematical programming, but to all scientists in various disciplines who use optimization methods in solving problems in computational chemistry and biology.
Lecture Notes On Computational Structural Biology
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Author : Zhijun Wu
language : en
Publisher: World Scientific
Release Date : 2008
Lecture Notes On Computational Structural Biology written by Zhijun Wu and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Science categories.
While the field of computational structural biology or structural bioinformatics is rapidly developing, there are few books with a relatively complete coverage of such diverse research subjects studied in the field as X-ray crystallography computing, NMR structure determination, potential energy minimization, dynamics simulation, and knowledge-based modeling. This book helps fill the gap by providing such a survey on all the related subjects. Comprising a collection of lecture notes for a computational structural biology course for the Program on Bioinformatics and Computational Biology at Iowa State University, the book is in essence a comprehensive summary of computational structural biology based on the author's own extensive research experience, and a review of the subject from the perspective of a computer scientist or applied mathematician. Readers will gain a deeper appreciation of the biological importance and mathematical novelty of the research in the field.
Global Optimization
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Author : János D. Pintér
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-10-13
Global Optimization written by János D. Pintér 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 2006-10-13 with Mathematics categories.
Optimization models based on a nonlinear systems description often possess multiple local optima. The objective of global optimization (GO) is to find the best possible solution of multiextremal problems. This volume illustrates the applicability of GO modeling techniques and solution strategies to real-world problems. The contributed chapters cover a broad range of applications from agroecosystem management, assembly line design, bioinformatics, biophysics, black box systems optimization, cellular mobile network design, chemical process optimization, chemical product design, composite structure design, computational modeling of atomic and molecular structures, controller design for induction motors, electrical engineering design, feeding strategies in animal husbandry, the inverse position problem in kinematics, laser design, learning in neural nets, mechanical engineering design, numerical solution of equations, radiotherapy planning, robot design, and satellite data analysis. The solution strategies discussed encompass a range of practically viable methods, including both theoretically rigorous and heuristic approaches.
Large Scale Optimization With Applications
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Author : Lorenz T. Biegler
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
Large Scale Optimization With Applications written by Lorenz T. Biegler 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 2012-12-06 with Mathematics categories.
Many important molecular conformation problems, such as protein folding, are expressed as global minimization problems. It is the fact that local minimization is insufficient, that markedly differentiates this volume from the previous two. Unfortunately, global minimization problems that result from models of molecular conformation are usually intractable. For example, simple 1-dimensional versions of distance conformation problems are NP-hard. Nevertheless, there has been significant recent progress in the design of promising heuristic strategies (often involving the use of high- performance parallel computers) for computing approximate global minimizers. The purpose of the sessions represented in this volume was to discuss the new algorithmic advances for global minimization in the context of protein folding and related molecular minimization problems. Emphasis was on practical shortcomings of current approaches, outstanding problems and questions, and the use of high-performance parallel computers.
A New Parallel Algorithm For Global Optimization With Application To The Molecular Cluster Problem
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Author : Aiping Liao
language : en
Publisher:
Release Date : 1994
A New Parallel Algorithm For Global Optimization With Application To The Molecular Cluster Problem written by Aiping Liao and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1994 with Mathematical optimization categories.
Foundations Of Global Genetic Optimization
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Author : Robert Schaefer
language : en
Publisher: Springer
Release Date : 2007-07-07
Foundations Of Global Genetic Optimization written by Robert Schaefer and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-07-07 with Technology & Engineering categories.
Genetic algorithms today constitute a family of e?ective global optimization methods used to solve di?cult real-life problems which arise in science and technology. Despite their computational complexity, they have the ability to explore huge data sets and allow us to study exceptionally problematic cases in which the objective functions are irregular and multimodal, and where information about the extrema location is unobtainable in other ways. Theybelongtotheclassofiterativestochasticoptimizationstrategiesthat, during each step, produce and evaluate the set of admissible points from the search domain, called the random sample or population. As opposed to the Monte Carlo strategies, in which the population is sampled according to the uniform probability distribution over the search domain, genetic algorithms modify the probability distribution at each step. Mechanisms which adopt sampling probability distribution are transposed from biology. They are based mainly on genetic code mutation and crossover, as well as on selection among living individuals. Such mechanisms have been testedbysolvingmultimodalproblemsinnature,whichiscon?rmedinpart- ular by the many species of animals and plants that are well ?tted to di?erent ecological niches. They direct the search process, making it more e?ective than a completely random one (search with a uniform sampling distribution). Moreover,well-tunedgenetic-basedoperationsdonotdecreasetheexploration ability of the whole admissible set, which is vital in the global optimization process. The features described above allow us to regard genetic algorithms as a new class of arti?cial intelligence methods which introduce heuristics, well tested in other ?elds, to the classical scheme of stochastic global search.
Scientific And Technical Aerospace Reports
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Author :
language : en
Publisher:
Release Date : 1995
Scientific And Technical Aerospace Reports written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1995 with Aeronautics categories.
Lists citations with abstracts for aerospace related reports obtained from world wide sources and announces documents that have recently been entered into the NASA Scientific and Technical Information Database.
Advances In Classification And Data Analysis
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Author : Simone Borra
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
Advances In Classification And Data Analysis written by Simone Borra 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 2012-12-06 with Business & Economics categories.
This volume contains a selection of papers presented at the biannual meeting of the Classification and Data Analysis Group of Societa Italiana di Statistica, which was held in Rome, July 5-6, 1999. From the originally submitted papers, a careful review process led to the selection of 45 papers presented in four parts as follows: CLASSIFICATION AND MULTIDIMENSIONAL SCALING Cluster analysis Discriminant analysis Proximity structures analysis and Multidimensional Scaling Genetic algorithms and neural networks MUL TIV ARIA TE DATA ANALYSIS Factorial methods Textual data analysis Regression Models for Data Analysis Nonparametric methods SPATIAL AND TIME SERIES DATA ANALYSIS Time series analysis Spatial data analysis CASE STUDIES INTERNATIONAL FEDERATION OF CLASSIFICATION SOCIETIES The International Federation of Classification Societies (IFCS) is an agency for the dissemination of technical and scientific information concerning classification and data analysis in the broad sense and in as wide a range of applications as possible; founded in 1985 in Cambridge (UK) from the following Scientific Societies and Groups: British Classification Society -BCS; Classification Society of North America - CSNA; Gesellschaft fUr Klassifikation - GfKI; Japanese Classification Society -JCS; Classification Group of Italian Statistical Society - CGSIS; Societe Francophone de Classification -SFC. Now the IFCS includes also the following Societies: Dutch-Belgian Classification Society - VOC; Polish Classification Society -SKAD; Associayao Portuguesa de Classificayao e Analise de Dados -CLAD; Korean Classification Society -KCS; Group-at-Large.