Download or read book Theory and Applications of Distance Geometry written by Leonard Mascot Blumenthal and published by Chelsea Publishing Company, Incorporated. This book was released on 1970 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Theory and applications of distance geometry written by and published by . This book was released on 1970 with total page 347 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Distance Geometry written by Antonio Mucherino and published by Springer Science & Business Media. This book was released on 2012-12-22 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of research surveys on the Distance Geometry Problem (DGP) and its applications. It will be divided into three parts: Theory, Methods and Applications. Each part will contain at least one survey and several research papers. The first part, Theory, will deal with theoretical aspects of the DGP, including a new class of problems and the study of its complexities as well as the relation between DGP and other related topics, such as: distance matrix theory, Euclidean distance matrix completion problem, multispherical structure of distance matrices, distance geometry and geometric algebra, algebraic distance geometry theory, visualization of K-dimensional structures in the plane, graph rigidity, and theory of discretizable DGP: symmetry and complexity. The second part, Methods, will discuss mathematical and computational properties of methods developed to the problems considered in the first chapter including continuous methods (based on Gaussian and hyperbolic smoothing, difference of convex functions, semidefinite programming, branch-and-bound), discrete methods (based on branch-and-prune, geometric build-up, graph rigidity), and also heuristics methods (based on simulated annealing, genetic algorithms, tabu search, variable neighborhood search). Applications will comprise the third part and will consider applications of DGP to NMR structure calculation, rational drug design, molecular dynamics simulations, graph drawing and sensor network localization. This volume will be the first edited book on distance geometry and applications. The editors are in correspondence with the major contributors to the field of distance geometry, including important research centers in molecular biology such as Institut Pasteur in Paris.

Download or read book Euclidean Distance Geometry written by Leo Liberti and published by Springer. This book was released on 2017-09-20 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook, the first of its kind, presents the fundamentals of distance geometry: theory, useful methodologies for obtaining solutions, and real world applications. Concise proofs are given and step-by-step algorithms for solving fundamental problems efficiently and precisely are presented in Mathematica®, enabling the reader to experiment with concepts and methods as they are introduced. Descriptive graphics, examples, and problems, accompany the real gems of the text, namely the applications in visualization of graphs, localization of sensor networks, protein conformation from distance data, clock synchronization protocols, robotics, and control of unmanned underwater vehicles, to name several. Aimed at intermediate undergraduates, beginning graduate students, researchers, and practitioners, the reader with a basic knowledge of linear algebra will gain an understanding of the basic theories of distance geometry and why they work in real life.

Download or read book Lecture Notes on Computational Structural Biology written by Zhijun Wu and published by World Scientific. This book was released on 2008 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt: 1. Introduction. 1.1. Protein structure. 1.2. Structure determination. 1.3. Dynamics simulation. 1.4. The myth of protein folding -- 2. X-ray crystallography computing. 2.1. The phase problem. 2.2. Least squares solutions. 2.3. Entropy maximization. 2.4. Indirect methods -- 3. NMR structure determination. 3.1. Nuclear magnetic resonance. 3.2. Distance geometry. 3.3. Distance-based modeling. 3.4. Structural analysis -- 4. Potential energy minimization. 4.1. Potential energy function. 4.2. Local optimization. 4.3. Global optimization. 4.4. Energy transformation -- 5. Molecular dynamics simulation. 5.1. Equations of motion. 5.2. Initial-value problem. 5.3. Boundary-value problem. 5.4. Normal mode analysis -- 6. Knowledge-based protein modeling. 6.1. Sequence/structural alignment. 6.2. Fold recognition/inverse folding. 6.3. Knowledge-based structural refinement. 6.4. Structural computing and beyond

Download or read book An Introduction to Distance Geometry applied to Molecular Geometry written by Carlile Lavor and published by Springer. This book was released on 2017-07-12 with total page 54 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a pedagogical presentation aimed at advanced undergraduate students, beginning graduate students and professionals who are looking for an introductory text to the field of Distance Geometry, and some of its applications. This versions profits from feedback acquired at undergraduate/graduate courses in seminars and a number of workshops.

Download or read book Encyclopedia of Distances written by Michel Marie Deza and published by Springer. This book was released on 2014-10-08 with total page 731 pages. Available in PDF, EPUB and Kindle. Book excerpt: This updated and revised third edition of the leading reference volume on distance metrics includes new items from very active research areas in the use of distances and metrics such as geometry, graph theory, probability theory and analysis. Among the new topics included are, for example, polyhedral metric space, nearness matrix problems, distances between belief assignments, distance-related animal settings, diamond-cutting distances, natural units of length, Heidegger’s de-severance distance, and brain distances. The publication of this volume coincides with intensifying research efforts into metric spaces and especially distance design for applications. Accurate metrics have become a crucial goal in computational biology, image analysis, speech recognition and information retrieval. Leaving aside the practical questions that arise during the selection of a ‘good’ distance function, this work focuses on providing the research community with an invaluable comprehensive listing of the main available distances. As well as providing standalone introductions and definitions, the encyclopedia facilitates swift cross-referencing with easily navigable bold-faced textual links to core entries. In addition to distances themselves, the authors have collated numerous fascinating curiosities in their Who’s Who of metrics, including distance-related notions and paradigms that enable applied mathematicians in other sectors to deploy research tools that non-specialists justly view as arcane. In expanding access to these techniques, and in many cases enriching the context of distances themselves, this peerless volume is certain to stimulate fresh research.

Download or read book Convex Optimization Euclidean Distance Geometry written by Jon Dattorro and published by Meboo Publishing USA. This book was released on 2005 with total page 776 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of Euclidean distance matrices (EDMs) fundamentally asks what can be known geometrically given onlydistance information between points in Euclidean space. Each point may represent simply locationor, abstractly, any entity expressible as a vector in finite-dimensional Euclidean space.The answer to the question posed is that very much can be known about the points;the mathematics of this combined study of geometry and optimization is rich and deep.Throughout we cite beacons of historical accomplishment.The application of EDMs has already proven invaluable in discerning biological molecular conformation.The emerging practice of localization in wireless sensor networks, the global positioning system (GPS), and distance-based pattern recognitionwill certainly simplify and benefit from this theory.We study the pervasive convex Euclidean bodies and their various representations.In particular, we make convex polyhedra, cones, and dual cones more visceral through illustration, andwe study the geometric relation of polyhedral cones to nonorthogonal bases biorthogonal expansion.We explain conversion between halfspace- and vertex-descriptions of convex cones,we provide formulae for determining dual cones,and we show how classic alternative systems of linear inequalities or linear matrix inequalities and optimality conditions can be explained by generalized inequalities in terms of convex cones and their duals.The conic analogue to linear independence, called conic independence, is introducedas a new tool in the study of classical cone theory; the logical next step in the progression:linear, affine, conic.Any convex optimization problem has geometric interpretation.This is a powerful attraction: the ability to visualize geometry of an optimization problem.We provide tools to make visualization easier.The concept of faces, extreme points, and extreme directions of convex Euclidean bodiesis explained here, crucial to understanding convex optimization.The convex cone of positive semidefinite matrices, in particular, is studied in depth.We mathematically interpret, for example,its inverse image under affine transformation, and we explainhow higher-rank subsets of its boundary united with its interior are convex.The Chapter on "Geometry of convex functions",observes analogies between convex sets and functions:The set of all vector-valued convex functions is a closed convex cone.Included among the examples in this chapter, we show how the real affinefunction relates to convex functions as the hyperplane relates to convex sets.Here, also, pertinent results formultidimensional convex functions are presented that are largely ignored in the literature;tricks and tips for determining their convexityand discerning their geometry, particularly with regard to matrix calculus which remains largely unsystematizedwhen compared with the traditional practice of ordinary calculus.Consequently, we collect some results of matrix differentiation in the appendices.The Euclidean distance matrix (EDM) is studied,its properties and relationship to both positive semidefinite and Gram matrices.We relate the EDM to the four classical axioms of the Euclidean metric;thereby, observing the existence of an infinity of axioms of the Euclidean metric beyondthe triangle inequality. We proceed byderiving the fifth Euclidean axiom and then explain why furthering this endeavoris inefficient because the ensuing criteria (while describing polyhedra)grow linearly in complexity and number.Some geometrical problems solvable via EDMs,EDM problems posed as convex optimization, and methods of solution arepresented;\eg, we generate a recognizable isotonic map of the United States usingonly comparative distance information (no distance information, only distance inequalities).We offer a new proof of the classic Schoenberg criterion, that determines whether a candidate matrix is an EDM. Our proofrelies on fundamental geometry; assuming, any EDM must correspond to a list of points contained in some polyhedron(possibly at its vertices) and vice versa.It is not widely known that the Schoenberg criterion implies nonnegativity of the EDM entries; proved here.We characterize the eigenvalues of an EDM matrix and then devisea polyhedral cone required for determining membership of a candidate matrix(in Cayley-Menger form) to the convex cone of Euclidean distance matrices (EDM cone); \ie,a candidate is an EDM if and only if its eigenspectrum belongs to a spectral cone for EDM^N.We will see spectral cones are not unique.In the chapter "EDM cone", we explain the geometric relationship betweenthe EDM cone, two positive semidefinite cones, and the elliptope.We illustrate geometric requirements, in particular, for projection of a candidate matrixon a positive semidefinite cone that establish its membership to the EDM cone. The faces of the EDM cone are described,but still open is the question whether all its faces are exposed as they are for the positive semidefinite cone.The classic Schoenberg criterion, relating EDM and positive semidefinite cones, isrevealed to be a discretized membership relation (a generalized inequality, a new Farkas''''''''-like lemma)between the EDM cone and its ordinary dual. A matrix criterion for membership to the dual EDM cone is derived thatis simpler than the Schoenberg criterion.We derive a new concise expression for the EDM cone and its dual involvingtwo subspaces and a positive semidefinite cone."Semidefinite programming" is reviewedwith particular attention to optimality conditionsof prototypical primal and dual conic programs,their interplay, and the perturbation method of rank reduction of optimal solutions(extant but not well-known).We show how to solve a ubiquitous platonic combinatorial optimization problem from linear algebra(the optimal Boolean solution x to Ax=b)via semidefinite program relaxation.A three-dimensional polyhedral analogue for the positive semidefinite cone of 3X3 symmetricmatrices is introduced; a tool for visualizing in 6 dimensions.In "EDM proximity"we explore methods of solution to a few fundamental and prevalentEuclidean distance matrix proximity problems; the problem of finding that Euclidean distance matrix closestto a given matrix in the Euclidean sense.We pay particular attention to the problem when compounded with rank minimization.We offer a new geometrical proof of a famous result discovered by Eckart \& Young in 1936 regarding Euclideanprojection of a point on a subset of the positive semidefinite cone comprising all positive semidefinite matriceshaving rank not exceeding a prescribed limit rho.We explain how this problem is transformed to a convex optimization for any rank rho.

Download or read book Mathematical Challenges from Theoretical Computational Chemistry written by National Research Council and published by National Academies Press. This book was released on 1995-03-29 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational methods are rapidly becoming major tools of theoretical, pharmaceutical, materials, and biological chemists. Accordingly, the mathematical models and numerical analysis that underlie these methods have an increasingly important and direct role to play in the progress of many areas of chemistry. This book explores the research interface between computational chemistry and the mathematical sciences. In language that is aimed at non-specialists, it documents some prominent examples of past successful cross-fertilizations between the fields and explores the mathematical research opportunities in a broad cross-section of chemical research frontiers. It also discusses cultural differences between the two fields and makes recommendations for overcoming those differences and generally promoting this interdisciplinary work.

Download or read book Reviews in Computational Chemistry Volume 2 written by Kenny B. Lipkowitz and published by John Wiley & Sons. This book was released on 2009-09-22 with total page 547 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second volume of the series 'Reviews in Computational Chemistry' explores new applications, new methodologies, and new perspectives. The topics covered include conformational analysis, protein folding, force field parameterizations, hydrogen bonding, charge distributions, electrostatic potentials, electronic spectroscopy, molecular property correlations, and the computational chemistry literature. Methodologies described include conformational search strategies, distance geometry, molecular mechanics, molecular dynamics, ab initio and semiempirical molecular orbital calculations, and quantitative structure-activity relationships (QSAR) using topological and electronic descriptors. A compendium of molecular modeling software will help users select the computational tools they need. Each chapter in 'Reviews in Computational Chemistry' serves as a brief tutorial for organic, physical, pharmaceutical, and biological chemists new to the field. Practitioners will be interested in the recent advances.

Download or read book Theory of Distances in NeutroGeometry written by and published by Infinite Study. This book was released on 2024-01-01 with total page 11 pages. Available in PDF, EPUB and Kindle. Book excerpt: NeutroGeometry is one of the most recent approaches to geometry. In NeutroGeometry mod-els, the main condition is to satisfy an axiom, definition, property, operator and so on, that is neither entirely true nor entirely false. When one of these concepts is not satisfied at all it is called AntiGeometry. One of the problems that this new theory has had is the scarcity of models. Another open problem is the definition of angle and distance measurements within the framework of NeutroGeometry. This paper aims to introduce a general theory of distance measures in any NeutroGeometry. We also present an algorithm for distance measurement in real-life problems.

Download or read book Rigidity Theory and Applications written by M.F. Thorpe and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although rigidity has been studied since the time of Lagrange (1788) and Maxwell (1864), it is only in the last twenty-five years that it has begun to find applications in the basic sciences. The modern era starts with Laman (1970), who made the subject rigorous in two dimensions, followed by the development of computer algorithms that can test over a million sites in seconds and find the rigid regions, and the associated pivots, leading to many applications. This workshop was organized to bring together leading researchers studying the underlying theory, and to explore the various areas of science where applications of these ideas are being implemented.

Download or read book New Foundations for Physical Geometry written by Tim Maudlin and published by Oxford University Press. This book was released on 2014-02 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tim Maudlin sets out a completely new method for describing the geometrical structure of spaces, and thus a better mathematical tool for describing and understanding space-time. He presents a historical review of the development of geometry and topology, and then his original Theory of Linear Structures.

Download or read book Frontiers And Prospects Of Contemporary Applied Mathematics written by Pingwen Zhang and published by World Scientific. This book was released on 2006-04-17 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection of articles covers the hottest topics in contemporary applied mathematics. Multiscale modeling, material computing, symplectic methods, parallel computing, mathematical biology, applied differential equations and engineering computing problems are all included. The book contains the latest results of many leading scientists and provides a window on new trends in research in the field.

Download or read book Encyclopedia of Optimization written by Christodoulos A. Floudas and published by Springer Science & Business Media. This book was released on 2008-09-04 with total page 4646 pages. Available in PDF, EPUB and Kindle. Book excerpt: The goal of the Encyclopedia of Optimization is to introduce the reader to a complete set of topics that show the spectrum of research, the richness of ideas, and the breadth of applications that has come from this field. The second edition builds on the success of the former edition with more than 150 completely new entries, designed to ensure that the reference addresses recent areas where optimization theories and techniques have advanced. Particularly heavy attention resulted in health science and transportation, with entries such as "Algorithms for Genomics", "Optimization and Radiotherapy Treatment Design", and "Crew Scheduling".

Download or read book Topics in Semidefinite and Interior Point Methods written by Panos M. Pardalos and Henry Wolkowicz and published by American Mathematical Soc.. This book was released on with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents refereed papers presented at the workshop Semidefinite Programming and Interior-Point Approaches for Combinatorial Problems: held at The Fields Institute in May 1996. Semidefinite programming (SDP) is a generalization of linear programming (LP) in that the non-negativity constraints on the variables is replaced by a positive semidefinite constraint on matrix variables. Many of the elegant theoretical properties and powerful solution techniques follow through from LP to SDP. In particular, the primal-dual interior-point methods, which are currently so successful for LP, can be used to efficiently solve SDP problems. In addition to the theoretical and algorithmic questions, SDP has found many important applications in combinatorial optimization, control theory and other areas of mathematical programming. The papers in this volume cover a wide spectrum of recent developments in SDP. The volume would be suitable as a textbook for advanced courses in optimization. It is intended for graduate students and researchers in mathematics, computer science, engineering and operations.

Download or read book Handbook of Geometric Constraint Systems Principles written by Meera Sitharam and published by CRC Press. This book was released on 2018-07-20 with total page 605 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Handbook of Geometric Constraint Systems Principles is an entry point to the currently used principal mathematical and computational tools and techniques of the geometric constraint system (GCS). It functions as a single source containing the core principles and results, accessible to both beginners and experts. The handbook provides a guide for students learning basic concepts, as well as experts looking to pinpoint specific results or approaches in the broad landscape. As such, the editors created this handbook to serve as a useful tool for navigating the varied concepts, approaches and results found in GCS research. Key Features: A comprehensive reference handbook authored by top researchers Includes fundamentals and techniques from multiple perspectives that span several research communities Provides recent results and a graded program of open problems and conjectures Can be used for senior undergraduate or graduate topics course introduction to the area Detailed list of figures and tables About the Editors: Meera Sitharam is currently an Associate Professor at the University of Florida’s Department of Computer & Information Science and Engineering. She received her Ph.D. at the University of Wisconsin, Madison. Audrey St. John is an Associate Professor of Computer Science at Mount Holyoke College, who received her Ph. D. from UMass Amherst. Jessica Sidman is a Professor of Mathematics on the John S. Kennedy Foundation at Mount Holyoke College. She received her Ph.D. from the University of Michigan.