Theory and Applications of Distance Geometry PDF Download
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Author: Leonard Mascot Blumenthal
Publisher: Chelsea Publishing Company, Incorporated
ISBN:
Category : Mathematics
Languages : en
Pages : 392
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Book Description
Author: Leonard Mascot Blumenthal
Publisher: Chelsea Publishing Company, Incorporated
ISBN:
Category : Mathematics
Languages : en
Pages : 392
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Book Description
Author: Antonio Mucherino
Publisher: Springer
ISBN: 9781489985781
Category : Mathematics
Languages : en
Pages : 0
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Book Description
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.
Author: Leo Liberti
Publisher: Springer
ISBN: 3319607928
Category : Mathematics
Languages : en
Pages : 141
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Book Description
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.
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 347
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Author: Abdo Y. Alfakih
Publisher: Springer
ISBN: 3319978462
Category : Mathematics
Languages : en
Pages : 258
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Book Description
This book offers a comprehensive and accessible exposition of Euclidean Distance Matrices (EDMs) and rigidity theory of bar-and-joint frameworks. It is based on the one-to-one correspondence between EDMs and projected Gram matrices. Accordingly the machinery of semidefinite programming is a common thread that runs throughout the book. As a result, two parallel approaches to rigidity theory are presented. The first is traditional and more intuitive approach that is based on a vector representation of point configuration. The second is based on a Gram matrix representation of point configuration. Euclidean Distance Matrices and Their Applications in Rigidity Theory begins by establishing the necessary background needed for the rest of the book. The focus of Chapter 1 is on pertinent results from matrix theory, graph theory and convexity theory, while Chapter 2 is devoted to positive semidefinite (PSD) matrices due to the key role these matrices play in our approach. Chapters 3 to 7 provide detailed studies of EDMs, and in particular their various characterizations, classes, eigenvalues and geometry. Chapter 8 serves as a transitional chapter between EDMs and rigidity theory. Chapters 9 and 10 cover local and universal rigidities of bar-and-joint frameworks. This book is self-contained and should be accessible to a wide audience including students and researchers in statistics, operations research, computational biochemistry, engineering, computer science and mathematics.
Author: Jon Dattorro
Publisher: Meboo Publishing USA
ISBN: 0976401304
Category : Mathematics
Languages : en
Pages : 776
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Book Description
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.
Author: Zhijun Wu
Publisher: World Scientific
ISBN: 9812814787
Category : Science
Languages : en
Pages : 243
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Book Description
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
Author: William Kirk
Publisher: Springer
ISBN: 3319109278
Category : Mathematics
Languages : en
Pages : 176
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Book Description
This is a monograph on fixed point theory, covering the purely metric aspects of the theory–particularly results that do not depend on any algebraic structure of the underlying space. Traditionally, a large body of metric fixed point theory has been couched in a functional analytic framework. This aspect of the theory has been written about extensively. There are four classical fixed point theorems against which metric extensions are usually checked. These are, respectively, the Banach contraction mapping principal, Nadler’s well known set-valued extension of that theorem, the extension of Banach’s theorem to nonexpansive mappings, and Caristi’s theorem. These comparisons form a significant component of this book. This book is divided into three parts. Part I contains some aspects of the purely metric theory, especially Caristi’s theorem and a few of its many extensions. There is also a discussion of nonexpansive mappings, viewed in the context of logical foundations. Part I also contains certain results in hyperconvex metric spaces and ultrametric spaces. Part II treats fixed point theory in classes of spaces which, in addition to having a metric structure, also have geometric structure. These specifically include the geodesic spaces, length spaces and CAT(0) spaces. Part III focuses on distance spaces that are not necessarily metric. These include certain distance spaces which lie strictly between the class of semimetric spaces and the class of metric spaces, in that they satisfy relaxed versions of the triangle inequality, as well as other spaces whose distance properties do not fully satisfy the metric axioms.
Author: M.F. Thorpe
Publisher: Springer Science & Business Media
ISBN: 0306470896
Category : Computers
Languages : en
Pages : 435
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Book Description
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.
Author: J. M. Landsberg
Publisher: American Mathematical Soc.
ISBN: 0821869078
Category : Mathematics
Languages : en
Pages : 464
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Book Description
Tensors are ubiquitous in the sciences. The geometry of tensors is both a powerful tool for extracting information from data sets, and a beautiful subject in its own right. This book has three intended uses: a classroom textbook, a reference work for researchers in the sciences, and an account of classical and modern results in (aspects of) the theory that will be of interest to researchers in geometry. For classroom use, there is a modern introduction to multilinear algebra and to the geometry and representation theory needed to study tensors, including a large number of exercises. For researchers in the sciences, there is information on tensors in table format for easy reference and a summary of the state of the art in elementary language. This is the first book containing many classical results regarding tensors. Particular applications treated in the book include the complexity of matrix multiplication, P versus NP, signal processing, phylogenetics, and algebraic statistics. For geometers, there is material on secant varieties, G-varieties, spaces with finitely many orbits and how these objects arise in applications, discussions of numerous open questions in geometry arising in applications, and expositions of advanced topics such as the proof of the Alexander-Hirschowitz theorem and of the Weyman-Kempf method for computing syzygies.
