An Introduction to Distance Geometry applied to Molecular Geometry

An Introduction to Distance Geometry applied to Molecular Geometry
Author: Carlile Lavor
Publisher: Springer
Total Pages: 59
Release: 2017-07-12
Genre: Computers
ISBN: 3319571834

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.

Distance Geometry

Distance Geometry
Author: Antonio Mucherino
Publisher: Springer
Total Pages: 0
Release: 2015-01-28
Genre: Mathematics
ISBN: 9781489985781

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.

Convex Optimization & Euclidean Distance Geometry

Convex Optimization & Euclidean Distance Geometry
Author: Jon Dattorro
Publisher: Meboo Publishing USA
Total Pages: 776
Release: 2005
Genre: Mathematics
ISBN: 0976401304

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.

Euclidean Distance Geometry

Euclidean Distance Geometry
Author: Leo Liberti
Publisher: Springer
Total Pages: 141
Release: 2017-09-20
Genre: Mathematics
ISBN: 3319607928

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.

Geometric Science of Information

Geometric Science of Information
Author: Frank Nielsen
Publisher: Springer
Total Pages: 863
Release: 2013-08-19
Genre: Computers
ISBN: 3642400205

This book constitutes the refereed proceedings of the First International Conference on Geometric Science of Information, GSI 2013, held in Paris, France, in August 2013. The nearly 100 papers presented were carefully reviewed and selected from numerous submissions and are organized into the following thematic sessions: Geometric Statistics on Manifolds and Lie Groups, Deformations in Shape Spaces, Differential Geometry in Signal Processing, Relational Metric, Discrete Metric Spaces, Computational Information Geometry, Hessian Information Geometry I and II, Computational Aspects of Information Geometry in Statistics, Optimization on Matrix Manifolds, Optimal Transport Theory, Probability on Manifolds, Divergence Geometry and Ancillarity, Entropic Geometry, Tensor-Valued Mathematical Morphology, Machine/Manifold/Topology Learning, Geometry of Audio Processing, Geometry of Inverse Problems, Algebraic/Infinite dimensional/Banach Information Manifolds, Information Geometry Manifolds, and Algorithms on Manifolds.

Reviews in Computational Chemistry, Volume 5

Reviews in Computational Chemistry, Volume 5
Author: Kenny B. Lipkowitz
Publisher: John Wiley & Sons
Total Pages: 482
Release: 2009-09-22
Genre: Science
ISBN: 0470126094

Führende Experten auf dem Gebiet der Computer-Chemie präsentieren in dem fünften Band der erfolgreichen Reihe 'Reviews in Computational Chemistry' die neuesten Entwicklungen. Um den interessierten Chemiker auf dem aktuellen Stand zu halten, ist der Reihe im Anhang eine Liste mit der Software zum Thema beigefügt

The Power of Geometric Algebra Computing

The Power of Geometric Algebra Computing
Author: Dietmar Hildenbrand
Publisher: CRC Press
Total Pages: 189
Release: 2021-09-30
Genre: Computers
ISBN: 1000461238

Geometric Algebra is a very powerful mathematical system for an easy and intuitive treatment of geometry, but the community working with it is still very small. The main goal of this book is to close this gap from a computing perspective in presenting the power of Geometric Algebra Computing for engineering applications and quantum computing. The Power of Geometric Algebra Computing is based on GAALOPWeb, a new user-friendly, web-based tool for the generation of optimized code for different programming languages as well as for the visualization of Geometric Algebra algorithms for a wide range of engineering applications. Key Features: Introduces a new web-based optimizer for Geometric Algebra algorithms Supports many programming languages as well as hardware Covers the advantages of high-dimensional algebras Includes geometrically intuitive support of quantum computing This book includes applications from the fields of computer graphics, robotics and quantum computing and will help students, engineers and researchers interested in really computing with Geometric Algebra.

Computational Physics

Computational Physics
Author: D.k. Jha
Publisher: Discovery Publishing House
Total Pages: 324
Release: 2009
Genre: Mathematical physics
ISBN: 9788183564519