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 59 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 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 141 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 Distance Geometry and Molecular Conformation written by G. M. Crippen and published by . This book was released on 1988 with total page 566 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The VSEPR Model of Molecular Geometry written by Ronald J Gillespie and published by Courier Corporation. This book was released on 2013-03-21 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: Valence Shell Electron Pair Repulsion (VSEPR) theory is a simple technique for predicting the geometry of atomic centers in small molecules and molecular ions. This authoritative reference was written by Istvan Hartiggai and the developer of VSEPR theory, Ronald J. Gillespie. In addition to its value as a text for courses in molecular geometry and chemistry, it constitutes a classic reference for professionals. Starting with coverage of the broader aspects of VSEPR, this volume narrows its focus to a succinct survey of the methods of structural determination. Additional topics include the applications of the VSEPR model and its theoretical basis. Helpful data on molecular geometries, bond lengths, and bond angles appear in tables and other graphics.
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 Molecular Geometry written by Alison Rodger and published by Butterworth-Heinemann. This book was released on 2014-05-16 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Geometry discusses topics relevant to the arrangement of atoms. The book is comprised of seven chapters that tackle several areas of molecular geometry. Chapter 1 reviews the definition and determination of molecular geometry, while Chapter 2 discusses the unified view of stereochemistry and stereochemical changes. Chapter 3 covers the geometry of molecules of second row atoms, and Chapter 4 deals with the main group elements beyond the second row. The book also talks about the complexes of transition metals and f-block elements, and then covers the organometallic compounds and transition metal clusters. The last chapter tackles the consequences of small, local variations in geometry. The text will be of great use to chemists who primarily deal with the properties of molecules and atoms.
Download or read book Reviews in Computational Chemistry Volume 5 written by Kenny B. Lipkowitz and published by John Wiley & Sons. This book was released on 2009-09-22 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book The Combinatorial Distance Geometry Approach to the Calculation of Molecular Conformation written by Timothy Franklin Havel and published by . This book was released on 1982 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book A Geometric Algebra Invitation to Space Time Physics Robotics and Molecular Geometry written by Carlile Lavor and published by Springer. This book was released on 2018-07-12 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers a gentle introduction to key elements of Geometric Algebra, along with their applications in Physics, Robotics and Molecular Geometry. Major applications covered are the physics of space-time, including Maxwell electromagnetism and the Dirac equation; robotics, including formulations for the forward and inverse kinematics and an overview of the singularity problem for serial robots; and molecular geometry, with 3D-protein structure calculations using NMR data. The book is primarily intended for graduate students and advanced undergraduates in related fields, but can also benefit professionals in search of a pedagogical presentation of these subjects.
Download or read book Molecular Geometry written by Ronald James Gillespie and published by . This book was released on 1972 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 From Chemical Topology to Three Dimensional Geometry written by Alexandru T. Balaban and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: Even high-speed supercomputers cannot easily convert traditional two-dimensional databases from chemical topology into the three-dimensional ones demanded by today's chemists, particularly those working in drug design. This fascinating volume resolves this problem by positing mathematical and topological models which greatly expand the capabilities of chemical graph theory. The authors examine QSAR and molecular similarity studies, the relationship between the sequence of amino acids and the less familiar secondary and tertiary protein structures, and new topological methods.
Download or read book Distance Geometry written by Springer and published by . This book was released on 2012-12-22 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book New Trends in Mathematical Programming written by F. Giannessi and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 315 pages. Available in PDF, EPUB and Kindle. Book excerpt: Though the volume covers 22 papers by 36 authors from 12 countries, the history in the background is bound to Hungary where, in 1973 Andras Pn§kopa started to lay the foundation of a scientific forum, which can be a regular meeting spot for experts of the world in the field. Since then, there has been a constant interest in that forum. Headed at present by Tamas Rapcsak, the Laboratory of Operations Research and Decisions Systems of the Computer and Automation Institute, Hungarian Academy of Sciences followed the tradition in every respect, namely conferences were organized almost in every second year and in the same stimulating area, in the Matra mountains. The basic fields were kept, providing opportunities for the leading personalities to give voice to their latest results. The floor has been widened recently for the young generation, ensuring this way both a real location for the past, present and future experts to meet and also the possibility for them to make the multicoloured rainbow of the fields unbroken and continuous. The volume is devoted to the memory of Steven Vajda, one of the pioneers on mathematical programming, born is Hungary. In 1992 he took part in the XIth International Conference on Mathematical Programming at Matrafiired where, with his bright personality, he greatly contributed to the good spirituality of the event. We thank Jakob Krarup for his reminiscence on the life and scientific activities of late Steven Vajda.
Download or read book Global Optimization written by János D. Pintér and published by Springer Science & Business Media. This book was released on 2006-10-13 with total page 559 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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. Coverage extends to a broad range of applications, from agroecosystem management to robot design. Proposed solutions encompass a range of practical and viable methods.
