Antonio Mucherino; et al (eds.)'s Distance geometry : theory, methods, and applications PDF

By Antonio Mucherino; et al (eds.)

ISBN-10: 1461451280

ISBN-13: 9781461451280

Distance Geometry: idea, tools, and functions is the 1st number of study surveys devoted to distance geometry and its purposes. the 1st a part of the e-book discusses theoretical features of the space Geometry challenge (DGP), the place the relation among DGP and different comparable topics also are offered. lined themes comprise distance matrix thought, Euclidean distance matrix of completion, multispherical constitution of distance matrices, geometric algebra, algebraic distance geometry conception, visualization of K-dimensional buildings within the airplane, graph pressure, and concept of discretizable DGP.The moment a part of this quantity offers mathematical and computational homes of equipment constructed to the issues mentioned within the first component, together with non-stop equipment (based on Gaussian and hyperbolic smoothing, distinction of convex features, semidefinite programming, branch-and-bound), discrete tools (based on branch-and-prune, geometric build-up, graph rigidity), and in addition heuristics tools (based on simulated annealing, genetic algorithms, tabu seek, variable local search).Applications contain the 3rd a part of the booklet, that's in most cases dedicated to the appliance of DGP to NMR constitution calculation. this can be a tremendous and strongly multidisciplinary software in biology and biomedicine. learn more... concept -- common stress of Bar Frameworks normally place: A Euclidean Distance Matrix procedure / Abdo Y. Alfakih -- combined quantity and Distance Geometry concepts for Counting Euclidean Embeddings of inflexible Graphs / Ioannis Z. Emiris, Elias P. Tsigaridas, Antonios Varvitsiotis -- The Discretizable Molecular Distance Geometry challenge turns out more uncomplicated on Proteins / Leo Liberti, Carlile Lavor, Antonio Mucherino -- Spheres Unions and Intersections and a few in their functions in Molecular Modeling / Michel Petitjean -- Is the space Geometry challenge in NP? / Nathanael Beeker, Stéphane Gaubert, Christian Glusa, Leo Liberti -- fixing Spatial Constraints with Generalized Distance Geometry / Lu Yang -- A Topological Interpretation of the stroll Distances / Pavel Chebotarev, Michel Deza -- equipment -- Distance Geometry equipment for Protein constitution choice / Zachary Voller, Zhijun Wu -- fixing the Discretizable Molecular Distance Geometry challenge through a number of awareness timber / Pedro Nucci, Loana Tito Nogueira, Carlile Lavor -- ASAP: An Eigenvector Synchronization set of rules for the Graph awareness challenge / Mihai Cucuringu -- international Optimization for Atomic Cluster Distance Geometry difficulties / Marco Locatelli, Fabio Schoen -- fixing Molecular Distance Geometry difficulties utilizing a continuing Optimization method / Rodrigo S. Lima, J. M. Martínez -- DC Programming ways for Distance Geometry difficulties / Hoai An Le Thi, Tao Pham Dinh -- Stochastic Proximity Embedding: an easy, speedy and Scalable set of rules for fixing the gap Geometry challenge / Dimitris okay. Agrafiotis, Deepak Bandyopadhyay, Eric Yang -- functions to Protein Conformations -- Distance Geometry for practical Molecular Conformations / Gordon M. Crippen -- Distance Geometry in Structural Biology: New views / Thérèse E. Malliavin, Antonio Mucherino, Michael Nilges -- utilizing a disbursed SDP method of clear up Simulated Protein Molecular Conformation difficulties / Xingyuan Fang, Kim-Chuan Toh -- an outline on Protein constitution choice by way of NMR: old and destiny views of using Distance Geometry tools / Fabio C. L. Almeida, Adolfo H. Moraes, Francisco Gomes-Neto

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Extra resources for Distance geometry : theory, methods, and applications

Example text

In sparse (or toric) elimination theory, a polynomial is characterized by its support. Given a polynomial f in n variables, its support is the set of exponents in Nn corresponding to nonzero terms (or monomials). The Newton polytope of f is the convex hull of its support and lies in Rn . Consider polytopes Pi ⊂ Rn and parameters λi ∈ R, λi ≥ 0, for i = 1, . . , n. We denote by λi Pi the corresponding scalar multiple of Pi . Consider the Minkowski sum of the scaled polytopes λ1 P1 + · · · + λn Pn ∈ Rn ; 2 Euclidean Embeddings of Rigid Graphs 29 its n-dimensional (Euclidean) volume is a homogeneous polynomial of degree n in the λi .

20) Then Zˆ is a Gale matrix of G(p) since both Ψ and Z2 are nonsingular. Furthermore, ˆ S = ZΨ Z T = ZΨ [Z1T Z2T ] = [ZΨ Z1T Z]. In other words, Zˆ consists of the last r¯ columns of S. Thus zˆi j = si, j+r+1 . It follows by the definition of S that si, j+r+1 = 0 for all i, j such that i = ( j + r + 1) and (i, j + ¯ j + r + 1). r + 1) ∈ E(G). Therefore, zˆi j = 0 for all j = 1, . . 10. Let the Gale matrix in Eq. 17) be Zˆ as defined in Eq. 20). Then the system of Eq. 17) is equivalent to the system of equations E (y)Zˆ = 0.

12. Let Sn−1 = Sn + Z ξn ξn T Z T = Z(I + ξn ξn T )Z T . Then 1. , PSn−1 = 0. 2. Sn−1 0 and the rank of Sn−1 remains n − r − 1. 3. sn−1 in = 0 for all i : i < n, (i, n) ∈ E(G). Proof. The first statement is obvious. The second statement follows since I + ξn ξnT 0. The third statement is also true by construction. , for all i ∈ N¯ (n), we have sn−1 in = sin + bi bn = sin − sin = 0. We continue this purification process for columns (n − 1), . . , k, . . , (r + 3). Before the kth purification step, we have Sk 0, PSk = 0, rank Sk = n − r − 1, and skij = 0, for all i j : i = j, (i, j) ∈ E(G), and for all j = k + 1, .

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Distance geometry : theory, methods, and applications by Antonio Mucherino; et al (eds.)


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