Convex Hulls (3D)
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												  Compact Hyperbolic Tetrahedra with Non-Obtuse Dihedral AnglesCompact hyperbolic tetrahedra with non-obtuse dihedral angles Roland K. W. Roeder ∗ January 7, 2006 Abstract Given a combinatorial description C of a polyhedron having E edges, the space of dihedral angles of all compact hyperbolic polyhe- dra that realize C is generally not a convex subset of RE [9]. If C has five or more faces, Andreev’s Theorem states that the correspond- ing space of dihedral angles AC obtained by restricting to non-obtuse angles is a convex polytope. In this paper we explain why Andreev did not consider tetrahedra, the only polyhedra having fewer than five faces, by demonstrating that the space of dihedral angles of com- pact hyperbolic tetrahedra, after restricting to non-obtuse angles, is non-convex. Our proof provides a simple example of the “method of continuity”, the technique used in classification theorems on polyhe- dra by Alexandrow [4], Andreev [5], and Rivin-Hodgson [19]. 2000 Mathematics Subject Classification. 52B10, 52A55, 51M09. Key Words. Hyperbolic geometry, polyhedra, tetrahedra. Given a combinatorial description C of a polyhedron having E edges, the space of dihedral angles of all compact hyperbolic polyhedra that realize C is generally not a convex subset of RE. This is proved in a nice paper by D´ıaz [9]. However, Andreev’s Theorem [5, 13, 14, 20] shows that by restricting to compact hyperbolic polyhedra with non-obtuse dihedral angles, E the space of dihedral angles is a convex polytope, which we label AC R . It is interesting to note that the statement of Andreev’s Theorem requires⊂ ∗rroeder@fields.utoronto.ca 1 that C have five or more faces, ruling out the tetrahedron which is the only polyhedron having fewer than five faces.
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												  Using Information Theory to Discover Side Chain Rotamer ClassesPacific Symposium on Biocomputing 4:278-289 (1999) U S I N G I N F O R M A T I O N T H E O R Y T O D I S C O V E R S I D E C H A I N R O T A M E R C L A S S E S : A N A L Y S I S O F T H E E F F E C T S O F L O C A L B A C K B O N E S T R U C T U R E J A C Q U E L Y N S . F E T R O W G E O R G E B E R G Department of Molecular Biology Department of Computer Science The Scripps Research Institute University at Albany, SUNY La Jolla, CA 92037, USA Albany, NY 12222, USA An understanding of the regularities in the side chain conformations of proteins and how these are related to local backbone structures is important for protein modeling and design. Previous work using regular secondary structures and regular divisions of the backbone dihedral angle data has shown that these rotamers are sensitive to the protein’s local backbone conformation. In this preliminary study, we demonstrate a method for combining a more general backbone structure model with an objective clustering algorithm to investigate the effects of backbone structures on side chain rotamer classes and distributions. For the local structure classification, we use the Structural Building Blocks (SBB) categories, which represent all types of secondary structure, including regular structures, capping structures, and loops.
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												  Equivelar Octahedron of Genus 3 in 3-SpaceEquivelar octahedron of genus 3 in 3-space Ruslan Mizhaev ([email protected]) Apr. 2020 ABSTRACT . Building up a toroidal polyhedron of genus 3, consisting of 8 nine-sided faces, is given. From the point of view of topology, a polyhedron can be considered as an embedding of a cubic graph with 24 vertices and 36 edges in a surface of genus 3. This polyhedron is a contender for the maximal genus among octahedrons in 3-space. 1. Introduction This solution can be attributed to the problem of determining the maximal genus of polyhedra with the number of faces - . As is known, at least 7 faces are required for a polyhedron of genus = 1 . For cases ≥ 8 , there are currently few examples. If all faces of the toroidal polyhedron are – gons and all vertices are q-valence ( ≥ 3), such polyhedral are called either locally regular or simply equivelar [1]. The characteristics of polyhedra are abbreviated as , ; [1]. 2. Polyhedron {9, 3; 3} V1. The paper considers building up a polyhedron 9, 3; 3 in 3-space. The faces of a polyhedron are non- convex flat 9-gons without self-intersections. The polyhedron is symmetric when rotated through 1804 around the axis (Fig. 3). One of the features of this polyhedron is that any face has two pairs with which it borders two edges. The polyhedron also has a ratio of angles and faces - = − 1. To describe polyhedra with similar characteristics ( = − 1) we use the Euler formula − + = = 2 − 2, where is the Euler characteristic. Since = 3, the equality 3 = 2 holds true.
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												  A Theory of Nets for Polyhedra and Polytopes Related to Incidence GeometriesDesigns, Codes and Cryptography, 10, 115–136 (1997) c 1997 Kluwer Academic Publishers, Boston. Manufactured in The Netherlands. A Theory of Nets for Polyhedra and Polytopes Related to Incidence Geometries SABINE BOUZETTE C. P. 216, Universite´ Libre de Bruxelles, Bd du Triomphe, B-1050 Bruxelles FRANCIS BUEKENHOUT [email protected] C. P. 216, Universite´ Libre de Bruxelles, Bd du Triomphe, B-1050 Bruxelles EDMOND DONY C. P. 216, Universite´ Libre de Bruxelles, Bd du Triomphe, B-1050 Bruxelles ALAIN GOTTCHEINER C. P. 216, Universite´ Libre de Bruxelles, Bd du Triomphe, B-1050 Bruxelles Communicated by: D. Jungnickel Received November 22, 1995; Revised July 26, 1996; Accepted August 13, 1996 Dedicated to Hanfried Lenz on the occasion of his 80th birthday. Abstract. Our purpose is to elaborate a theory of planar nets or unfoldings for polyhedra, its generalization and extension to polytopes and to combinatorial polytopes, in terms of morphisms of geometries and the adjacency graph of facets. Keywords: net, polytope, incidence geometry, prepolytope, category 1. Introduction Planar nets for various polyhedra are familiar both for practical matters and for mathematical education about age 11–14. They are systematised in two directions. The most developed of these consists in the drawing of some net for each polyhedron in a given collection (see for instance [20], [21]). A less developed theme is to enumerate all nets for a given polyhedron, up to some natural equivalence. Little has apparently been done for polytopes in dimensions d 4 (see however [18], [3]). We have found few traces of this subject in the literature and we would be grateful for more references.
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												  Predicting Backbone Cα Angles and Dihedrals from Protein Sequences by Stacked Sparse Auto-Encoder Deep Neural NetworkPredicting backbone C# angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network Author Lyons, James, Dehzangi, Abdollah, Heffernan, Rhys, Sharma, Alok, Paliwal, Kuldip, Sattar, Abdul, Zhou, Yaoqi, Yang, Yuedong Published 2014 Journal Title Journal of Computational Chemistry DOI https://doi.org/10.1002/jcc.23718 Copyright Statement © 2014 Wiley Periodicals, Inc.. This is the accepted version of the following article: Predicting backbone Ca angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network Journal of Computational Chemistry, Vol. 35(28), 2014, pp. 2040-2046, which has been published in final form at dx.doi.org/10.1002/jcc.23718. Downloaded from http://hdl.handle.net/10072/64247 Griffith Research Online https://research-repository.griffith.edu.au Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network James Lyonsa, Abdollah Dehzangia,b, Rhys Heffernana, Alok Sharmaa,c, Kuldip Paliwala , Abdul Sattara,b, Yaoqi Zhoud*, Yuedong Yang d* aInstitute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia bNational ICT Australia (NICTA), Brisbane, Australia cSchool of Engineering and Physics, University of the South Pacific, Private Mail Bag, Laucala Campus, Suva, Fiji dInstitute for Glycomics and School of Information and Communication Technique, Griffith University, Parklands Dr. Southport, QLD 4222, Australia *Corresponding authors ([email protected], [email protected]) ABSTRACT Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between Cαi-1−Cαi−Cαi+1 (θ) and a dihedral angle rotated about the Cαi−Cαi+1 bond (τ).
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												  Toroidal Diffusions and Protein Structure EvolutionToroidal diffusions and protein structure evolution Eduardo García-Portugués1;7, Michael Golden2, Michael Sørensen3, Kanti V. Mardia2;4, Thomas Hamelryck5;6, and Jotun Hein2 Abstract This chapter shows how toroidal diffusions are convenient methodological tools for modelling protein evolution in a probabilistic framework. The chapter addresses the construction of ergodic diffusions with stationary distributions equal to well-known directional distributions, which can be regarded as toroidal analogues of the Ornstein–Uhlenbeck process. The important challenges that arise in the estimation of the diffusion parameters require the consideration of tractable approximate likelihoods and, among the several approaches introduced, the one yielding a spe- cific approximation to the transition density of the wrapped normal process is shown to give the best empirical performance on average. This provides the methodological building block for Evolutionary Torus Dynamic Bayesian Network (ETDBN), a hidden Markov model for protein evolution that emits a wrapped normal process and two continuous-time Markov chains per hid- den state. The chapter describes the main features of ETDBN, which allows for both “smooth” conformational changes and “catastrophic” conformational jumps, and several empirical bench- marks. The insights into the relationship between sequence and structure evolution that ETDBN provides are illustrated in a case study. Keywords: Directional statistics; Evolution; Probabilistic model; Protein structure; Stochastic differential equation; Wrapped
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												  H2O2 and NH 2 OHInt. J. Mol. Sci. 2006 , 7, 289-319 International Journal of Molecular Sciences ISSN 1422-0067 © 2006 by MDPI www.mdpi.org/ijms/ A Quest for the Origin of Barrier to the Internal Rotation of Hydrogen Peroxide (H 2O2) and Fluorine Peroxide (F 2O2) Dulal C. Ghosh Department of Chemistry, University of Kalyani, Kalyani-741235, India Email: [email protected], Fax: +91-33 25828282 Received: 2 July 2006 / Accepted: 24 July 2006 / Published: 25 August 2006 Abstract: In order to understand the structure-property relationship, SPR, an energy- partitioning quest for the origin of the barrier to the internal rotation of two iso-structural molecules, hydrogen peroxide, H 2O2, and fluorine peroxide, F 2O2 is performed. The hydrogen peroxide is an important bio-oxidative compound generated in the body cells to fight infections and is an essential ingredient of our immune system. The fluorine peroxide is its analogue. We have tried to discern the interactions and energetic effects that entail the nonplanar skew conformation as the equilibrium shape of the molecules. The physical process of the dynamics of internal rotation initiates the isomerization reaction and generates infinite number of conformations. The decomposed energy components faithfully display the physical process of skewing and eclipsing as a function of torsional angles and hence are good descriptors of the process of isomerization reaction of hydrogen peroxide (H 2O2) and dioxygen difluoride (F 2O2) associated with the dynamics of internal rotation. It is observed that the one-center, two-center bonded and nonbonded interaction terms are sharply divided in two groups. One group of interactions hinders the skewing and favours planar cis/trans forms while the other group favours skewing and prefers the gauche conformation of the molecule.
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												  Klein 4A Alkanes+IsomerismGrossman, CHE 230 4a. Alkanes. Conformational Stereoisomerism. Structural Isomerism. 4a.1 Derivatives of methane. We can replace one of the H atoms in methane with another atom or group. These atoms or groups are called heteroatoms. Examples: Methyl bromide, methyl iodide, methanol, methylamine, methanethiol. Here the central C atom is not quite as perfectly tetrahedral, but for our purposes, it is close enough. If the H atom is replaced with nothing, we have three possibilities. – • We can remove just the H nucleus and leave behind two electrons -- this gives CH3 , with sp3 hybridization. It has the same structure as ammonia, just one fewer proton (and neutron) in the nucleus in the center. + • We can take away the H nucleus and both electrons. This gives us CH3 . The hybridization here? We don't want to waste valuable low-energy s orbital in a hybrid orbital in which there are no electrons. Instead, the valuable s electron is divided equally among the six electrons (three bonds) remaining. Three bonds means three orbitals, one s and two p. That means the third p orbital remains unhybridized. This situation is called sp2 hybridization. Two p orbitals occupy a plane, so in sp2 hybridization, the three hybrid orbitals are coplanar. They point 120° apart, to the corners of a triangle. The unhybridized p orbital is perpendicular to this plane. • What if we take away the H nucleus and one electron? We have a situation in which CH3· (methyl radical) is between sp2 and sp3 hybridization. It's a shallow pyramid. These species are high in energy and don't exist for long.
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												  Zipper Unfoldings of Polyhedral ComplexesZipper Unfoldings of Polyhedral Complexes The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Demaine, Erik D. et al. "Zipper Unfoldings of Polyhedral Complexes." 22nd Canadian Conference on Computational Geometry, CCCG 2010, Winnipeg MB, August 9-11, 2010. As Published http://www.cs.umanitoba.ca/~cccg2010/accepted.html Publisher University of Manitoba Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/62237 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike 3.0 Detailed Terms http://creativecommons.org/licenses/by-nc-sa/3.0/ CCCG 2010, Winnipeg MB, August 9{11, 2010 Zipper Unfoldings of Polyhedral Complexes Erik D. Demaine∗ Martin L. Demainey Anna Lubiwz Arlo Shallitx Jonah L. Shallit{ Abstract We explore which polyhedra and polyhedral complexes can be formed by folding up a planar polygonal region and fastening it with one zipper. We call the reverse tetrahedron icosahedron process a zipper unfolding. A zipper unfolding of a polyhedron is a path cut that unfolds the polyhedron to a planar polygon; in the case of edge cuts, these are Hamiltonian unfoldings as introduced by Shephard in 1975. We show that all Platonic and Archimedean solids have Hamiltonian unfoldings. octahedron dodecahedron We give examples of polyhedral complexes that are, Figure 2: Doubly Hamiltonian unfoldings of the other and are not, zipper [edge] unfoldable. The positive ex- Platonic solids. amples include a polyhedral torus, and two tetrahedra joined at an edge or at a face. The physical model of a zipper provides a natural 1 Introduction extension of zipper unfolding to polyhedral complexes which generalize polyhedra, either by allowing positive A common way to build a paper model of a polyhe- genus (these are polyhedral manifolds), or by allowing dron is to fold and glue a planar polygonal shape, called an edge to be incident to more than two faces, or allow- a net of the polyhedron.
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												  Representing the Sporadic Archimedean Polyhedra As Abstract Polytopes$CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Discrete Mathematics 310 (2010) 1835–1844 Contents lists available at ScienceDirect Discrete Mathematics journal homepage: www.elsevier.com/locate/disc Representing the sporadic Archimedean polyhedra as abstract polytopesI Michael I. Hartley a, Gordon I. Williams b,∗ a DownUnder GeoSolutions, 80 Churchill Ave, Subiaco, 6008, Western Australia, Australia b Department of Mathematics and Statistics, University of Alaska Fairbanks, PO Box 756660, Fairbanks, AK 99775-6660, United States article info a b s t r a c t Article history: We present the results of an investigation into the representations of Archimedean Received 29 August 2007 polyhedra (those polyhedra containing only one type of vertex figure) as quotients of Accepted 26 January 2010 regular abstract polytopes. Two methods of generating these presentations are discussed, Available online 13 February 2010 one of which may be applied in a general setting, and another which makes use of a regular polytope with the same automorphism group as the desired quotient. Representations Keywords: of the 14 sporadic Archimedean polyhedra (including the pseudorhombicuboctahedron) Abstract polytope as quotients of regular abstract polyhedra are obtained, and summarised in a table. The Archimedean polyhedron Uniform polyhedron information is used to characterize which of these polyhedra have acoptic Petrie schemes Quotient polytope (that is, have well-defined Petrie duals). Regular cover ' 2010 Elsevier B.V. All rights reserved. Flag action Exchange map 1. Introduction Much of the focus in the study of abstract polytopes has been on the regular abstract polytopes. A publication of the first author [6] introduced a method for representing any abstract polytope as a quotient of regular polytopes.
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												  Nomenclature and Conformations of Alkanes and Cycloalkanes1 on TheAndrew Rosen Chapter 4 - Nomenclature and Conformations of Alkanes and Cycloalkanes1 4.1 - Introduction to Alkanes and Cycloalkanes - Alkanes are hydrocarbons with all carbon-carbon single bonds - Alkenes are hydrocarbons with a carbon-carbon double bond - Alkynes are hydrocarbons with a carbon-carbon triple bond - Cycloalkanes are alkanes in which all or some of the carbon atoms are arranged in a ring - Alkanes have the general formula of CnH2n+2 - Cycloalkanes with a single ring have the formula CnH2n 4.2 - Shapes of Alkanes - An unbranched chain means that each carbon atom is bonded to no more than two other carbon atoms and that there are only primary and secondary carbon atoms 4.3 - IUPAC Nomenclature of Alkanes, Alkyl Halides, and Alcohols - Endings of alkane names end in −ane, and the standard prexes apply to how many carbon atoms there are (meth-, eth-, prop-, but-, pent-, etc.) - An alkyl group has one hydrogen removed from an alkane, and the names have a sux of −yl Rules for naming branched-chain alkanes: 1) Locate the longest continuous chain of carbon atoms. This chain determines the parent (prex) name for the alkane. Always start numbering from the end of a chain 2) Number the longest chain begining with the end of the chain nearer the substitutent 3) Use the numbers obtained by application of Rule 2 to designate the location of the substitutent group 4) When two or more substitutents are present, give each substituent a number corresponding to its location on the longest chain. Name them in alphabetical order 5) When two
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												  Of Rigid Motions) to Make the Simplest Possible Analogies Between Euclidean, Spherical,Toroidal and Hyperbolic GeometrySPHERICAL, TOROIDAL AND HYPERBOLIC GEOMETRIES MICHAEL D. FRIED, 231 MSTB These notes use groups (of rigid motions) to make the simplest possible analogies between Euclidean, Spherical,Toroidal and hyperbolic geometry. We start with 3- space figures that relate to the unit sphere. With spherical geometry, as we did with Euclidean geometry, we use a group that preserves distances. The approach of these notes uses the geometry of groups to show the relation between various geometries, especially spherical and hyperbolic. It has been in the background of mathematics since Klein’s Erlangen program in the late 1800s. I imagine Poincar´e responded to Klein by producing hyperbolic geometry in the style I’ve done here. Though the group approach of these notes differs philosophically from that of [?], it owes much to his discussion of spherical geometry. I borrowed the picture of a spherical triangle’s area directly from there. I especially liked how Henle has stereographic projection allow the magic multiplication of complex numbers to work for him. While one doesn’t need the rotation group in 3-space to understand spherical geometry, I used it gives a direct analogy between spherical and hyperbolic geometry. It is the comparison of the four types of geometry that is ultimately most inter- esting. A problem from my Problem Sheet has the name World Wallpaper. Map making is a subject that has attracted many. In our day of Landsat photos that cover the whole world in its great spherical presence, the still mysterious relation between maps and the real thing should be an easy subject for the classroom.