On Polyhedral Realization with Isosceles Triangles
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Descartes, Euler, Poincaré, Pólya and Polyhedra Séminaire De Philosophie Et Mathématiques, 1982, Fascicule 8 « Descartes, Euler, Poincaré, Polya and Polyhedra », , P
Séminaire de philosophie et mathématiques PETER HILTON JEAN PEDERSEN Descartes, Euler, Poincaré, Pólya and Polyhedra Séminaire de Philosophie et Mathématiques, 1982, fascicule 8 « Descartes, Euler, Poincaré, Polya and Polyhedra », , p. 1-17 <http://www.numdam.org/item?id=SPHM_1982___8_A1_0> © École normale supérieure – IREM Paris Nord – École centrale des arts et manufactures, 1982, tous droits réservés. L’accès aux archives de la série « Séminaire de philosophie et mathématiques » implique l’accord avec les conditions générales d’utilisation (http://www.numdam.org/conditions). Toute utilisation commerciale ou impression systématique est constitutive d’une infraction pénale. Toute copie ou impression de ce fichier doit contenir la présente mention de copyright. Article numérisé dans le cadre du programme Numérisation de documents anciens mathématiques http://www.numdam.org/ - 1 - DESCARTES, EULER, POINCARÉ, PÓLYA—AND POLYHEDRA by Peter H i l t o n and Jean P e d e rs e n 1. Introduction When geometers talk of polyhedra, they restrict themselves to configurations, made up of vertices. edqes and faces, embedded in three-dimensional Euclidean space. Indeed. their polyhedra are always homeomorphic to thè two- dimensional sphere S1. Here we adopt thè topologists* terminology, wherein dimension is a topological invariant, intrinsic to thè configuration. and not a property of thè ambient space in which thè configuration is located. Thus S 2 is thè surface of thè 3-dimensional ball; and so we find. among thè geometers' polyhedra. thè five Platonic “solids”, together with many other examples. However. we should emphasize that we do not here think of a Platonic “solid” as a solid : we have in mind thè bounding surface of thè solid. -
Compact Hyperbolic Tetrahedra with Non-Obtuse Dihedral Angles
Compact 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. -
Using Information Theory to Discover Side Chain Rotamer Classes
Pacific 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. -
Polyhedral Surfaces, Discrete Curvatures, Shape Analysis, 3D Modelling, Segmentation
JOURNAL OF MEDICAL INFORMATICS & TECHNOLOGIES Vol. 9/2005, ISSN 1642-6037 polyhedral surfaces, discrete curvatures, shape analysis, 3D modelling, segmentation. Alexandra BAC, Marc DANIEL, Jean-Louis MALTRET* 3D MODELLING AND SEGMENTATION WITH DISCRETE CURVATURES Recent concepts of discrete curvatures are very important for Medical and Computer Aided Geometric Design applications. A first reason is the opportunity to handle a discretisation of a continuous object, with a free choice of the discretisation. A second and most important reason is the possibility to define second-order estimators for discrete objects in order to estimate local shapes and manipulate discrete objects. There is an increasing need to handle polyhedral objects and clouds of points for which only a discrete approach makes sense. These sets of points, once structured (in general meshed with simplexes for surfaces or volumes), can be analysed using these second-order estimators. After a general presentation of the problem, a first approach based on angular defect, is studied. Then, a local approximation approach (mostly by quadrics) is presented. Different possible applications of these techniques are suggested, including the analysis of 2D or 3D images, decimation, segmentation... We finally emphasise different artefacts encountered in the discrete case. 1. INTRODUCTION This paper offers a review of work on discrete curvatures for Computer Aided Geometric Design applications and a discussion about some ideas for further studies. We consider the discrete curvatures computed on a set of points and their relevance to continuous curvatures when the density of the points increases. First of all, it is interesting to recall that curvatures are fundamental tools for studying curves and surfaces. -
Predicting Backbone Cα Angles and Dihedrals from Protein Sequences by Stacked Sparse Auto-Encoder Deep Neural Network
Predicting 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). -
Toroidal Diffusions and Protein Structure Evolution
Toroidal 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 -
H2O2 and NH 2 OH
Int. 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. -
Binding Regular Polyhedra
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Repository of the Academy's Library Optimal packages: binding regular polyhedra F. Kovacs´ Department of Structural Mechanics Budapest University of Technology and Economics ABSTRACT: Strings on the surface of gift boxes can be modelled as a special kind of cable-and-joint struc- ture. This paper deals with systems composed of idealised (frictionless) closed loops of strings that provide stable binding to the underlying convex polyhedron (‘package’). Optima are searched in both the sense of topology and geometry in finding minimal number of closed loops as well as the minimal (total) length of cables to ensure such a stable binding for simple cases of polyhedra. 1 INTRODUCTION and concave otherwise (for example, ‘zigzag’ loops with alternating turns are concave). In these terms, the 1.1 Loops on a polyhedral surface loop on the left hand side of Fig. 1 is complex due to the self-intersection at the top and concave because of There are some practical occurrences of closed strings the two rectangular turns with different handedness on polyhedral surfaces. For example, mailed pack- at the bottom (such connections will be called self- ages are traditionally bound by some pieces of string. binding from now on); whereas the skew string to the Another example is from basketry, when a woven right is simple and convex (by having no turns within pattern over a polyhedral surface is also formed by the polyhedral surface at all). some (mainly closed) strings (Tarnai, Kov´acs, Fowler, & Guest 2012, Kov´acs 2014). -
Parity Check Schedules for Hyperbolic Surface Codes
Parity Check Schedules for Hyperbolic Surface Codes Jonathan Conrad September 18, 2017 Bachelor thesis under supervision of Prof. Dr. Barbara M. Terhal The present work was submitted to the Institute for Quantum Information Faculty of Mathematics, Computer Science und Natural Sciences - Faculty 1 First reviewer Second reviewer Prof. Dr. B. M. Terhal Prof. Dr. F. Hassler Acknowledgements Foremost, I would like to express my gratitude to Prof. Dr. Barbara M. Terhal for giving me the opportunity to complete this thesis under her guidance, insightful discussions and her helpful advice. I would like to give my sincere thanks to Dr. Nikolas P. Breuckmann for his patience with all my questions and his good advice. Further, I would also like to thank Dr. Kasper Duivenvoorden and Christophe Vuillot for many interesting and helpful discussions. In general, I would like to thank the IQI for its hospitality and everyone in it for making my stay a very joyful experience. As always, I am grateful for the constant support of my family and friends. Table of Contents 1 Introduction 1 2 Preliminaries 2 3 Stabilizer Codes 5 3.1 Errors . 6 3.2 TheBitFlipCode ............................... 6 3.3 The Toric Code . 11 4 Homological Code Construction 15 4.1 Z2-Homology .................................. 18 5 Hyperbolic Surface Codes 21 5.1 The Gauss-Bonnet Theorem . 21 5.2 The Small Stellated Dodecahedron as a Hyperbolic Surface Code . 26 6 Parity Check Scheduling 32 6.1 Seperate Scheduling . 33 6.2 Interleaved Scheduling . 39 6.3 Coloring the Small Stellated Dodecahedron . 45 7 Fault Tolerant Quantum Computation 47 7.1 Fault Tolerance . -
Winter Break "Homework Zero"
\HOMEWORK 0" Last updated Friday 27th December, 2019 at 2:44am. (Not officially to be turned in) Try your best for the following. Using the first half of Shurman's text is a good start. I will possibly add some notes to supplement this. There are also some geometric puzzles below for you to think about. Suggested winter break homework - Learn the proof to Cauchy-Schwarz inequality. - Find out what open sets, closed sets, compact set (closed and bounded in Rn, as well as the definition with open covering cf. Heine-Borel theorem), and connected set means in Rn. - Find out what supremum (least upper bound) and infimum (greatest lower bound) of a subset of real numbers mean. - Find out what it means for a sequence and series to converge. - Find out what does it mean for a function f : Rn ! Rm to be continuous. There are three equivalent characterizations: (1) Limit preserving definition. (2) Inverse image of open sets are open. (3) −δ definition. - Find the statements to extreme value theorem, intermediate value theorem, and mean value theorem. - Find out what is the fundamental theorem of calculus. - Find out how to perform matrix multiplication, computation of matrix inverse, and matrix deter- minant. - Find out what is the geometric meaning of matrix determinantDecember, 2019 . - Find out how to solve a linear system of equation using row reduction. n m - Find out what a linear map from R to R is, and what is its relationth to matrix multiplication by an m × n matrix. How is matrix product related to composition of linear maps? - Find out what it means to be differentiable at a point a for a multivariate function, what is the derivative of such function at a, and how to compute it. -
Elysée Wilson-Egolf Topic: Polygons, Polyhedra, Polytope Series
Berkeley Math Circle Intermediate I, 1/23, 1/20, 2/6 Presenter: Elysée Wilson-Egolf Topic: Polygons, Polyhedra, Polytope Series Part 1 – Polygon Angle Formula Let’s start simple. How do we find the sum of the interior angles of a convex polygon? • Write down as many methods as you can. • Think about: how can you adapt your method to concave polygons? Formula for the interior angles of a polygon: _________________ . Q: There is an equality between the number of ways to triangulate an n+2-gon and the number of expressions containing n pairs of parentheses that are correctly matched. Prove that these numbers are the same. Can you find a closed formula? Part 2 – Platonic Solids and Angular Defect Definition: A platonic solid is a polyhedron which a. has only one kind of regular polygon for a face and b. has the same number of faces at each vertex. One simple example is that of a cube. Each face is a square (=regular quadrilateral) and each vertex is connected to exactly three squares. In Schläfli notation, this is {4, 3}: the regular polyhedron with 3 regular 4-gons at each vertex. • Can there be polyhedra with exactly one or two squares at each vertex? • Can there be polyhedra with exactly four squares at each vertex? For future reference, we’ll need the notion of the “angular defect” as well. Rather than focusing on what is present at the vertex, we focus on what is absent: the deviation from 360 degrees at the vertex, or “leftover” angle. In this case, it is 360−90×3=90 . -
Klein 4A Alkanes+Isomerism
Grossman, 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.