214 research outputs found
Grid Vertex-Unfolding Orthogonal Polyhedra
An edge-unfolding of a polyhedron is produced by cutting along edges and
flattening the faces to a *net*, a connected planar piece with no overlaps. A
*grid unfolding* allows additional cuts along grid edges induced by coordinate
planes passing through every vertex. A vertex-unfolding permits faces in the
net to be connected at single vertices, not necessarily along edges. We show
that any orthogonal polyhedron of genus zero has a grid vertex-unfolding.
(There are orthogonal polyhedra that cannot be vertex-unfolded, so some type of
"gridding" of the faces is necessary.) For any orthogonal polyhedron P with n
vertices, we describe an algorithm that vertex-unfolds P in O(n^2) time.
Enroute to explaining this algorithm, we present a simpler vertex-unfolding
algorithm that requires a 3 x 1 refinement of the vertex grid.Comment: Original: 12 pages, 8 figures, 11 references. Revised: 22 pages, 16
figures, 12 references. New version is a substantial revision superceding the
preliminary extended abstract that appeared in Lecture Notes in Computer
Science, Volume 3884, Springer, Berlin/Heidelberg, Feb. 2006, pp. 264-27
Steinitz Theorems for Orthogonal Polyhedra
We define a simple orthogonal polyhedron to be a three-dimensional polyhedron
with the topology of a sphere in which three mutually-perpendicular edges meet
at each vertex. By analogy to Steinitz's theorem characterizing the graphs of
convex polyhedra, we find graph-theoretic characterizations of three classes of
simple orthogonal polyhedra: corner polyhedra, which can be drawn by isometric
projection in the plane with only one hidden vertex, xyz polyhedra, in which
each axis-parallel line through a vertex contains exactly one other vertex, and
arbitrary simple orthogonal polyhedra. In particular, the graphs of xyz
polyhedra are exactly the bipartite cubic polyhedral graphs, and every
bipartite cubic polyhedral graph with a 4-connected dual graph is the graph of
a corner polyhedron. Based on our characterizations we find efficient
algorithms for constructing orthogonal polyhedra from their graphs.Comment: 48 pages, 31 figure
Unfolding and Reconstructing Polyhedra
This thesis covers work on two topics: unfolding polyhedra into the plane and reconstructing polyhedra from partial information. For each topic, we describe previous work in the area and present an array of new research and results.
Our work on unfolding is motivated by the problem of characterizing precisely when overlaps will occur when a polyhedron is cut along edges and unfolded. By contrast to previous work, we begin by classifying overlaps according to a notion of locality. This classification enables us to focus upon particular types of overlaps, and use the results to construct examples of polyhedra with interesting unfolding properties.
The research on unfolding is split into convex and non-convex cases. In the non-convex case, we construct a polyhedron for which every edge unfolding has an overlap, with fewer faces than all previously known examples. We also construct a non-convex polyhedron for which every edge unfolding has a particularly trivial type of overlap. In the convex case, we construct a series of example polyhedra for which every unfolding of various types has an overlap. These examples disprove some existing conjectures regarding algorithms to unfold convex polyhedra without overlaps.
The work on reconstruction is centered around analyzing the computational complexity of a number of reconstruction questions. We consider two classes of reconstruction problems. The first problem is as follows: given a collection of edges in space, determine whether they can be rearranged by translation only to form a polygon or polyhedron. We consider variants of this problem by introducing restrictions like convexity, orthogonality, and non-degeneracy. All of these problems are NP-complete, though some are proved to be only weakly NP-complete. We then consider a second, more classical problem: given a collection of edges in space, determine whether they can be rearranged by translation and/or rotation to form a polygon or polyhedron. This problem is NP-complete for orthogonal polygons, but polynomial algorithms exist for non-orthogonal polygons. For polyhedra, it is shown that if degeneracies are allowed then the problem is NP-hard, but the complexity is still unknown for non-degenerate polyhedra
Unfolding some classes of polycubes
An unfolding of a polyhedron is a cutting along its surface such that the surface remains connected and it can be flattened to the plane without any overlap. An edge- unfolding is a restricted kind of unfolding, we are only allowed to cut along the edges of the faces of the polyhedron. A polycube is a special case of orthogonal polyhedron formed by glueing several unit cubes together face-to-face. In the case of polycubes, the edges of all cubes are available for cuts in edge-unfolding. We focus on one-layer polycubes and present several algorithms to unfold some classes of them. We show that it is possible to edge-unfold any one-layer polycube with cubic holes, thin horizontal holes and separable rectangular holes. The question of edge-unfolding general one-layer polycubes remains open. We also briefly study some classes of multi-layer polycubes. 1Rozklad mnohostěnu je tvořen řezy jeho povrchu takovými, že rozřezaný povrch je možné rozložit do roviny, aniž by vznikl překryv. Hranový rozklad je omezený typ roz- kladu, ve kterém je povolené řezy vést jen po hranách mnohostěnu. Kostičkový mno- hostěn je speciální druh mnohostěnu, který je tvořen jednotkovými krychlemi slepenými k sobě celými stěnami. V případě kostičkových mnohostěnů můžeme v hranovém roz- kladu řezat po hranách všech jednotkových krychlí. V této práci se zabýváme zejména jednovrstvými kostičkovými mnohostěny a popíšeme několik algoritmů pro rozklad růz- ných speciálních tříd. Ukážeme, že je možné hranově rozložit jednovrstvé krychličkové mnohostěny s krychlovými dírami, tenkými horizontálními dírami a oddělitelnými ob- délníkovými dírami. Otázka hranového rozkladu obecných jednovrstvých krychličkových zůstává otevřena. Také se krátce zabýváme rozklady některých tříd vícevrstvých krych- ličkových mnohostěnů. 1Department of Applied MathematicsKatedra aplikované matematikyMatematicko-fyzikální fakultaFaculty of Mathematics and Physic
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Predicting multibody assembly of proteins
textThis thesis addresses the multi-body assembly (MBA) problem in the context of protein assemblies. [...] In this thesis, we chose the protein assembly domain because accurate and reliable computational modeling, simulation and prediction of such assemblies would clearly accelerate discoveries in understanding of the complexities of metabolic pathways, identifying the molecular basis for normal health and diseases, and in the designing of new drugs and other therapeutics. [...] [We developed] F²Dock (Fast Fourier Docking) which includes a multi-term function which includes both a statistical thermodynamic approximation of molecular free energy as well as several of knowledge-based terms. Parameters of the scoring model were learned based on a large set of positive/negative examples, and when tested on 176 protein complexes of various types, showed excellent accuracy in ranking correct configurations higher (F² Dock ranks the correcti solution as the top ranked one in 22/176 cases, which is better than other unsupervised prediction software on the same benchmark). Most of the protein-protein interaction scoring terms can be expressed as integrals over the occupied volume, boundary, or a set of discrete points (atom locations), of distance dependent decaying kernels. We developed a dynamic adaptive grid (DAG) data structure which computes smooth surface and volumetric representations of a protein complex in O(m log m) time, where m is the number of atoms assuming that the smallest feature size h is [theta](r[subscript max]) where r[subscript max] is the radius of the largest atom; updates in O(log m) time; and uses O(m)memory. We also developed the dynamic packing grids (DPG) data structure which supports quasi-constant time updates (O(log w)) and spherical neighborhood queries (O(log log w)), where w is the word-size in the RAM. DPG and DAG together results in O(k) time approximation of scoring terms where k << m is the size of the contact region between proteins. [...] [W]e consider the symmetric spherical shell assembly case, where multiple copies of identical proteins tile the surface of a sphere. Though this is a restricted subclass of MBA, it is an important one since it would accelerate development of drugs and antibodies to prevent viruses from forming capsids, which have such spherical symmetry in nature. We proved that it is possible to characterize the space of possible symmetric spherical layouts using a small number of representative local arrangements (called tiles), and their global configurations (tiling). We further show that the tilings, and the mapping of proteins to tilings on arbitrary sized shells is parameterized by 3 discrete parameters and 6 continuous degrees of freedom; and the 3 discrete DOF can be restricted to a constant number of cases if the size of the shell is known (in terms of the number of protein n). We also consider the case where a coarse model of the whole complex of proteins are available. We show that even when such coarse models do not show atomic positions, they can be sufficient to identify a general location for each protein and its neighbors, and thereby restricts the configurational space. We developed an iterative refinement search protocol that leverages such multi-resolution structural data to predict accurate high resolution model of protein complexes, and successfully applied the protocol to model gp120, a protein on the spike of HIV and currently the most feasible target for anti-HIV drug design.Computer Science
Reshaping Convex Polyhedra
Given a convex polyhedral surface P, we define a tailoring as excising from P
a simple polygonal domain that contains one vertex v, and whose boundary can be
sutured closed to a new convex polyhedron via Alexandrov's Gluing Theorem. In
particular, a digon-tailoring cuts off from P a digon containing v, a subset of
P bounded by two equal-length geodesic segments that share endpoints, and can
then zip closed.
In the first part of this monograph, we primarily study properties of the
tailoring operation on convex polyhedra. We show that P can be reshaped to any
polyhedral convex surface Q a subset of conv(P) by a sequence of tailorings.
This investigation uncovered previously unexplored topics, including a notion
of unfolding of Q onto P--cutting up Q into pieces pasted non-overlapping onto
P.
In the second part of this monograph, we study vertex-merging processes on
convex polyhedra (each vertex-merge being in a sense the reverse of a
digon-tailoring), creating embeddings of P into enlarged surfaces. We aim to
produce non-overlapping polyhedral and planar unfoldings, which led us to
develop an apparently new theory of convex sets, and of minimal length
enclosing polygons, on convex polyhedra.
All our theorem proofs are constructive, implying polynomial-time algorithms.Comment: Research monograph. 234 pages, 105 figures, 55 references. arXiv
admin note: text overlap with arXiv:2008.0175
Collection of abstracts of the 24th European Workshop on Computational Geometry
International audienceThe 24th European Workshop on Computational Geomety (EuroCG'08) was held at INRIA Nancy - Grand Est & LORIA on March 18-20, 2008. The present collection of abstracts contains the 63 scientific contributions as well as three invited talks presented at the workshop
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