Geometric discretization through primal-dual meshes

This thesis introduces new tools for geometric discretization in computer graphics and computational physics. Our work builds upon the duality between weighted triangulations and power diagrams to provide concise, yet expressive discretization of manifolds and differential operators. Our exposition begins with a review of the construction of power diagrams, followed by novel optimization procedures to fully control the local volume and spatial distribution of power cells. Based on this power diagram framework, we develop a new family of discrete differential operators, an effective stippling algorithm, as well as a new fluid solver for Lagrangian particles. We then turn our attention to applications in geometry processing. We show that orthogonal primal-dual meshes augment the notion of local metric in non-flat discrete surfaces. In particular, we introduce a reduced set of coordinates for the construction of orthogonal primal-dual structures of arbitrary topology, and provide alternative metric characterizations through convex optimizations. We finally leverage these novel theoretical contributions to generate well-centered primal-dual meshes, sphere packing on surfaces, and self-supporting triangulations.

Computational design of self-assembling proteins and protein-DNA nanowires

Computational protein design (CPD) is a burgeoning field that uses a physical-chemical or knowledge-based scoring function to create protein variants with new or improved properties. This exciting approach has recently been used to generate proteins with entirely new functions, ones that are not observed in naturally occurring proteins. For example, several enzymes were designed to catalyze reactions that are not in the repertoire of any known natural enzyme. In these designs, novel catalytic activity was built de novo (from scratch) into a previously inert protein scaffold. In addition to de novo enzyme design, the computational design of protein-protein interactions can also be used to create novel functionality, such as neutralization of influenza. Our goal here was to design a protein that can self-assemble with DNA into nanowires. We used computational tools to homodimerize a transcription factor that binds a specific sequence of double-stranded DNA. We arranged the protein-protein and protein-DNA binding sites so that the self-assembly could occur in a linear fashion to generate nanowires. Upon mixing our designed protein homodimer with the double-stranded DNA, the molecules immediately self-assembled into nanowires. This nanowire topology was confirmed using atomic force microscopy. Co-crystal structure showed that the nanowire is assembled via the desired interactions. To the best of our knowledge, this is the first example of a protein-DNA self-assembly that does not rely on covalent interactions. We anticipate that this new material will stimulate further interest in the development of advanced biomaterials.

Logarithmic Potential Theory on Riemann Surfaces

We develop a logarithmic potential theory on Riemann surfaces which generalizes logarithmic potential theory on the complex plane. We show the existence of an equilibrium measure and examine its structure. This leads to a formula for the structure of the equilibrium measure which is new even in the plane. We then use our results to study quadrature domains, Laplacian growth, and Coulomb gas ensembles on Riemann surfaces. We prove that the complement of the support of the equilibrium measure satisfies a quadrature identity. Furthermore, our setup allows us to naturally realize weak solutions of Laplacian growth (for a general time-dependent source) as an evolution of the support of equilibrium measures. When applied to the Riemann sphere this approach unifies the known methods for generating interior and exterior Laplacian growth. We later narrow our focus to a special class of quadrature domains which we call Algebraic Quadrature Domains. We show that many of the properties of quadrature domains generalize to this setting. In particular, the boundary of an Algebraic Quadrature Domain is the inverse image of a planar algebraic curve under a meromorphic function. This makes the study of the topology of Algebraic Quadrature Domains an interesting problem. We briefly investigate this problem and then narrow our focus to the study of the topology of classical quadrature domains. We extend the results of Lee and Makarov and prove (for n ≥ 3) c ≤ 5n-5, where c and n denote the connectivity and degree of a (classical) quadrature domain. At the same time we obtain a new upper bound on the number of isolated points of the algebraic curve corresponding to the boundary and thus a new upper bound on the number of special points. In the final chapter we study Coulomb gas ensembles on Riemann surfaces.

The isolation and partial biochemical analysis of Sindbis virus proteins

Recently, the amino acid sequences have been reported for several proteins, including the envelope glycoproteins of Sindbis virus, which all probably span the plasma membrane with a common topology: a large N-terminal, extracellular portion, a short region buried in the bilayer, and a short C-terminal intracellular segment. The regions of these proteins buried in the bilayer correspond to portions of the protein sequences which contain a stretch of hydrophobic amino acids and which have other common characteristics, as discussed. Reasons are also described for uncertainty, in some proteins more than others, as to the precise location of some parts of the sequence relative to the membrane.

The signal hypothesis for the transmembrane translocation of proteins is briefly described and its general applicability is reviewed. There are many proteins whose translocation is accurately described by this hypothesis, but some proteins are translocated in a different manner.

The transmembraneous glycoproteins E1 and E2 of Sindbis virus, as well as the only other virion protein, the capsid protein, were purified in amounts sufficient for biochemical analysis using sensitive techniques. The amino acid composition of each protein was determined, and extensive N-terminal sequences were obtained for E1 and E2. By these techniques E1 and E2 are indistinguishable from most water soluble proteins, as they do not contain an obvious excess of hydrophobic amino acids in their N-terminal regions or in the intact molecule.

The capsid protein was found to be blocked, and so its N-terminus could not be sequenced by the usual methods. However, with the use of a special labeling technique, it was possible to incorporate tritiated acetate into the N-terminus of the protein with good specificity, which was useful in the purification of peptides from which the first amino acids in the N-terminal sequence could be identified.

Nanomole amounts of PE2, the intracellular precursor of E2, were purified by an immuno-affinity technique, and its N-terminus was analyzed. Together with other work, these results showed that PE2 is not synthesized with an N-terminal extension, and the signal sequence for translocation is probably the N-terminal amino acid sequence of the protein. This N-terminus was found to be 80-90% blocked, also by Nacetylation, and this acetylation did not affect its function as a signal sequence. The putative signal sequence was also found to contain a glycosylated asparagine residue, but the inhibition of this glycosylation did not lead to the cleavage of the sequence.

Paranormal operator on a Hilbert space

In this thesis an extensive study is made of the set P of all paranormal operators in B(H), the set of all bounded endomorphisms on the complex Hilbert space H. T ϵ B(H) is paranormal if for each z contained in the resolvent set of T, d(z, σ(T))//(T-zI)^-1 = 1 where d(z, σ(T)) is the distance from z to σ(T), the spectrum of T. P contains the set N of normal operators and P contains the set of hyponormal operators. However, P is contained in L, the set of all T ϵ B(H) such that the convex hull of the spectrum of T is equal to the closure of the numerical range of T. Thus, N≤P≤L.

If the uniform operator (norm) topology is placed on B(H), then the relative topological properties of N, P, L can be discussed. In Section IV, it is shown that: 1) N P and L are arc-wise connected and closed, 2) N, P, and L are nowhere dense subsets of B(H) when dim H ≥ 2, 3) N = P when dimH ˂ ∞ , 4) N is a nowhere dense subset of P when dimH ˂ ∞ , 5) P is not a nowhere dense subset of L when dimH ˂ ∞ , and 6) it is not known if P is a nowhere dense subset of L when dimH ˂ ∞.

The spectral properties of paranormal operators are of current interest in the literature. Putnam [22, 23] has shown that certain points on the boundary of the spectrum of a paranormal operator are either normal eigenvalues or normal approximate eigenvalues. Stampfli [26] has shown that a hyponormal operator with countable spectrum is normal. However, in Theorem 3.3, it is shown that a paranormal operator T with countable spectrum can be written as the direct sum, N ⊕ A, of a normal operator N with σ(N) = σ(T) and of an operator A with σ(A) a subset of the derived set of σ(T). It is then shown that A need not be normal. If we restrict the countable spectrum of T ϵ P to lie on a C²-smooth rectifiable Jordan curve G_o, then T must be normal [see Theorem 3.5 and its Corollary]. If T is a scalar paranormal operator with countable spectrum, then in order to conclude that T is normal the condition of σ(T) ≤ G_o can be relaxed [see Theorem 3.6]. In Theorem 3.7 it is then shown that the above result is not true when T is not assumed to be scalar. It was then conjectured that if T ϵ P with σ(T) ≤ G_o, then T is normal. The proof of Theorem 3.5 relies heavily on the assumption that T has countable spectrum and cannot be generalized. However, the corollary to Theorem 3.9 states that if T ϵ P with σ(T) ≤ G_o, then T has a non-trivial lattice of invariant subspaces. After the completion of most of the work on this thesis, Stampfli [30, 31] published a proof that a paranormal operator T with σ(T) ≤ G_o is normal. His proof uses some rather deep results concerning numerical ranges whereas the proof of Theorem 3.5 uses relatively elementary methods.

Locally convex Riesz spaces and Archimedean quotient spaces

A Riesz space with a Hausdorff, locally convex topology determined by Riesz seminorms is called a locally convex Riesz space. A sequence {x_n} in a locally convex Riesz space L is said to converge locally to x ϵ L if for some topologically bounded set B and every real r ˃ 0 there exists N (r) and n ≥ N (r) implies x – x_n ϵ r^b. Local Cauchy sequences are defined analogously, and L is said to be locally complete if every local Cauchy sequence converges locally. Then L is locally complete if and only if every monotone local Cauchy sequence has a least upper bound. This is a somewhat more general form of the completeness criterion for Riesz – normed Riesz spaces given by Luxemburg and Zaanen. Locally complete, bound, locally convex Riesz spaces are barrelled. If the space is metrizable, local completeness and topological completeness are equivalent.

Two measures of the non-archimedean character of a non-archimedean Riesz space L are the smallest ideal A_o (L) such that quotient space is Archimedean and the ideal I (L) = { x ϵ L: for some 0 ≤ v ϵ L, n |x| ≤ v for n = 1, 2, …}. In general A_o (L) ᴝ I (L). If L is itself a quotient space, a necessary and sufficient condition that A_o (L) = I (L) is given. There is an example where A_o (L) ≠ I (L).

A necessary and sufficient condition that a Riesz space L have every quotient space Archimedean is that for every 0 ≤ u, v ϵ L there exist u₁ = sup (inf (n v, u): n = 1, 2, …), and real numbers m₁ and m₂ such that m₁ u₁ ≥ v₁ and m₂ v₁ ≥ u₁. If, in addition, L is Dedekind σ – complete, then L may be represented as the space of all functions which vanish off finite subsets of some non-empty set.

Two and Three Finger Caging of Polygons and Polyhedra

Multi-finger caging offers a rigorous and robust approach to robot grasping. This thesis provides several novel algorithms for caging polygons and polyhedra in two and three dimensions. Caging refers to a robotic grasp that does not necessarily immobilize an object, but prevents it from escaping to infinity. The first algorithm considers caging a polygon in two dimensions using two point fingers. The second algorithm extends the first to three dimensions. The third algorithm considers caging a convex polygon in two dimensions using three point fingers, and considers robustness of this cage to variations in the relative positions of the fingers.

This thesis describes an algorithm for finding all two-finger cage formations of planar polygonal objects based on a contact-space formulation. It shows that two-finger cages have several useful properties in contact space. First, the critical points of the cage representation in the hand’s configuration space appear as critical points of the inter-finger distance function in contact space. Second, these critical points can be graphically characterized directly on the object’s boundary. Third, contact space admits a natural rectangular decomposition such that all critical points lie on the rectangle boundaries, and the sublevel sets of contact space and free space are topologically equivalent. These properties lead to a caging graph that can be readily constructed in contact space. Starting from a desired immobilizing grasp of a polygonal object, the caging graph is searched for the minimal, intermediate, and maximal caging regions surrounding the immobilizing grasp. An example constructed from real-world data illustrates and validates the method.

A second algorithm is developed for finding caging formations of a 3D polyhedron for two point fingers using a lower dimensional contact-space formulation. Results from the two-dimensional algorithm are extended to three dimension. Critical points of the inter-finger distance function are shown to be identical to the critical points of the cage. A decomposition of contact space into 4D regions having useful properties is demonstrated. A geometric analysis of the critical points of the inter-finger distance function results in a catalog of grasps in which the cages change topology, leading to a simple test to classify critical points. With these properties established, the search algorithm from the two-dimensional case may be applied to the three-dimensional problem. An implemented example demonstrates the method.

This thesis also presents a study of cages of convex polygonal objects using three point fingers. It considers a three-parameter model of the relative position of the fingers, which gives complete generality for three point fingers in the plane. It analyzes robustness of caging grasps to variations in the relative position of the fingers without breaking the cage. Using a simple decomposition of free space around the polygon, we present an algorithm which gives all caging placements of the fingers and a characterization of the robustness of these cages.

Structure theorems for noncommutative complete local rings

If R is a ring with identity, let N(R) denote the Jacobson radical of R. R is local if R/N(R) is an artinian simple ring and ∩N(R)ⁱ = 0. It is known that if R is complete in the N(R)-adic topology then R is equal to (B)_n, the full n by n matrix ring over B where E/N(E) is a division ring. The main results of the thesis deal with the structure of such rings B. In fact we have the following.

If B is a complete local algebra over F where B/N(B) is a finite dimensional normal extension of F and N(B) is finitely generated as a left ideal by k elements, then there exist automorphisms g_i,...,g_k of B/N(B) over F such that B is a homomorphic image of B/N[[x₁,…,x_k;g₁,…,g_k]] the power series ring over B/N(B) in noncommuting indeterminates x_i, where x_ib = g_i(b)x_i for all b ϵ B/N.

Another theorem generalizes this result to complete local rings which have suitable commutative subrings. As a corollary of this we have the following. Let B be a complete local ring with B/N(B) a finite field. If N(B) is finitely generated as a left ideal by k elements then there exist automorphisms g₁,…,g_k of a v-ring V such that B is a homomorphic image of V [[x₁,…,x_k;g₁,…,g_k]].

In both these results it is essential to know the structure of N(B) as a two sided module over a suitable subring of B.

Análise cladística de táxons atribuídos aos peixes euteleósteos basais

Os teleósteos são o grupo mais diversificado entre os vertebrados e seu registro mais antigo data do Jurássico. Sua atual classificação inclui quatro clados, dentre os quais Euteleostei é o mais avançado e variado. Apesar de todos os trabalhos a respeito do grupo, ele ainda não possui diagnose, definição e composição precisas. A discordância entre autores é ilustrada pelas nove diferentes propostas filogenéticas elaboradas nos últimos 30 anos. Muitos fósseis do Cretáceo são classificados como euteleósteos basais por falta de conhecimento morfológico, enquanto outros fósseis possuem classificação sistemática controversa ou compartilham aspectos estruturais com euteleósteos basais. Nesse contexto, os objetivos da presente dissertação são avaliar o monofiletismo de euteleósteos basais e recuperar relações filogenéticas de táxons do Nordeste do Brasil, África, Europa, Ásia e América do Norte atribuídos aos euteleósteos basais. Sete táxons brasileiros (i.e., Beurlenichthys ouricuriensis, Britoichthys marizalensis, Clupavus brasiliensis, Santanasalmo elegans, Santanichthys diasii, Scombroclupeoides scutata e novo euteleósteo da Bacia de Pelotas) e 14 táxons de localidades estrangeiras (i.e., Avitosmerus canadensis, Barcarenichthys joneti, Chanoides macropoma, Clupavus maroccanus, Gaudryella gaudryi, Humbertia operta, Kermichthys daguini, Leptolepides spratiiformis, Lusitanichthys characiformis, Nybelinoides brevis, Orthogonikleithrus leichi, Pattersonella formosa, Wenzichthys congolensis e Tchernovichthys exspectatum) foram analisados através de observação direta, fotografias, desenhos e descrições e submetidos a uma análise de Sistemática Filogenética utilizando o princípio da parcimônia. Três espécies recentes (i.e., Elops saurus, Hoplias malabaricus e Salmo trutta) foram usadas como grupo externo. Sessenta e dois caracteres foram selecionados e, como resultado, seis árvores igualmente parcimoniosas foram obtidas com 325 passos, índice de consistência (CI) de 0,2523 e índice de retenção (RI) de 0,4309. O consenso estrito é representado pela seguinte topologia: ((C. marocanus), (C. brasiliensis, (H. malabaricus + S. diasii))) ((G. gaudryi, (C. macropoma + L. characiformis)), (K. daguini), ((A. canadensis, (novo euteleósteo, (S. elegans + W. congolensis), (B. ouricuriensis + B. marizalensis)), (L. spratiiformis, (S. scutata, (N. brevis + P. formosa))), (B. joneti), (O. leichi), (H. operta + T. exspectatum), indicando que euteleósteos basais não formam um grupo monofilético e que as atuais sinapomorfias propostas são insuficientes para suportar o grupo.

Estudo do comportamento caótico e determinação de dimensão fractal em modelos pré-inflacionários não compactos

O caos determinístico é um dos aspectos mais interessantes no que diz respeito à teoria moderna dos sistemas dinâmicos, e está intrinsecamente associado a pequenas variações nas condições iniciais de um dado modelo. Neste trabalho, é feito um estudo acerca do comportamento caótico em dois casos específicos. Primeiramente, estudam-se modelos préinflacionários não-compactos de Friedmann-Robertson-Walker com campo escalar minimamente acoplado e, em seguida, modelos anisotrópicos de Bianchi IX. Em ambos os casos, o componente material é um fluido perfeito. Tais modelos possuem constante cosmológica e podem ser estudados através de uma descrição unificada, a partir de transformações de variáveis convenientes. Estes sistemas possuem estruturas similares no espaço de fases, denominadas centros-sela, que fazem com que as soluções estejam contidas em hipersuperfícies cuja topologia é cilíndrica. Estas estruturas dominam a relação entre colapso e escape para a inflação, que podem ser tratadas como bacias cuja fronteira pode ser fractal, e que podem ser associadas a uma estrutura denominada repulsor estranho. Utilizando o método de contagem de caixas, são calculadas as dimensões características das fronteiras nos modelos, o que envolve técnicas e algoritmos de computação numérica, e tal método permite estudar o escape caótico para a inflação.

Análise da viabilidade de aplicações de monitoramento e controle utilizando redes acústicas submarinas.

A acústica submarina vem sendo estudada por décadas, mas redes submarinas com transmissão acústica e protocolos específicos para a comunicação neste meio são campos de pesquisa que estão iniciando. Recentemente alguns simuladores, baseados no NS-2, foram desenvolvidos para o estudo destas redes. Este trabalho avalia através de simulações a viabilidade de aplicações genéricas de monitoramento e controle em redes acústicas submarinas. São propostas e utilizadas três topologias básicas para redes acústicas submarinas: linha, quadro e cubo e dois protocolos MAC: Broadcast e R-MAC. Em nossas análises comparamos esses dois protocolos em relação ao consumo total de energia e o atraso total na rede. Os resultados mostram que essas topologias associadas aos protocolos MAC atendem as necessidades e as peculiaridades da grande maioria das aplicações de monitoramento e controle que utilizam redes acústicas submarinas. O objetivo deste estudo não foi determinar qual a melhor topologia ou o melhor tipo de protocolo de acesso ao meio, mais sim determinar qual a configuração de rede mais indicada para determinada aplicação levando em consideração as características da cada uma delas.

Frame presentations: variants of the reals, rings of functions, their Dedekind completions, and the unit circle

176 p.

20-W average power, high repetition rate, nanosecond pulse with diffraction limit from an all-fiber MOPA system

In this article, we report an all-fiber master oscillator power amplifier (MOPA) system, which can provide high repetition rate and nanosecond pulse with diffraction-limit. The system was constructed using a (2 + 1) X 1 multimode combiner. The Q-Switched, LD pumped Nd:YVO4 solid-state laser wets used (is master oscillator. The 976-nm fiber-coupled module is used as pump source. A 10-m long China-made Yb3+-doped D-shape double-clad large-mode-area fiber was used as amplifier fiber. The MOPA produced as much as 20-W average power with nanosecond pulse and near diffraction limited. The pulse duration is maintained at about 15 its during 50-175 kHz. The system employs a simple and compact architecture and is therefore suitable for the use in practical applications such as scientific and military airborne LIDAR and imaging. Based oil this system. the amplification performances of. the all fiber amplifier is investigated. (C) 2008 Wiley Periodicals, Inc.

Helmholtz Fermi surface harmonics: an efficient approach for treating anisotropic problems involving Fermi surface integrals

We present a new efficient numerical approach for representing anisotropic physical quantities and/or matrix elements defined on the Fermi surface (FS) of metallic materials. The method introduces a set of numerically calculated generalized orthonormal functions which are the solutions of the Helmholtz equation defined on the FS. Noteworthy, many properties of our proposed basis set are also shared by the FS harmonics introduced by Philip B Allen (1976 Phys. Rev. B 13 1416), proposed to be constructed as polynomials of the cartesian components of the electronic velocity. The main motivation of both approaches is identical, to handle anisotropic problems efficiently. However, in our approach the basis set is defined as the eigenfunctions of a differential operator and several desirable properties are introduced by construction. The method is demonstrated to be very robust in handling problems with any crystal structure or topology of the FS, and the periodicity of the reciprocal space is treated as a boundary condition for our Helmholtz equation. We illustrate the method by analysing the free-electron-like lithium (Li), sodium (Na), copper (Cu), lead (Pb), tungsten (W) and magnesium diboride (MgB2)

Thermal stability and crystallochemical analysis for CoII based coordination polymers with TPP and TPPS porphyrins

Artículo CrystEngComm 2013