<p>A distributed, real-time database could be used to implement a shared whiteboard architecture used for communication between mobile nodes, in an ad-hoc network. This kind of application implies specific requirements on how the database handles replication and consistency between replicas (global consistency). Since mobile nodes are likely to disconnect from the network and connect again at unpredictable times, and since a node may be disconnected an arbitrary amount of time, this needs to be treated as normal operation, and not as failures.</p><p>The replication scheme used in the DeeDS architecture, and the PRiDe replication protocol are both suitable for a shared whiteboard architecture as described above. Since the mobile nodes are likely to be some kind of hand-held device (e.g., used by rescue personnel to exchange information), the database system should be suitable for use in embedded systems. The Polyhedra Real-Time Relational Database (RTRDB) and the TimesTen database are two such systems. A problem is that neither of these two database systems have a replication scheme suitable for use in the previously described type of architecture.</p><p>This dissertation presents two design proposals for how to extend the Polyhedra RTRDB with support for multi-master replication of data using full replication and eventual consistency. One design proposal is based on the DeeDS architecture and the other is based on the PRiDe replication protocol. The proposal based on DeeDS puts a number of requirements on the underlying database and is not easy to port to another DBMS since it makes use of Polyhedra specific API’s. The proposal based on PRiDe on the other hand requires no instrumentation of the underlying database and is thus easier to port to other database systems.</p>

Despite the plethora of information regarding cellular crowding and its importance on modulating protein function the effects of confinement on biological molecules are often overlooked when investigating their physiological function. Recently however, the encapsulation of biomolecules in solid state matrices (NafionTM, sol-gels, zirconium phosphate,etc.) has increased in importance as a method for examining protein conformation and dynamics in confined space as well as novel applications in biotechnology. Biotechnological applications include, but are not limited to, bioremediation, biosensors, biocatalysts, etc. In order to better utilize solid state materials as substrates for biological molecules an understanding of the effects of encapsulation on the detailed dynamics associated with physiological function is required as well as a complete characterization of the physical properties associated with the space in which the biological molecule is to be confined. The focus of this research is to probe the effects of confinement on the thermodynamics of ligand photo-release/rebinding to the prototypical heme protein, myoglobin, encapsulated within sol-gel glasses utilizing photoacoustic calorimetry (PAC) and photothermal beam deflection (PBD). Optical spectroscopies (including optical absorption and fluorescence) have also been employed to characterize the molecular environments of materials including Zr-phosphate and metal organic polyhedral (MOPs), thought to be good candidates for novel bio-hybrid materials. The assembly mechanisms associated with MOPs were also examined in order to develop a foundation through which new, bio-compatible MOPs can be designed. Overall the results presented here represent a technological breakthrough in the application of fast calorimetry to the study of proteins in confined space. This will allow for the first time the acquisition of detailed thermodynamic maps associated with the well-choreographed biomolecular dynamics in confined environments.

Cette thèse revisite de deux manières le domaine abstrait des polyèdres utilisé pour l'analyse statique de programmes.D'abord, elle montre comment utiliser l'assistant à la preuve Coq pour apporter des garanties sur la correction des opérations sur les polyèdres sans compromettre l'efficacité de l'outil VP Lissu de ces travaux.L'outil est fondé sur le principe de la vérification de résultats :un oracle, auquel on ne fait pas confiance, fait les calculs,puis les résultats sont vérifiés par un validateur dont la correction est prouvée avec Coq. De plus, l'oracle fournit des témoins de la correction des résultats afin d'accélérer la vérification.L'autre caractéristique de VPL est l' utilsation de la seule représentation par contraintes des polyèdres,par opposition à l'approche habituelle qui consiste à utiliser à la fois des contraintes et des générateurs.Malgré ce choix inhabituel,les performances de VPL s'avèrent compétitives.Comme on pouvait le prévoir,l'opérateur "join",qui calcule l'enveloppe convexe de deux polyèdres,est le plus coûteux.Puisqu'il nécessite un grand nombre de projections,cette thèse explore plusieurs nouvelles approches de l'opérateur de projection,basées sur la programmation linéaire paramétrique.Elle propose une synthèse des variantes et des combinaisons possibles.La thèse se termine sur les éléments clés d'un nouvel algorithme de résolution tirant parti des spécificités de l'encodage afin d'obtenir de bonnes performances. / The work reported in this thesis revisits in two waysthe abstract domain of polyhedraused for static analysis of programs.First, strong guarantees are provided on the soundness of the operationson polyhedra,by using of the Coq proof assistant to check the soundness proofs.The means used to ensure correctnessdon't hinder the performance of the resultingVerimag Polyhedra Library (VPL).It is built on the principle of result verification:computations are performed by an untrusted oracleand their results are verified by a checkerwhose correctness is proved in Coq.In order to make verification cheap,the oracle computes soundness witnesses along with the results.The other distinguishing feature of VPL is thatit relies only on the constraint representation of polyhedra,as opposed to the common practice of using both constraints and generators.Despite this unusual choice,VPL turns out to be a competitive abstract domain of polyhedra,performance-wise.As expected, the join operator of VPL,which performs the convex hull of two polyhedra,is the costliest operator.Since it builds on the projection operator,this thesis also investigates a new approach toperforming projections,based on parametric linear programming.A new understanding of projection encoded asa parametric linear problem is presented.The thesis closes on a progress report in the design of a new solvingalgorithm,tailored to the specifics of the encodingso as to achieve good performance.

Submitted by MARCOS LUCHIARI BARALDI (marcosbrld@yahoo.com.br) on 2018-09-12T03:42:53Z No. of bitstreams: 1 DISSERTAÇÃO-12.09.18.pdf: 3346423 bytes, checksum: a92ab36f4ef9b546a9685be711a2f4b5 (MD5) / Approved for entry into archive by Elza Mitiko Sato null (elzasato@ibilce.unesp.br) on 2018-09-12T13:24:07Z (GMT) No. of bitstreams: 1 baraldi_ml_me_sjrp.pdf: 3346423 bytes, checksum: a92ab36f4ef9b546a9685be711a2f4b5 (MD5) / Made available in DSpace on 2018-09-12T13:24:07Z (GMT). No. of bitstreams: 1 baraldi_ml_me_sjrp.pdf: 3346423 bytes, checksum: a92ab36f4ef9b546a9685be711a2f4b5 (MD5) Previous issue date: 2018-08-03 / Este trabalho apresenta uma verificação de uma das relações mais importantes da matemática elementar: a relação de Euler. Ela expressa uma relação entre o número vértices, arestas e faces de poliedros convexos, podendo ser estendida aos poliedros estrelados, particularmente aos de Kepler-Poinsot. Para analisar tal relação, a proposta é utilizar material concreto, como jujubas, canudos e varetas de fibra. A princípio é realizada a construção dos poliedros de Platão, canudos rígidos e coloridos, onde é possível verificar com facilidade a veracidade da Relação de Euler. Na sequência utilizam-se as varetas de fibra de vidro 1,4 mm que com a introdução nas arestas dos poliedros, verifica-se facilmente que apenas o dodecaedro e o icosaedro são passíveis da estrelação, por prolongamento das arestas obtendo assim, dois dos poliedros estrelados de Kepler-Poinsot. Por fim, é analisado que a Relação de Euler, também se verifica para esses estrelados. Com tal procedimento fica mais perceptível a não existência de outros poliedros estrelados, pois a partir de sua construção com canudos e a ampliação de suas arestas com varetas fica claro a não intersecção delas. Vale lembrar que tais atividades lúdicas são incentivadas no ensino da matemática e algumas já foram abordadas em dissertações do PROFMAT e em documentos oficiais de ensino no Brasil, como nos Parâmetros Curriculares Nacionais, no Currículo do Estado de São Paulo, matrizes de referências de avaliações tais como: Saresp (Sistema de avaliação de rendimento escolar do estado de São Paulo), Saeb (Sistema nacional de avaliação do ensino básico) e ENEM (Exame nacional do ensino médio). / This paper presents a verification of one of the most important relations of elementary mathematics: Euler's relation. It expresses a relation between the number of vertices, edges and faces of convex polyhedra, and can be extended to the starry polyhedra, particularly to those of Kepler-Poinsot. To analyze this relationship, the proposal is to use concrete material, such as jelly beans, straws and fiber rods. At first the construction of Plato's polyhedrons, rigid and colored straws, is carried out, where it is possible to verify with ease the veracity of the Euler Relation. The 1.4 mm glass fiber rods are then used which, with the introduction of polyhedron edges, can easily be verified that only the dodecahedron and the icosahedron are capable of staring by prolonging the edges, thus obtaining two of the polyhedra starring Kepler-Poinsot. Finally, it is analyzed that the relation of Euler, also is verified for these stars. With such a procedure it is more noticeable the existence of other starry polyhedra, since from its construction with straws and the enlargement of its edges with rods it is clear the nonintersection of them. It is worth remembering that such play activities are encouraged in the teaching of mathematics and some have already been addressed in PROFMAT dissertations and in official teaching documents in Brazil, such as in the National Curriculum Parameters, in the Curriculum of the State of São Paulo, references reference matrices such as: Saresp (System of evaluation of school performance of the state of São Paulo), Saeb (National system of evaluation of basic education) and ENEM (National High School Examination).

Cette thèse présente la nouvelle implémentation de la Verified Polyhedra Library (VPL), une bibliothèque efficace de calcul polyédral.Elle fournit des opérateurs certifiés en Coq, s'appliquant sur des représentations en contraintes.La version précédente souffrait d'inefficacité lors d'opérateurs cruciaux, à savoir l'élimination de variables et l'enveloppe convexe.Dans ce document, je présente des améliorations importantes qui bénéficient à la modularité, la simplicité et au passage à l'échelle de la bibliothèque:le processus de certification est généralisé et simplifié;les conditions polynomiales sont maintenant traitées;Les calculs qui n'impliquent pas de certification sont effectués en flottant;de nouveaux algorithmes sont fournis pour la minimisation de représentation et la détection d'égalités implicites.D'un côté, l'implémentation d'un solveur de problèmes de Programmation Linéaire Paramétrique (PLP) a mené à une meilleure efficacité tant en nombre de contraintes que de générateurs.L'élimination de variables et l'enveloppe convexe sont tous deux encodés en problème PLP.Le PLP est un outil générique possédant de nombreuses applications, et qui permet d'éviter la génération de redondances grâce à l'utilisation d'une contrainte de normalisation.De plus, nous proposons de nouveaux opérateurs pour la gestion des contraintes polynomiales, l'un d'entre eux étant également encodé en tant que problème PLP.De l'autre, la certification de la bibliothèque a été grandement optimisée et simplifiée.La VPL suit un paradigme de vérification a posteriori, où les calculs non triviaux sont effectués par des oracles externes générant des témoins de correction.Ces témoins sont ensuite validés par un vérifieur écrit en Coq.Grâce à un cadre de certification puissant et innovant, le Polymorphic Factory Style (PFS), la plupart des aspects délicats de la génération de témoins sont maintenant évitée.La souplesse du PFS est démontrée par la création d'une tactique en COQ qui découvre les égalités implicites en arithmétique linéaire. / This thesis presents the design and implementation of the Verified Polyhedra Library (VPL), a scalable library for polyhedral calculus.It provides Coq-certified polyhedral operators that work on constraints-only representation.The previous version was inefficient on crucial operations, namely variable elimination and convex hull.In this work, I present major improvements that have been made in scalability, modularity and simplicity:The certification process is generalized and simplified;Polynomial guards can now be handled;Computations that do not involve certification use floating-points;New algorithms are presented for minimization and detection of implicit equalities.On the one hand, the implementation of a solver for Parametric Linear Programming (PLP) problems led to an improved scalability both in dimension and in number of constraints.Variable elimination and convex hull are now encoded as such.PLP is a generic tool that has many applications, and that avoids generating redundancies thanks to a normalization constraint.Additionally, we provide new operators for handling multivariate polynomials, one of which being also encoded as a PLP problem.On the other hand, the certification part of the library has been greatly optimized and simplified.The VPL follows a result-verification paradigm, where complex computations are performed by untrusted oracles that generate witnesses of correctness, themselves validated by a certified Coq checker.Thanks to an innovative and powerful certification framework known as Polymorphic Factory Style (PFS), most cumbersome parts of the witness generation are now avoided.The flexibility of PFS is attested by the creation of a Coq tactic for learning equalities in linear arithmetic.

Submitted by Cássia Santos (cassia.bcufg@gmail.com) on 2015-01-30T10:50:40Z No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Alceny Garcia Filho - 2014.pdf: 2219421 bytes, checksum: 7bccfbe2cdaf663705c07a9d9017bda7 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-01-30T13:07:22Z (GMT) No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Alceny Garcia Filho - 2014.pdf: 2219421 bytes, checksum: 7bccfbe2cdaf663705c07a9d9017bda7 (MD5) / Made available in DSpace on 2015-01-30T13:07:22Z (GMT). No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Alceny Garcia Filho - 2014.pdf: 2219421 bytes, checksum: 7bccfbe2cdaf663705c07a9d9017bda7 (MD5) Previous issue date: 2014-08-08 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The work proposed aims to provide a reflection about the importance of promoting a dynamic teaching. Therefore it proposes the use of a software , A Plethora of Polyhedra, that considers the learning needs of students in order to assist them in the viewing and understanding of space around them and so they can use the geometric and mathematical knowledge in benefit of everyday issues. This is a free software for d ynamic mathematics that gathers resources of spatial geometry such as: rotation, translation, enlargement, reduction, and counting of the number of vertices, edges and faces, which enables the students understand the main presented contents. By manipulating the software chosen, teacher and student can identify their main characteristics and essential elements, not just only through the development and resolution of mathematical expressions algebraically presented. This work also is willing to motivate the activities to be proposed by a theoretical basis and analyze the possible difficulties encountered by students and teachers, and the opportunities for improvement in the teaching of geometry. / O trabalho ora proposto tem como objetivo proporcionar uma reflexão sobre a importância de se promover um ensino dinâmico. Para tanto, propõe -se a utilização de um software – Uma Pletora de Poliedros – que leve em consideração as necessidades de aprendizagem dos alunos, de modo a ajudá-los na visualização e no entendimento do espaço que os cerca e para que eles possam utilizar o conhecimento geométrico e matemático em benefício das questões cotidianas. Trata-se de um software livre para matemática dinâmica que reúne recursos de geometria espacial como: rotação, translação, ampliação, redução e contagem do número de vértices, arestas e faces, o que permite aos alunos compreenderem os principais conteúdos apresentados. Ao manipular o software escolhido, professor e aluno podem identificar suas principais características e elementos essenciais, não mais apenas somente por meio da elaboração e resolução de expressões matemáticas algebricamente apresentadas. Este trabalho dispõe-se, ainda, a motivar as atividades a serem propostas por meio de uma fundamentação teórica, bem como analisar as possíveis dificuldades encontradas por parte de alunos e professores, assim como as possibilidades de melhoria no ensino de geometria.

A distributed, real-time database could be used to implement a shared whiteboard architecture used for communication between mobile nodes, in an ad-hoc network. This kind of application implies specific requirements on how the database handles replication and consistency between replicas (global consistency). Since mobile nodes are likely to disconnect from the network and connect again at unpredictable times, and since a node may be disconnected an arbitrary amount of time, this needs to be treated as normal operation, and not as failures. The replication scheme used in the DeeDS architecture, and the PRiDe replication protocol are both suitable for a shared whiteboard architecture as described above. Since the mobile nodes are likely to be some kind of hand-held device (e.g., used by rescue personnel to exchange information), the database system should be suitable for use in embedded systems. The Polyhedra Real-Time Relational Database (RTRDB) and the TimesTen database are two such systems. A problem is that neither of these two database systems have a replication scheme suitable for use in the previously described type of architecture. This dissertation presents two design proposals for how to extend the Polyhedra RTRDB with support for multi-master replication of data using full replication and eventual consistency. One design proposal is based on the DeeDS architecture and the other is based on the PRiDe replication protocol. The proposal based on DeeDS puts a number of requirements on the underlying database and is not easy to port to another DBMS since it makes use of Polyhedra specific API’s. The proposal based on PRiDe on the other hand requires no instrumentation of the underlying database and is thus easier to port to other database systems.

This 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. / text

A highly porous metal–organic framework Cu2(BBCDC) (BBCDC = 9,9′-([1,1′-[b with combining low line]iphenyl]-4,4′-diyl)[b with combining low line]is(9H-[c with combining low line]arbazole-3,6-[d with combining low line]i[c with combining low line]arboxylate) (DUT-49) with a specific surface area of 5476 m2 g−1, a pore volume of 2.91 cm3 g−1, a H2 excess uptake of 80 mg g−1 (77 K, 50 bar), a CO2 excess uptake of 2.01 g g−1 (298 K, 50 bar) and an exceptionally high excess methane storage capacity of 308 mg g−1 (298 K, 110 bar) was obtained using an extended tetratopic linker. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2017-01-12T13:19:24Z No. of bitstreams: 1 2015 - Wellington Gon?alves Lemos.pdf: 9868472 bytes, checksum: c653096dd1677c18027859c47248be69 (MD5) / Made available in DSpace on 2017-01-12T13:19:24Z (GMT). No. of bitstreams: 1 2015 - Wellington Gon?alves Lemos.pdf: 9868472 bytes, checksum: c653096dd1677c18027859c47248be69 (MD5) Previous issue date: 2015-08-31 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / Currently working with stellar polyhedra in high school is not registered in official national proposals. Such polyhedra arouse interest in teachers and also the students because of its beauty and also for its conceptual struture. Therefore, the presente work aims to analyze how a classroom dedicated to diversity, and not just to students skill limitations, cognitive and contribues differently for learning each of them when the topic studied are the stellar polyhedra. We show you an interactive room is able to include students who easily exclude school due to a difficulty to perform activity with a feature that exposes its limitations. This architeture of classroom challenges educators to rethink different possiblities for analysis of teaching-learning process. In addition to curricular innovations, we believe that the results of the work bring new perspectives for the analysis of mathematical learning through the use of foldings, adjutments, animations and instutional videos / Atualmente o trabalho com poliedros estrelados no ensino m?dio n?o possui registro nas propostas oficiais nacionais. Tais poliedros despertam interesse nos professores, tamb?m nos alunos, devido sua beleza e tamb?m pela sua estrutura conceitual. Assim, o presente trabalho tem o objetivo de analisar como uma sala de aula interativa voltada para a diversidade, e n?o apenas para limita??es de habilidades dos alunos, contribui cognitiva e diferentemente no aprendizado de cada um deles quando o tema estudado s?o os poliedros estrelados. Mostramos como uma sala interativa ? capaz de incluir alunos que facilmente se excluem da aula devido a uma dificuldade apresentada ao realizar atividade com um recurso que exp?e suas limita??es. Essa arquitetura de sala de aula desafia os educadores a repensarem as diferentes possibilidades para an?lise do processo ensino-aprendizagem. Al?m de propor inova??es curriculares, acreditamos que os resultados do trabalho tragam novas perspectivas para a an?lise do aprendizado matem?tico mediante o uso de dobraduras, planifica??es, anima??es e v?deos did?ticos