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In recent years pervasive computing has enjoyed an amazing growth in both research and commercial fields. Not only have the number of available techniques and tools expanded, but the number of actual deployments has been underwhelming. With this growth however, we are also experiencing a divergence of software interfaces, languages, and techniques. This leads to an understandably confusing landscape which needlessly burdens the development of applications. It is our sincere hope that through the use of specialized interfaces, languages, and tools, we can make pervasive computing environments more approachable and efficient to software developers and thereby increase the utility and value of pervasive computing applications. In this dissertation, we present a new method for creating and managing the long-term conversations between peers in pervasive computing environments. The Application Sessions Model formally describes these conversations and specifies techniques for managing them over their lifetimes. In addition to these descriptions, this dissertation presents a prototype implementation of the model and results from its use for realistic scenarios. To address the Application Sessions Model's unique needs for resource discovery in pervasive computing environments, we also present the Evolving Tuples Model. This model is also formally defined in this dissertation and practical examples are used to clarify its features. A prototype for both sensor hardware and software simulation of this model is described along with results characterizing the behavior of the model. The models, prototypes, and evaluations of both models presented here form the basis of a new and interesting line of research into support structures for pervasive computing application development. / text

A graph is a mathematical structure for modelling the pairwise relations between objects. This thesis studies two types of graphs, namely, similarity-based graphs and evolving graphs. We look at ways to traverse an evolving graph. In particular, we examine the influence of temporal information on node centrality. In the process, we develop EvolvingGraphs.jl, a software package for analyzing time-dependent networks. We develop Etymo, a search system for discovering interesting research papers. Etymo utilizes both similarity-based graphs and evolving graphs to build a knowledge graph of research articles in order to help users to track the development of ideas. We construct content similarity-based graphs using the full text of research papers. And we extract key concepts from research papers and exploit the temporal information in research papers to construct a concepts evolving graph.

The photosynthetic water oxidation reaction is catalyzed by an inorganic Mn4OxCaClyHCO3-z cluster at the heart of the oxygen evolving complex (OEC) in photosystem II. In the absence of an atomic resolution crystal structure, the precise molecular organization of the OEC remains unresolved. Accordingly, the role of the protein and inorganic cofactors of PSII (Ca2+, HCO3- and Cl-) in the mechanism of O2-evolution await clarification. In this study, rapid 18O-isotope exchange measurements were applied to monitor the substrate-water binding kinetics as a function of the intermediate S-states of the catalytic site (i.e. S3, S2 and S1) in Triton X-100 solubilized membrane preparations that are enriched in photosystem II activity and are routinely used to evaluate cofactor requirements. Consistent with the previous determinations of the 18O exchange behavior in thylakoids, the initial 18O exchange measurements of native PSII membranes at m/e = 34 (which is sensitive to the 16O18O product) show that the ‘fast’ and ‘slowly’ exchanging substrate-waters are bound to the catalytic site in the S3 state, immediately prior to O2 release. Although the slowly exchanging water is bound throughout the entire S-state cycle, the kinetics of the fast exchanging water remains too fast in the S2, S1 [and S0] states to be resolved using the current instrumentation, and left open the possibility that the second substrate-water only binds to the active site after the formation of the S3 state. Presented is the first direct evidence to show that fast exchanging water is already bound to the OEC in the S2 state. Rapid 18O-isotope exchange measurements for Ex-depleted PSII (depleted of the 17- and 23-kDa extrinsic proteins) in the S2 state reveals a resolvable fast kinetic component of 34k2 = 120 ± 14 s-1. The slowing down of the fast phase kinetics is discussed in terms of increased water permeation and the effect on the local dielectric following removal of the extrinsic subunits. In addition, the first direct evidence to show the involvement of calcium in substrate-water binding is also presented. Strontium replacement of the OEC Ca2+-site reveals a factor of ~3-4 increase in the 18O exchange of the slowly exchanging water across the S3, S2 and S1 states while the kinetics of the fast exchanging water remain unchanged. Finally, a re-investigation of the proposed role for bicarbonate as an oxidizable electron donor to photosystem II was unable to discern any 18O enrichment of the photosynthetically evolved O2 in the presence of 18O-bicarbonate. A working model for O2-evolution in terms of these results is presented.

The focus of this research is on identification, location, interruption, characterization and overall management of faults in conventional AC distribution systems as well as isolated MVDC power systems. The primary focus in AC distributions systems is on identifying and locating underground cable faults using voltage and current waveforms as the input data. Cable failure process is gradual and is characterized by a series of single-phase sub-cycle incipient faults with high arc voltage. They often go undetected and eventually result in a permanent fault in the same phase. In order to locate such incipient cable faults, a robust yet practical algorithm is developed taking into account the fault arc voltage. The algorithm is implemented in the time-domain and utilizes power quality monitor data to estimate the distance to the fault in terms of the line impedance. It can be applied to locate both sub-cycle as well as permanent faults. The proposed algorithm is evaluated and proved out using field data collected from utility distribution circuits. Furthermore, this algorithm is extended to locate evolving faults on overhead distribution lines. Evolving faults are faults beginning in one phase of a distribution circuit and spreading to another phase after a few cycles. The algorithm is divided into two parts, namely, the single line-to-ground portion of the fault and the line-to-line-to-ground portion of the fault. For the single line-to-ground portion of the fault, the distance to the fault is estimated in terms of the loop or self-reactance between the monitor and the fault. On the other hand, for the line-to-line-to-ground and line-to-line portion of the fault the distance is estimated in terms of the positive-sequence reactance. The secondary focus of fault management in AC distribution systems is on identifying fault cause employing voltage and current waveform data as well as meteorological information. As the first step, unique characteristics of cable faults are examined along with methods to identify such faults with suitable accuracy. These characteristics are also used to distinguish underground cable faults from other overhead distribution line faults. The overhead line faults include tree contact, animal contact and lightning induced faults. Waveform signature analysis, wavelet transforms and arc voltages during the fault event are used for fault cause identification and classification. A statistical based classification methodology to identify fault cause is developed by utilizing promising characteristics. Unlike the AC system infrastructure which is already in place, the DC system considered in this document is that of a notional electric ship. The nature of DC current, with the absence of a current zero as well as the presence of power electronic devices influencing the current behavior, makes interrupting DC fault currents challenging. As a part of this research an innovative DC fault interruption scheme is proposed for rectifier- fed MVDC systems. A fault at the terminals of a phase-controlled rectifier results in a high magnitude current impulse caused by the filter capacitor discharging into the fault resistance. It is proposed to use a series inductor to limit the magnitude of this current impulse. The addition of the inductor results in an underdamped series RLC circuit at the output terminals of the rectifier which causes the fault current to oscillate about zero. Furthermore, it is proposed to utilize a conventional AC circuit breaker to interrupt this fault current by exploiting the zero crossings resulting from the oscillations. Using the proposed scheme for the example case, the peak fault current magnitude as well as the interruption time is significantly reduced. / text

Hepatitis C Virus (HCV) infects more than 170 million people worldwide but no vaccine is available yet. HCV entry may represent a promising target for therapies and is mediated by two envelope glycoproteins, E1 and E2, assembled as heterodimer onto the virus surface. However, how E1 and E2 dialog, structurally rearrange and act together during these steps remain poorly defined. In this work, we aimed to clarify the interrelation of E1E2 during virus entry, thus opening ways to potential new therapeutic strategies. We first investigated whether a strong genetic divergence between E1E2 heterodimers may highlight distinct functions. We observed that B-cell derived E1E2 were specialized for B-cell infection, suggesting that new functions can emerge from the E1E2 conformational plasticity. In a second approach, we identified a conserved dialog between E1 and the domain III of E2 that was critical for virus binding and fusion. Moreover, a computational model predicted a strong co-evolution between E1 and E2 as well as potential structural rearrangements, suggesting that HCV E2 is likely a fusion protein able to fold over via its domain III through the mediation of E1. Altogether, these different works highlight that E1 and E2 are involved in complex dialogs that regulate the heterodimer folding and functions, suggesting that E1E2 heterodimer is more likely a single functional protein entity than an association of two proteins with specific functions.

Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2017-03-17T12:24:22Z No. of bitstreams: 1 DissCOSF.pdf: 3751345 bytes, checksum: 50050f093a497de77a404a0a957ad02c (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-04-24T13:10:09Z (GMT) No. of bitstreams: 1 DissCOSF.pdf: 3751345 bytes, checksum: 50050f093a497de77a404a0a957ad02c (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-04-24T13:10:17Z (GMT) No. of bitstreams: 1 DissCOSF.pdf: 3751345 bytes, checksum: 50050f093a497de77a404a0a957ad02c (MD5) / Made available in DSpace on 2017-04-24T13:13:58Z (GMT). No. of bitstreams: 1 DissCOSF.pdf: 3751345 bytes, checksum: 50050f093a497de77a404a0a957ad02c (MD5) Previous issue date: 2016-11-22 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The expansion of different areas of knowledge through many types of information brought the necessity to support complex data (images, sounds, videos, strings, DNA chains, etc.), that do not have a Total Order Relationship and need other management mechanisms, like the contentbased retrieval. In general, they are represented in metric space domains, where we have only the elements and the distances between them. Through the characteristics extracted from them, we perform the similarity search. Considering the necessity to associate temporal information on these data in many applications, this work aims to analyze the temporal evolve of metric data. One alternative for this is embedding them into a multidimensional space to allow trajectories estimates. We studied different methods of embedding and analyzed how this affected the data’s distribution and, consequently, the estimates. Two new methods were purposed to estimate an element’s status on a different time from that available in database, in order to reduce the number of non-relevant elements on search results. These methods are based on radius search reduction (range) and evaluation of retrieved element’s proximity by using an approximation of reverse k- NN. We performed experiments which showed that purposed methods could improve the estimate’s result, that used to be performed only using k-NN searches. / A expansão de diferentes áreas do conhecimento com os diversos tipos de informação tornou necessário o suporte a dados complexos (imagens, sons, vídeos, cadeias de DNA, entre outros), que por não possuírem uma Relação de Ordem Total (ROT), necessitam de outros mecanismos de gerenciamento, como a recuperação por conteúdo. Em geral, esses dados são representados em domínios de espaços métricos, onde apenas se tem os elementos e as distâncias entre eles. Através das características extraídas dos mesmos, realiza-se consultas por similaridade. Considerando a necessidade de associar a informação temporal a esses dados em muitas aplicações, este trabalho visa analisar a evolução temporal dos dados métricos. Para isso, uma alternativa é mapeá-los para um espaço multidimensional, a fim possibilitar a estimativa de trajetórias. Neste trabalho, foram estudados diferentes métodos de mapeamento, sendo também analisado como o mapeamento afetou a distribuição dos mesmos e, por conseguinte, a realização das estimativas. Foram propostos dois novos métodos para estimar o estado de um elemento em um tempo diferente daqueles disponíveis na base de dados, com o objetivo de reduzir no conjunto resposta a quantidade de elementos não relevantes. Os métodos propostos são baseados na redução do raio de consulta na região estimada pela delimitação do raio de consulta (range) e a avaliação da proximidade dos elementos retornados utilizando verificação (aproximação) do k-NN reverso. Foram realizados experimentos que mostraram que os métodos propostos melhoraram o resultado final das estimativas, que anteriormente eram realizadas apenas com consultas aos vizinhos mais próximos.

abstract: This dissertation presents a novel algorithm for recovering missing values of co-evolving time series with partial embedded network information. The idea is to connect two sources of data through a shared low dimensional latent space. The proposed algorithm, named NetDyna, is an Expectation-Maximization algorithm, and uses the Kalman filter and matrix factorization approaches to infer the missing values both in the time series and embedded network. The experimental results on real datasets, including a Motes dataset and a Motion Capture dataset, show that (1) NetDyna outperforms other state-of-the-art algorithms, especially with partially observed network information; (2) its computational complexity scales linearly with the time duration of time series; and (3) the algorithm recovers the embedded network in addition to missing time series values. This dissertation also studies a load balancing algorithm, the so called power-of-two-choices(Po2), for many-server systems (with N servers) and focuses on the convergence of stationary distribution of Po2 in the both light and heavy traffic regimes to the solution of mean-field system. The framework of Stein’s method and state space collapse (SSC) are used to analyze both regimes. In both regimes, the thesis first uses the argument of state space collapse to show that the probability of the state being far from the mean-field solution is small enough. By a simple Markov inequality, it is able to show that the probability is indeed very small with a proper choice of parameters. Then, for the state space close to the solution of mean-field model, the thesis uses Stein’s method to show that the stochastic system is close to a linear mean-field model. By characterizing the generator difference, it is able to characterize the dominant terms in both regimes. Note that for heavy traffic case, the lower and upper bound analysis of a tridiagonal matrix, which arises from the linear mean-field model, is needed. From the dominant term, it allows to calculate the coefficient of the convergence rate. In the end, comparisons between the theoretical predictions and numerical simulations are presented. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2020

The purpose of this master's thesis was to design and implement the simulation server for the DEVS that is using already existing SmallDEVS system. The work is aimed to description of the DEVS formalism, SmallDEVS and implemented simulation server. This server provides functions to create new DEVS models, edit already existing models and control simulation. In addition server saves information about state changes during the simulation process, so we can find out the state of the model at any simulation time. It allows to analyze this data and get more information about the simulation process, which was not possible until now. There is a complete description of the communication protocol between client and server in this document. If a new function is implemented in the SmallDEVS system, this protocol can be easily updated. A prototype of client was implemented during this project to test the implemented simulation server. The client implements this communication protocol and allows the user to work with the SmallDEVS system on the server.