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Increasing interest, from the U.S. Army Corps of Engineers (USACE) and other agencies, in using deep-mixing methods (DMM) to improve the stability of levees constructed on soft ground is driven by the need to reduce levee footprints and environmental impacts and to allow for more rapid construction. Suitable methods for analysis and design of these systems are needed to ensure that the DMM technology is properly applied. DMM shear walls oriented perpendicular to the levee alignment are an effective arrangement for supporting unbalanced lateral loads. Shear walls constructed by overlapping individual DMM columns installed with single-axis or multiple axis equipment include vertical joints caused by the reduced width of the wall at the overlap between adjacent columns. These joints can be made weaker by misalignment during construction, which reduces the efficiency of the overlap. Depending on the prevalence and strength of these joints, complex failure mechanisms, such as racking due to slipping along vertical joints between adjacent installations in the shear walls, can occur. Ordinary limit equilibrium analyses only account for a composite shearing failure mode; whereas, numerical stress-strain analyses can account for other failure modes. Five case studies provided by the USACE were analyzed to evaluate the behavior of levee and floodwall systems founded on soft ground stabilized with DMM shear walls. These identified and illustrated potential failure mechanisms of these types of systems. Two-dimensional numerical stability and settlement analyses were performed for the case studies using the FLAC computer program. The key findings and conclusions for the individual case studies were assessed and integrated into general conclusions about design of deep-mixing support for levees and floodwalls. One of the significant findings from this research was to identify the potential for a partial depth racking failure, which can control design when the DMM shear walls are socketted into a relatively strong bearing layer. The potential for partial depth racking failure is not discussed in the literature and represents a new failure mode identified by this research. This discovery also highlights the importance of adapting suitable methods for analysis and design of these systems to address all potential failure modes. / Ph. D.

Yes / This work presents a combination of a cup-shaped monopole antenna and an E-shaped Multi-Mode Resonator (MMR) with the presence of a pair of PIN diodes and a varactor diode to form a compact reconfigurable communication filtering antenna for interweave Cognitive Radio (CR) systems. The proposed filtering antenna operates in the WiMAX band, and it is fabricated on an FR4 substrate with overall dimensions normalized to the wavelength ( λ o ) of the first resonant frequency (0.413λ o × 0.516λ o × 0.0165λ o ). The step and continuous tuning serve the secondary user of the WiMAX CR system to communicate in the absence of the primary users at modifiable resonant frequencies and data rates.When the PIN diodes are OFF, the filtering antenna operates with a fixed odd mode resonant frequency and tunable even mode resonant frequency. This state results in a tunable antenna bandwidth covering a maximum measured frequency range of 3.25-4.02~ GHz and a minimum measured range equal to 3.25-3.58~ GHz. The ON state of the PIN diodes eliminates the antenna matching at the even mode resonant frequency while keeping a strong matching at the odd mode resonant frequency. The resulted operational measured frequency range of the antenna in this state is fixed at 2.9-3.28~ GHz. The filtering antenna has acceptable gain values at the pass band of the E-shaped MMR with a maximum simulated gain value equal to 2.5~ dB and a measured maximum gain equal to 2.48~ dB. The simulated and measured power patterns of the antenna for all diodes states are omnidirectional, which are convenient for portable CR gadgets. / This work was supported in part by the Innovation Programme under Grant H2020-MSCA-ITN-2016 SECRET-722424, and in part by the U.K. Engineering and Physical Sciences Research Council (EPSRC) under Grant EP/E022936/1.

In general, this dissertation is concerned with modeling of mechanical behavior of protein molecules. In particular, we focus on coarse-grained models, which bridge the gap in time and length scale between the atomistic simulation and biological processes. The dissertation presents three independent studies involving such models. The first study is concerned with a rigorous coarse-graining method for dynamics of linear systems. In this method, as usual, the conformational space of the original atomistic system is divided into master and slave degrees of freedom. Under the assumption that the characteristic timescales of the masters are slower than those of the slaves, the method results in Langevin-type equations of motion governed by an effective potential of mean force. In addition, coarse-graining introduces hydrodynamic-like coupling among the masters as well as non-trivial inertial effects. Application of our method to the long-timescale part of the relaxation spectra of proteins shows that such dynamic coupling is essential for reproducing their relaxation rates and modes. The second study is concerned with calibration of elastic network models based on the so-called B-factors, obtained from x-ray crystallographic measurements. We show that a proper calibration procedure must account for rigid-body motion and constraints imposed by the crystalline environment on the protein. These fundamental aspects of protein dynamics in crystals are often ignored in currently used elastic network models, leading to potentially erroneous network parameters. We develop an elastic network model that properly takes rigid-body motion and crystalline constraints into account. This model reveals that B-factors are dominated by rigid-body motion rather than deformation, and therefore B-factors are poorly suited for identifying elastic properties of protein molecules. Furthermore, it turns out that B-factors for a benchmark set of three hundred and thirty protein molecules can be well approximated by assuming that the protein molecules are rigid. The third study is concerned with the polymer mediated interaction between two planar surfaces. In particular, we consider the case where a thin polymer layer bridges two parallel plates. We consider two models of monodisperse and polydisperse for the polymer layer and obtain an analytical expression for the force-distance relationship of the two plates. / text

A abordagem de modos normais de baixa frequência na descrição das flutuações conformacionais dos estados nativos das proteínas globulares tem ajudado na caracterização das suas funções biológicas. Vários métodos teóricos e experimentais têm sido empregados para a determinação destas flutuações internas. Estes movimentos podem ser caracterizados pelo fator Debye-Waller (fator-B), correspondente à mobilidade local do resíduo em nível atômico. A análise de modos normais utilizando os modelos de rede elástica (ENM) demonstra ser uma técnica robusta. Fatores-B experimentais são reproduzidos teoricamente por meio desta técnica em tempos computacionais relativamente curtos, mostrando-se competitiva com as técnicas mais sofisticadas. O modelo de rede elástica é uma abordagem t ipo coarse-grain na qual a proteína no seu estado enovelado é representada por uma rede elástica tridimensional de carbonos conectados por molas. As molas representam as interações ligantes e não ligantes entre os carbonos . Neste trabalho, inicialmente, estudamos os modelos de rede elástica já conhecidos na literatura. Em seguida, realizamos um estudo comparativo entre eles. Neste estudo, comprovamos que os modelos pfGNM e pfANM apresentam melhor correlação com os fatores-B experimentais que os os modelos GNM e ANM tradicionais. Desenvolvemos também uma nova abordagem, a qual intitulamos número de contatos ponderados anisotrópica (AWCN). Mostramos que a abordagem AWCN apresenta um desempenho significativamente melhor que o modelo de rede elástica anisotrópica tradicional. Por fim, realizamos um estudo de caráter investigativo do comportamento do peso das interações entre resíduos. Este estudo re velou que, para os modelos WCN e AWCN, a correlação exibe o seu valor máximo para interações ponderadas $1/R^p$, entre resíduos $i$ e $j$j, para valores de $p$ em torno de 2. Nos modelos pfGNM e pfANM a correlação é maximizada para dois valores de $p$, o primeiro em torno de 2 e o segundo em torno de 4,75, indicando que a ponderação pelo recíproco do quadrado da distância, usualmente empregada na literatura, pode não ser adequada para obter a melhor correlação. / Low frequency normal mode approach to describe conformational fluctuations of globular proteins has helped to characterize their biological functions. Various theoretical and experimental methods have been employed to det ermine the magnitudes of those internal motions. Those motions can be characterized by the Debye-Waller factor (B-factor), co rresponding to the local mobility of the residue at the atomic level. Normal mode analysis using elastic network models (ENM) has demonstrated to be a robust technique. Experimental B-factors has been reproduced theoretically by means of this techniq ue in a short computational time and it has been shown to be competitive with more sophisticated techniques. The ENM is a coarse-grained approach in which the protein is represented by a three-dimensional elastic network of alpha-carbon atoms connect ed by springs. Springs represent bonded and non-bonded interactions between the alpha-carbon atoms. In this work, we study th e elastic network models known in the literature. Next, we perform a comparative study between them. We show that the pfGNM a nd pfANM models present better correlation with experimental B-factors than the traditional GNM and ANM models. We also devel op a new approach, which we entitled anisotropic weighted contact number (AWCN). We show that it presents results significantly better than the traditional anisotropic elastic network model. Finally, we perform a study of investigative character of the behavior for the weight of the interactions between residues. This study revealed that, for the WCN and AWCN models, the correlation exhibits its maximum value for weighted interactions $1/R^p$, between residues $i$ and $j$, for values of $p$ around 2. In the pfGNM and pfANM models the correlation is max imized for two values of $p$, the first one around 2 and the second one around 4.75. This indicates that the weighting by the reciprocal of the square of the distance, usually employed in the literature, may not be appropriate to obtain the best correlation.

Sistemas alostéricos são característicos de proteínas com um ou mais estados de equilíbrio. Nesse sentido, uma enzima passa por modificações de sua atividade quando um substrato cooperativo se liga a um estado ou outro (1). Estes estados são reconhecidos por possuírem uma conformação mais estável e coexistirem num ensemble. Este trabalho sustenta que tais proteínas oscilem naturalmente entre esses estados. Experimentos de difração de raios-X e RMN, que proporcionam parâmetros de deslocamento anisotrópicos e tempos de relaxação de spin nuclear, já demonstram a coexistência de ambos estados em solução e descrevem o movimento como uma mudança de equilíbrio populacional dos confórmeros (2). Também é possível desenvolver métodos numéricos, como o cálculo de modos normais e a simulação de dinâmica molecular, para associar a geometria proteica a um movimento sobre determinado potencial de campos de força. O sistema adotado para o desenvolvimento desses estudos é a enzima alostérica Glucosamina-6-fosfato Desaminase. Características que defendem seu uso são sua reversibilidade catalítica, rápido equilíbrio cinético e muito baixa afinidade do estado T por ligantes. Sua estrutura também já foi resolvida por experimentos de cristalografia, identificando ambos estados alostéricos. E a caracterização das mudanças estruturais entre os estados T e R está bem estabelecida, identificando diferentes subunidades a distintos graus de rotação e prevendo uma oscilação de baixa frequência entre eles (3). Resultados obtidos neste projeto constituem: (a) uma dinâmica de 100ns partindo do estado T de toda a proteína (hexamérica) solvatada explicitamente, formando um ensemble NVT de 92000 átomos através do programa NAMD, usando o campo de forças CHARMM; (b) análise de componentes principais aproveitando esta dinâmica e usando algoritmos do programa Gromacs; (c) e análise de modos normais, em que os cálculos de minimização de energia foram feitos pelo programa Gromacs sob o campo de forças ENCADV, no vácuo. Análises desses resultados envolvem cálculos de RMSDs e flutuações, trajetórias calculadas para os autovetores oriundos de NMA ou de PCA, fatores de Debye-Waller e a confirmação visual (e gráficos de distância entre resíduos) de aproximação a um estado ou outro. Como a prévia caracterização da movimentação alostérica, identificava duas regiões para cada monômero como representativas de corpos rígidos, também é desenvolvida uma análise por tensores de inércia. Espera-se que, ao longo do tempo, essas subunidades se comportem como corpos quase rígidos e os movimentos destas regiões rígidas correspondam a uma maior representatividade da transição alostérica. Assim, a caracterização dos tensores seria capaz de filtrar movimentos de mais alta frequência que constituem ruído em relação a movimentos funcionais da proteína. - Algoritmos para cálculos matriciais dos tensores foram escritos em Fortran e em TCl. / Allosteric systems are characteristic of proteins with one or more equilibrium states. Such an enzyme experiences a modification of its activity when a cooperative substrate binds to a state or another, thus, establishing a change in population equilibrium (1). These states are recognized by having a more stable conformation, and they coexist in an ensemble. X-ray diffraction and NMR experiments already demonstrated this dynamic equilibrium, and simulation methods, as molecular dynamics and normal mode analysis, generally provide a more complete proof (2).The allosteric enzyme Glucosamine-6-Phosphate Deaminase appeared to be a good model to better understand the equilibrium dynamics as essential to the protein function, given its reversibility of the catalysis and rapid-equilibrium kinetic mechanism. It also has the structure elucidated for both its conformers (3). A computational approach would now give better perspective on how the conformational changes occur. A set of results of this latter kind were obtained: (a) a 100ns dynamic starting at the hexameric T conformer, explicitly solvated, building a NVT ensemble using NAMD program and CHARMM force field; (b) a principal components analysis making use of the calculated dynamic and of the Gromacs algorithms; (c) and normal mode analysis of the T conformer structure (pdb code 1fsf) minimized with Gromacs program using ENCADV vacuum force field. Not only the conventional analyses for these results (fluctuations and projections) were taken, but also an inertia tensor analysis was developed. As the allosteric conformational change, for this protein, was described by the displacement of only two rigid body subunits³, its description by inertia tensors should act as a filter for the high frequency and functionally uninteresting motions, which normally constitute only noise.

Robots must plan and execute tasks in the presence of uncertainty. Uncertainty arises from sensing errors, control errors, and uncertainty in the geometry of the environment. The last, which is called model error, has received little previous attention. We present a framework for computing motion strategies that are guaranteed to succeed in the presence of all three kinds of uncertainty. The motion strategies comprise sensor-based gross motions, compliant motions, and simple pushing motions.

This thesis focuses on the realist life mode analysis, especially the independent life mode, and the empirical field of entrepreneurship – running a small firm. The aim is to broaden the general understanding for entrepreneurship to include non-capitalistic rationality through application and development of realist life mode analysis. The application of the analysis is done by studying different social phenomena within the field of entrepreneurship. The two phenomena in question are expansion of small firms and trust between an entrepreneur and an employee, and flexibility in small firms. The problem concerning this theoretical application has to do with showing how life mode analysis can be used to explain that entrepreneurship does not have to be about capitalism. The problem concerning theoretical development has to do with identifying social relations and mechanisms that constitute the everyday life of entrepreneurs. The study has been carried out as a qualitative interview study and it is based on the methodology of critical realism. Concerning expansion and trust between an entrepreneur and an employee, my study shows that as an expression of an entrepreneur’s socio centric life mode specific way to interpret reality trust can be an obstacle for employing extra labour-force outside the own firm. Trust can also be an obstacle for an existing relationship to function smoothly if the entrepreneur and the employee live different life modes. However, my study shows that trust can also function as a possible incitement for employment. My conclusion concerning flexibility is that the concept of flexibility, defined with a starting point in the capitalist principles of the economic market, is occasionally misused in literature. My structural perspective shows that not all small firms are driven by these motives powers. Capitalistic small firms do exist and are to be described as flexible, but not all small firms. The size of the firm conditions entrepreneurship in many ways but it does not condition the rationality. My study also shows that the independent life mode as described in the theory so far characterizes simple commodity production and not production of services. Structural changes seem to have resulted in two different life modes for independent entrepreneurs; a commodity specific independent life mode and a service specific independent life mode.

Made available in DSpace on 2014-10-09T12:27:40Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:04:16Z (GMT). No. of bitstreams: 0 / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Sistemas alostéricos são característicos de proteínas com um ou mais estados de equilíbrio. Nesse sentido, uma enzima passa por modificações de sua atividade quando um substrato cooperativo se liga a um estado ou outro (1). Estes estados são reconhecidos por possuírem uma conformação mais estável e coexistirem num ensemble. Este trabalho sustenta que tais proteínas oscilem naturalmente entre esses estados. Experimentos de difração de raios-X e RMN, que proporcionam parâmetros de deslocamento anisotrópicos e tempos de relaxação de spin nuclear, já demonstram a coexistência de ambos estados em solução e descrevem o movimento como uma mudança de equilíbrio populacional dos confórmeros (2). Também é possível desenvolver métodos numéricos, como o cálculo de modos normais e a simulação de dinâmica molecular, para associar a geometria proteica a um movimento sobre determinado potencial de campos de força. O sistema adotado para o desenvolvimento desses estudos é a enzima alostérica Glucosamina-6-fosfato Desaminase. Características que defendem seu uso são sua reversibilidade catalítica, rápido equilíbrio cinético e muito baixa afinidade do estado T por ligantes. Sua estrutura também já foi resolvida por experimentos de cristalografia, identificando ambos estados alostéricos. E a caracterização das mudanças estruturais entre os estados T e R está bem estabelecida, identificando diferentes subunidades a distintos graus de rotação e prevendo uma oscilação de baixa frequência entre eles (3). Resultados obtidos neste projeto constituem: (a) uma dinâmica de 100ns partindo do estado T de toda a proteína (hexamérica) solvatada explicitamente, formando um ensemble NVT de 92000 átomos através do programa NAMD, usando o campo de forças CHARMM; (b) análise de componentes principais aproveitando esta dinâmica e usando algoritmos do programa Gromacs; (c) e análise de modos normais, em que os cálculos de minimização de energia foram feitos pelo programa Gromacs sob o campo de forças ENCADV, no vácuo. Análises desses resultados envolvem cálculos de RMSDs e flutuações, trajetórias calculadas para os autovetores oriundos de NMA ou de PCA, fatores de Debye-Waller e a confirmação visual (e gráficos de distância entre resíduos) de aproximação a um estado ou outro. Como a prévia caracterização da movimentação alostérica, identificava duas regiões para cada monômero como representativas de corpos rígidos, também é desenvolvida uma análise por tensores de inércia. Espera-se que, ao longo do tempo, essas subunidades se comportem como corpos quase rígidos e os movimentos destas regiões rígidas correspondam a uma maior representatividade da transição alostérica. Assim, a caracterização dos tensores seria capaz de filtrar movimentos de mais alta frequência que constituem ruído em relação a movimentos funcionais da proteína. - Algoritmos para cálculos matriciais dos tensores foram escritos em Fortran e em TCl. / Allosteric systems are characteristic of proteins with one or more equilibrium states. Such an enzyme experiences a modification of its activity when a cooperative substrate binds to a state or another, thus, establishing a change in population equilibrium (1). These states are recognized by having a more stable conformation, and they coexist in an ensemble. X-ray diffraction and NMR experiments already demonstrated this dynamic equilibrium, and simulation methods, as molecular dynamics and normal mode analysis, generally provide a more complete proof (2).The allosteric enzyme Glucosamine-6-Phosphate Deaminase appeared to be a good model to better understand the equilibrium dynamics as essential to the protein function, given its reversibility of the catalysis and rapid-equilibrium kinetic mechanism. It also has the structure elucidated for both its conformers (3). A computational approach would now give better perspective on how the conformational changes occur. A set of results of this latter kind were obtained: (a) a 100ns dynamic starting at the hexameric T conformer, explicitly solvated, building a NVT ensemble using NAMD program and CHARMM force field; (b) a principal components analysis making use of the calculated dynamic and of the Gromacs algorithms; (c) and normal mode analysis of the T conformer structure (pdb code 1fsf) minimized with Gromacs program using ENCADV vacuum force field. Not only the conventional analyses for these results (fluctuations and projections) were taken, but also an inertia tensor analysis was developed. As the allosteric conformational change, for this protein, was described by the displacement of only two rigid body subunits³, its description by inertia tensors should act as a filter for the high frequency and functionally uninteresting motions, which normally constitute only noise.