This thesis focuses on the task of dexterous manipulation of deformable objects, and in particular, clothing and garments. The task of manipulating deformable objects such as clothing can be broken down into a series of sub-tasks: (1) perceive and pick up garment, and then identify garment and recognize its pose; (2) using a manipulation strategy, regrasp the object to put it into a canonical state; (3) scan the surface of the object to find wrinkles, and use an iron to remove the wrinkles; (4) starting from the wrinkle-free state, fold the garment according to pre-planned sequence of manipulations with optimized trajectories; In this thesis, we will address all the phases of this process. A key contribution of the work is innovative use of simulation. We use offline simulation results to predict states of deformable objects (i.e. cloth, fabric, clothing) that are then recognized by a robotic vision/grasping system to correctly pick up and manipulate these objects. The recognition will use the simulation engine to deform the models in real time to find correct matches. The simulation will also be used to find the optimized trajectories for the manipulation of the garments, such as the garment folding.

Este trabalho tem como foco a dobradura em sala de aula, auxiliando o professor em sua prática docente. Com dobras simples de serem realizadas a dobradura pode auxiliar o aluno a desenvolver a concentração, estimular a criatividade, concretizar uma ideia ou pensamento no momento em que surge a foma no papel e, consequentemente, o aluno interioriza o aprendizado desejado. Os tópicos estudados versam sobre a construção dos principais polígonos regulares e de um sólido espacial, o tetraedro. São também estudadas algumas aplicações aritméticas, como divisão de segmentos e raízes quadradas e cúbicas. / This work aims to study the activity of paper folding in the classroom as an auxiliary resource for the teacher. The folders are quite simple and will improve the students skills on concentration, creativity, and the ability to realize on paper his/her thoughts and ideas. The covered topics range from the construction of the main regular poligons, a spatial solid (tetrahedron), through some arithmetic applications, like division of a segment and square and cubic roots.

Orientador: Luis Paulo Barbour Scott. / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós-Graduação em Engenharia da Informação.

O problema do folding de proteínas tem sido investigado intensamente há mais de sessenta anos. Entretanto ainda não é encontrado na literatura um modelo que seja capaz de explicar plenamente qual é o mecanismo responsável pelo processo de folding. Neste contexto, a presente tese de doutorado é uma proposta minimalista para investigar o papel de um código estereoquímico, que é centrado no efeito hidrofóbico e nos vínculos estéricos dos aminoácidos (o modelo estereoquímico), no processo em pauta. Esse modelo quando combinado com um método para incluir a flutuação térmica local no sistema cadeia protéica-solvente, possibilita a investigação de um dos aspectos mais extraordinários do problema, a saber, a rapidez do processo de folding, considerado aqui por meio da correlação entre a complexidade da estrutura nativa (alvo) e a taxa de folding. Esse método é motivado por argumentos físico-químicos e biológicos, e é fundamentado na Mecânica Estatística Não Extensiva, via o uso do peso de Tsallis em simulações Monte Carlo (MC). O tempo característico de folding (obtido daquelas simulações e utilizado aqui como um parâmetro analítico do problema), cobre várias ordens de grandeza para cadeias com o mesmo tamanho. Dois conjuntos principais de simulações foram considerados com a finalidade de análise: (i) alguns alvos foram especialmente selecionados e submetidos a simulações MC a várias temperaturas T do reservatório térmico (o meio solvente); e (ii) um total de duzentos alvos com topologias diversas foram submetidos a simulações à mesma temperatura T = 1 (unidades arbitrárias). Com essas simulações foi possível verificar comparativamente o efeito dos dois pesos estatísticos, o de Boltzmann e o de Tsallis, sobre a cinética do processo de folding, e assim revelar comportamentos intrigantes, porém consistentes com o fenômeno focado, como a robustez do processo de folding e , este último emergindo como uma grandeza que depende da complexidade da estrutura nativa. Para estruturas distintas, cobre quatro ordens de grandeza. Os resultados da investigação da correlação entre e parâmetros globais destinados a avaliar a complexidade da topologia da estrutura nativa, como a ordem de contato e a cooperatividade estrutural, corroboram com a noção de que a rapidez do processo de folding é determinada fundamentalmente pela complexidade da topologia da estrutura nativa. / The protein folding problem has been investigated for more than sixty years. However is not yet found in literature a model that is able to fully explain the mechanism behind the folding process. In this context, the present doctoral thesis is a speculative and minimalist proposal to investigate the role of a stereochemical code -grounded in the hydrophobic effect and steric constraints of amino acids (the stereochemical model), in the discussed process. This model, when combined with a method to include local thermal fluctuations in the protein chain-solvent system, enables the investigation of one of the most extraordinary aspects of the problem, namely, the fastness of the folding process, which is studied here by means of the correlation between the complexity of the native structure (target) and the folding process rate. This method is motivated by physical chemistry and biological arguments, and is based on the Nonextensive Statistical Mechanics, by the use of the Tsallis weight in Monte Carlo simulations (MC), where the entropic index q is adjusted at each new conformation of the protein chain. For chains with the same length, the characteristic folding time (estimated from those simulations and used here as an analytical parameter of the problem) span several order of magnitude. Two main sets of simulations were performed for analysis purposes. First, some targets were specially selected and submitted to MC simulations with several temperatures of the thermal reservoir (the solvent), and then a total of two hundred targets with diverse topologies were submitted to simulations with the same reservoir temperature T = 1 (arbitrary units). With such set of simulations, we could compare the effect of two statistical weights, namely the Boltzmann and the Tsallis weight, on the kinetics of the folding process. Intriguing but consistent behavior with respect to the folding phenomenon was reveled, such as the robustness of the process, and about the characteristic folding time , which emerges as an amount that depends on the complexity of the native structure. For distinct structures, covers four orders of magnitude. Our results about the correlation between and global parameters to assess the complexity of the topology of the native structure, such as contact order and structural cooperativity, support the notion that the fastness of the folding process is essentially determined by the complexity of the topology of native structure.

Objective: To assess neck angulation and endograft oversizing as factors contributing to folding. Endograft folding will then be assessed on its role in endograft fixation strength. Methods: Bench top flow loop experiments were performed with barbless Gore Excluder endovascular grafts (EVG) that were deployed into silicone aorta-AAA models with neck angles of 0, 30, and 60. A total of five oversizings were tested: -7%, 2%, 12%, 24%, and 38% with N= 3 for each oversizing at each neck angle for a total of 45 experiments. Photographs of the stent apex to apex distances were taken for the entire circumference of the device for a total of 8 photos per experiment. Measurements of the apex to apex distance were taken for the top three stent layers and variance for each stent layer was calculated. Variances for all three stent layers were summed to represent the folding metric. The silicone model was then removed from the flow loop and placed on the uniaxial extension tester to for pull out testing to assess impact on attachment strength. Results: Neck angle and oversizing increases folding risk at oversizing ≥12% for 0° and 30° neck angles, and ≥ 2% oversizing for a 60° neck angle. Folding metric comparison between 0° vs. 30° and 0° vs. 60° across all oversizings had statistical significance (Mann-Whitney U, p

Intrinsically disordered proteins (IDPs) do not form stable tertiary structures like their ordered partners. They exist as heterogeneous ensembles that fluctuate over a time scale. Intrinsically disordered regions and proteins are found across different phyla and exert crucial biological functions. They exhibit transient secondary structures in their free state and become folded upon binding to their protein partners via a mechanism called coupled folding and binding. Some IDPs form alpha helices when bound to their protein partners. We observed a set of cancer associated IDPs where the helical binding segments of IDPs are flanked by prolines on both the sides. Helix-breaking prolines are frequently found in IDPs flanking the binding segment and are evolutionarily conserved across phyla. Two studies have shown that helix flanking prolines modulate the function of IDPs by regulating the levels of disorder in their free state and in turn regulating the binding affinities to their partners. We aimed to study if this is a common phenomenon in IDPs that exhibit similar pattern in the conservation of helix flanking prolines. We chose to test the hypothesis in c-Myb-KIX : IDP-target system in which the disordered protein exhibits high residual helicity levels in its free state. c-Myb is a hematopoietic regulator that plays a crucial role in cancer by binding to the KIX domain of CBP. Studying the functional regulation of c-Myb by modulating the disorder levels in c-Myb and in IDPs in general provides a better understanding of the way IDPs function and can be used in therapeutic strategies as IDPs are known to be involved in regulating various cellular processes and diseases. To study the effect of conserved helix flanking prolines on the residual helicity levels of c-Myb and its binding affinity to the KIX domain of CBP, we mutated the prolines to alanines. Mutating prolines to alanines increased the helicity levels of c-Myb in its free state. This small increase in the helicity levels of a highly helical c-Myb showed almost no effect on the binding affinity between cMyb and KIX. We hypothesized that there is a helical threshold for coupled folding and binding beyond which helicity levels of the free state IDP have no effect on its binding to their ordered protein partner. To test this hypothesis, we mutated solvent exposed amino acid residues in c-Myb that reduce its overall helicity and studied its effect on the binding affinity between c-Myb and KIX. Over a broad range of reduction in helicity levels of the free state did not show an effect on the binding affinity but beyond a certain level, decrease in helicity levels showed pronounced effects on the binding affinity between c-Myb and KIX.

Abstract not available

<p>Today's radio frequency receivers for digital wireless communication are getting more and more complex. A single receiver unit should support multiple bands, have a wide bandwidth, be flexible and show good performance. To fulfil these requirements, new receiver architectures have to be developed and used. One possible alternative is the RF undersampling architecture. </p><p>This thesis evaluates the RF undersampling architecture, which make use of an undersampling track-and-hold circuit with very wide bandwidth to perform direct sampling of the RF carrier before the analogue-to-digital converter. The architecture’s main advantages and drawbacks are identified and analyzed. Also, techniques and improvements to solve or reduce the main problems of the RF undersampling receiver are proposed.</p>

<p>This thesis is based on studies, described in four papers, in which the folding energy landscape of MerP was investigated by various techniques. MerP is a water-soluble 72 amino acid protein with a secondary structure consisting of four anti-parallel β-strands and two α-helices on one side of the sheet in the order β1α1β2β3α2β4. </p><p>The first paper describes the use of CD and fluorescence analysis to examine the folding/unfolding process of MerP. From these experiments it was found that the protein folds according to a two-state model in which only the native and unfolded forms are populated without any visible intermediates. With a rate constant of 1.2 s^-1, the folding rate was found to be unusually slow for a protein of this size.</p><p>The studies presented in the second and third papers were based on measurements of native-state amide proton exchange at different temperatures (Paper II) and GuHCl concentrations (Paper III) in the pre-transitional region. In these studies partially unfolded forms were found for MerP which are essentially unrelated to each other. Thus, in the folding energy landscape of MerP, several intermediates seem to occur on different folding trajectories that are parallel to each other. The slow folding rate of MerP might be coupled to extensive visitation of these conformations. Hydrogen exchange in MerP did also reveal structure-dependent differences in compactness between the denatured states in GuHCl and H₂O.</p><p>In the last paper multivariate data analysis was applied to 2-dimensional NMR data to detect conformational changes in the structure of MerP induced by GuHCl. From this analysis it was suggested that regions involved in the most flexible part of the protein structure are disrupted at rather low denaturant concentrations (< 2.1 M GuHCl) while the native structures of the most stable parts are still not completely ruptured at 2.9 M GuHCl.</p><p>Finally, the stability, kinetics, contact order and folding nuclei of six proteins with similar topology (MerP, U1A, S6, ADA2h, AcP and HPr) were compared. In this analysis it was found that their folding properties are quite diverse, despite their topological similarities, and no general rules that have been formulated yet can adequately predict their folding behaviour.</p>

<p>Protein folding and export to the membrane are crucial events in the cell. Both processes may be initiated already at the ribosome, assisted by factors that bind to the polypeptide as it emerges from the ribosome. The signal recognition particle (SRP) scans the ribosome for nascent peptides destined for membrane insertion and targets these ribosomes to the site for translocation in the membrane. Trigger factor (TF) is a folding chaperone that interacts with nascent chains to promote their correct folding, prevent misfolding and aggregation. </p><p>In this thesis, we first investigated membrane targeting and insertion of two heterologous membrane proteins in E. coli by using in vitro translation, membrane targeting and cross-linking. We found that these proteins are dependent on SRP for targeting and that they initially interact with translocon components in the same way as native nascent membrane proteins. </p><p>Moreover we have characterised the SRP and TF interactions with the ribosome both with cross-linking experiments and with quantitative binding experiments. Both SRP and TF bind to ribosomal L23 close to the nascent peptide exit site where they are strategically placed for binding to the nascent polypeptide. </p><p>Quantitative analysis of TF and SRP binding determined their respective KD values for binding to non translating ribosomes and reveals that they bind simultaneously to the ribosome, thus having separate binding sites on L23. </p><p>Finally, binding studies on ribosome nascent chain adds clues as to how TF functions as a chaperone.</p>