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<p>Granular systems are ensembles of inelastic particles which dissipate energy during collisions. Granular systems serve as excellent models for a wide variety of materials such as sand, soils, corn, and powder. A rather remarkable property of granular systems is when excited, whether due to an interstitial fluid or via the boundaries, the granular particlesdisplay fluid-like behavior. As a result, there has been decades of granular research with the overarching goal of formulating a general granular hydrodynamic theory.</p> <p>However, the granular hydrodynamic theory is limited, and the underlying transport coefficients often require modifications which are based on empirical observations, and assuch, are system-specific. It is ideally better to devise a general theory which minimizes the information needed about the systema priori. The main thrust of the work undertaken shown here strives to develop such a model by using kinetic theory as the basis. More specifically, I investigate granular gases via the direct simulation Monte Carlo (DSMC) methodand modify the governing equations. In this thesis, two idealized cases of granular gases areconsidered: the homogeneous cooling state and a boundary-heated gas (or the pure conduc-tion case). In the former, the effects of polydispersity are probed. In the latter, the evolutionof the local hydrodynamics due to strong rarefaction effects are divulged. Additionally, amodified, more generalized constitutive relation for the heat flux is proposed and comparedwith DSMC results. Extensions of the DSMC method for dense granular gases and granulargases composed of non-spherical particles are also discussed.</p>

It remains a major challenge in biophysics to understand the conformational dynamics of biomolecules. As powerful tools, molecular dynamics (MD) simulations have become increasingly important in studying the full atomic details of conformational dynamics of biomolecules. In addition, many statistical models have been developed to give insight into the big datasets from MD simulations. In this work, I first describe three statistical models used to analyze MD simulation data: Lifson-Roig Helix-Coil theory, Bayesian inference models, and Markov state models. Then I present the applications of each model in analyzing MD simulations and revealing insight into the conformational dynamics of biomolecules. These statistical models allow us to bridge microscopic and macroscopic mechanisms of biological processes and connect simulations with experiments. / Chemistry

The research reported in this dissertation focuses on the response of grain boundaries in polycrystalline metallic nanostructures to applied strain using molecular dynamics simulations and empirical interatomic force laws. The specific goals of the work include establishing how local grain boundary structure affects deformation behavior through the quantitative estimation of various plasticity mechanisms, such as dislocation emission and grain boundary sliding. The effects of strain rate and temperature on the plastic deformation process were also investigated. To achieve this, molecular dynamics simulations were performed on both thin-film and quasi-2D virtual samples constructed using a Voronoi tessellation technique. The samples were subjected to virtual mechanical testing using uniaxial strain at strain rates ranging from 105s-1 to 109s-1. Seven different interatomic embedded atom method potentials were used in this work. The model potentials describe different metals with fcc or bcc crystal structures. The model was validated against experimental results from studying the tensile deformation of irradiated austenitic stainless steels performed by collaborators at the University of Michigan. The results from the model validation include a novel technique for detecting strain localization through adherence of gold nanoparticles to the surface of an experimental sample prior to deformation. Similar trends with respect to intergranular crack initiation were observed between the model and the experiments. Simulations of deformation in the virtual samples revealed for the first time that equilibrium grain boundary structures can be non-planar for model potentials representing fcc materials with low stacking fault energy. Non-planar grain boundary features promote dislocation as deformation mechanisms, and hinder grain boundary sliding. This dissertation also reports the effects of temperature and strain rate on deformation behavior and correlates specific deformation mechanisms that originate from grain boundaries with controlling material properties, deformation temperature and strain rate. / Ph. D.

No / Review article. No abstract.

Multicomponent high-entropy and amorphous alloys represent relatively new classes of structural materials with complex atomic configurations and exceptional mechanical properties. However, there are several knowledge gaps in the relationships between their atomic structure and mechanical properties. Understanding these critical relationships will enable novel alloy design and tailoring of their mechanical properties for desired engineering applications. In this dissertation, first-principles calculations and molecular dynamics simulations are applied to investigate the local atomic configurations and ordering in high-entropy and amorphous alloys. Our findings suggest that fluctuations in local atomic configurations for high- entropy alloys result in significant changes in stacking fault energy, twin energy, dislocation behavior, dislocation-twin interactions, and critical shear stress. For amorphous alloys or metallic glasses, the short-range order (SRO) and medium-range order (MRO) were found to play decisive roles in determination of their mechanical properties. Structural relaxation was found to lead to shear localization, which was attributed to free volume change and evolution of SRO and MRO to more brittle nature. In contrast, rejuvenated metallic glasses had relatively large and uniform free volume distribution giving rise to homogeneous flow and increased plasticity.

Over one million amputees are living in the United States with major lower limb loss (Ziegler-Graham et al. 2008). Lower limb amputation leads to the functional loss of the ankle plantar flexor muscles, which are important contributors to body support, forward propulsion, and leg swing initiation during walking (Neptune et al. 2001; Liu et al. 2006). Effective prosthetic component design is essential for successful rehabilitation of amputees to return to an active lifestyle by partially replacing the functional role of the ankle muscles. The series of experimental and computer simulation studies presented in this research showed that design characteristics of energy storage and return prosthetic ankles, specifically the elastic stiffness, significantly influence residual and intact leg ground reaction forces, knee joint moments, and muscle activity, thus affecting muscle output. These findings highlight the importance of proper prosthetic foot stiffness prescription for amputees to assure effective rehabilitation outcomes. The research also showed that the ankle muscles serve to stabilize the body during turning the center of mass. When amputees turn while supported by their prosthetic components, they rely more on gravity to redirect the center of mass than active muscle generation. This mechanism increases the risks of falling and identifies a need for prosthetic components and rehabilitation focused on increasing amputee stability during turning. A proper understanding of the effects of prosthetic components on amputee walking mechanics is critical to decreasing complications and risks that are prevalent among lower-limb amputees. The presented research is an important step towards reaching this goal. / text

Les propriétés mécaniques des polymères et des copolymères à blocs ont été étudiées par simulation de type dynamique moléculaire (modèle billes-ressorts). Les échantillons polymères ont été générés par la méthode de « radical like polymerisation ». Ces échantillons ont été soumis à des essais de traction uniaxiaux et triaxiaux dans le but d’étudier leurs réponses mécaniques. Dans la première partie de ce travail on a comparé deux méthodes de traction : « méthode de traction homogène» et la traction « pilotée par les bords » de l’échantillon. Les résultats montrent que les deux méthodes sont équivalentes à faible vitesse de traction. Le changement de distance entre enchevêtrement dans un polymère modèle sous traction est analysé, les résultats montrent que le désenchevêtrèrent des chaines est plus prononcé lorsque la déformation de l’échantillon est uniaxiale du fait de la relaxation latérale de l’échantillon. La nucléation des cavités dans les polymères amorphes soumis à une déformation triaxial a été également étudiée. On a trouvé que les cavités se forment dans des zones qui sont caractérisées par un faible module d’incompressibilité élastique. Ces zones sont identifiables dès le début de la déformation à une température très basse (T~0K). La seconde partie de ce travail se concentre sur la simulation de la réponse mécanique des copolymères à blocs. L’influence de l’architecture moléculaire sur le comportement mécanique de l’échantillon a été analysée. Les résultats montrent que le comportement mécanique des échantillons est piloté par le taux des chaines liantes qui assurent la transmission des contraintes entre les phases. Le flambement des lamelles dans les copolymères à blocs a été également étudié, l’influence de la taille de l’échantillon et de la vitesse de déformation sur la réponse mécanique de l’échantillon a été explorée. Les résultats montrent un changement de mode du flambement selon la vitesse de déformation imposée. Un nouveau modèle qui prend en compte le facteur cinétique du flambement est proposé pour décrire la compétition entre les modes. / We use molecular dynamics simulation of a coarse grained model to investigate the mechanical properties of homogenous polymers and lamellar block copolymers. Polymer samples have been generated using “radical like polymerisation” method. These samples were submitted to uniaxial and triaxial tensile tests in order to study their mechanical responses. First we compare two tensile test methods: the “homogenous deformation method” and the “boundary driven deformation method”. We find that the two methods lead to similar results at low strain rate. The change of the entanglement network in polymer sample undergoing a tensile deformation was investigated. We have found that the sample exhibits an increase of its entanglement length in uniaxial deformation test compared to triaxial deformation one. Our finding was interpreted by the pronounced chain disentanglement observed in the uniaxial deformation test due to the lateral relaxation of the sample. The cavity nucleation in amorphous polymers has been also studied. We have found that the cavities nucleate preferentially in zones that exhibit a low elastic bulk modulus. These zones can be identified from the initial undeformed state of the sample at low temperature (T~0K). The second part of the work focused in the simulation of the mechanical response of block copolymers. The influence of chain architecture on the mechanical properties was investigated: our finding reveals an important role of the bridging molecules (cilia chains and knotted loop chains) on the stress transmission between phases at high strain. The initiation of plasticity in copolymer samples was also studied. The role of the buckling has been found to be determinant in the mechanical response of the sample The dependence of the buckling instability with the sample size and the deformation rate was investigated. We have found that the fundamental (first) mode of buckling develops at relatively low strain rate whereas at high strain rate the buckling of the sample occurs with the second or higher mode of buckling. A new model that takes into account the buckling kinetic was developed to describe this competition between the buckling modes.

As cisteíno-proteases da família da papaína desempenham funções essenciais em processos biológicos, entre eles o desenvolvimento e crescimento do organismo, vias de sinalização celular e apoptose, invasão de parasitas em células hospedeiras. Assim, trata-se de uma classe de proteínas de grande interesse para as indústrias farmacêuticas, sendo utilizada como alvo para o tratamento de doenças como o câncer e metástases, osteoporose. Disfunções relacionadas ao sistema imune, doenças parasitárias como malária, leishmaniose, doença do sono e doença de Chagas. Esta última é uma enfermidade considerada negligenciada pelas grandes indústrias farmacêuticas, sem nenhum tratamento eficaz e seguro disponível, que gera um problema econômico de mais de sete bilhões de dólares anuais devido à perda de mão de obra e gastos com tratamento para amenizar os efeitos da doença. A cisteíno protease cruzaína de Trypanosoma cruzi, causador da Doença de Chagas, desponta como um alvo validado na busca de novos fármacos contra essa enfermidade. Essa enzima apresenta um par de aspartatos que interagem entre si, para os quais foi predito um pKa de 7, sendo possível a forma desprotonada desse par em condições biológicas. Neste caso, pode levar à exposição de uma nova cavidade por meio do movimento da alça entre os resíduos 57-62, segundo as simulações de dinâmica molecular desse trabalho, que se trata de uma possível candidata a ponto de seletividade de inibidores de cisteínoproteases de parasitos em relação às suas ortólogas em Homo sapiens que não possuem o par de aspartatos. Em pH ácido, foi mostrado por meio de análise de componentes principais de simulações de dinâmica molecular que as cisteíno protease apresentam uma restrição gradual na amostragem conformacional do sítio ativo quando complexadas com as formas não covalente e covalente de inibidores derivados de dipeptidil nitrilas. Isso sugere que esse sistema segue o modelo de seleção conformacional para flexibilidade de proteína. Notou-se também que o perfil de restrição de ligantes que inibem na faixa de nmol.L-1 difere daqueles a µmol.L-1 , o que possibilitou a construção de uma árvore de decisão para identificar os complexos que apresentam afinidade a nmol.L-1 . / The papain-like cysteine proteases are essentials for biological process, performing important roles on the parasite development, growth and also in the parasite invasion process on the host cell, in cellular signaling pathways and apoptosis, among others. Thus, the pharmaceutical industry widely uses this class of protein as target for the development of new drugs, against cancer and metastasis, osteoporosis and immune system disorders, resulting in many approved drugs. Additionally, these enzymes are validated target against parasitic diseases as leishmaniose, malaria and African and American trypanosomiasis. The last one, also known as Chagas\' disease, is neglected disease for which, further a century form this discovery, there is no effective and safe chemotherapy and is responsible for an economic loss of around seven billion dollars in the world per year due to the health care and lost productivity from infected people. Faced with this situation, the Cruzain, a cysteine protease from the Trypanosoma cruzi, the causative agent of Chagas\' disease, is emerging as interesting and validated target to the search for new drugs against this sickness. This enzyme has a pair of interactiong Asp for which was predicted a pKa of 7, by computational methods. By this way, this pair under neutral to alkaline pH adopts the deprotonated form, which exposed a new cavity through a movement of loop of residues 57-62, as we showed here by molecular dynamics simulations. This cavity emerges as a possible selectivity point of the cruzain inhibitors, once Homo sapiens enzynes does not present the aspartic acid - aspartate pair. In condition of acidic pH, principal component analysis of molecular dynamics simulations showed a gradual reduction of the conformational space covered by the active site of cruzain, cathepsin K and cathepsin L in it free form and complexed with dipeptidyl nitrilelike molecules in it noncovalent e covalent forms. This suggests these systems follows the conformational selection model of protein flexibility. Furthermore, we observed the ligands that inhibits the protein at nmol.L-1 induces the protein flexibility in a similar way, while the µmol.L-1 ones leads to another pattern. That made possible the construction of a decision tree which is able to identify nmol.L-1 from µmol.L-1 complexes.

As alquilfosfocolinas (APC) são uma classe de fármacos derivados de fosfolipídios endógenos que apresentam potencial antitumoral. Diferentemente de outros fármacos antitumorais que agem no DNA da célula, as APCs têm como primeiro local de ação a membrana plasmática e proteínas de sinalização, como a PKC. O objetivo desse trabalho é elucidar, através de metodologias computacionais, os possíveis mecanismos de ação das APCs que provocam hemólise, inibição da PKC e interação com membranas celulares. Inicialmente, a toxicidade de um conjunto de 34 APCs foi estudada pelos métodos quimiométricos de Análise de Agrupamentos Hierárquicos (HCA) e Componentes Principais (PCA). As moléculas foram simuladas com dinâmica molecular (DM) e propriedades físico-químicas e estruturais foram calculadas para os confôrmeros de menor energia. Após aplicação de HCA e PCA, as APCs foram divididas em 3 grupos, de acordo com suas características estruturais. Os resultados sugerem que a presença de grupos catiônicos volumosos, ou anéis como adamantila e ciclohexila, aumentam a hemólise de compostos de cadeia alquílica longa. Anéis macrocíclicos como ciclopentadecila parecem ser importantes para o potencial hemolítico de compostos com cadeia alquílica curta. Com relação a compostos sem anéis e de cadeia linear, grupos catiônicos menos volumosos parecem favorecer a hemólise. Na próxima etapa do estudo, 7 derivados de APC, com diferentes grupos catiônicos, foram selecionados e ancorados no domínio C2 da PKC&#945;. O intuito foi mapear resíduos de aminoácidos importantes para a interação dos ligantes com a enzima, e comparar com o modo de ligação do ativador endógeno fosfatidilserina (PS). Mais uma vez, HCA e PCA foram aplicados para extrair informação relevante do mapeamento. Os resultados mostraram que as cadeias laterais de Pro188, Asn189, Arg216, Trp247, Asp249 e Thr250 não permitem a aproximação adequada do ligante, o que impede que a porção fosforila se coordene com um dos átomos de cálcio. A porção catiônica da PS, em contrapartida, consegue estabelecer ligação-hidrogênio com Asn189 de forma a posicionar os oxigênios da fosforila para interagir, ao mesmo tempo, com o átomo de cálcio. Com menos pontos de coordenação, a afinidade de ligação do cálcio pela PKC&#945; diminui e a ativação da enzima fica comprometida, interrompendo toda a cascata de sinalização que depende dela. A parte final desse trabalho se dedicou ao estudo da interação da miltefosina com diferentes bicamadas lipídicas sob o ponto de vista termodinâmico. Oito bicamadas de diferentes fosfolipídios foram simuladas por DM e a interação energética da miltefosina foi calculada por Umbrella Sampling. Os resultados mostraram que a miltefosina apresenta maior partição em bicamadas contendo colesterol, sendo a miscibilidade nesses sistemas cerca de 76 vezes maior que os valores encontrados para bicamadas sem colesterol. Além disso, verificou-se que a internalização da miltefosina é mais fácil em regiões contendo lipídeos poli-insaturados, provavelmente devido ao empacotamento mais frouxo da bicamada. Os dados sugerem que a miltefosina age principalmente em rafts lipídicos e que células contendo mais lipídicos poli-insaturados podem incorporar maior quantidade do fármaco. / Alquilfosfocolines (APCs) comprise a class of drugs with antitumor activity derived from endogenous phospholipids. Differently from other drugs whose primary site of action is the DNA, APCs act firstly in the plasma membrane and signaling proteins, such as PKC. The main objective of this work is to elucidate, via computational approaches, the possible mechanisms of actions that cause hemolysis, PKC inhibition and interaction with cellular membranes. Initially, a set of 34 APCs was studied by means of Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA). The molecules were simulated by means of molecular dynamics simulations (MD) and molecular and structural properties were calculated for the lowest-energy conformer. After HCA and PCA methodologies, the set was divided into 3 groups according to their structural features. The findings suggest that the presence of bulky cationic moieties, or the adamantyl and cyclohexil rings, increase the hemolytic potential of compounds with long alkyl chains. Macrocyclic rings, such as cyclopentadecyl, seem to be important to elevate the hemolysis of compounds with short alkyl chains. Regarding linear carbon chain derivatives with no ring substitution, less bulky cationic head groups seem to favor hemolysis. In the next step of this work, 7 APC derivatives were selected and docked in the C2 domain of PKC&#945;. The aim now was to map the residues relevant for ligands interaction compared to the binding mode of the endogenous activator, phosphatidylserine (PS). HCA and PCA were again applied in order to extract relevant information from the mapping. The results showed that the lateral chains of Pro188, Asn189, Arg216, Trp247, Asp249 and Thr250 do not allow the proper approximation of the ligands, impeding the phosphoryl moiety from coordinating with one of the calcium atoms. On the other hand, the cationic moiety of PS forms hydrogen-bonding with Asn189 in order to position the oxygens to interact, at the same time, with a calcium atom. With less coordination sites, calcium binding affinity diminishes and the enzyme activation is compromised, interrupting the signaling cascade. The final part of this work was dedicated to the study of miltefosine interaction with different lipid bilayers from the thermodynamics standpoint. Eight bilayers were simulated with MD and the energetic interaction was calculated via Umbrella Sampling simulations. The findings showed that miltefosine has higher partition in bilayers containing cholesterol, with miscibility of about 76 times higher than the values referring to bilayers without cholesterol. Moreover, it was observed that the internalization of miltefosine is facilitated in regions containing polyunsaturated lipids, probably due to the looser packing. The data suggest that miltefosine acts primarily in lipid rafts, and that cells containing more polyunsaturated lipids in their membranes can incorporate higher quantities of this drug.