Molecular dynamics simulations of the liquid crystal phases of 2-(4-butyloxyphenyl)-5-octyloxypyrimidine (2PhP) and 5-(4-butyloxyphenyl)-2-octyloxy-pyrimidine (5PhP) are the focus of this thesis. The 2PhP and 5PhP mesogens display different liquid crystalline phase sequences, despite having very similar molecular structures. Specifically, both mesogens consist of aromatic phenyl and pyrimidine cores in between two flexible alkoxy tails, but they differ in the preferred core conformation. A multi-site coarse-grained model, in which the aromatic rings are represented by soft quadrupolar ellipsoids and the alkoxy chains are given a united atom representation, is proposed in this thesis. A parameterization route for the intra- and intermolecular potentials appropriate for liquid crystal simulations is developed. The ab initio based derivation of suitable molecular models for the two mesogens is discussed in detail, with particular emphasis on capturing proper phenyl-pyrimidine interactions which proved to be essential to correctly represent core-core interactions between neighboring molecules. A systematic determination of suitable Gay-Berne (GB) parameters has been adopted for the aromatic rings of 2PhP and 5PhP. To account for the pi-electron cloud below and above the ring plane, a quadrupole was added perpendicular to the ring. In the end, four parameterizations for aromatic rings have been selected for the simulations. Model characterization via pair interactions proved to be valuable in identifying and analyzing the short range structure in the phases. Extensive molecular dynamics simulations of these fluids at various temperatures are performed. Intermolecular structure and order, in aromatic core and the flexible tail regions, are analyzed. Intermolecular structure is divided into contributions parallel and perpendicular to the layers, as indicated by a layer normal or by a director, to differentiate smectic A (SmA) from smectic C (SmC). The presence of a ring quadrupole in the molecular model is shown to be essential to the correct reproduction of the experimentally observed phases. Simulations correctly indicate phases in agreement with experiment: SmC and SmA phases for 2PhP, and only a SmA phase for 5PhP. / Thesis (Ph.D, Chemistry) -- Queen's University, 2009-10-27 20:23:37.89

No description available.

We conduct a comprehensive and systematic study of the Fermi-Pasta-Ulam (FPU) model using both equilibrium and non-equilibrium molecular dynamics simulations, with the aim being to explain the cause of the anomalous energy-transport behaviour in the model. In the equilibrium scenario, our motivation stems from the lack of a complete understanding of the effects of initial conditions on the energy dissipation among Fourier modes. We also critically reconsider the ????probes' that had been widely used to quantitatively describe the types of energy sharing in a system, and then decide on a preferred choice to be used in our equilibrium study. We establish, from strong numerical evidence, that there exists a critical energy density of approximately 0:1, above which the energy dissipation among the modes becomes independent of initial conditions and system parameters, and that the full equipartition of mode energy is never attained in the FPU model. We report, for the first time, the violation of particle positions in the FPU model at high energies, where the particles are found to pass through one another. In the non-equilibrium scenario, we critically review the Nos???Se-Hoover algorithm thermostatting method largely used by other works, and identify its weaknesses. We also review some other alternative methods and decide on the most appropriate one to be implemented throughout our work. We confirm the divergence of the thermal conductivity of the FPU model as the chain length increases, and that kfpu [symbol] No.41, in agreement with other works. Our study further shows that there exists an upper limit of the anharmonicity in the FPU model, and that any attempt to increase the strength of this anharmonicity will not succeed. We also introduce elastic collisions into the original FPU model and find that the Modified model (FPUC) still exhibits anomalous thermal conductivity. We conclude that a one-dimensional FPU-type model with ????only' nearest-neighbour interaction, regardless of being soft or hard, does not exhibit a finite thermal conductivity as the system size increases, due to the non-chaotic nature of its microscopic dynamics, the origin of which we are unable to account for. Finally, we briefly outline possible research directions.

CAMARÃO, Diego de Lucena. Propriedades difusivas de sistemas clássicos confinados. 2011. 79 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2011. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-04-28T21:29:36Z No. of bitstreams: 1 2011_dis_dlcamarao.pdf: 2441556 bytes, checksum: ff4cb229929b646cece7ef667144d79d (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-04-29T17:54:40Z (GMT) No. of bitstreams: 1 2011_dis_dlcamarao.pdf: 2441556 bytes, checksum: ff4cb229929b646cece7ef667144d79d (MD5) / Made available in DSpace on 2015-04-29T17:54:41Z (GMT). No. of bitstreams: 1 2011_dis_dlcamarao.pdf: 2441556 bytes, checksum: ff4cb229929b646cece7ef667144d79d (MD5) Previous issue date: 2011 / Nesta dissertação, fizemos um estudo das propriedades difusivas de um sistema de partículas clássicas carregadas em canais quasi-unidimensionais. Mais especificamente, no Capítulo 2, apresentamos uma revisão do problema da difusão e do movimento browniano. Mostramos que as abordagens de Einstein e de Langevin para o movimento browniano são equivalentes no limite de tempos longos. Isto foi feito através do cálculo analítico do deslocamento quadrático médio (MSD) de um sistema unidimensional de N partículas não--interagentes através da solução da equação de difusão. No Capítulo 3, introduzimos o método de Dinâmica Molecular (DM), amplamente utilizado em simulações computacionais de sistemas de N partículas clássicas. Apresentamos dois métodos de integração numérica das equações de movimento: o algoritmo de Verlet e o algoritmo leapfrog. Abordamos brevemente o método de Dinâmica Molecular de Langevin (DML), que inclui um termo de flutuações térmicas (força estocástica), devido às colisões das moléculas do fluido com as partículas do sistema. Finalmente, apresentamos uma aproximação do método de DML chamada Dinâmica Browniana (DB). No Capítulo 4, estudamos as propriedades difusivas, através da análise do deslocamento quadrático médio, de um sistema de partículas clássicas carregadas sujeitas à ação de um potencial de confinamento unidimensional, analisando a transição do regime de difusão em linha (SFD) para o regime de difusão bidimensional (2D). Vimos como ocorre essa transição em função dos parâmetros que regulam o potencial de confinamento. Discutimos a validade dos resultados numéricos obtidos em relação a resultados analíticos teóricos encontrados na literatura. Finalmente, no Capítulo 5, apresentamos um resumo dos resultados obtidos, bem como discutimos perspectivas e sugestões para futuros trabalhos.

Orientador: Munir Salomão Skaf / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-21T17:39:27Z (GMT). No. of bitstreams: 1 daSilva_JulioCesarAraujo_D.pdf: 43361733 bytes, checksum: 212cdef85174d1daf286133ff839cfb2 (MD5) Previous issue date: 2012 / Resumo: Receptores de androgênio (AR) são membros da superfamília de receptores nucleares que incluem os receptores de esteroides, entre outros. O AR liga os esteroides sexuais endógenos diidrotestosterona e testosterona. O desenvolvimento normal do fenótipo masculino e do sistema reprodutivo necessita de ações pré- e pósnatais promovidas pela interação do AR com esses hormônios. Mutações no gene do receptor de androgênio podem levar a várias doenças como o câncer de próstata e a síndrome de insensibilidade ao androgênio (AIS). Substituições diferentes no mesmo resíduo de aminoácido podem resultar em impactos variáveis na atividade do receptor levando a diferentes graus de AIS. Um grande número de mutações tem sido reportado para o AR envolvendo AIS e células tumorais de câncer de próstata e sua localização e função podem ajudar a entender como essas doenças devem ser tratadas. Entretanto, pouco se sabe sobre como as mutações mudam a estrutura e a dinâmica do AR, uma vez que apenas poucas estruturas cristalográficas de mutantes foram obtidas. Neste trabalho, apresentamos estudos de simulação de dinâmica molecular de algumas estruturas do AR humano com mutações localizadas no domínio de ligação do ligante (LBD) em comparação com a estrutura nativa complexadas com o ligante sintético metiltrienolona (R1881). Nosso objetivo é investigar as bases moleculares das mudanças sutis no receptor causadas pelas mutações que afetam sua afinidade pelo ligante R1881. Embora nenhum dos resíduos mutados deste estudo interajam diretamente com o ligante, os resultados das simulações indicaram que as mutações causam mudanças estruturais e dinâmicas no AR-LBD na região onde se localiza a mutação e na cavidade de ligação do ligante (LBP). A principal mudança observada foi o deslocamento do resíduo Arg752, facilitando a entrada de moléculas de água no LBP e o reposicionamento de cadeias laterais dos resíduos do domínio F, uma importante região que contribui para a estabilidade da estrutura do AR-LBD e da conformação ativa da hélice 12. Os resultados obtidos mostram que essas mutações, que ocorrem naturalmente, são exemplos de resíduos que não estão em contato direto com o ligante e não pertencem à região de recrutamento do coativador, mas que possuem um importante papel na ligação do ligante e na ativação do receptor por estabilizar a hélice 12 e o domínio F na conformação ativa / Abstract: Androgen receptors (AR) are members of the superfamily of nuclear receptors that includes the steroid receptors, among others. AR binds the male endogenous sex steroids, dihydrotestosterone and testosterone. Normal development of the male phenotype and reproductive system requires pre- and postnatal actions promoted by AR interaction with these hormones. Mutations in the androgen receptor gene may lead to several diseases like prostate cancer (PCa) and the androgen insensitivity syndrome (AIS). Different substitutions at the same amino acid residue may result in variable impact on the activity of the receptor leading to different degrees of AIS. A number of mutations have been reported for the AR in AIS and PCa tumor cells and their location and function may help us to understand how these diseases should be treated. Nevertheless, not much is known about how the mutations change the structure and dynamics of the AR since only a few crystallographic structures of mutants were obtained. In this work we present molecular dynamics simulation (MD) studies of some human AR mutations located in the ligand binding domain (LBD) in comparison with wild type (WT) structure in complex with the synthetic ligand methyltrienolone (R1881). Our goal is to investigate the molecular basis of subtle changes in the receptor caused by mutations in the AR-LBD/R1881 affinity. Although the mutated residues do not interact with the ligand, the simulations results indicated that the mutants cause structural and dynamical changes in the AR-LBD in the region in which the mutation is placed and in the binding pocket (LBP). The principal change observed was the displacement of residue Arg752, facilitating water penetration in LBP, and the repositioning of F-domain side chains, which makes important contributions to the stability of the AR-LBD structure and helix 12 active conformation. The results obtained show that these naturally occurring mutations are examples of residues that are not in contact with the ligand and do not belong to coactivator recruitment region, but which do have an important role in ligand binding and receptor activation by stabilizing the helix H12 and the F-domain in the active conformation / Doutorado / Físico-Química / Doutor em Ciências

The intrinsic plasticity of biological systems provides opportunities for rational design of selective and potent ligands. Increasingly, computational methods are being applied to predict biomolecular flexibility. However, the motions involved in these processes can be large and occur on time scales generally difficult to achieve with standard simulation methods. In order to overcome the intrinsic limitations of classical molecular dynamics, this Ph.D. project focuses on the application of advanced sampling computational techniques to capture the plasticity of diverse biological systems. The first of these applications involved the evaluation of the secondary structure of the N-terminal portion of p53 and its inverse, reverse and retro-inverso sequences by using replica exchange molecular dynamics simulations in implicit solvent. In this study, we also evaluated the effects of reversal of sequence and stereochemistry in mimicking an inhibitory pharmacophoric conformation. The results showed how the ability to mimic the parent peptide is severely compromised by backbone orientation (for D-amino acids) and side-chain orientation (for reversed sequences). Moreover, the structural information obtained from simulations showed good agreement with NMR and circular dichroism studies, confirming the validity of the combination of replica exchange molecular dynamics with the ff99SB force field and Generalized Born solvent model for computational modelling of D-peptide conformations.In a second work, we explored conformations of the DFG motif of the p38α mitogen-activated protein (MAP) kinase. To achieve this, we employed an advanced sampling simulation method that has been developed in-house, called swarm-enhanced sampling molecular dynamics (sesMD). In contrast to multiple independent MD simulations, swarm-coupled sesMD trajectories were able to sample a wide range of DFG conformations, some of which map onto existing crystal structures. Simulated structures intermediate between DFG-in and DFG-out conformations were predicted to have druggable pockets of interest for structure-based ligand design. Overall, sesMD shows promise as a useful tool for enhanced sampling of complex conformational landscapes. Finally, we used microsecond MD simulations to evaluate the molecular plasticity of R-spondins, a class of proteins involved in the activation of the Wnt pathway. The unbound R-spondin 1 is characterised by a closed conformation, while, when complexed to proteins LGR and RNF43/ZNRF3, assumes an open and more extended arrangement. This is true also for R-spondin 2, in both its unbound or bound forms. From our simulation, we find that the closed R-spondin 1 conformation is stable, whilst, R-spondin 1 and 2 from their open conformation explore several intermediate structures. In addition, we evaluated the druggability of a potential binding site located at the interface between the second and the third β-hairpin moiety of the first furin domain. The computational screening with small molecular fragments provided interesting insights about the druggability and the pharmacophoric features of the potential binding pockets identified, outlining promising future perspectives of structure-based design of Wnt pathway inhibitors.

No description available.

<p>To achieving successfully commercial nuclear fusion energy, fully understanding of the interaction between plasma particles and plasma facing components is one of the essential issues. Tungsten, due to good thermal and mechanical properties such as high thermal conductivity and melting temperature, is one of the most promising candidates. However, the plasma facing components interacting with the extreme environmental conditions such as high temperature and radiation may lead to nanostructure formation, sputtering and erosion that will lead to material degradation. And these deformations may influence not only properties of plasma facing components but also might affect the plasma itself. For example, the contamination of plasma with a few amounts of tungsten, a high Z element, as a result of erosion or sputtering may cause core plasma cooling that results in loss of plasma confinement. Additionally, the retention of hydrogen isotopes, especially tritium, in tungsten is essential issue because of its radioactivity and market value.</p> In this study, deuterium trapping in tungsten is analyzed by molecular dynamics method and the effect of pre-irradiation on trapping is studied. Non-cumulative studies show that the increase in the energy of hydrogen isotopes rises the absorption rate, the initial implantation depth, and the average resting time for initial implantation. Additionally, the effect of implanted deuterium due to pre-irradiation on the hydrogen isotopes trapping is analyzed by combining both cumulative and non-cumulative simulations, and results indicate that while the increase in the pre-irradiation time raises the absorption rate of deuterium with higher energy than 80 eV, it causes a decrease the initial implantation depth and the average resting time for initial implantation because of deuterium-deuterium interactions. Additionally, the deuterium-deuterium interactions may transfer enough energy to implanted deuterium to start a motion which may lead to deeper implantation or escaping from the surface of tungsten. The escaping from surface as a result of deuterium-deuterium interaction could explain the decrease in accumulation rate of deuterium while absorption rate rises.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Misregulation of protein signaling pathways is the basis for many human diseases, and thus 95% of Food and Drug Administration approved drugs target proteins. Proteins are dynamic entities which can undergo transitions to reach different conformational states. The conformational state of a protein, or its three-dimensional shape, is intricately linked to functions, such as association with endogenous or exogenous binding partners, or catalysis. Thus, it is of interest to the pharmacological community to understand the mechanisms of protein conformational state transitions in order to better target and control protein functions. In two case studies, I show the importance of understanding protein dynamics in protein function and drug design. In the case of human immunodeficiency virus-1 (HIV-1) protease, a tremendous “open-and-closed” conformational transition is revealed by Molecular Dynamics Simulations (MDS). Through observing the dramatic difference in effectiveness of two Darunavir inhibitor derivatives differentiated by a single atom at locking the protease in the closed conformation, we discovered the residues and mechanism that lead to the protease’s conformational transition. This mechanism also explained the significant difference in the binding conformation and binding affinity of these two inhibitors. This study provides insight on how to improve the potency and anti-viral capacity of these compounds. In the second case study, MDS enabled us to observe the conformational transitions of a family of seven isoforms known as the 14-3-3 proteins. Many vital cellular processes involve all or select 14-3-3 isoforms, making this family very difficult to target. Through MDS, I discovered different conformational samplings among these 14-3-3 isoforms which were then validated by SAXS. Subsequently, a FRET-based ligand binding assay was developed which can screen for preferential 14-3-3 isoform binding of endogenous ligands, giving hope that using conformations unique to a 14-3-3 isoform of interest can provide a method for selective drug design. / 2022-03-09