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Dissertations / Theses on the topic 'Monte Carlo; Molecules; Ligands'
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Parretti, Martin Frank. "Molecular similarity : alignment and advanced applications." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325831.
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Lecina, Casas Daniel. "Studying protein-ligand interactions using a Monte Carlo procedure." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/459297.
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Biomolecular simulations have been widely used in the study of protein-ligand interactions; comprehending the mechanisms involved in the prediction of binding affinities would have a significant repercussion in the pharmaceutical industry. Notwithstanding the intrinsic difficulty of sampling the phase space, hardware and methodological developments make computer simulations a promising candidate in the resolution of biophysically relevant problems. In this context, the objective of the thesis is the development of a protocol that permits studying protein-ligand interactions, in view to be applied in drug discovery pipelines.
The author contributed to the rewriting PELE, our Monte Carlo sampling procedure, using good practices of software development. These involved testing, improving the readability, modularity, encapsulation, maintenance and version control, just to name a few. Importantly, the recoding resulted in a competitive cutting-edge software that is able to integrate new algorithms and platforms, such as new force fields or a graphical user interface, while being reliable and efficient. The rest of the thesis is built upon this development.
At this point, we established a protocol of unbiased all-atom simulations using PELE, often combined with Markov (state) Models (MSM) to characterize the energy landscape exploration. In the thesis, we have shown that PELE is a suitable tool to map complex mechanisms in an accurate and efficient manner. For example, we successfully conducted studies of ligand migration in prolyl oligopeptidases and nuclear hormone receptors (NHRs). Using PELE, we could map the ligand migration and binding pathway in such complex systems in less than 48 hours. On the other hand, with this technique we often run batches of 100s of simulations to reduce the wall-clock time. MSM is a useful technique to join these independent simulations in a unique statistical model, as individual trajectories only need to characterize the energy landscape locally, and the global characterization can be extracted from the model. We successfully applied the combination of these two methodologies to quantify binding mechanisms and estimate the binding free energy in systems involving NHRs and tyorsinases. However, this technique represents a significant computational effort.
To reduce the computational load, we developed a new methodology to overcome the sampling limitations caused by the ruggedness of the energy landscape. In particular, we used a procedure of iterative simulations with adaptive spawning points based on reinforcement learning ideas. This permits sampling binding mechanisms at a fraction of the cost, and represents a speedup of an order of magnitude in complex systems. Importantly, we show in a proof-of-concept that it can be used to estimate absolute binding free energies.
Overall, we hope that the methodologies presented herein help streamline the drug design process.Las simulaciones biomoleculares se han usado ampliamente en el estudio de interacciones proteína-ligando. Comprender los mecanismos involucrados en la predicción de afinidades de unión tiene una gran repercusión en la industria farmacéutica. A pesar de las dificultades intrínsecas en el muestreo del espacio de fases, mejoras de hardware y metodológicas hacen de las simulaciones por ordenador un candidato prometedor en la resolución de problemas biofísicos con alta relevancia. En este contexto, el objetivo de la tesis es el desarrollo de un protocolo que introduce un estudio más eficiente de las interacciones proteína-ligando, con vistas a diseminar PELE, un procedimiento de muestreo de Monte Carlo, en el diseño de fármacos. Nuestro principal foco ha sido sobrepasar las limitaciones de muestreo causadas por la rugosidad del paisaje de energías, aplicando nuestro protocolo para hacer analsis detallados a nivel atomístico en receptores nucleares de hormonas, receptores acoplados a proteínas G, tirosinasas y prolil oligopeptidasas, en colaboración con una compañía farmacéutica y de varios laboratorios experimentales. Con todo ello, esperamos que las metodologías presentadas en esta tesis ayuden a mejorar el diseño de fármacos.
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Cabeza, de Vaca López Israel. "Mapping biophysics through enhanced Monte Carlo techniques." Doctoral thesis, Universitat Politècnica de Catalunya, 2015. http://hdl.handle.net/10803/334172.
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This thesis is focused on the study of molecular interactions at the atomistic detail and is divided into one introductory chapter and four chapters referencing different problems and methodological approaches. All of them are focused on the development and improvement of computational Monte Carlo algorithms to study, in an efficient manner, the behavior of these systems at a classical molecular mechanics level. The four biophysical problems studied in this thesis are: induced fit docking between protein-ligand and between DNA-ligand to understand the binding mechanism, protein stretching response, and generation/ scoring of protein-protein docking poses.
The thesis is organized as follows: First chapter corresponds to the state of the art in computational methods to study biophysical interactions, which is the starting point of this thesis. Our in-house PELE algorithm and the main standard methods such as molecular dynamics will be explained in detail. Chapter two is focused on the main PELE modifications to add new features, such as the addition of a new force field, implicit solvent and an anisotropic network specific for DNA simulation studies. We study, compare and validate the conformations generated by six representative DNA fragments with the new PELE features using molecular dynamics as a reference.
Chapter three is devoted to applying the new methods implemented and tested in PELE to study protein-ligand interactions and DNA-ligand interactions using four systems. First, we study the porphyrin binding to Gun4 protein combining PELE and molecular dynamics simulations. Besides, we provide a docking pose that has been corroborated by a new crystal structure published during the revision process of the submitted study showing the accuracy of our predictions. In the second project, we use our improved version of PELE to generate the first structural model of an alpha glucose 1,6-bisphosphate substrate bound to the human Phosphomannomutase 2 demonstrating that this ligand can adopt two low-energy orientations.
The third project is the study of DNA-ligand interactions for three cisplatin drugs where we evaluate the binding free energy using Markov state models. We show excellent results respect another free energy methods studied with molecular dynamics. The last project is the study of the daunomycin DNA intercalator where we simulate and study the binding process with PELE. Chapter four is focused on the computational study of force extension profiles during the protein unfolding. We added a dynamic harmonic constraint following a similar procedure applied in steered molecular dynamics to our Monte Carlo approach to fix or pull some selected atoms forcing the protein unfolding in a defined direction. We implement and compare with steered molecular dynamics this technique with Ubiquitin and Azurin proteins. Moreover, we add this feature to a well-known algorithm called MCPRO from William Jorgensen¿s group at YALE University to evaluate the free energy associated to the unfolding of the deca-alanine system.
Chapter five corresponds to the introduction of a multiscale approach to study protein-protein docking. A coarse-grained model will be combined with a Monte Carlo exploration reducing the degrees of freedom to generate thousands of protein-protein poses in a quick way. Poses produced by this procedure will be refined and ranked through a protonation, hydrogen bond optimization, and minimization protocol at the all-atom representation to identify the best poses. I present two test cases where this procedure has been applied showing a good accuracy in the predictions: tryptogalinin and ferredoxin/flavodoxin systems.Aquesta tesi es centra en l'estudi de les interaccions moleculars amb detall atomic i es divideix en un capítol d'introducció i quatre capítols que fan referència a diferents problemes i enfocaments metodològics. Tots ells se centren en el desenvolupament i millora dels algoritmes computacionals de Monte Carlo per estudiar, de manera eficient, el comportament d'aquests sistemes a un nivell mecànica molecular clàssica. Els quatre problemes biofísics estudiats en aquesta tesi són: acoblament induït entre la proteïna-lligand i entre DNA-lligant per comprendre el mecanisme d'unió, resposta de les proteïnes a l'estirament, i la generació/puntuació d'acoblament entre poses proteïna-proteïna. La tesi s'organitza de la següent manera: El primer capítol correspon a l'estat de l'art en mètodes computacionals per estudiar les interaccions biofísiques, que és el punt de partida d'aquesta tesi. El nostre PELE algoritme i els principals mètodes estàndard com ara la dinàmica molecular s'explicaran en detall. El capítol dos es centra en les principals modificacions PELE per afegir noves característiques, com ara l'addició d'un nou camp de força, solvent implícit i modes normals per aquests estudis de simulació d'ADN. Es fa un estudi, comparació i validació de les conformacions generades per sis fragments d'ADN representatius amb PELE utilitzant dinàmica molecular com a referència. El tercer capítol està dedicat a l'aplicació dels nous mètodes implementats i provats en PELE per estudiar les interaccions proteïna-lligand i la interacció lligand-DNA utilitzant quatre sistemes. En primer lloc, se estudia la unió a proteïnes GUN4 combinant PELE i simulacions de dinàmica molecular. A més, es proposa un acoblament que ha sigut corroborat per una nova estructura cristal·lina publicada durant el procés de revisió de l'estudi mostrant l'exactitud de les nostres prediccions. En el segon projecte, hem utilitzat la nostra versió millorada de PELE per generar el primer model estructural d'una glucosa alfa substrat 1,6-bisfosfat unit a la fosfomanomutasa humana 2, que demostra que aquest lligant pot adoptar dues orientacions de baiza energia. El tercer projecte és l'estudi de les interaccions d'ADN lligant per tres medicaments cisplatí on se avalua l'energia lliure d'unió utilitzant Markov States Models. Es mostren excel·lents resultats respecte d'altres mètodes d'energia lliure estudiats amb dinàmica molecular. L'últim projecte és l'estudi de l'intercalador d'ADN anomenat daunomicina on es simula i estudia el procés d'unió amb PELE. El capítol 4 es centra en l'estudi computacional dels perfils d'extensió de la força durant el desplegament de la proteïna. Hem afegit una restricció harmònica dinàmica seguint un procediment similar al aplicat en dinàmica molecular en el nostre algoritme Monte Carlo per fixar o moure alguns àtoms seleccionats obligant a desplegar la proteïna en una direcció definida. Aquesta tècnica s'ha implementat i comparat amb dinàmica molecular per les proteïnes ubiquitina i azurin. D'altra banda, hem afegit aquesta modificació a un algoritme ben conegut anomenat MCPRO del grup de William Jorgensen a la Universitat de Yale per avaluar l'energia lliure associada al desplegament del sistema deca alanina. El capítol cinc correspon a la introducció d'un enfocament multiescala per estudiar l'acoblament proteïna-proteïna. Un model de gra gruixut es combinat amb una exploració Monte Carlo per reduir els graus de llibertat i generar milers de poses proteïna-proteïna d'una manera ràpida. Les poses produides per aquest procediment es perfeccionan i evaluan a través d'una protonació, optimització d'enllaços d'hidrogen, i minimització a escala atòmica per identificar les millors poses. Es presenten dos casos de prova on s'ha aplicat aquest procediment que mostra una bona precisió en les prediccions: tryptogalinin i ferredoxina / flavodoxina systems.
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Lin, Fei Berlinsky A. J. Kallin C. Sørensen Erik S. "A quantum Monte Carlo study on the fullerene molecules and solids." *McMaster only, 2006.
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Parker, S. D. "Monte Carlo modelling of Case I and Case II solvent diffusion in polymers." Thesis, University of Surrey, 1999. http://epubs.surrey.ac.uk/843853/.
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The development of two original Monte Carlo models of solvent diffusion into a polymer is described. Employing a coarse grained model of a polymer solution on a regular lattice, the dynamic properties of both the solvent and polymer molecules can be observed. The "Simple" Monte Carlo model reliably reproduces Case I dynamics, but no departure from this is seen for any reasonable model parameters. This "Simple" Monte Carlo model is unable to reproduce Case II diffusion dynamics. One reason for this is that in this Monte Carlo model the processes of solvent diffusion and polymer relaxation are entirely independent processes. In this thesis it is suggested that a simple Monte Carlo model of this type will always produce Case I diffusion dynamics. The dynamic algorithm described in this work relies on simple instantaneous molecular motions between neighbouring lattice sites. It is shown that a diffusion process based on these motions is purely concentration dependent, relying only on the current state of the system. To use the Monte Carlo method to simulate Case II diffusion dynamics, the diffusion process is made time dependent by incorporating a history dependent model of diffusion first proposed by Crank (CRANK 1953). In this "History Dependent" Monte Carlo model the motions of both the solvent and the polymer are no longer instantaneous, but occur at a rate that approaches equilibrium by a first order process governed by a relaxation time characteristic of the viscoelastic relaxation of the polymer. This "History Dependent" Monte Carlo model successfully simulates most of the features of Case II diffusion and also demonstrates a return to Case I diffusion in the limit of long times. Unlike many models of Case II diffusion, this Monte Carlo model is able to simultaneously model the microscopic motions of both the solvent and the polymer molecules. This novel feature demonstrates the formation of a discontinuous moving boundary between the rubbery polymer and the glassy polymer that is typical of Case II diffusion dynamics.
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Lin, Haiping. "Simulations of chiral ordering of achiral molecules by Density Functional Theory and Monte Carlo." Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490915.
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The self-organization of organic molecules on metal surfaces can play a crucial role in various subjects of science such as electrochemistry and heterogeneous catalysis. However, their practical applications have been suffering from lack of atomic scale understanding of the ordering behavior. Theoretically, however, the description of the self-assembly processes has been limited by the inability of microscopic models to account for the interplay of all elementary processes at realistic temperatures and pressures. In this work, we take the succinate molecules and Cu(1IO) surface as a model system to study the nature of the asymmetric self-assembly behavior of the achiral adsorbates on an achiral surface. In the first step, density-functional theory (DFT) is used to accurately characterize the molecule-surface system on the microscopic level. The obtained energetics is then employed to parameterize a lattice gas Hamiltonian, which subsequently allows to address the mesoscopic ordering behavior at finite temperatures by means of ~v1onte Carlo simulations. Two well-defined ordered structures have appeared in the rvlonte Carlo simulations. The (5 0, 3 2) structure has been confirmed to be the ground state configuration by direct DFT calculations. This structure has not been reported before and it can be the ordering configuration observed in some STrvI experiments. By summing up all the calculations, the nature of the self-organization behavior of succinate molecules on Cu(llO) is attributed to the indirect lateral interactions of the adsorbates. This result may provide a new understanding of designing two dimensional periodic architectures on metal surfaces. Supplied by The British Library - 'The world's knowledge'
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Suewattana, Malliga. "Monte Carlo simulations of ferroelectric crystal growth and molecular electronic structure of atoms and molecules." W&M ScholarWorks, 2005. https://scholarworks.wm.edu/etd/1539623487.
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In this thesis, we explore two stochastic techniques to study properties of materials in realistic systems. Specifically, the kinetic Monte Carlo (KMC) method is utilized to study the crystal growth process of ferroelectric materials and the quantum Monte Carlo (QMC) approach is used to investigate the ground state properties of atoms and molecules.;In the growth simulations, we study the growth rates and chemical ordering of ferroelectric alloys using an electrostatic model with long-range Coulomb interactions. Crystal growth is characterized by thermodynamic processes involving adsorption and evaporation, with solid-on-solid restrictions and excluding diffusion. A KMC algorithm is formulated to simulate this model efficiently in the presence of long-range interactions. The growth process is simulated as a function of temperature, chemical composition, and substrate orientation. We carried out the simulations on two heterovalent binaries, those of the NaCl and the Ba(Mg1/3Nb2/3))O3(BMN) structures. Compared to the simple rocksalt ordered structures, ordered BMN grows only at very low temperatures and only under finely tuned conditions. For materials with tetravalent compositions, such as (1-x)Ba(Mg 1/3Nb2/3))O3 + x BaZrO3 (BMN-BZ), the model does not incorporate tetravalent ions at low-temperature, exhibiting a phase-separated ground state instead. at higher temperatures, tetravalent ions can be incorporated, but the resulting crystals show no chemical ordering in the absence of diffusive mechanisms.;In the second part of the thesis, we present results from an auxiliary field quantum Monte Carlo (AFQMC) study of ground state properties, in particular dissociation and ionization energy, of second-row atoms and molecules. The method projects the many-body ground state from a trial wavefunction by random walks in the space of Slater determinants. The Hubbard-Stratonovich transformation is employed to decouple the Coulomb interaction between electrons. A trial wave function is used in the approximation to control the "phase problem". We also carry out Hartree-Fock (HF) and Density Functional Theory (DFT) calculations for comparison to AFQMC results and to serve as starting wavefunctions for our AFQMC calculations. Results of dissociation energy are in excellent agreement with experimental values. Ionization energy errors are somewhat larger than those of other methods. We conclude with a discussion of several possible sources of error as well as a direction for the improvement.
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Petit, Andrew S. "Monte Carlo Methods for the Study of the Ro-Vibrational States of Highly Fluxional Molecules." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1366136698.
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Cleland, Deidre Mary. "The initiator full configuration interaction quantum Monte Carlo method : development and applications to molecular systems." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610385.
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Ferrando, Nicolas. "Potentiels intermoléculaires et algorithmes de monte carlo : application à l'étude des composés oxygénés." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA112080/document.
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Ce travail de thèse a pour but de proposer des potentiels d'interaction et des méthodologies pour prédire, au travers de simulations Monte Carlo, les équilibres et propriétés de phases de systèmes oxygénés rencontrés dans les procédés de conversion de la biomasse. Le potentiel AUA4 a ainsi été étendu aux alcools, éthers, cétones, aldéhydes et esters carboxyliques. Une attention particulière a été portée à la transférabilité de ce champ de forces, afin de pouvoir simuler de manière prédictive un grand nombre de molécules oxygénées. Différentes propriétés d'équilibre de corps purs sont correctement prédites (masses volumiques, pressions de saturation, enthalpies de vaporisation, propriétés critiques, tensions de surface, structure de la phase liquide). De nombreux mélanges ont également été simulés dans le pseudo-ensemble point de bulle, qui a été étendu aux molécules polaires dans le cadre de ce travail. Les résultats de simulation de mélanges complexes comme des bioessences ont été validés par l'acquisition de nouvelles mesures expérimentales. Enfin, une nouvelle méthodologie pour le calcul des interactions électrostatiques intramoléculaires a été mise au point dans ce travail pour la simulation de molécules oxygénées multifonctionnelles (polyols, éthers de glycol, composés aromatiques oxygénés). L'utilisation de cette méthode, qui permet d'éviter l'emploi de paramètres empiriques additionnels, conduit à des résultats très encourageants, ce qui laisse entrevoir de nombreuses perspectives pour la prédiction de propriétés de mélanges industriels complexesThe goal of this thesis work is to propose interaction potentials and numerical methods to predict through Monte Carlo simulations the phase equilibrium and properties of oxygenated systems involved in biomass conversion processes. The AUA4 potential was therefore extended to alcohols, ethers, ketones, aldehydes and carboxylic esters. A special care was paid to the transferability of this force field to allow the predictive simulation of a large number of oxygenated compounds. Various equilibrium properties of pure compounds are correctly predicted (densities, saturation pressures, vaporization enthalpies, critical properties, surface tensions, liquid phase structure). Many mixtures have also been simulated in the bubble point pseudo-ensemble which was extended in this work to polar molecules. The simulation results of complex mixtures such as biofuels have been validated through new experimental data acquisition. Finally, a new methodology for the intramolecular electrostatic energy interaction has been developed in this work to simulate multifunctional oxygenated molecules (polyols, glycol ethers, oxygenated aromatic compounds). The use of this method, which allows to avoid the use of additional empirical parameters, leads to promising results, giving thus future opportunities to predict properties of complex mixtures of industrial interest
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Luukkonen, Sohvi. "Hydration of drug-like molecules with molecular density functional theory and the hybrid-4th-dimension Monte Carlo approach." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASF030.
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Le développement d’un médicament prend en moyenne plus de 10 ans pour un coût de 1 Mrd de dollars. Pour accélérer le processus et diminuer le coût, on utilise des méthodes in-silico lors de l’étape de découverte qui consiste à cribler ~10⁵ molécules de type médicament pour proposer quelques candidats à l’étape préclinique. Le critère majeur est l’affinité entre la molécule potentielle et la cible biologique. L’interaction se passant dans notre corps: cette affinité doit être prédite dans l’eau et le médicament doit être soluble dans l’eau pour avoir accès à la cible. Globalement, les effets de solvatation ont un rôle important dans la conception de médicaments. Numériquement, pour un champ de force donné, la solvatation peut être étudiée par des méthodes de simulation exactes mais coûteuses, par des modèles de continuum rapides mais qui ignorent la nature moléculaire du solvant, enfin par des théories des liquides approximatives mais capables de garder l’information moléculaire du solvant tout en diminuant le temps de calcul. L’objectif de cette thèse étant la prédiction des énergies libres d’hydratation (ELH) de molécules de type médicament par des méthodes qui soient les plus précises et plus rapides possibles, elle se concentre sur deux approches originales: Le Monte-Carlo hybride à 4ème dimension, une nouvelle méthode pour calculer les ELH selon le principe de Jarzynski à partir simulations courtes hors-équilibre pendant lesquelles on introduit ou retire le soluté doucement depuis le solvant avec un paramètre de couplage dépendant du temps. Nous montrons que cette approche est capable de prédire les ELH de molécules de type pharmaceutique 4-6 fois plus rapidement que l’approche classique de perturbation de l’énergie libre. La théorie de la fonctionnelle de densité moléculaire, une approche de théorie des liquides qui permet l’étude des propriétés de solvatation de n’importe quelle soluté rigide. Dans son état actuel, dans l’approximation hyper-netted-chain couplée à une correction de pression, nous montrons qu’elle est capable de prédire les ELH des mêmes molécules avec une précision de respectivement 0.5 ou 1.0 kcal/mol par rapport aux simulations ou aux données expérimentales, avec une accélération de calcul de l’ordre de 10³-10⁴ par rapport aux simulations. H4D-MC est considéré ici comme une source de références pour développer plus avant la MDFT, elle-même une méthode suffisamment rapide pour être envisagée dans un processus de criblage haut-débitThe development of a drug takes on average over 10 yr. for a cost of 1B dollars. To speed up the process, and reduce its cost, in-silico methods are used at the drug discovery stage. It consists of screening ~10⁵ drug-like molecules to propose few candidates to the pre-clinical stages. The main criterion is the affinity between the potential drug molecule and biological target. As the interaction happens the body, these affinities need to be predicted in water and the molecule needs to be water-soluble to access the receptor. Overall, solvation properties play an important role in drug design. Numerically, for a given force-field, solvation can be studied either with exact but time-consuming simulation methods, fast continuum models that lose the molecular nature of the solvent, or approximate liquid state theories that keep the solvent molecular information while speeding-up the computation. In this thesis, we focus on the prediction of the hydration free energies (HFE) of drug-like molecules with methods that are as fast and precise as possible, and we concentrate on two original approaches: Hybrid-4th-dimension Monte Carlo, a novel method that computes the HFEs according to the Jarzynski principle from short non-equilibrium simulations in which the solute is inserted or removed from the solvent with a time-depending coupling parameter. This approach is shown to predict the HFEs of drug-like molecules 4-6 times faster than the classical free energy perturbation approach. Molecular density functional theory, a liquid-state-theory approach that allows the study of the equilibrium solvation properties of any rigid solute. In its current level, the hyper netted-chain approximation coupled with a pressure correction, it is shown to predict the HFEs of drug-like molecules within 0.5 and 1.0 kcal/mol of simulations and experimental data, respectively, for an average computational speed-up 10³-10⁴ with respect to simulations. H4D-MC is considered here as a source of reference data for MDFT developments. MDFT is itself fast enough to be foreseen in a high-throughput screening pipeline
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Ayissi, Serge Olivier. "Simulation of chiral ordering process in the adsorption of chiral organic molecules on metal surfaces by Monte Carlo methods." Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490608.
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Experimental observations have shown that haloalkane molecules, e.g. l-cWorododecane, physisorbed on Si(111)-(7 x 7) self-assemble to form dimers stable to 100° C which corral silicon adatoms. The corral size is governed by the haloalkane chain-length. Spectroscopic and theoretical evidence shows that the haloalkane dimer induces electron transfer to the corralled adatom. The enclosed silicon adatom, within a bistable dimeric corral of self-assembled chlorododecane molecules, switches its energy levels permanently (Type-II corrals) or discontinuously (Type-I corrals). Both types of corral, switching and stable, can be seen to alter the local surface charge distribution. Density Functional Theory and electron transport (STM) simulations of the switch and the stable molecular configurations can help the theoretical understanding of both phenomena in order to characterized the exact molecular conformations that produce field effects to the corralled silicon adatom and local surface charge distribution. Chiral heterogeneous catalysts are mostly fabricated from chiral molecules on a metal support. They playa crucial role in intermediate reactions in the fabrication of pharmacies, itself and important part of today's health econolPY. However, the key parameters in the fabrication of these catalysts, a requirements for their rational design, are still poorly understood despite years of experimental research. In essence, such an understanding can only come from high-level simulations. Here, we present the first predictions about the structure of such a catalyst, tartaric acid on a copper support, over the whole phase space of temperature and coverage. Interestingly, we find that molecular vibrations playa key role in the ensuing ordered structures, and that tuning the fabrication temperature should allow for a wide range of molecular separations, which can be targeted at specific molecules and reactions in chiral heterogeneous catalysis.
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Michelon, Mateus Fontana. "Transições de fase em ligas substitucionais e líquidos polimórficos através de simulações atomísticas." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/277258.
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Orientador: Alex AntonelliTese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin
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Resumo: Um dos objetivos da simulação atomística na ciência dos materiais é calcular as propriedades de um material virtual e propor rotas para sua fabricação em laboratório. Uma das principais propriedades que o material deve apresentar antes de ser sintetizado é a estabilidade termodinâmica. Como a estabilidade é determinada pela energia livre, o cálculo preciso desta quantidade é de fundamental importância na construção de um laboratório virtual. Neste contexto, desenvolvemos uma metodologia alternativa para a determinação da energia livre de ligas substitucionais, que leva em conta os graus de liberdade vibracionais e configuracionais com precisão controlada. A metodologia utiliza o método de Monte Carlo para simular a dinâmica de trocas e vibrações atômicas e determina a energia livre através dos métodos de ligação adiabática e escalamento reversível. Além disso, a metodologia é capaz de avaliar a influência de mecanismos associados à entropia vibracional, através da relaxação sucessiva de vínculos na dinâmica. Especificamente, permite quantificar os mecanismos de a) proporção de ligações entre átomos distintos, b) discrepância entre volumes atômicos e c) relaxação volumétrica, e identificar a origem da diferença de entropia vibracional na transição ordem-desordem. Testamos e aplicamos a metodologia para estudar um modelo semiempírico da liga Ni3Al. Observamos um aumento da entropia vibracional na transição ordem-desordem comparável com o aumento da entropia configuracional e explicado pelo aumento de volume na transição. Outra característica de um laboratório virtual é possuir modelos que descrevam satisfatoriamente os sistemas de interesse. Investigamos um potencial do tipo tight-binding e descobrimos que não é transferível para descrever fenômenos de ordem-desordem em diversas ligas. Além de investigar o fenômeno ordem-desordem em ligas, estudamos transições de fase líquido-líquido em substâncias puras. Apresentamos uma evidência teórica de transição líquido-líquido de primeira ordem em um modelo semiempírico do gálio, fornecendo suporte a uma recente evidência experimental de transição líquido-líquido no regime super-resfriado deste elemento. Além disso, as simulações atomísticas sugerem um mecanismo microscópico para esta transição. Outras características de um laboratório virtual são a possibilidade de estudar sistemas em condições experimentais inacessíveis e a capacidade de propor novos experimentos. Neste contexto, apresentamos uma evidência teórica de transição líquido-líquido em um modelo ab initio para o dióxido de carbono. A transição ocorre entre um líquido molecular e um líquido polimérico em uma região do diagrama de fases atualmente inacessível experimentalmente. Em um futuro próximo, esperamos que seja possível testar esta previsão teórica e sintetizar fases poliméricas por meios físicos.
Abstract: One of the goals of atomistic simulation in materials science is to calculate properties of a virtual material and suggest routes for its fabrication in laboratory. One of the main properties that the material must have before being synthesized is the thermodynamical stability. As the thermodynamical stability is determined by the free energy, its accurate calculation is of fundamental importance for the construction of a virtual laboratory. In this context, we developed an alternative methodology to determine the free energy of substitutional alloys, which takes into account both the vibrational and configurational degrees of freedom with controlled accuracy. The methodology uses the Monte Carlo method to simulate both the vibrational and exchange dynamics and uses the adiabatic switching and reversible scaling methods to calculate the free energy efficiently. In addition, the methodology is able to evaluate the effect of three mechanisms in the vibrational entropy, through successive relaxations of constraints associated with the dynamics. Specifically, it allows to quantify the mechanisms of a) bond proportion, b) atomic size mismatch and c) bulk volume, and thus identify the origin of the vibrational entropy difference at the order-disorder transition. We tested and applied the methodology to study a semiempirical model of the Ni3Al alloy. We observed an increasing of the vibrational entropy at the order-disorder transition comparable to the configurational entropy increasing and explained by an increasing of the bulk volume. Another expected feature of a virtual laboratory is to offer models that describe satisfactorily the systems of interest. We investigated a tight-binding potential and found out that it is not transferable to describe the order-disorder phenomena in several alloys. In addition to the study of the order-disorder phenomena in alloys, we investigated phase transitions between two liquids of a pure substance. We present a theoretical evidence of a first-order liquid-liquid phase transition in a semiempirical model of gallium, which lend support to the recent experimental evidence of a first-order liquid-liquid transition in the supercooled regime of this element. Moreover, the atomistic simulations suggest a microscopic mechanism for this phase transition. Another expected features of a virtual laboratory are the possibility to investigate systems in unreachable experimental conditions and the capacity to suggest new experiments. In this context, we present an ab initio theoretical evidence of a liquid-liquid phase transition in carbon dioxide. We predict a transition between a molecular liquid and a polymeric liquid at a temperature and pressure which are presently unreachable experimentally. We hope that in the near future it will be possible to test this theoretical prediction and synthesize polymeric phases through physical means.
Doutorado
Física da Matéria Condensada
Doutor em Ciências
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Mahajan, Thejus. "Excitation and fragmentation of CnN⁺ (n=1-3) molecules in collisions with He atoms at intermediate velocity ; fundamental aspects and application to astrochemistry." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS311/document.
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Dans cette thèse nous avons étudié des collisions entre des projectiles CnN⁺ (n=0,1,2,3) et des atomes d’Hélium à vitesse intermédiaire (2.25 u.a). A cette vitesse, proche de la vitesse des électrons sur les couches de valence externe des atomes et molécules, de nombreux processus électroniques prennent place avec une forte probabilité : ionisation (simple et multiple), excitation électronique, capture d’électron (simple et double). Nous avons mesuré les sections efficaces absolues de tous ces processus. Un autre aspect intéressant de la collision concerne la fragmentation des molécules excitées, que nous avons également mesurée précisément grâce à un dispositif dédié. Les expériences ont été effectuées auprès de l’accélérateur Tandem d’Orsay avec des faisceaux de quelques MeV d’énergie cinétique. Le dispositif AGAT a permis de réaliser les collisions (en condition de collision unique) et de mesurer tout à la fois les sections efficaces des processus et la fragmentation associée. Parallèlement nous avons simulé ces collisions d’un point de vue théorique en utilisant le modèle à Atomes et Electrons Indépendants (IAE) couplé à des calculs CTMC (Classical trajectory Monte Carlo). Sur cette base, nous avons prédit les sections efficaces qui se sont trouvées être en bon accord avec les mesures, à l’exception de la double capture d’électrons. Par ailleurs les rapports de branchement de dissociation des CnN⁺ après excitation électronique sont bien reproduits en utilisant la distribution d’énergie interne des espèces calculées avec le même modèle IAE/CTMC. Ces expériences nous ont permis de construire des « Breakdown Curves » (BDC), véritables cartes d’identité des molécules qui permettent de prévoir, dans le cadre d’une fragmentation statistique comment va fragmenter un système dont on connait l’énergie interne. Avec ces BDC nous avons pu prédire et recommander des rapports de branchement pour des voies de sortie de processus physiques et chimiques d’intérêt astrochimique. Ces données seront insérées dans la base internationale d'astrochimie the Kinetic Data Base for Astrochemistry KIDA. Cette thèse a été réalisée dans le cadre de l’Ecole Doctorale Ondes et Matière (EDOM) à l’Institut des Sciences Moléculaires d’Orsay (ISMO), à l’Université Paris-Sud Paris SaclayThis thesis studies the aftermath of collision between singly positively charged Nitrogenated carbon species CnN⁺ (n=0,1,2,3) and neutral Helium atom at a velocity of 2.25 au. At this velocity, close to the velocity of outer electrons in atoms and molecules, several electronic processes take place and are near their maximum of probability such as ionisation (single, double, triple …), electronic excitation and electron capture (single and double). We looked at their cross sections and how their evolution with the molecule size. Following the collision the molecule can fragment, which leads to another interesting aspect, the fragmentation branching ratios. Collision experiments were done using a Tandem accelerator at Orsay that produced the CnN⁺ projectiles and a dedicated set-up, AGAT, to capture the flying fragments/intact molecule after collision according to their charge to mass ratio. Knowing the number of particles that are shot and the fact that our set-up allows no loss of fragments/intact molecule, we could get the probabilities of various fragments formed. Using these probabilities and a knowledge of the Helium jet profile used, we could measure their cross sections. The probabilities alone are sufficient to obtain the fragmentation branching ratios.The next step was to use a theoretical model to simulate the collision. We used Independent Atom and Electron (IAE) model coupled with Classical Trajectory Monte Carlo (CTMC) method to calculate the desired cross sections. A general good agreement was obtained, with the exception of double electron capture. The model could also predict, through the calculation of the species internal energy, the fragmentation branching ratios of cations CnN⁺ after electronic excitation. Also, the branching ratios were used to construct semi-empirical Breakdown Curves (BDCs), which are internal energy dependent dissociation branching ratios specific to each molecule, type, size and charge. With those, we could recommend products branching ratios to be used for various processes of astrochemical interest. The products branching ratios will be made available for a wider network of researchers under the international Kinetic Database for Astrochemistry (KIDA).This thesis was realized under the doctoral programme of Ecole Doctorale Ondes et Matiere (EDOM) with Institut des Sciences Moléculaires d’Orsay (ISMO) where the author was given an office and Université Paris-Sud where the author is formally enrolled
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Blaudeck, Thomas. "Self-Assembly of Functionalized Porphyrin Molecules on Semiconductor Nanocrystal Surfaces." Doctoral thesis, Universitätsbibliothek Chemnitz, 2007. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-200701451.
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Im Fokus dieser Dissertation stehen anorganisch-organische Hybridaggregate aus Kadmiumselenid-Nanokristallen und funktionalisierten Porphyrinmolekülen in Lösung. Mit Hilfe von statischen und zeitaufgelösten Methoden der optischen Spektroskopie wird nachgewiesen, daß die Bildung der Aggregate durch spontane Adsorption der funktionalisierten Moleküle an der Nanokristalloberfläche erfolgt. Dabei ist von einem dynamischen Gleichgewicht zwischen den Porphyrinmolekülen und den ursprünglichen Nanokristall-Liganden (TOPO) auszugehen. In der Photophysik der Hybridaggregate lassen sich ein resonanter Energietransfer nach Förster, der vom Nanokristall zum Porphyrinmolekül gerichtet ist, sowie eine Elektronen-Austauschwechselwirkung zwischen beiden Komponenten nach Dexter nachweisen. Mit Hilfe einer Erweiterung des Stern-Volmer-Ansatzes zur Beschreibung der Fluoreszenzlöschung für bimolekulare Reaktionen können die jeweiligen Anteile für eine Serie von Nanokristallen unterschiedlicher Größe und zweierlei Beschaffenheit grob quantifiziert werden. Ferner wird der Einfluß diffundierender Ladungen auf die Quantenausbeute von Halbleiternanokristallen anhand von zeitkorrelierter Einzelphotonenerfassung untersucht. Mit Hilfe einer Detektionsmethode, die die Zeitreihe der Ankunftszeiten einzelner Photonen erhält (tt-TCSPC), ist es möglich, den in eine Polymermatrix eingebetteten Halbleiternanokristallen charakteristische Fluktuationen der Fluoreszenzlebensdauer mit individueller Zeitkonstante zuzuordnenThis Thesis is devoted to the formation and the photophysics of inorganic/organic hybride nanoaggregates designed from CdSe semiconductor nanocrystals and pyridyl-functionalized porphyrin molecules in solution at ambient conditions. The formation of the aggregates is revealed to be based on a spontaneous adsorption of the functionalized porphyrin molecules on the nanocrystal surfaces, with a dynamic equilibrium sustained due to the competition with TOPO, ie. the original surface ligand. The evidence for the existence of the self-assembled aggregates is furnished by the proof of a directed Förster resonant energy transfer from the nanocrystal to the porphyrin molecules at low compound concentrations. By means of steady-state and time-resolved optical spectroscopy, the resonant energy transfer (RET) is valued to be accompanied by at least one more secondary quenching mechanism. Motivated by the aptitude of the nanocrystals to host more than one molecule at once, the detection and quantification of this process is done by an extension of the conventional Stern-Volmer kinetics valid for bimolecular reactions. With that, the secondary interaction process aside from RET is explained in terms of a Dexter-type energy transfer that, on ist part, can be put down to a generation of charge-induced shallow trap states within the semiconductor nanocrystal. This model is in qualitative accordance with the known phenomena of fluorescence intermittency and spectral diffusion. The role of a fluctuating environment to affect the fluorescence quantum yield of the nanocrystals is confirmed by time-tagged time-correlated single-photon counting (tt-TCSPC) on single nanocrystals in a polymer matrix. The measurements show that the fluorescence lifetime of the nanocrystals is characterized by individual characteristic fluctuations possibly induced by temporal and spatial inhomogeneities in the distribution of the dielectric constants
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Garcia, Claudio J. "Investigation of single molecule and monolayer properties with Monte Carlo simulations of a coarse-grained model for alpha-sexithiophene." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron1511314081783002.
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Chang, Qiang. "Continuous-time random-walk simulation of surface kinetics." The Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=osu1166592142.
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Franz, Douglas M. "Simulation and Software Development to Understand Interactions of Guest Molecules inPorous Materials." Scholar Commons, 2019. https://scholarcommons.usf.edu/etd/7788.
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The effect of inclusion of explicit polarization is investigated through several theoret- ical studies of crystalline porous materials herein. In addition to the use of Monte Carlo simulation for such studies, a robust molecular dynamics software is presented which is suitable for analyzing time dependent properties of gases or other molecules in porous materials and other condensed phase systems. Metal-organic frameworks (MOFs) are the main focus of the work included here, a relatively young class of materials originally in- troduced in the early 1990s. These are usually three dimensional crystalline nanoporous materials that exhibit unique properties such as gas separation, storage and catalysis. They are synthesized by the combination of a metal ion e.g. Cu2+ with an organic linker e.g. benzene dicarboxylate. They are a very popular topic of scientific research due to the diversity in possible structures and manifold utility – finding applications in electron transfer, sensing, drug release etc. Industrially, MOFs like HKUST-1 and others are on the global market for use in gas storage and separation in fuel cell and raw materials processing.
These materials are often ideal candidates for computer simulation owing to their crystalline nature – a very large atomic system (that is, moles of particles) can be under- stood by only evaluating one or a few unit cells of the MOF, usually less than 5,000 atoms, and macroscopic properties such as gas sorption capacity and diffusion coefficients can be calculated through extrapolation of atomistic interactions in a mathematically infinite lattice. The software developed by the space group as of 2005, Massively Parallel Monte Carlo (MPMC), allows for sophisticated calculation of repulsion dispersion, electrostatic and polarization energies. In this work, Monte Carlo Molecular Dynamics (MCMD) is in- troduced, which can hybridize both methods to explore the phase space of a system with ease and better efficiency, as well as explore the effects of MOF flexibility and dynamic properties which to-date are rarely studied.
Studies involving primarily CO2, H2 and CH4 will be presented, but other gases investigated include C2 H2 , C2 H4 , C2 H6 , N2 , H2 O and others. Metal-organic materials with a wide variety of composition and structure will also be presented. Finally, features of the software MCMD will be presented for use by future studies.
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Rooy, Vincent Jean Bernard. "Investigation of the limits of the study of the adsorption of aromatic molecules inside the zeolite ZSM-5 Silicalite : from experimental data interpolations to Monte Carlo simulation approaches." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/14319.
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Zeolite ZSM-5 is a standard material in the petrochemical industry used as a catalyst in oil refining processes. Its shape selectivity toward parasubstituted aromatics has been very valuable in the processing of BTX (benzene, toluene, xylene). The adsorption of aromatic molecules inside the zeolite ZSM-5 presents also some unusual adsorption isotherms which has generated a great body of experimental and theoretical articles with only partial agreements. It is believed that the source of these discrepancies originates from the main characteristic of this system, a tight fit situation between the diameter of the aromatic ring and the size of the zeolite pore. The aim of this thesis is to achieve a consistent explanation between the experimental data measurements and the theoretical models. The determination of some adsorption values such as the Henry coefficient or the isosteric heat of adsorption by data interpolations or calculation from theoretical simulation is the numerical criterion to check this consistency. It is also the prerequisite to validate the parameters used to carry out the Monte Carlo simulation of such system. This work studies the limits of this epistemological approach. We start from a review of the different standard interpolation models and a discussion of the relevance of the Henry and isosteric heat values calculated. We continue with the investigation of the limits of a Monte Carlo simulation; from the difficulties to assess a heterogeneous set of Force Field simulation parameters, to the study of new bias Monte Carlo algorithms used to carry out an efficient simulation.
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Brunet, Annaël. "Etude à l'échelle de la molécule unique des changements conformationnels de la molécule d'ADN : influence de la présence de défauts locaux présents sur l'ADN et de paramètres physico-chimiques de la solution environnante." Thesis, Toulouse 3, 2015. http://www.theses.fr/2015TOU30168/document.
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Les ions jouent un rôle majeur sur les processus biologiques affectant la molécule d'ADN que ce soit en termes d'activité de liaison de protéines à l'ADN ou d'encapsulation de l'ADN dans les capsides virales ou le noyau. L'activité de protéines sur l'ADN est, par ailleurs, fréquemment liée à une courbure locale de l'axe de la double hélice, que ce soit en raison d'une séquence intrinsèquement courbée, ou, via la capacité de protéines à courber la séquence sur laquelle elles se fixent. Être capable de caractériser et comprendre l'effet des ions présents en solution, de la courbure et de la dénaturation locale de la molécule d'ADN sur les conformations de cette dernière est donc crucial pour approfondir la compréhension de nombreux processus biologiques. Des travaux, tant expérimentaux que théoriques, ont déjà été menés sur ces questions mais celles-ci sont encore largement débattues. En effet, pour y répondre, doivent notamment être développées des méthodes expérimentales qui ne perturbent pas significativement la conformation de l'ADN ou le complexe ADN-protéine, ainsi que des modèles théoriques associés permettant une analyse précise des données expérimentales et leur compréhension physique. L'objectif de ce travail est de proposer des outils expérimentaux et théoriques permettant de décrire physiquement l'influence de défauts locaux présents sur la molécule d'ADN et de paramètres physico-chimiques de la solution environnante. A cette fin, des données expérimentales ont été acquises à l'échelle de la molécule unique grâce à la technique haut-débit de "Tethered Particle Motion" (HT-TPM). Le TPM consiste à enregistrer, au cours du temps, les positions d'une particule accrochée à l'extrémité d'une molécule d'ADN, immobilisée par son autre extrémité sur un support en verre. L'utilisation d'une biopuce permettant la parallélisation des complexes ADN/particule et l'acquisition "à haut débit" de données TPM a permis d'obtenir une grande accumulation de statistiques individuelles. Une procédure d'analyse efficace a été élaborée afin de déterminer les amplitudes du mouvement des assemblages ADN-particules valides. En parallèle, ont été effectuées des simulations basées sur un modèle de physique statistique mésoscopique dans lequel la molécule d'ADN est assimilée à une chaîne de billes de rayons variables dont les déplacements sont régis par la diffusion brownienne et une énergie potentielle d'interaction prenant en compte notamment l'énergie de courbure du polymère ADN. Une première étude a porté sur l'effet de la force ionique de la solution environnante sur la longueur de persistance Lp, qui traduit la rigidité du polymère d'ADN. Les valeurs de Lp extraites des données de HT-TPM ont fait apparaître une décroissance de la longueur de persistance de 55 à 30 nm, corrélée à l'augmentation de la force ionique, avec une décroissance plus forte observée pour les ions divalents Mg2+ que pour les ions monovalents Na+. Les valeurs de Lp déterminées sur une plage étendue de force ionique ont permis de valider l'approche théorique proposée par Manning en 2006 dans la cas Na+. Une deuxième étude a conduit à l'élaboration d'une méthode permettant de quantifier l'angle de courbure locale induite par une séquence spécifique ou la liaison d'une protéine sur la molécule d'ADN. L'échantillon modèle a été obtenu en insérant de une à sept séquences CAAAAAACGG en phase. Une description théorique de la chaîne d'ADN appelée "kinked Worm-Like Chain" a été proposée. Elle conduit à une formule simple de la distance bout-à-bout de l'ADN qui permet d'extraire la valeur de l'angle de courbure à partir des mesures de HT-TPM. Ainsi, il a pu être montré que la séquence CAAAAAACGG induit un angle de 19° ± 4° en accord avec les données de la littérature. Une troisième étude concernant la mesure de l'impact de la dénaturation partielle de l'ADN, induite par la température, sur sa rigidité apparente globale a été menée. Des résultats préliminaires sont proposésIons play an important role in many biological processes affecting the DNA molecule, both for binding activities of DNA-protein interaction, and the DNA packaging in viral capsids or in the cell nucleus. Proteins actions on DNA are also often associated to the double helix curvature, be it because of an intrinsic curved sequence, or of the ability of the proteins, to curve the sequence they are trying to bind. Being able to characterize and understand the effects on the DNA conformation of ions present in solution, DNA local curvature, and local denaturation bubble is essential and crucial for the thorough understanding of many biological processes. Many experimental, and theoretical studies have already been conducted to address these questions. However they remain highly debated. To answer then one must notably develop experimental approaches that minimize alteration of the conformation of the DNA molecule or the complex protein-DNA, as well as associated theoretical models that permit a precise analysis of experimental data as well as their physical understanding. The goal of this work is to develop and propose experimental and theoretical tools which would provide a physical description of the influence of DNA local defects on the DNA molecule as well as of physicochemical conditions of the DNA environmental solution. For this purpose, experimental data have been collected, at a single molecule level, using the High-Throughput Tethered Particle Motion" (HT-TPM) technique. TPM consists of recording the location of a particle grafted by one end of a single DNA molecule and immobilized, at the other end, to a glass surface. The use of a biochip that enables the parallelization of DNA/particle complexes and the ensuing high-throughput data acquisition permitted to obtain a large accumulation of individual statistics. A strong analysis procedure has been developed to extract and quantify the amplitude of motion of the valid DNA/particle complexes . Alongside that, simulations have been run, based on a mesoscopic statistical mechanics model in which the DNA molecule is related to a chain of monomers with varying radius and in which the amplitude of motion is governed by both the Brownian motion and by the interaction potential associated to stretching and bending energies of the polymer. A first study was conducted on the effect of the ionic strength induced by surrounding ions in solution on the DNA persistence length (Lp) which characterizes the DNA polymer rigidity. The extracted Lp values of HT-TPM measurement decrease from 55 to 30 nm when the ionic strength increases. A stronger decrease was observed in presence of divalent ions Mg2+ than with monovalent ions Na+. This quantification of Lp dependence, on a large and strongly prospected range of ionic strengthes, tends to validate the theoretical approach proposed in 2006 by Manning in presence of monovalent ions Na+. A second project allows us to develop a method of evaluation and quantification of local DNA bending angles, induced either by specific intrinsic sequence, or by the binding of proteins on DNA. Constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven sequences CAAAAAACGG was used. A theoretical description of the polymer chain, named "kinked Worm-Like Chain" was proposed which leads to a simple formulation of the end-to-end distance of DNA molecules allowing to extract local bend angles from HT-TPM measurement. As a result, we find that the sequence CAAAAAACGG induces a bend angle of 19° ± 4° in agreement with other value from the literature. A third study concerning the influence of temperature-induced partial denaturation on the global apparent rigidity parameters of the polymer was conducted. Preliminary results are proposed
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Yazaydin, Ahmet Ozgur. "Molecular simulation of the adsorption of organics from water." Link to electronic thesis, 2007. http://www.wpi.edu/Pubs/ETD/Available/etd-042507-023605/.
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Mouawad, Lena. "Monte Carlo simulations and a theoretical study of the damage induced by ionizing particles at the macroscopic scale as well as the molecular scale." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAE009/document.
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Le travail présenté dans cette thèse se place dans le contexte de la simulation de dommages biologiques. D'abord une étude macroscopique met en question la pertinence des plans de traitement basés sur la dose absorbée et le passage à une étude de micro-dosimétrie permet l'utilisation de paramètres biologiques plus pertinents, tels que les cassures de brins d'ADN. La validité des sections efficaces d'interaction sur lesquelles se basent ces simulations est discutée en plus de détails. Suite à la complexité du milieu biologique, les sections efficaces d'interaction avec l'eau sont souvent utilisées. Nous développons un algorithme qui permet de fournir les sections efficaces d'ionisation pour n'importe quelle cible moléculaire, en utilisant des outils qui permettent de surmonter les difficultés de calcul, ce qui rend notre programme particulièrement intéressant pour les molécules complexes. Nous fournissons des résultats pour l'eau, l'ammoniac, l'acide formique et le tétrahydrofuraneThe work presented in this thesis can be placed in the context of biological damage simulation. Webegin with a macroscopic study where we question the relevance of absorbed-dose-based treatmentplanning. Then we move on to a micro-dosimetry study where we suggest the use of morebiologically relevant probes for damage, such as DNA strand breaks. More focus is given to thefundamental considerations on which the simulations are based, particularly the interaction crosssections. Due to the complexity of the biological medium, the interaction cross sections with waterare often used to simulate the behavior of particles. We develop a parallel user-friendly algorithmthat can provide the ionization cross sections for any molecular target, making use of particular toolsthat allow to overcome the computational difficulties, which makes our program particularlyinteresting for complex molecules. We provide preliminary results for water, ammonia, formic acidand Tetrahydrofuran
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Bouissou, Thomas. "Modélisation de la structure électronique et de la spectroscopie de chromophores solvatés par un agrégat de gaz rare." Toulouse 3, 2010. http://thesesups.ups-tlse.fr/1215/.
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Le travail présenté dans cette thèse constitue une première contribution de l'étude de la structure électronique du système Ca2Arn. La première partie de la thèse porte sur le calcul ab initio du spectre des états électroniques du dimère de calcium. Les calculs ont mis en lumière la richesse de la structure du spectre électronique de Ca2 : interaction entre états électroniques monoexcités et diexcités et rôle des états zwitterioniques. Plus de 70 états électroniques ont été calculés et caractérisés par leurs constantes spectroscopiques. Les moments dipolaires de transitions depuis l'état fondamental ont également été déterminés. Ces calculs confirment les résultats théoriques et expérimentaux disponibles dans la littérature sur le bas du spectre (transition électroniques inférieures à 20 000 cm-1), mais étendent les informations spectrales jusqu'à 35 000 cm-1 au dessus de l'état fondamental. Ces calculs ont permis dans une seconde étape de construire un modèle de la structure électronique efficace pour les systèmes Ca2Arn. Nous avons mis au point un modèle Diatomics-In-Molecules (DIM) pour modéliser l’interaction de Ca2 électroniquement excité avec des atomes d’argon. Ce modèle utilise une base de configuration Valence Bond pour exprimer l'hamiltonien de l’agrégat. La paramétrisation du hamiltonien DIM a été réalisée à partir des résultats obtenus par une procédure de diabatisation des états électroniques ab initio des fragments Ca2 et de CaAr. Après avoir déterminé les propriétés structurales des agrégats Ca2Arn dans leur état fondamental, nous avons mis en oeuvre des simulations Monte-Carlo des spectres d’absorption visible depuis le fondamentalThe work introduced in the present thesis is a first contribution to the investigation of the electronic structure of the Ca2Arn system. The first part reports the ab initio calculations of the electronics states of the calcium dimer. The calculations highlight the very rich nature of the electronic spectrum of Ca2 : interaction between singly and doubly excited states, role of zwitterionic states. More than 70 electronics states have been investigated and characterized via the determination of their spectroscopic constants. The transition dipole moments from the ground state have also been determined. These calculations confirm previous theoretical and experimental results available in the literature (electronic transitions below 20 000 cm-1) and extend the spectral knowledge up to 35 000 cm-1 above the ground state. In a second step, a Diatomics-In-Molecules model has been designed to describe the interaction between Ca2 electronic excited an argon atoms. This model is expressed in a basis of Valence Bond configurations. The parameterization of the DIM Hamiltonian is achieved a diabatization of the electronic states of Ca2 and CaAr fragments. After determining the structural properties of Ca2Arn clusters in their ground state, we have achieved Monte-Carlo simulations to investigate their visible absorption spectra from the ground state
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Peudon, Aude. "Prise en compte de la structure moléculaire pour la modélisation des dommages biologiques radio-induits." Toulouse 3, 2007. http://www.theses.fr/2007TOU30125.
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Pour améliorer la modélisation des effets des rayonnements sur le milieu biologique, l'objectif de ce travail fût la prise en compte de la structure moléculaire. Pour cela des sections efficaces moléculaires photoniques et électroniques ont été calculées à partir des données moléculaires ab-initio (énergies de liaison des orbitales, population…). Un modèle dynamique de réorganisation moléculaire a également été développé pour évaluer l'impact des électrons Auger et des photons de fluorescence émis suite à une ionisation interne. L'influence de ces changements, sur le nombre et la répartition des dommages radio-induits, a été étudiée sur le nucléosome, élément unitaire de l'ADN. Des modifications ont ensuite été réalisées pour permettre la modélisation d'expériences in vitro. Une simulation a permis d'évaluer le nombre de cytosines mutagènes sur le plasmide P53, et une autre, la quantité de dommages provoquée par les isotopes 125 et 123 de l'iode sur le plasmide pBR322. Le bon accord entre les résultats confirme la complémentarité nécessaire du modèle et de l'expérienceTo improve modelling of biological radio-induced damage, the aim of this work was to take into account molecular structure. Based on ab-initio molecular data (molecular binding energy, population analysis…), photonic and electronic cross sections have been calculated. An interactive model of molecular reorganization has been also developed to evaluate efficiency of Auger electrons and fluorescent photons after inner shell ionization. The improvement impact on number and distribution of SSB and DSB has been studied with one core particle. Then, modifications have been performed to model in-vitro experiments. One simulation allows mutagenic cytosines number evaluation on P53 plasmid. And another one deals with I-125 and I-123 impact on pBR322 plasmid. The good agreement in the results confirms the necessary complement of model and experiment
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Kotdawala, Rasesh R. "Adsorption studies of hazardous air pollutants in microporous adsorbents using statistical mechanical and molecular simulation techniques." Worcester, Mass. : Worcester Polytechnic Institute, 2007. http://www.wpi.edu/Pubs/ETD/Available/etd-050407-112429/.
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Dissertation (Ph.D.) -- Worcester Polytechnic Institute.Keywords: Activated carbons; Hydrogen cyanide; Methyl ethyl ketone; Adsorption; Mercury; Monte-Carlo; Solvents; Molecular simulations; Zeolites; Water; Methanol; Nanopores. Includes bibliographical references (leaves 147-150).
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Barreau, Alain. "Contribution à l'étude de la diffusion collisionnelle de la lumière : modélisations et simulations par la méthode de Monte-Carlo des milieux denses, comparaisons aux résultats expérimentaux et de dynamique moléculaire." Angers, 1987. http://www.theses.fr/1987ANGE0012.
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Calculs numériques, à l'approximation D. I. D, de la diffusion collisionnelle de la lumière par des milieux denses composes de molécules isotropes ou faiblement anisotropes, à l'aide de deux simulations ou l'algorithme de résolution est la méthode de Monte-Carlo. Cas de la première simulation pour les molécules isotropes, avec un modèle réticulaire avec prise en compte des seules interactions entre molécules voisines : intensités collisionnelles des doublets, triplets et quadruplets à différentes températures et densités, facteurs d'interférences Rayleigh et Raman ; bon accord à toutes densités pour les gaz et aux densités élevées pour les liquides. Cas de la deuxième simulation pour des molécules linéaires anisotropes : les corrélations entre axes moléculaires et intermoléculaires sont prépondérantes pour déterminer les taux de dépolarisation Rayleigh de n::(2).
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Ramezani-Dakhel, Hadi. "Bioengineered Metal Nanoparticles: Shape Control, Structure, and Catalytic Functionality." University of Akron / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=akron1426184509.
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Exler, Matthias. "On classical and quantum mechanical energy spectra of finite Heisenberg spin systems." Doctoral thesis, [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=980110440.
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Harrison, Ryan M. "Molecular biophysics of strong DNA bending and the RecQ DNA helicase." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:f02fc167-b705-4275-a413-21d13b5d94c3.
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Molecular biophysics is a rapidly evolving field aimed at the physics-based investigation of the biomolecular processes that enable life. In this thesis, we explore two such processes: the thermodynamics of DNA bending, and the mechanism of the RecQ DNA helicase. A computational approach using a coarse-grained model of DNA is employed for the former; an experimental approach relying heavily on single-molecule fluorescence for the latter. There is much interest in understanding the physics of DNA bending, due to both its biological role in genome regulation and its relevance to nanotechnology. Small DNA bending fluctuations are well described by existing models; however, there is less consensus on what happens at larger bending fluctuations. A coarse-grained simulation is used to fully characterize the thermodynamics and mechanics of duplex DNA bending. We then use this newfound insight to harmonize experimental results between four distinct experimental systems: a 'molecular vise', DNA cyclization, DNA minicircles and a 'strained duplex'. We find that a specific structural defect present at large bending fluctuations, a 'kink', is responsible for the deviation from existing theory at lengths below about 80 base pairs. The RecQ DNA helicase is also of much biological and clinical interest, owing to its essential role in genome integrity via replication, recombination and repair. In humans, heritable defects in the RecQ helicases manifest clinically as premature aging and a greatly elevated cancer risk, in disorders such as Werner and Bloom syndromes. Unfortunately, the mechanism by which the RecQ helicase processes DNA remains poorly understood. Although several models have been proposed to describe the mechanics of helicases based on biochemical and structural data, ensemble experiments have been unable to address some of the more nuanced questions of helicase function. We prepare novel substrates to probe the mechanism of the RecQ helicase via single-molecule fluorescence, exploring DNA binding, translocation and unwinding. Using this insight, we propose a model for RecQ helicase activity.
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Engelhardt, Larry Paul. "Quantum Monte Carlo calculations applied to magnetic molecules /." 2006.
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Galbraith, Aysa Lamia. "Phase equilibria of diatomic Lennard-Jones molecules using Monte Carlo simulation." 2006. http://www.lib.ncsu.edu/theses/available/etd-04282006-140847/unrestricted/etd.pdf.
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Madsen, Jonathan R. "Monte Carlo Electromagnetic Cross Section Production Method for Low Energy Charged Particle Transport Through Single Molecules." Thesis, 2013. http://hdl.handle.net/1969.1/151357.
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The present state of modeling radio-induced effects at the cellular level neglects to account for the microscopic inhomogeneity of the nucleus from the non-aqueous contents by approximating the entire cellular nucleus as a homogenous medium of water. Charged particle track-structure calculations utilizing this principle of superposition are thereby neglecting to account for approximately 30% of the molecular variation within the nucleus. To truly understand what happens when biological matter is irradiated, charged particle track-structure calculations need detailed knowledge of the secondary electron cascade, resulting from interactions with not only the primary biological component – water – but also the non-aqueous contents, down to very low energies.
This paper presents developments for a novel approach, which to our knowledge has never been done before, to reducing the homogenous water approximation. The purpose of our work is to develop of a completely self-consistent computational method for predicting molecule-specific ionization, excitation, and scattering cross sections in the very low energy regime that can be applied in a condensed history Monte Carlo track-structure code. The present methodology begins with the calculation of a solution to the many-body Schrödinger equation and proceeds to use Monte Carlo methods to calculate the perturbations in the internal electron field to determine the aforementioned processes. Results are computed for molecular water in the form of linear energy loss, secondary electron energies, and ionization-to-excitation ratios and compared against the low energy predictions of the GEANT4-DNA physics package of the Geant4 simulation toolkit.
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Vincent, Jordan Eric. "Quantum Monte Carlo calculations of the electronic excitations of Ge atoms, molecules and nanoclusters using core-polarization potentials /." 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3243017.
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Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2006.Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6466. Adviser: Richard M. Martin. Includes bibliographical references (leaves 226-238) Available on microfilm from Pro Quest Information and Learning.
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Liu, Susan Marisa. "Energetic and conformational studies of nonspecific adsorption of simple protein-like chain molecules using dynamic Monte Carlo simulations." Thesis, 2004. http://hdl.handle.net/2429/17135.
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Dynamic Monte Carlo simulations of short HP (hydrophobic-polar) protein-like chains to
solid-liquid surfaces are used to probe thermodynamic and dynamic aspects of protein
adsorption. The HP model enables the enumeration of all chain conformations, thereby
aiding understanding of the relation between adsorption thermodynamics and changes in
accessible chain conformations resulting from the sorption process. Simulation results
indicate that HP chains having a single conformation at their lowest energy in solution
adsorb such that the new lowest energy state of the system is conformationally
degenerate. As a result, adsorption can lead to an increase in chain entropy.
Entropically-driven adsorption is found to be likely when the interaction energy between
the hydrophobic segments of the chain and the sorbent is weak and equals the contact
energy between two hydrophobic units within the chain.
Chain sequence and sorbent properties are shown to profoundly influence adsorption
thermodynamics. Simulations are carried out where intra- and intermolecular
hydrophobic interaction energies are varied to examine the influence of the stability of
the native-state conformation on adsorption thermodynamics over a range of sorbent
hydrophobicities. Lower stability chains tend to adsorb more readily on hydrophilic
sorbents and experience greater average changes in conformation, usually accompanied
by a loss in entropy. Adsorption to more hydrophobic sorbents leads to a loss in chain
conformational entropy, irrespective of the stability of the native state.
Lateral confinement on the sorbent surface is shown to greatly reduce the degrees of
freedom in the chain, thereby resulting in a strong stabilization of the native-state
conformation of the chain in its adsorbed state. This effect is compared to experimental data for nonspecific adsorption of hen egg-white lysozyme to silica to explain the
increase in adsorbed enzyme activity as a function of surface loading and geometry.
Studies of run-averaged energy trajectories for chain adsorption indicate that the process
follows a basic energy path characterized by well-defined energy levels, suggesting the
presence of natural kinetic barriers.
This thesis demonstrates the value of simple mesoscopic protein-like chain models and
dynamic Monte Carlo simulations of their adsorption behavior in understanding better the
mechanisms and forces driving nonspecific protein adsorption.Applied Science, Faculty of
Chemical and Biological Engineering, Department of
Graduate
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Weymouth, Alfred John. "Scanning Tunneling Microscopy Studies of Small Aromatic Molecules on Semiconductor Surfaces." Thesis, 2009. http://hdl.handle.net/1974/7328.
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Understanding the behaviour of molecules on a semiconductor surface is necessary if molecular self-assembly is going to be employed, with existing semiconductor technology, to create useful devices. Si(111)-7x7 is an invaluable surface upon which to study molecular adsorption. The surface reconstruction has been well characterized and it possesses seven symmetrically distinct dangling bonds that can serve as reaction sites. Aromatic molecules on Si(111)-7x7 have been investigated with a variety of techniques and have been shown to chemisorb at room temperature. However, it is not trivial to predict how an ensemble of aromatic molecules might distribute themselves amongst the available bonding sites on this surface. The work presented in this thesis begins with a joint STM and ab initio investigation of thiophene on 7x7 that demonstrates kinetics are necessary to describe the chemisorption sites occupied at various coverages. A kinetic Monte Carlo model, taking into account a mobile physisorbed state, is shown to accurately describe this site occupancy at room temperature. This model disregards molecule-molecule interaction because thiophene does not sterically hinder chemisorption to a neighbouring dangling bond. A larger molecule, mesitylene, was then studied on Si(111)-7x7, and shown to form an ordered molecular lattice on the Si(111)-7x7 surface. This is the first demonstration of a porous molecular lattice grown on Si(111)-7x7 at room temperature. Finally, molecular chemisorption on the related 5x5 reconstruction, grown by depositing Ge on 7x7, is studied. It is found that the presence of Ge hinders molecular chemisorption, preventing formation of the mesitylene lattice.Thesis (Ph.D, Physics, Engineering Physics and Astronomy) -- Queen's University, 2009-09-11 10:14:10.118
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Mendoza-Cortes, Jose Luis. "Design of Molecules and Materials for Applications in Clean Energy, Catalysis and Molecular Machines Through Quantum Mechanics, Molecular Dynamics and Monte Carlo Simulations." Thesis, 2012. https://thesis.library.caltech.edu/7091/1/JoseMendozaCortes_Thesis.pdf.
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We use a multiparadigm, multiscale strategy based on quantum mechanics (QM), first-principles QM-based molecular mechanics (MD) and grand canonical Monte Carlo (GCMC) to rationally design new molecules and materials for clean energy (H2 and CH4 storage), catalysis (O2 evolution, metal organic complexes) and molecular architectures (rotaxanes, hydrogels). This thesis is organized in seven chapters and shows that it is crucial to understand the scale of the system to be studied, the insight obtained can be used to rationally design new molecules and materials for desirable applications; as well as to guide and complement experimental studies. Chapter 1 discusses the specific details of the proposed methodology, including the theoretical underpinning of each modeling paradigm, potential limitations, and how we use these for in silico characterization and design optimization. Chapter 2 covers the structure prediction and characterization of metal-organic complex arrays (MOCA) through QM and force-field-based molecular mechanics. The methodology is inspired by the approach used for enzymatic systems, considering that experimentally determining their three-dimensional structure remains an open challenge. Chapter 3 describes the use of transition state theory for the calculation of reaction rates in polymer hydrogel network formation. This enables the determination of optimum concentrations for polymerization reactions and preparation of coarse-grained force elds. Chapter 4 describes the work performed on Stoddard's rotaxane dumbbells, where we explained origin for the template-directed synthesis through QM-derived free energies. We also give a consistent explanation for the role of the counter anion. Chapter 5 presents the simulation results for a tetranuclear cluster model for O2 evolution, based on CaMn304 and Mn4O4 clusters. We demonstrate how to calculate their oxidation potentials and propose new molecular designs that resemble the oxygen evolution complex (OEC) both structurally and electronically. Chapter 6 presents our findings for CH4 storage. Using a second-order Moller-Plesset perturbation theory force field and GCMC we propose a framework for optimal delivery. Chapter 7 presents our designed materials for hydrogen storage and the validation of our methodology against experimental results. We based our predictions in QM and GCMC calculations through the development of our own first-principles vdW force eld. Our results demonstrate novel frameworks capable of achieving the DOE energy density target for 2015. Finally, we show the generalization of adsorption phenomena for any porous material based on topological constraints.
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Geser, Federico Alejandro. "Caracterización dosimétrica y monitoreo in situ para hadronterapia." Doctoral thesis, 2019. http://hdl.handle.net/11086/14465.
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Tesis (Dr. en Física)--Universidad Nacional de Córdoba, Facultad de Matemática, Astronomía, Física y Computación, 2019.Actualmente, se cuenta con modernas técnicas para el tratamiento del cáncer incluidas dentro del marco de la radioterapia, conocidas como radioterapias no-convencionales. Estas técnicas fueron investigadas bajo el mismo precepto que todas las terapias de cáncer que utilizan radiaciones ionizantes: realizar la conformación de la dosis en el interior del paciente de la forma más precisa posible, sin dañar tejidos sanos o radio-sensibles. Entre estas técnicas no-convencionales, se encuentra la hadronterapia, que consiste básicamente en la utilización de partı́culas cargadas pesadas (protones, partı́culas alfa, iones de carbono, etc) para la conformación de dosis en pequeños volumenes. Las principales ventajas de la hadronterapia, se deben a la naturaleza del depósito de energı́a descripto por la fı́sica del problema. Dada la alta transferencia lineal de energı́a que poseen los iones utilizados en hadronterapia, los daños biológicos resultan superiores a los de la radioterapia convencional, y por ende es necesario contar con herramientas que permitan establecer el “control / verificación del rango de los iones” en el interior del paciente durante el procedimiento de irradiación. Para este fin, es necesario identificar procesos fı́sicos que produzcan alguna señal interpretable desde el exterior del paciente que sea potencialmente útil para monitorear el haz terapéutico. Una posibilidad consiste en aprovechar las propiedades del agua lı́quida equivalente a las del tejido blando, y analizar los procesos nucleares que den lugar a estados excitados del núcleo de oxı́geno con consecuente emisión foto-nuclear. En este trabajo de tesis, se investigó un nuevo enfoque basado en la posibilidad de monitorear el haz de terapia por medio de algún elemento no presente, en forma natural, en el tejido biológico; que al interactuar de alguna forma con la radiación incidente produzca alguna consecuencia correlacionada con los procesos de interés. Asimismo, se analiza la potencial detección de fotones de aniquilación en la radioterapia convencional debido a la inclusión de nanopartı́culas de oro en el material tejido-equivalente a modo de aproximación experimental a la detección, y correlación con el proceso de irradiación. En términos de hadronterapia, y particularmente la protonterapia, se estudia la factibilidad de aprovechar la fusión nuclear entre protones de energı́as bajas (respecto de las energı́as incidentes de terapia) y el isótopo de boro 11, dando lugar a dos significativas ventajas: la mejora dosimétrica debido a la emisión de partı́culas alfa resultantes del proceso de fusión; y la verificación online e in-situ del rango de los protones, con la consecuente herramienta de diagnóstico por imágenes médicas, debido a la emisión de fotones gamma prompt (“rápidos”).
Nowadays, different techniques are being used for the treatment of cancer in the framework of radiotherapy, thoroughly known as non-conventional radiotherapies. These techniques were researched with the same goal than most cancer therapies utilizing ionizing radiation: conforming the dose inside the patient in the more accurate way possible, sparing healthy or radiosensitive tissues. Among these non-conventional techniques is the hadrontherapy, consisting mainly in using heavy charged particles (protons, alpha particles, carbon ions, etc) to perform the dose conformation in small volumes. The principal advantages of hadrontherapy are due to the nature of the energy deposition mechanism of the charged particles in matter, as described by the physics of the problem. Given the high linear energy transfer (LET) the ions used in hadrontherapy possess, the biological damage is higher than the conventional radiotherapy, and for this reason it is necessary to provide tools that allows the medical physicists to establish the “control / verification of the range of the ions” inside the patient during the irradiation procedure. To this aim, it is necessary to identify physical processes that leads to an interpretable signal outside the patient that are potentially useful for the therapeutic beam monitoring. A posibility consists of taking advantage of the water-equivalent properties of the biological tissue, and analyze the nuclear processes with excited states of the oxygen nuclei with the consecuent emission of a photo-nuclear photon. In this thesis work, a new approach is studied, based on the possibility of monitoring the therapeutic beam using an element not naturally present in the biological tissue, and whose interaction with the ionizing radiation used in the therapy produces a consequence correlated with the process of interest. These are called the “theranostics” methods. Likewise, the potential detection of annihilation photons in conventional radiotherapy is analyzed, using gold nanoparticles inside a tissue-equivalent material, mostly as an experimental approach to the detection and correlation with the irradiation process. In terms of hadrontherapy, particularly regarding protontherapy, this work shows the feasibility of taking advantage of the so-called proton-boron fusion, consisting of using the low-energy protons (respect therapy incident energies) interaction with boron 11 isotopes, which leads to two significant advantages: dosimetric improvement due to the alpha particles produced in the reaction; and an online and in-situ verification of the range of the protons, with the consequent tool for medical imaging, due to the emission of prompt-gamma photons.
Fil: Geser, Federico Alejandro. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía, Física y Computación; Argentina.
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Nostheide, Sandra. "Kinetics and thermodynamics of unfolding processes in DNA molecules with several conformational states: theory and experiments." Doctoral thesis, 2014. https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2014101512898.
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The modelling of single-molecule experiments is of vital interest to gain new insights into processes which were hitherto not accessible by measurements performed on bulk systems. In the first part of this thesis, the kinetics of a triple-branch DNA molecule with four conformational states is investigated by employing pulling experiments
with optical tweezers and theoretical modelling. Probability distributions of first rupture forces, which are calculated by
applying transition rate theory to a free energy model, show good agreement with experimental findings. Permanently frayed molecules could be identified by analysing the number of opening base pairs in
force jumps. In the second part of the thesis, DNA hairpin molecules with periodic base sequences are studied. Their unfolding kinetics allows an analytical treatment, because they exhibit a regular coarse-grained free energy landscape as a function of the number of opened base pairs. A procedure is developed for determining all relevant parameters of the landscape, which relies on probabilities that can be
easily sampled from the unfolding trajectories. By means of Monte
Carlo simulations it is shown that already 300 trajectories, as typically measured in single-molecule experiments, provide faithful
results for the energetic parameters. The approach in particular opens a new access to improve loop contributions in the free energy landscape. In the third part of the thesis, a simulation method is developed for
modelling the unfolding kinetics of DNA molecules with arbitrary base sequences. The method is validated against experimental data for five DNA hairpin molecules with different length of the end-loop.
Applications of the method enable one, among others, to improve the parameter determination in functional forms suggested for the tail behaviour of work distributions. Such work distributions enter detailed and integral fluctuation theorems, which are useful for estimating free energy differences between folded and unfolded states from nonequilibrium measurements.
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"Molecular simulation of vapour-liquid equilibrium using beowulf clusters." Thesis, 2010. http://hdl.handle.net/10413/1541.
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