Dissertations / Theses on the topic 'Molecular simulation'
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Cai, Qiong. "Hybrid molecular dynamics simulation." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/10849.
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Bekker, Hendrik. "Molecular dynamics simulation methods revised." [Groningen] : [Groningen] : Rijksuniversiteit Groningen ; [University Library Groningen] [Host], 1996. http://irs.ub.rug.nl/ppn/14860532X.
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Do, Hainam. "Molecular simulation of simple fluids." Thesis, University of Nottingham, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546280.
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Free energy is the criterion of stability and is essential for determining phase equilibrium properties, for example. However, calculation of free energies for complex systems, such as fluids by computer simulation, is extremely difficult. In this thesis, we show how the partition function of fluids can be calculated directly from simulations; this allows us to obtain the absolute Helmholtz free energy (F) via F- -k8TInQ. Our method radically simplifies the process of calculating absolute free energies of continuous systems. As the method has been developed in the past few months, we have not yet applied it to the study of phase equilibria. This task will be part of our future work. In the rest of the thesis, we have focused on the application of more established simulation techniques to the urgent problem of finding environmentally friendly refrigerant fluids. Methane and fluoromethanes are possible candidates. However, they are flammable. 1-1-1-2-tetrafluoroethane, on the other hand, has for a long time been used in domestic refrigeration and automobile air-conditioning systems. However, it will be banned in Europe from 2011, due to concerns about its global warming impact. Carbon dioxide has received much attention as a fluid that can be used in combination with other refrigerants to minimise flammability and toxicity, and has a very low global warming potential. Thus, it could be mixed with those refrigerants to form new environmentally friendly refrigerant mixtures. Unfortunately, little information on the thermophysical properties of these mixtures is available. We simulate the thermophysical properties of these important industrial refrigerants and their mixtures with carbon dioxide using both empirical and in-house firstprinciples potentials. Simulations also provide a microscopic-level understanding of the structure of liquids, which is not accessible via experiment. Our high-quality ab initio force fields have reproduced the thermophysical properties for carbon dioxide, methane, fluorinated methanes, and mixtures of carbon dioxide and methane and carbon dioxide and fluorinated methanes. Multi-body effects play a crucial role in determining the thermophysical properties of fluids and inclusion of a three-body effect substantially improves the prediction of the phase-coexistence properties. Our studies should be of relevance to a broad range of mixtures of fluoroalkanes and carbon dioxide. Our efforts in making the first-principle force fields for carbon dioxide and fluorinated methanes pave the way for larger fluorinated hydrocarbons to come in the future.
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Foulger, Stephen Hans. "Molecular simulation of liquid crystalline." Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/11246.
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Boothroyd, Simon. "Phase equilibria from molecular simulation." Thesis, Lancaster University, 2018. http://eprints.lancs.ac.uk/126751/.
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Phase equilibria are at the heart of many properties of substances, such as their solubility, manufacturability, and stability. They are of significant industrial and commercial interest, perhaps most importantly to the pharmaceutical industry where drug stability and solubility are two of the largest challenges of drug development. The focus of this thesis then was to develop a molecular level understanding of phase equilibria, and produce tools and models to predict phase stability. An emphasis was given to exploring solid-solid and solid-liquid equilibria and stability. Specifically, the work presented here aimed to elucidate what drives the formation of multicomponent crystals, improve available models for exploring phase equilibria phenomena and explore solubility prediction from first principles as a potentially more powerful alternative to correlation based methods. These three fundamental areas were explored by employing molecular simulation in combination with the machinery of statistical mechanics, utilising advanced sampling methods and free energy calculations. This approach has led to the development of a foundation for understanding multicomponent crystal formation in terms of molecular affinities and packing, the characterisation of a set of soft coarse-grained potentials for use in phase equilibria studies, which overcome the main limitations of the most widely used potential, and finally, the development of a novel method for solubility prediction from first principles. Here, this novel method was successfully applied to an ionic (aqueous sodium chloride) and small molecular (urea in methanol and aqueous urea) system. In the future, these results are expected to lead to a set of guidelines for predicting (and perhaps prohibiting) multicomponent crystal formation, the development of a higher class of coarse-grained transferable force field with utility in studying phase equilibria, and powerful approach for predicting solubility of even large, flexible molecules (such as pharmaceuticals).
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Durandurdu, Murat. "Molecular Statics Simulation in Aluminum." Thesis, Virginia Tech, 1999. http://hdl.handle.net/10919/33528.
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Effects of dislocation emission from a mode I crack and of pinning distances on the behavior of the crack and on fracture toughness in aluminum were studied by using the Molecular Statics Technique with atomic interactions described in terms of the Embedded Atom Method.
It was found that aluminum is a ductile material in which the cracks generate dislocations, blunting the cracks. The blunting and the dislocation shielding reduce the local stress intensity factor. Also, twinning, which has not been observed experimentally in Aluminum due to the high stacking fault, was obtained in the simulation. Probably, the low temperature facilitates twin formation.
The applied stress intensity factor required to propagate the crack tip increases at first, and then becomes constant as the maximum distance that the first dislocation can travel away from the crack tip increases. These effects can be attributed to dislocation shielding and crack blunting. The maximum distance of the emitted dislocations from the crack tip is the equilibrium distance for the largest simulation performed (400,000 atoms) while for the smaller simulations the dislocations are hindered by the fixed boundary condition of the model. On the other hand, the total local stress intensity factor at the crack tip and the local stress intensity factor along the slip plane remain basically constant as the maximum distance of the emitted dislocations from the crack tip increases. For distances larger than , these local stress intensity factors start to increase slightly.
Master of Science
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Burgos, Marmol Jose Javier. "Molecular simulation of polymer nanocomposites." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/molecular-simulation-of-polymer-nanocomposites(56a195bb-81ed-4eb8-81d7-b3357d7f2316).html.
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Polymer nanocomposites (PNCs) are hybrid materials incorporating organic or inorganic nanoparticles (NPs) with at least one dimension in the submicron scale. Over the last two decades, these materials have drawn a remarkable attention due to their central role in industrial formulations and technological applications, extending from food packaging to smart coatings. Incorporating nanoparticles (NPs) to a polymer matrix can significantly alter the conformation and the mobility of the polymer chains in their proximity. Moreover, understanding the delicate balance between the enthalpic and entropic interactions is crucial to control and predict the ability of NPs to diffuse and disperse in the polymer matrix. The impact of these interactions on the structure and the dynamics of polymer chains and NPs is fully revealed in how a number of macroscopic properties changes, justifying the high interest on these materials for industrial applications. In this thesis, the impact on the structure, dynamics, viscosity and thermal conductivity of a number of microscopic properties is investigated by performing Molecular Dynamics (MD) simulations. Specifically, the PNC is represented by a coarse-grained model of a melt of linear homopolymer chains containing spherical NPs. Throughout this work, a number of parameters are modified in order to unveil possible patterns in the PNCâs performance. To this end, this work focuses on the consequences of modifying the NP size dispersity, NP-polymer chain relative size, and chainsâ degree of stiffness. Four theoretical models describing the diffusivity of NPs, three of which include nano-scale corrections, have been averaged to study the dependence of dilute NPsâ diffusivity on the NP polydispersity index. By comparing these models to the simulation results at different degrees of polydispersity, it is possible to obtain a more complete picture of their validity as compared to the monodisperse case. Regarding the diffusion of polymer chains, simulation results were in good agreement with the experimental results previously obtained by Composto and coworkers (Soft Matter 2012, 8, 6512), which relate the chainsâ diffusivity to the average interparticle distance. As far as the transport properties are concerned, they show a weaker dependence on the polydispersity index. By contrast, results on viscosity and thermal conducitivity show that they are conditioned by the polymer-NP specific interfacial area and the inverse average mass, respectively. These results are in good agreement with previous experimental results. A deeper examination of this intriguing deviation from viscosity predictions in traditional composites, reveals a non-trivial combination of thickening and thinning effects contributing to the final viscosity of the PNC. This thesis also address the influence of the chainsâ stiffness on the dynamical and viscous behaviour. An isotropic-to-nematic phase transition is observed, regardless of the NP-monomer interactions, below which a monotonic increase of both properties is observed, whereas orientationally ordered systems dramatically modify them, resulting into a steep increase or a smooth decrease depending on the direction in which they are measured.
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Freitas, Rodrigo Moura 1989. "Molecular simulation = methods and applications = Simulações moleculares : métodos e aplicações." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/278440.
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Orientador: Maurice de KoningDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin
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Resumo: Devido aos avanços conceptuais e técnicos feitos em física computacional e ciência dos materiais computacional nos estamos aptos a resolver problemas que eram inacessíveis a alguns anos atrás. Nessa dissertação estudamos a evolução de alguma destas técnicas, apresentando a teoria e técnicas de simulação computacional para estudar transições de fase de primeira ordem com ênfase nas técnicas mais avançadas de calculo de energia livre (Reversible Scaling) e métodos de simulação de eventos raros (Forward Flux Sampling) usando a técnica de simulação atomística da Dinâmica Molecular. A evolução e melhora da e ciência destas técnicas e apresentada junto com aplicações a sistemas simples que permitem solução exata e também ao caso mais complexo da transição de fase Martenstica. Também apresentamos a aplicação de métodos numéricos no estudo do modelo de Pauling para o gelo. Nos desenvolvemos e implementamos um novo algoritmo para a criação e ciente de estruturas de gelo desordenadas. Este algoritmo de geração de cristais de gelo nos permitiu criar células de gelo Ih de tamanhos que não eram possíveis antes. Usando este algoritmo abordamos o problema de efeitos de tamanho finito não estudados anteriormente
Abstract: Due to the conceptual and technical advances being made in computational physics and computational materials science we have been able to tackle problems that were inaccessible a few years ago. In this dissertation we study the evolution of some of these techniques, presenting the theory and simulation methods to study _rst order phase transitions with emphasis on state-of-the-art free-energy calculation (Reversible Scaling) and rare event (Forward Flux Sampling) methods using the atomistic simulation technique of Molecular Dynamics. The evolution and efficiency improvement of these techniques is presented together with applications to simple systems that allow exact solution as well as the more the complex case of Martensitic phase transitions. We also present the application of numerical methods to study Pauling\'s model of ice. We have developed and implemented a new algorithm for efficient generation of disordered ice structures. This ice generator algorithm allows us to create ice Ih cells of sizes not reported before. Using this algorithm we address finite size effects not studied before
Mestrado
Física
Mestre em Física
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Vaitheeswaran, Subramanian. "Computer Simulations of Partially Confined Water." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/VaitheeswaranS2004.pdf.
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Ernst, Matthew Brian. "Molecular dynamics simulation of DNA lesions." Online access for everyone, 2005. http://www.dissertations.wsu.edu/Thesis/Fall2005/m%5Fernst%5F121305.pdf.
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Naser, Md Abu. "Molecular dynamics simulation of protein adsorption." Thesis, Heriot-Watt University, 2008. http://hdl.handle.net/10399/2187.
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Wicks, Thomas J. "Molecular simulation of nucleation in polymers." Thesis, University of Nottingham, 2016. http://eprints.nottingham.ac.uk/32012/.
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We develop several new algorithms using molecular simulation to investigate the nucleation barrier of a single, freely-jointed polymer chain. In the first part of the thesis, we use a free particle model to develop a new biasing technique, which uses an automated feedback mechanism to overcome the poor sampling of crystal states in a thermodynamic system. Our feedback technique does not require any prior knowledge of the nucleation barrier and enables good representative sampling of all available states of interest. In the second part of the thesis, we simulate the nucleation barrier of the single, freely-jointed, square-well chain. We use our feedback technique and parallel tempering with a nonstandard temperature distribution to overcome poor sampling of crystal states and configuration mixing issues respectively. We also provide some comparative analysis of different choices of configurational order parameters for the single chain. Finally, we apply stretching to the chain to approximate flow-induced crystallisation and investigate the effect of different degrees of stretch on the nucleation barrier. We verify the quality of our simulation with careful monitoring of several criteria, including the acceptance ratios of configuration swaps between simulations with adjacent temperatures, evolution of the energy traces as a result of configuration swaps between tempering levels, and ensuring effective de-correlation of configurations through reptation moves. Our simulations provide strong reproducible results for the base, the peak and beyond the peak of the barrier for the quiescent and stretched single chain. We observe a remarkably strong effect of modest stretching on the nucleation barrier for a single chain, which can potentially lead to dramatic effects on the nucleation rate. Our simulation code has been made publicly available, with details provided in an appendix.
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Bos�ko, Jaroslaw Tomasz, and jbosko@unimelb edu au. "Molecular simulation of dendrimers under shear." Swinburne University of Technology. Centre for Molecular Simulation, 2005. http://adt.lib.swin.edu.au./public/adt-VSWT20050804.141034.
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In this work flow properties of dendrimers are studied with the aid of molecular simulations. For the first time the results of the nonequilibrium molecular dynamics simulations of the dendrimers in the melt are reported. Molecules are modelled at the coarse-grained level using the bead-spring model. The objective of this research is to analyse the influence of the molecular topology in the macroscopic flow behaviour of the melts. Systems of dendrimers of generations 1 to 4 undergoing planar shear are compared to the melts composed of linear chain polymers. The internal structure and shape of dendrimers is extensively analysed. The response of the molecules to the shearing in the form of stretching and alignment is studied. The correlation between the onset of shear thinning and the onset of deformation of molecules is observed. The changes in the fractal dimensionality of dendrimers due to shearing are also analysed. Dendrimers, due to their highly branched structure and compact globular conformations in the melt, are found to behave differently when sheared, compared to traditional linear polymers. Unlike linear polymers, they do not undergo transition form the Rouse to the reptation regimes. This effect is explained in terms of the suppressed entanglement between molecules. Moreover, dendrimers when compared to linear chain systems exhibit lower Newtonian viscosity, onset of the shear thinning at higher strain rates, and less pronounced shear thinning in the non-Newtonian regime. They can be used as rheology modifiers, as it is shown in the preliminary results obtained from the simulations of the dendrimers-linear polymer blends. In agreement with other theoretical and experimental studies, dendrimers in the melt are found to have compact space-filling structure with terminal groups distributed throughout the interior of the molecule. Suggestions for the further study of dendrimers via molecular simulations are made.
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Lu, Lanyuan Berkowitz Max L. "Molecular dynamics simulation of amphiphilic aggregates." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,787.
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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.Title from electronic title page (viewed Dec. 18, 2007). " ... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.
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Sturdy, Yvette Katherine. "Molecular simulation with path integral methods." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.436950.
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Sun, Jizhong. "Molecular dynamics simulation of colloidal monolayers." Thesis, University of Hull, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397087.
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Poter, Simon Christopher. "Fluid phase coexistence by molecular simulation." Thesis, University of Southampton, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242790.
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Ding, Wei. "Molecular dynamics simulation of biomembrane systems." Thesis, Queen Mary, University of London, 2018. http://qmro.qmul.ac.uk/xmlui/handle/123456789/36217.
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The fundamental structure of all biological membranes is the lipid bilayer. At- tributed to the multifaceted features of lipids and its dynamical interaction with other membrane-integrated molecules, the lipid bilayer is involved in a variety of physiological phenomena such as transmembrane transportation, cellular signalling transduction, energy storage, etc. Due to the nanoscale but high complexity of the lipid bilayer system, experimental investigation into many important processes at the molecular level is still challenging. Molecular dynamics (MD) simulation has been emerging as a powerful tool to study the lipid membrane at the nanoscale. Utilizing atomistic MD, we have quantitatively investigated the effect of lamellar and nonlamellar lipid composition changes on a series of important bilayer properties, and how membranes behave when exposed to a high-pressure environment. A series of membrane properties such as lateral pressure and dipole potential pro les are quanti ed. Results suggest the hypothesis that compositional changes, involving both lipid heads and tails, modulate crucial mechanical and electrical features of the lipid bilayer, so that a range of biological phenomena, such as the permeation through the membrane and conformational equilibria of membrane proteins, may be regulated. Furthermore, water also plays an essential role in the biomembrane system. To balance accuracy and efficiency in simulations, a coarse-grained ELBA water model was developed. Here, the ELBA water model is stress tested in terms of temperature- and pressure-related properties, as well as hydrating properties. Results show that the accuracy of the ELBA model is almost as good as conventional atomistic water models, while the computational efficiency is increased substantially.
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Yim, Shon W. 1973. "Molecular dynamics simulation of boundary lubrication." Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/44493.
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Dullweber, Andreas. "Simulation of atomic and molecular complexes." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624109.
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Banerjee, Soumik. "Molecular Simulation Of Nanoscale Transport Phenomena." Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/28252.
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Interest in nanoscale heat and mass transport has been augmented through current trends in nanotechnology research. The theme of this dissertation is to characterize electric charge, mass and thermal transport at the nanoscale using a fundamental molecular simulation method, namely molecular dynamics. This dissertation reports simulations of (1) ion intake by carbon nanotubes, (2) hydrogen storage in carbon nanotubes, (3) carbon nanotube growth and (4) nanoscale heat transfer. Ion transport is investigated in the context of desalination of a polar solution using charged carbon nanotubes. Simulations demonstrate that when either a spatially or temporally alternating charge distribution is applied, ion intake into the nanotubes is minimal. Thus, the charge distribution can either be maintained constant (for ion encapsulation) or varied (for water intake) in order to achieve different effects. Next, as an application of mass transport, the hydrogen storage characteristics of carbon nanotubes under modified conditions is reported. The findings presented in this dissertation suggest a significant increment in storage in the presence of alkali metals. The dependence of storage on the external thermodynamic conditions is analyzed and the optimal range of operating conditions is identified. Another application of mass transport is the growth mode of carbon nanostructures (viz. tip growth and base growth). A correct prediction of the dominant growth mode depends on the energy gain due to the addition of C-atoms from the carbon-metal catalyst solution to the graphene sheets forming the carbon nanostructures. This energy gain is evaluated through molecular dynamics simulations. The results suggest tip growth for Ni and base growth for Fe catalysts. Finally, unsteady nanoscale thermal transport at solid-fluid interfaces is simulated using non-equilibrium molecular dynamics simulations. It is found that the simulated temperature evolution deviates from an analytical continuum solution due to the overall system heterogeneity. Temperature discontinuities are observed between the solid-like interfaces and their neighboring fluid molecules. With an increase in the temperature of the solid wall the interfacial thermal resistance decreases.Ph. D.
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Sun, Mingqiu. "Molecular dynamics simulation of fluid systems /." The Ohio State University, 1994. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487849696964891.
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Yani, Yin. "Molecular dynamics simulation of nanocomposite materials." [Ames, Iowa : Iowa State University], 2009.
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Posocco, Paola. "Multiscale Molecular Simulation of Nanostructured Systems." Doctoral thesis, Università degli studi di Trieste, 2010. http://hdl.handle.net/10077/3445.
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2008/2009Computational materials science based on multiscale approach is very promising in the domain of nanoscience. It gives the modeler a route from the atomistic description of the system to a trust-worthy estimate of the properties of a material, obtained from the underlying molecules in a quantifiable manner. In this thesis we discuss general guidelines for its implementation in the field of nanomaterials and propose an alternative pathway to link effectively atomistic to mesoscopic scale and this, in turn, to the macroscopic scale. As proofs of concept for the reliability of the proposed approach, we consider several systems of industrial interest, ranging from polymeric nanocomposite materials, to epoxy resins, block copolymers, and gels for biomedical applications. In this context, we ascertain that multiscale molecular modelling can play a crucial role in the design of new materials whose properties are influenced by the structure at nanoscale. The results suggest that the combination of simulations at multiple scales can unleash the power of modeling and yield important insights.
Le tecniche computazionali fondate su un approccio multiscala costituiscono uno strumento molto promettente nel campo della nanoscienza e dei nanomateriali. Esse forniscono al modellatore un percorso quantitativo che parte dalla descrizione atomistica fino alle proprietà finali del materiale. In questo lavoro di tesi sono discusse le linee guida per l’implementazione della modellistica multiscala nel settore dei nanomateriali ed è proposta una strategia alternativa alle soluzioni attualmente esistenti per collegare la scala atomistica alla mesoscala e, successivamente, la mesoscala alla scala macroscopica. Per dimostrare la validità del metodo proposto, sono stati presi in esame differenti sistemi di interesse industriale, i quali comprendono materiali nanocompositi polimerici, resine epossidiche, copolimeri a blocchi, e gel per applicazioni biomediche. In questo contesto, si è evidenziato come la modellistica multiscala possa svolgere un ruolo cruciale nella progettazione di nuovi materiali le cui proprietà sono influenzate dalla struttura a scala nanometrica. I risultati suggeriscono che la combinazione di simulazioni su scale multiple amplifica sinergicamente la potenza della modellazione e può fornire importanti intuizioni.
XXII Ciclo
1978
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Stocker, Urs. "Computer simulation of biomolecules : investigation of molecular environment and simulation parameters /." [S.l.] : [s.n.], 2000. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=13686.
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Adrien, Berthault. "Molecular simulation of mixtures in lipid bilayers." Doctoral thesis, Universitat Rovira i Virgili, 2018. http://hdl.handle.net/10803/664727.
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L'objectiu principal d'aquesta tesi doctoral és estendre un mètode ràpid i fiable (camp simple de mitjana cadena) per estudiar barreges en equilibri i en particular mescles de lípids i petits col·loides inserits en membranes lipídiques, capaços de considerar la presència de components addicionals i unir models de simulació molecular i teories elàstiques per membranes anfifíliques. Per aconseguir aquest objectiu, proposem parametritzar els paràmetres amb el mètode de camp de mitjana cadena simple per reproduir les característiques de les bicapes de lípids DMPC en equilibri comparant amb resultats de simulació publicats prèviament i dades experimentals. La tesi presenta el treball realitzat per assolir els objectius específics d'aquesta tesi doctoral: dades moleculars fiables completament parametritzats capaços de reproduir el comportament de les membranes lipídiques amb un únic tipus de component, l'estudi de les seves propietats d'equilibri interactuant amb molècules addicionals i els seus efectes en la línia de tensió per al cas específic de la creació de porus i un enfocament dinàmic per a l'estudi de la dinàmica de les membranes fetes de diverses cadenes anfifíliques, en particular en presència de porusEl objetivo principal de esta tesis doctoral es extender un método rápido y confiable (campo simple de media cadena) para estudiar mezclas en equilibrio y en particular mezclas de lípidos y pequeños coloides insertados en membranas lipídicas, capaces de considerar la presencia de componentes adicionales y unir modelos de simulación molecular y teorías elásticas para membranas anfifílicas. Para lograr este objetivo, proponemos parametrizar los parámetros con el método de campo de media cadena simple para reproducir las características de las bicapas de lípidos DMPC en equilibrio comparando con resultados de simulación publicados previamente y datos experimentales. La tesis presenta el trabajo realizado para alcanzar los objetivos específicos de esta tesis doctoral: datos moleculares fiables completamente parametrizados capaces de reproducir el comportamiento de las membranas lipídicas con un único tipo de componente, el estudio de sus propiedades de equilibrio interactuando con moléculas adicionales y sus efectos en la línea de tensión para el caso específico de la creación de poros y un enfoque dinámico para el estudio de la dinámica de las membranas hechas de varias cadenas anfifílicas, en particular en presencia de poros
The main goal of this Doctoral thesis is to extend a fast and reliable method (Single Chain Mean Field) to study mixtures at equilibrium and in particular mixtures of lipids and small colloids inserted into lipid membranes, able to consider the presence of additional components and bridge molecular simulation models and elastic theories for amphiphilic membranes. In order to achieve this objective, we proposed to parametrise the parameters for the Single Chain Mean Field method to reproduce the features of DMPC lipid bilayers at equilibrium involving comparisons with previously published simulation results and experimental data. The thesis reports the work performed to achieve the specific objectives of this doctoral thesis: reliable fully parametrised molecular details able to reproduce the behaviour of lipid membranes made of a single type of component, the study of their equilibrium properties interacting with additional molecules and their effects on the line tension for the specific case of the pore creation and a dynamical approach to study the dynamics of membranes made of various amphiphilic chains, in particular in the presence of pores.
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Triandafilidi, Vasilii. "Molecular dynamics simulation of polymer crystallization process." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/54825.
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Large scale molecular dynamics simulations were carried out to study the kinetics of polymer melt crystallization. A coarse-grained model CG-PVA developed by Meyer and Muller-Plathe is applied. A new algorithm for analyzing crystallization is proposed. It is based on the alignment of individual chains which speeds up previous similar calculation by a factor of ten. Moreover, it is found to be more suitable for investigating chain crystallinity in polydisperse systems. Different thermodynamic protocols of polymer crystallization were studied: deep quench, shallow quench and cooling with various rates, as well as polymer pre-stretching and consequent cooling and quenching. Cooling with the slowest rate was shown to generate the highest terminal crystallinity values. Resulting curves were fitted using the Avrami equation that showed good agreement at the early stages of crystallization. As a result shorter chains were found to exhibit higher terminal crystallinity value than the longer ones. Pre-stretching and subsequent quenching was found to have a minor effect on thefinal crystallinity, whereas pre-stretching followed by an intermediate rate cooling was found to increase the terminal crystallinity. The effect of polydispersity was modeled via two bidisperse melts comprising of different proportion of short and long chains. Due to the presence of two relaxation times in the melt, initial stages of bidisperse polymers crystallization were found to be dominated by the short chains, whereas the final stages were dominated by the long ones. Further investigation concluded that the behavior of bidisperse melts is governed by the proportion of short and long chains in the melt. When a critical fraction of the long chains was reached, they appeared to act as baby nuclei for the short chains to attach themselves onto resulting in bundle-like fringed micelle structures. Otherwise, they acted as "molecular traps" hindering crystallization of the short chains. When a critical fraction of the short chains was reached, they were found to assist crystallization of the long chains at the initial stages of crystallization but impede crystallization dynamics at the final stages.Applied Science, Faculty of
Chemical and Biological Engineering, Department of
Graduate
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Vedell, Peter Thomas. "Boundary value approaches to molecular dynamics simulation." [Ames, Iowa : Iowa State University], 2007.
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Bjelic, Sinisa. "Molecular Simulation of Enzyme Catalysis and Inhibition." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7468.
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Anderson, K. L. "Simulation of molecular behaviour at polymeric interfaces." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596097.
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Monte Carlo computer simulation methods were used to understand molecular behaviour of polymeric materials in the condensed state near an interface. The 'interfaces' studied were between an amorphous polymer and (a) air, (b) another amorphous polymer, and (c) a polymer crystal. Three specific cases were examined: interfacial induced ordering and dynamics, diffusion across an interface and crystallisation and phase transitions. A calibrated model of a polymer system illustrates the computational possibilities that now exist in what has mainly been an experimental and theoretical approach to polymer surface science. Molecular ordering at the polymer-air interface was examined for various molecular weights of atactic poly(styrene), and directly compared to experiment and theory. The actual radius of gyration of polymer chains was shown to be directly observable using scanning force microscopy and lattice chain simulations, leading to a new method of molecular weight characterisation. Furthermore, dynamic analysis of this system hinted at a depression of the glass transition temperature near the free surface. Dynamic simulation of polymer-polymer interfaces, where diffusion across the interface leads to a loss of order and eventual disappearance of the interface, led to very promising results. The diffusion and disordering processes were examined in the cases of polydisperse and semi-flexible chain systems, in which there is inherent ordering. In polydisperse systems, the lower molecular weight polymer solubilises larger polymers, leading to shorter weld-times. However, this does not necessarily lead to increased weld strength. Chain stiffness had a tremendous effect on weld strength, with stiff chains oriented normal to the weld plane producing the most interdiffusion and strength development. A modified version of the Sadler/Gilmer model was used to probe interfacial growth kinetics and thermodynamics for forming a polymer crystal. A study of the phase transitions from amorphous polymer to mobile polymer crystal, and then to stable crystal, was undertaken within the context of competing energies of the crystal-amorphous interface and bulk crystalline regions. The model reproduced the theoretical and the experimental results published to date. Given more experimental data, these predictions could be tested even more rigorously.
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Lion, Thomas. "Osmosis : a molecular dynamics computer simulation study." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7877.
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Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modi cation to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modi cation on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures.
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Minoukadeh, Kimiya. "Deterministic and stochastic methods for molecular simulation." Phd thesis, Université Paris-Est, 2010. http://tel.archives-ouvertes.fr/tel-00597694.
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Molecular simulation is an essential tool in understanding complex chemical and biochemical processes as real-life experiments prove increasingly costly or infeasible in practice . This thesis is devoted to methodological aspects of molecular simulation, with a particular focus on computing transition paths and their associated free energy profiles. The first part is dedicated to computational methods for reaction path and transition state searches on a potential energy surface. In Chapter 3 we propose an improvement to a widely-used transition state search method, the Activation Relaxation Technique (ART). We also present a local convergence study of a prototypical algorithm. The second part is dedicated to free energy computations. We focus in particular on an adaptive importance sampling technique, the Adaptive Biasing Force (ABF) method. The first contribution to this field, presented in Chapter 5, consists in showing the applicability to a large molecular system of a new parallel implementation, named multiple-walker ABF (MW-ABF). Numerical experiments demonstrated the robustness of MW-ABF against artefacts arising due to poorly chosen or oversimplified reaction coordinates. These numerical findings inspired a new study of the longtime convergence of the ABF method, as presented in Chapter 6. By studying a slightly modified model, we back our numerical results by showing a faster theoretical rate of convergence of ABF than was previously shown
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Harrell, Anthony F. "Molecular dynamic modeling and simulation for polymers." Thesis, Monterey, California. Naval Postgraduate School, 2012.
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Approved for public release; distribution in unlimited.Polymers have been widely used in various engineering applications. For more than a quarter century, the materials have been utilized intensively for the binding materials for composites. The material properties of the binding materials called matrix materials play an important role for the composite material behaviors. As a result, the objective of this study was to understand the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity. To this end, molecular dynamics was used to model and simulate the polymeric behaviors. Polymeric chains were modeled using the bead and spring model along with interacting potentials. The study examined the effects of different sizes, densities, and numbers of molecules per chain on the shear moduli of the polymers. Furthermore, some preliminary study was also conducted for metallic particle reinforced polymer composites.
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Calmiano, Mark Daniel. "Computer simulation of molecular sorption in zeolites." Thesis, University College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.249244.
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Sanchez-Castillo, Francisco Xavier. "Compaction of powders by molecular dynamics simulation." Thesis, King's College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272141.
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Alsayegh, Rajab. "Vision-augmented molecular dynamics simulation of nanoindentation." Thesis, Brunel University, 2016. http://bura.brunel.ac.uk/handle/2438/13660.
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This thesis has contributed to the literature by providing a pathway to simplify the process of carrying out molecular dynamics simulation. As a part of the investigation, a user-friendly vision-augmented technique was developed to set up and carry out atomistic simulations using hand-gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of preparing and carrying out molecular dynamics simulations in a more intuitive way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by performing parallel molecular dynamics simulations to study (i) crystal anisotropy of a diamond cubic substrate (crystalline silicon) using nanoindentation with a long-range (Screened bond order) Tersoff potential and (ii) crystal anisotropy of a body centre cubic metal (tantalum) using nanoindentation with an Embedded Atomic Method (EAM) type potential. The MD data was post-processed to reveal size effects observed in anisotropy of both these materials, namely, silicon and tantalum. The value of hardness and elastic modulus obtained from the MD data was found in accordance with what has been discovered previously by experiments, thereby validating the simulations. Based on this, it is anticipated that the proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.
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Parris, P. "Molecular simulation studies in the supercritical region." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/134245/.
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In our work, we employed molecular dynamics and Monte Carlo (MC) simulations to investigate the supercritical phase of carbon dioxide near its critical point. Three systems have been studied. The pure carbon dioxide, mixture methane + carbon dioxide at infinite dilution of supercritical carbon dioxide and water + carbon dioxide at infinite dilution of supercritical carbon dioxide. The usage of molecular simulation methods in supercritical region gave us a distinct advantage of knowing the microstructure of the systems in a qualitative and quantitative way. The Kirkwood-Buff theory, which predicts the influence of the solvent on the solute, enabled us to predict thermodynamic properties of supercritical phase and compare them with experimental values. We have examined the density effect on structure of the pure carbon dioxide and its solutions along its critical isotherm 4 K above its critical point. We focused our research and we present results for two basic sections, A. Equilibrium and transport properties, namely Volumetric properties; Average configurational energy; Isothermal compressibility; Diffusivity; and the Isochoric heat capacity B. Solution structures at infinite solutions, namely Radial distribution function; and Coordination number We discuss the outcomes based on the density inhomogeneities of the solvent and critical fluctuations, which are maximised at the critical point. We found that the addition of methane to supercritical carbon dioxide increases the volume of the solution and a cavitation is formed around it. On the hand, the addition of water gives a cluster around it in local structure and decrease the volume of solution. We report results also of the diffusion coefficients for the pure carbon dioxide and the mixtures in this study, which it shows an anomalous decrease close to the critical point of the pure carbon dioxide. It is a general conclusion for all the properties we have studied that the density dependence along the isotherm is maximised at densities close to the critical one. Further, the usage of both molecular dynamics and Monte Carlo in supercritical regions validates the extension of the techniques in the supercritical region and reveals their limitations.
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Sweet, Christopher Richard. "Hamiltonian thermostatting techniques for molecular dynamics simulation." Thesis, University of Leicester, 2004. http://hdl.handle.net/2381/30526.
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Molecular dynamics trajectories that sample from a Gibbs, or canonical, distribution can be generated by introducing a modified Hamiltonian with additional degrees of freedom as described by Nose [46]. Although this method has found widespread use in its time re-parameterized Nose-Hoover form, the lack of a Hamiltonian, and the need to 'tune' thermostatting parameters has limited, its use compared to stochastic methods. In addition, since the proof of the correct sampling is based on an ergodic assumption, thermostatting small of stiff systems often does not given the correct distributions unless the Nose-Hoover chains [43] method is used, which inherits the Nose-Hoover deficiencies noted above. More recently the introduction of the Hamiltonian Nose-Poincare method [11], where symplectic integrators can be used for improved long term stability, has renewed interest in the possibility of Hamiltonian methods which can improve dynamical sampling. This class of methods, although applicable to small systems, has applications in large scale systems with complex chemical structure, such as protein-bath and quantum-classical models.;For Nose dynamics, it is often stated that the system is driven to equilibrium through a resonant interaction between the self-oscillation frequency of the thermostat variable and a natural frequency of the underlying system. By the introduction of multiple thermostat Hamiltonian formulations, which are not restricted to chains, it has been possible to clarify this perspective, using harmonic models, and exhibit practical deficiencies of the standard Nose-chain approach. This has led to the introduction of two Hamiltonian schemes, the Nose-Poincare chains method and the Recursive Multiple Thermostat (RMT) method. The RMT method obtains canonical sampling without the stability problems encountered with chains with the advantage that the choice of Nose mass is independent of the underlying system.
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Mitchell, Felicity. "Modelling protein flexibility using molecular simulation methods." Thesis, University of Manchester, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525167.
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Ahammed, Ballal. "MOLECULAR DYNAMICS SIMULATION OF SELF-HEALING POLYMERS." Miami University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=miami1564686567714321.
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Harrell, Anthony F. "Molecular dynamic modeling and simulation for polymers /." [United States] : Storming Media, 2003. http://library.nps.navy.mil/uhtbin/hyperion-image/03sep%5FHarrell.pdf.
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Chen, Jingzhi. "Molecular dynamics simulation of the self-assembly of icosahedral virus." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS326/document.
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Les virus sont connus pour infecter toutes les classes d’organismes vivants sur Terre, qu’elles soient végétales ou animales. Les virions consistent en un génome d'acide nucléique protégé par une enveloppe protéique unique ou multicouche appelée capside et, dans certains cas, par une enveloppe de lipides. La capside virale est généralement composée de centaines ou de milliers de protéines formant des structures ordonnées. La moitié des virus connus présentent une symétrie icosaédrique, les autres étant hélicoïdaux, prolats ou de structure irrégulière complexe. Récemment, les particules virales ont attiré une attention croissante en raison de leur structure extrêmement régulière et de leur utilisation potentielle pour la fabrication de nanostructures ayant diverses fonctions. Par conséquent, la compréhension des mécanismes d'assemblage sous-jacents à la production de particules virales est non seulement utile au développement d'inhibiteurs à des fins thérapeutiques, mais elle devrait également ouvrir de nouvelles voies pour l'auto-assemblage de matériaux supramoléculaires complexes. À ce jour, de nombreuses études expérimentales et théoriques sur l'assemblage de virus ont été effectuées. Des recherches expérimentales ont permis d'obtenir de nombreuses informations sur l'assemblage du virus, y compris les conditions appropriées requises pour l'assemblage et les voies cinétiques. En combinant ces informations et méthodes théoriques, une première compréhension du mécanisme d'assemblage des virus a été élaborée. Cependant, les informations provenant uniquement d'expériences ne peuvent donner une image complète, en particulier à l'échelle microscopique. Par conséquent, dans cette thèse, nous avons utilisé des simulations informatiques, y compris des techniques de Monte Carlo et de la dynamique moléculaire, pour sonder l’assemblage du virus, dans l’espoir de mieux comprendre les mécanismes moléculaires en jeuViruses are known for infecting all classes of living organisms on Earth, whether vegetal or animal. Virions consist of a nucleic acid genome protected by a single or multilayered protein shell called capsid, and in some cases by an envelope of lipids. The viral capsid is generally made of hundreds or thousands of proteins forming ordered structures. Half of all known viruses exhibit an icosahedral symmetry, the rest being helical, prolate or having a complex irregular structure. Recently, viral particles have attracted an increasing attention due to their extremely regular structure and their potential use for fabricating nanostructures with various functions. Therefore, understanding the assembly mechanisms underlying the production of viral particles is not only helpful to the development of inhibitors for therapeutic purpose, but it should also open new routes for the self-assembly of complex supramolecular materials. To date, numerous experimental and theoretical investigations on virus assembly have been performed. Through experimental investigations, a lot of information have been obtained on virus assembly, including the proper conditions required for the assembly and the kinetic pathways. Combining those information and theoretical methods, an initial understanding of the assembly mechanism of viruses has been worked out. However, information coming purely from experiments cannot give the whole picture, in particular at a microscopic scale. Therefore, in this thesis, we employed computer simulations, including Monte Carlo and molecular dynamics techniques, to probe the assembly of virus, with the expectation to gain new insights into the molecular mechanisms at play
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Gunnerson, Kim Noreen. "Computer simulation studies of molecular interactions by application of classical molecular dynamics /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/8668.
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Corry, Ben Alexander. "Simulation studies of biological ion channels." View thesis entry in Australian Digital Theses Program, 2002. http://thesis.anu.edu.au/public/adt-ANU20030423.162927/index.html.
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Chui, Yu-hang, and 崔宇恒. "Molecular simulations of metal nanoparticles." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B29288733.
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Chen, Zhaoyang. "Molecular dynamics simulation of charged dusts in plasmas." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=971847266.
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Vashisth, Harish Abrams Cameron F. "Molecular simulation studies of the insulin receptor family /." Philadelphia, Pa. : Drexel University, 2010. http://hdl.handle.net/1860/3295.
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Kormann, Katharina. "Efficient and Reliable Simulation of Quantum Molecular Dynamics." Doctoral thesis, Uppsala universitet, Avdelningen för beräkningsvetenskap, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-180251.
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The time-dependent Schrödinger equation (TDSE) models the quantum nature of molecular processes. Numerical simulations based on the TDSE help in understanding and predicting the outcome of chemical reactions. This thesis is dedicated to the derivation and analysis of efficient and reliable simulation tools for the TDSE, with a particular focus on models for the interaction of molecules with time-dependent electromagnetic fields. Various time propagators are compared for this setting and an efficient fourth-order commutator-free Magnus-Lanczos propagator is derived. For the Lanczos method, several communication-reducing variants are studied for an implementation on clusters of multi-core processors. Global error estimation for the Magnus propagator is devised using a posteriori error estimation theory. In doing so, the self-adjointness of the linear Schrödinger equation is exploited to avoid solving an adjoint equation. Efficiency and effectiveness of the estimate are demonstrated for both bounded and unbounded states. The temporal approximation is combined with adaptive spectral elements in space. Lagrange elements based on Gauss-Lobatto nodes are employed to avoid nondiagonal mass matrices and ill-conditioning at high order. A matrix-free implementation for the evaluation of the spectral element operators is presented. The framework uses hybrid parallelism and enables significant computational speed-up as well as the solution of larger problems compared to traditional implementations relying on sparse matrices. As an alternative to grid-based methods, radial basis functions in a Galerkin setting are proposed and analyzed. It is found that considerably higher accuracy can be obtained with the same number of basis functions compared to the Fourier method. Another direction of research presented in this thesis is a new algorithm for quantum optimal control: The field is optimized in the frequency domain where the dimensionality of the optimization problem can drastically be reduced. In this way, it becomes feasible to use a quasi-Newton method to solve the problem.eSSENCE
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Erastova, Valentina. "Molecular simulation studies of diesel and diesel additives." Thesis, Durham University, 2012. http://etheses.dur.ac.uk/6361/.
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As diesel fuel is cooled down, waxes are deposited, which are made up from crystals of long chain n-alkanes. Wax depositions are undesirable, since they can block anything from filters in diesel engines to pipelines. It is already known that wax formation can be inhibited by the addition of wax crystal modifiers to diesel fuel. This thesis em- ploys computational models at atomistic and coarse-grained levels to investigate the crystallisation of diesel fuel and the effect of additives upon the crystallisation process. In the first results section, a model for diesel fuel is introduced and a strategy for investigating its crystallisation is developed. Crystallisation was observed from pure n-tricosane, binary and tertiary mixtures of paraffins of similar chain lengths. These systems were found to crystallise into hexagonally arranged lamellae. The presence of different length alkanes was found to create gauche disorders, leading to the formation of lamellar layers with softer edges. It was also found that crystal growth could be simulated more efficiently in the presence of a positionally restrained crystal, acting as a nucleation centre. Subsequently, crystallisation of paraffins, and the solvent effect upon it, was studied. This allowed to establish behavioural trends characteristic for aromatic and aliphatic solvents. Finally, paraffin crystallisation in the presence of four common additives was investigated. A common mode of action for these additives was identified, based upon partial co-crystallisation of additive alkyl chains and paraffin molecules. The main drawback of atomistic simulation is the computational cost, which limits both the time and length scales accessible on modern computers. In order to overcome these inherent limitations, a coarse grained model was developed for a range of n-alkanes. Remarkably, the model shows transferability over 120 K, preserving thermodynamic and structural properties of both melt and crystal. In summary, this thesis provides a detailed picture of diesel crystallisation at a molecular level, and provides new insights into the mechanism of action of a number of common diesel additives.
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Klingelhoefer, Jochen W. "Biophysics of nanopores-multiscale molecular dynamics simulation studies." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540136.
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