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1
Grinberg, Farida. "Ultraslow molecular dynamics of organized fluids". Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-196884.
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Zhang, Junfang. "Computer simulation of nanorheology for inhomogenous fluids". Australasian Digital Thesis Program, 2005. http://adt.lib.swin.edu.au/public/adt-VSWT20050620.095154.
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Thesis (PhD) - Swinburne University of Technology, School of Information Technology, Centre for Molecular Simulation - 2005.A thesis submitted in fulfilment of requirements for the degree of Doctor of Philosophy, Centre for Molecular Simulation, School of Information Technology, Swinburne University of Technology - 2005. Typescript. Bibliography: p. 164-170.
3
Brookes, Sarah. "Fluids in Nanopores". Thesis, Griffith University, 2016. http://hdl.handle.net/10072/365467.
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Molecular modelling plays an important and complementary role to experimental studies. In this thesis we use molecular dynamic simulations and time correlation functions to examine the isomerization of n-butane and to perform a proof-of-concept demonstration, applying the dissipation theorem to calculating transport properties.
Equilibrium molecular dynamics are used to determine the solvent shift and rate constants in the isomerization process of n-butane. Furthermore the effects of confining n-butane to a nanopore are examined and compared to in two different wall-models. The structure and dynamics of a fluid can be affected when confined to pores of nanometre widths. An understanding of the effects of confinement on the equilibrium composition of reacting mixtures, diffusion and adsorption rates, can lead to improvements in industrial processes such as in the food and pharmaceutical industry. A known effect of confinement is wetting of the walls due to interactions between the wall and the fluid. Examination of the local molecular fluid density across the pore has shown that the degree of wetting is a function of pore width, mean fluid density and wall surface density.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Natural Sciences
Science, Environment, Engineering and Technology
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Siavosh-Haghighi, Ali. "Topics in molecular dynamics". free to MU campus, to others for purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p3164542.
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Vyalov, Ivan. "Molecular dynamics simulation of dissolution of cellulose in supercritical fluids and mixtures of cosolvents/supercritical fluids". Thesis, Lille 1, 2011. http://www.theses.fr/2011LIL10178/document.
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La cellulose est le polymère naturel le plus abondant. Cependant son utilisation est limitée par sa faible dissolution due à des liaisons hydrogènes intra et inter moléculaires. Jusqu’à aujourd’hui des solvants toxiques sont utilisés dans les procédés de dissolutions de la cellulose. Par conséquent de nouveaux solvants pour la dissolution de la cellulose ont été intensivement étudiés comme solutions de rechange de ces procédés polluants. Une des solutions est d’utiliser la technologie des fluides supercritiques utilisant le dioxyde de carbone. Malheureusement, la cellulose reste insoluble dans le CO2 dans les conditions supercritiques et il est donc important d'étudier un mélange binaire d’un co-solvant (organique ou liquide ionique) et le CO2 pour le développement d’un nouveau procédé. Cependant la connaissance du point fondamental des paramètres contrôlant le processus de dissolution dans ces fluides ralentit le développement de l’utilisation de cet outil propre et peu couteux en énergie. Nous avons donc utilisé la simulation de dynamique moléculaire pour caractériser le processus de dissolution de la cellulose dans ces fluides. Pour cela, nous nous sommes intéressés aux fluides supercritiques purs, puis aux mélanges des fluides supercritiques avec un co-solvant et enfin nous avons étudié le processus de dissolution de modèle de celluloses et de caractériser l’effet de la pression, la température, la composition du mélange ainsi que les propriétés structurales de ces modèles de cellulose sur le processus de dissolutionCellulose is insoluble in neat supercritical CO2 and the main objective of this work was to investigate mixtures of scCO2 with polar cosolvents for the development of new processing technologies for the cellulose dissolution. The objective is achieved by studying the dissolution process of monomer of cellulose and its various polymorphs. The effect of the t/d parameters on the dissolution process was analyzed by molecular dynamics simulation. We begin with analyzing structure of pure supercritical fluids and mixtures of supercritical fluids/cosolvents using unconvential tools: Voronoi tesselations and nearest neighbours approach.Thermodynamics of the mixtures of scCO2/cosolvents is analysed in order to check the validity of the potential models used in our simulations for what the method of thermodynamic integration to calculate the energy, entropy and free energy of mixing was applied. To analyze the dissolution of cellulose we started from studying the solvation free energy of cellobiose(cellulose monomer) which was calculated from molecular dynamics simulations using free energy perturbation method. The influence of conformational degrees of freedom on solvation free energy of cellobiose was also considered.Finally, the direct dissolution of cellulose crystals models in well-known good cellulose solvent(1-ethyl-3-methylimidazolium chloride) and then considered supercritical solvents. It was found that various mixtures of CO2 with cosolvents do not dissolve cellulose but they can considerably affect its crystalline structure whereas ammonia fluid can dissolve cellulose and this process is significantly influenced by temperature, pressure and density
6
Grinberg, Farida. "Ultraslow molecular dynamics of organized fluids: NMR experiments and Monte-Carlo simulations". Diffusion fundamentals 2 (2005) 119, S. 1-2, 2005. https://ul.qucosa.de/id/qucosa%3A14460.
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Muscatello, Jordan. "Heat transport in fluids and interfaces via non-equilibrium molecular dynamics simulations". Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/11081.
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In this thesis non-equilibrium molecular dynamics is used to investigate effects relating to thermal transport in fluids and interfacial systems. Non-equilibrium molecular dynamics (NEMD) simulations of liquid water were undertaken using the Modified Central Force model (MCFM) of water. Non-equilibrium thermodynamics predicts dipolar alignment as a response to an applied temperature gradient. This effect was systematically investigated by applying thermal gradients of up to 4 K/ Å to a system of MCFM water. This yielded induced electric fields of up to ~ 109 Vm-1. The predictions of non-equilibrium thermodynamics were supported by the simulations. The mechanism of thermal transport was investigated. The effect of electrostatic interactions on the thermal transport properties was also investigated in this model comparing the Ewald summation and Wolf methods. It was found that whilst the change in equation of state using each method is small, the truncation of the electrostatic interactions leads to a lower heat flux density and values for the thermal conductivity that are ~ 5 - 10% lower. The relaxation of the system to a steady-state temperature gradient was also investigated and the timescales involved were found to agree with the results using the macroscopic heat equation. The hydrogen bonding contribution to the heat flux vector was investigated. This was found to contribute to around 30-40% of the total heat flux for MCFM water. The potential energy contribution was found to become negative towards lower temperatures. Also investigated was the thermal conductivity of glassy water with the aim of identifying a difference in the thermal conductivity from liquid to the glass state. The SPC/E model was employed for this purpose but no significant change was identified. NEMD simulations were employed to investigate the interfacial thermal resistance of liquid/vapour and solid/vapour interfaces in a Lennard-Jones system. For energy fluxes of ≈107 Wm-2 a significant interfacial thermal resistance was observed, particularly at low temperatures. To investigate the microscopic origin of the interfacial thermal resistance, the intrinsic sampling method was employed in the liquid/vapour interface. The temperature drop was found to occur in front of the interface in a region where adsorbed atoms at the surface correspond to a density peak in the vapour phase.
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Alekseeva, Uliana [Verfasser]. "Adaptive resolution simulations : combining multi-particle-collision dynamics and molecular dynamics simulations for fluids / Uliana Alekseeva". Aachen : Hochschulbibliothek der Rheinisch-Westfälischen Technischen Hochschule Aachen, 2014. http://d-nb.info/105230351X/34.
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Bos�ko, Jaroslaw Tomasz, i 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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Liu, Qianli Zewail Ahmed H. Zewail Ahmed H. "Femtosecond real-time dynamics of solvation : molecular reactions in clusters and supercritical fluids /". Diss., Pasadena, Calif. : California Institute of Technology, 1997. http://resolver.caltech.edu/CaltechETD:etd-04072008-091702.
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Marcelli, Gianluca, i g. marcelli@imperial ac uk. "The role of three-body interactions on the equilibrium and non-equilibrium properties of fluids from molecular simulation". Swinburne University of Technology. Centre for Molecular Simulation, 2001. http://adt.lib.swin.edu.au./public/adt-VSWT20060112.082425.
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The aim of this work is to use molecular simulation to investigate the role of
three-body interatomic potentials in noble gas systems for two distinct
phenomena: phase equilibria and shear flow. In particular we studied the
vapour-liquid coexisting phase for pure systems (argon, krypton and xenon) and
for an argon-krypton mixture, utilizing the technique called Monte Carlo Gibbs
ensemble. We also studied the dependence of the shear viscosity, pressure and
energy with the strain rate in planar Couette flow, using a non-equilibrium
molecular simulation (NEMD) technique.
The results we present in this work demonstrate that three-body interactions
play an important role in the overall interatomic interactions of noble gases. This
is demonstrated by the good agreement between our simulation results and the
experimental data for both equilibrium and non-equilibrium systems.
The good results for vapour-liquid coexisting phases encourage performing
further computer simulations with realistic potentials. This may improve the
prediction of quantities like critical temperature and density, in particular of
substances for which these properties are difficult to obtain from experiment.
We have demonstrated that use of accurate two- and three-body potentials for
shearing liquid argon and xenon displays significant departure from the
expected strain rate dependencies of the pressure, energy and shear viscosity.
For the first time, the pressure is convincingly observed to vary linearly with an
apparent analytic y2 dependence, in contrast to the predicted y3/2 dependence
of mode -coupling theory. Our best extrapolation of the zero -shear viscosity for
argon gives excellent agreement (within 1%) with the known experimental data.
To the best of our knowledge, this the first time that such accuracy has been
achieved with NEMD simulations. This encourages performing simulations with
accurate potentials for transport properties.
12
Yang, Chenxing. "Simulation studies of liquids, supercritical fluids and radiation damage effects". Thesis, Queen Mary, University of London, 2017. http://qmro.qmul.ac.uk/xmlui/handle/123456789/24858.
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The work in this thesis aims to gain fundamental understanding of several important types of disordered systems, including liquids, supercritical fluids and amorphous solids on the basis of extensive molecular dynamics simulations. I begin with studying the diffusion in amorphous zirconolite, a potential waste form to encapsulate highly radioactive nuclear waste. I find that amorphization has a dramatic effect for diffusion. Interestingly and differently from previous understanding, diffusion increases as a result of amorphization at constant density. Another interesting insight is related to different response of diffusion of different atomic species to structural disorder. I calculate activation energies and diffusion pre-factors which can be used to predict long-term diffusion properties in this system. This improves our understanding of how waste forms operate and provides a quantitative tool to predict their performance. I subsequently study the effects of phase coexistence and phase decomposition in Y-stabilized zirconia, the system of interest in many industrial applications including in encapsulating nuclear waste due to its exceptional resistance to radiation damage. For the first time I show how the microstructure emerges and evolves in this system and demonstrate its importance for self-diffusion and other properties. This has not been observed before and is important for better understanding of existing experiments and planning the new ones. I subsequently address dynamical properties of subcritical liquids and supercritical fluids. I start with developing a new empirical potential for CO2 with improved performance. Using this and other potentials, I simulate the properties of supercritical H2O, CO2 and CH4 and map their Frenkel lines in the supercritical region of the phase diagram. I observe that the Frenkel line for CO2 coincides with experimentally found maxima of solubility and explain this finding by noting that the Frenkel line corresponds to the optimal combination of density and temperature where the density is maximal and the diffusion is still in the fast gas-like regime. This can serve as a guide in future applications of supercritical fluids and will result in their more efficient use in dissolving and extracting applications. I extend my study to collective modes in liquids. Here, my simulations provide first direct evidence that a gap emerges and evolves in the reciprocal space in transverse spectra of liquids. I show that the gap increases with temperature and is inversely proportional to liquid relaxation time. Interestingly, the gap emerges and evolves not only in subcritical liquids but also in supercritical fluids as long as they are below the Frenkel line. Given the importance of phonons in condensed matter physics and other areas of physics, I propose that the discovery of the gap represents a paradigm change. There is an active interest in the dynamics of liquids and supercritical fluids, and I therefore hope that my results will quickly stimulate high-temperature and high-pressure experiments aimed at detecting and studying the gap in several important systems.
13
Loya, Adil. "Large scale dynamic molecular modelling of metal oxide nanoparticles in engineering and biological fluids". Thesis, University of Hertfordshire, 2015. http://hdl.handle.net/2299/15336.
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Nanoparticles (NP) offer great merits over controlling thermal, chemical and physical properties when compared to their micro-sized counterparts. The effectiveness of the dispersion of the NP is the key aspect of the applications in nanotechnology. The project studies the characterization and modification of functional NPs aided by the means of large scale molecular thermal dynamic computerized dispersing simulations, in the level of Nanoclusters (NC). Carrying out NP functionality characterisation in fluids can be enhanced, and analysed through computational simulation based on their interactions with fluidic media; in terms of thermo-mechanical, dynamic, physical, chemical and rheological properties. From the engineering perspective, effective characterizations of the nanofluids have also been carried out based on the particles sizes and particle-fluids Brownian motion (BM) theory. The study covered firstly, investigation of the pure CuO NP diffusion in water and hydrocarbon fluids, secondly, examination of the modified CuO NP diffusion in water. In both cases the studies were put under experiments and simulations for data collection and comparison. For simulation the COMPASS forcefield, smoothed particle hydrodynamic potential (SPH) and discrete particle dynamics potential (DPD) were implemented through the system. Excellent prediction of BM, Van der Waals interaction, electrostatic interaction and a number of force-fields in the system were exploited. The experimental results trend demonstrated high coherence with the simulation results. At first the diffusion coefficient was found to be 1.7e-8m2/s in the study of CuO NC in water based fluidic system. Secondly highly concurrent simulation results (i.e. data for viscosity and thermal conductivity) have been computed to experimental coherence. The viscosity trend of MD simulation and experimental results show a high level of convergence for temperatures between 303-323K. The simulated thermal conductivity of the water-CuO nanofluid was between 0.6—0.75W•m−1•K−1, showing a slight increase following a rise in temperature from 303 to 323 K. Moreover, the alkane-CuO nanofluid experimental and simulated work was also carried out, for analysing the thermo-physical quantities. The alkane-CuO nanofluid viscosity was found 0.9—2.7mpas and thermal conductivity is between 0.1—0.4W•m−1•K−1. Finally, the successful modification of the NPs on experimental and simulation platform has been analysed using different characterization variables. Experimental modification data has been quantified by using Fourier Transformation Infrared (FTIR) peak response, from particular ranges of interest i.e. 1667-1609cm-1 and 1668-1557cm-1. These FTIR peaks deduced Carboxylate attachment on the surface of NPs. Later, MD simulation was approached to mimic experimental setup of modification chemistry and similar agglomerations were observed as during experimental conditions. However, this approach has not been presented before; therefore this study has a significant impact on describing the agglomeration of modified NPs on simulation and experimental basis. Henceforth, the methodology established for metal oxide nanoparticle dispersion simulation is a novelty of this work.
14
Shinto, Hiroyui. "Interfacial Microstructures and Interaction Forces between Colloidal Particles in Simple and complex Fluids-Molecular Dynamics Simulation-". Kyoto University, 1999. http://hdl.handle.net/2433/77943.
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Porras, Vazquez Alejandro. "A molecular approach to the ultimate friction response of confined fluids". Thesis, Lyon, 2019. http://www.theses.fr/2019LYSEI087.
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Afin de contrôler les pertes d'énergie dans les systèmes mécaniques, un film mince de lubrifiant est souvent introduit entre les solides en contact. Les contacts lubrifiés ponctuels fonctionnent en régime élastohydrodynamique, caractérisé par des pressions élevées (de l’ordre du GPa) et des épaisseurs de film minces (de l’ordre de 100 nanomètres). A des taux de cisaillement élevés, le fluide peut présenter une contrainte de cisaillement limite dont l’origine physique est encore incertaine. Actuellement, les modèles empiriques disponibles pour la prédiction du frottement ne décrivent pas la réponse ultime des lubrifiants dans ces conditions sévères. De plus, l'analyse expérimentale in-situ est très difficile à réaliser en raison du confinement et des fortes pressions. Ainsi, dans cette thèse, le problème est abordé sous l’angle de la modélisation à l’échelle atomique. Le comportement en cisaillement de trois de fluides (un fluide de traction, un lubrifiant modèle et un lubrifiant industriel pour le secteur aérospatial) est analysé par simulation Dynamique Moléculaire. Les résultats numériques sont ensuite comparés qualitativement et quantitativement à des essais expérimentaux. La réponse en frottement est indépendante du profile de vitesse dans l’épaisseur du confinement, ce dernier apparaissant plutôt comme une conséquence des conditions limites aux surfaces. Le régime de frottement limite apparaît naturellement lorsque le lubrifiant est soumis à des conditions thermodynamiques caractéristiques d’un état solide. Dans ce cas, la dynamique des molécules est fortement ralentie. L’énergie d’activation augmente rapidement avec la pression, de sorte que la diffusion devient négligeable à forte pression, même aux taux de cisaillement sévères imposés dans les simulations Dynamique Moléculaire. La réponse macroscopique à ce phénomène est donc une saturation de la valeur du frottement. Ce travail s’achève en jetant les bases d’une modélisation qui pourra permettre la prédiction du frottement lubrifié sous conditions sévèresIn order to control energy losses in mechanical systems, a thin film of lubricant is often introduced between the solids in contact. The lubricated point contacts operate in the elastohydrodynamic regime, characterized by high pressures (of the order of GPa) and thin film thicknesses (of the order of 100 nanometers). At high shear rates, the fluid may exhibit a limiting shear stress whose physical origin is still uncertain. At present, the empirical models available for the prediction of friction fail to describe the ultimate response of lubricants at these severe operating conditions. In addition, in-situ experimental analysis is very difficult to achieve due to confinement and high pressures. Thus, in this thesis, the problem is approached from the angle of modeling at the atomic scale. The shear behavior of three fluids (a traction fluid, a model lubricant and an industrial lubricant for the aerospace industry) is analyzed by Molecular Dynamics Simulation. The numerical results are then compared qualitatively and quantitatively with experimental tests. The friction response is independent of the velocity profile in the confinement thickness, the latter appearing rather as a consequence of boundary conditions at the surfaces. The limiting friction regime naturally occurs when the lubricant is subjected to thermodynamic conditions characteristic of a solid state. In this case, the dynamics of the molecules is strongly slowed down. The activation energy increases rapidly with the pressure, so that the diffusion becomes negligible at high pressure, even at the severe shear rates imposed in the Molecular Dynamics simulations. The macroscopic response to this phenomenon is thus a saturation of the value of friction. This work ends by laying the foundations of a modeling that will allow the prediction of lubricated friction under severe conditions
16
Merchan, Alvarez Lina Paola. "Alkane fluids confined and compressed by two smooth gold crystalline surfaces: pure liquids and mixtures". Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/47551.
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With the use of grand canonical molecular dynamics, we studied the slow ompression(0.01m/s) of very thin liquid films made of equimolar mixtures of short and long alkane chains (hexane and hexadecane), and branched and unbranched alkanes (phytane and hexadecane). Besides comparing how these mixtures behave under constant speed compression, we will compare their properties with the behavior and structure of
the pure systems undergoing the same type of slow compression. To understand the arrangement of the molecules inside the confinement, we present segmental and molecular density profiles, average length and orientation of the molecules inside well layered gaps. To observe the effects of the compression on the fluids, we present the number of confined molecules, the inlayer orientation, the solvation force and the inlayer diffusion coefficient, versus the thickness of the gap. We
observe that pure hexadecane, although liquid at this temperature, starts presenting strong solid-like behavior when it is compressed to thicknesses under 3nm, while pure hexane and pure phytane continue to behave liquid-like except at 1.3nm when they show some weak solid-like features. When hexadecane is mixed with the short straight hexane, it remains liquid down to 2.8nm at which point this mixture behaves solid-like with an enhanced alignment of the long molecules not seen in its pure form; but when hexadecane is mixed with the branched phytane the system does not present the solid-like features seen when hexadecane is compressed pure.
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Shukla, Charu L. "Computationally Probing the Cybotactic Region in Gas-Expanded Liquids". Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/14510.
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Gas-expanded liquids (GXLs) are novel and environmentally benign solvent systems with applications in reactions, separations, nanotechnology, drug delivery, and microelectronics. GXLs are liquid mixtures consisting of an organic solvent combined with a benign gas, such as CO2, in the nearcritical regime. In this work, molecular dynamics simulations have been combined with experimental techniques to elucidate the cybotactic region or local environment in gas-expanded liquids. Molecular dynamics simulations show clustering of methanol molecules in carbon dioxide-methanol mixtures. This clustering was not observed in carbon dioxide-acetone mixtures. Furthermore, addition of carbon dioxide enhances diffusivity of solutes in gas-expanded media as shown by both simulations and Taylor-Aris dispersion experiments. Finally, local structure and local compositions around pyrene in carbon dioxide-methanol and carbon-dioxide acetone were investigated using simulations and UV-vis spectroscopy.
18
Boromand, Arman. "Computational Studies on Multi-phasic Multi-componentComplex Fluids". Case Western Reserve University School of Graduate Studies / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=case1480500319335545.
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Razavi, Seyed Mostafa. "OPTIMIZATION OF A TRANSFERABLE SHIFTED FORCE FIELD FOR INTERFACES AND INHOMOGENEOUS FLUIDS USING THERMODYNAMIC INTEGRATION". University of Akron / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=akron1481881698375321.
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Hoang, Hai. "Modeling of Simple Fluids Confined in Slit Nanopores : Transport and Poromechanics". Thesis, Pau, 2013. http://www.theses.fr/2013PAUU3016/document.
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Ce travail vise à étudier les propriétés de transport et le comportement poromécaniquede fluides simples confinés dans des nanopores lamellaires par le biais de simulationsmoléculaires. Pour ce faire, nous avons proposé différents schémas de simulations de ladynamique moléculaire dans des ensembles adaptés aux propriétés étudiées (diffusion demasse, viscosité, force de friction, gonflement …). Il a été note que les propriétés de transportde fluides fortement inhomogènes variaient fortement dans la direction perpendiculaire auxmurs solides. Nous avons alors proposé une approche non-locale permettant de déterminerquantitativement la viscosité locale de fluides inhomogènes à partir du profil de densité etapplicable pour des sphères dures, molles et le fluide de Lennard-Jones. Il a été égalementmontré qu’un fluide de Lennard-Jones fortement confiné pouvait avoir un comportementviscoplastique (et rhéofluidifiant) si un ordre structurel était induit dans le fluide par laposition relative des murs solides. Enfin, nous avons montré qu’une modification importantede la pression de solvatation du fluide confiné peut être induite par cisaillement ce qui peutinduire un gonflement « dynamique » d’un nanopore lamellaireThis work aims at investigating the transport properties and the poromechanics of simple spherical fluids confined in slit nanopores through molecular simulations. To do so, we have proposed different schemes to perform molecular dynamics simulations in ensembles adequate to deal with the properties we were looking after (mass diffusion, shear viscosity,friction force, swelling …). The transport properties of strongly inhomogeneous fluids were found to be varying with space perpendicularly to the solid walls. We have then proposed a non-local approach to determine quantitatively the local shear viscosity of such inhomogeneous fluids from the density profile applicable from the Hard-Sphere to the Lennard-Jones fluids. In addition, it has been shown that highly confined Lennard-Jones fluid may exhibit a visco-plastic (+ shear thinning) behavior when a strong structural order is induced in the whole confined fluid because of the relative position of the solid walls. Finally, it was demonstrated that shear induced modifications of the solvation pressure of a confined fluid may exist that leads to a “dynamic” swelling when a slit micropore is sheared
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Shagolsem, Lenin Singh. "Morphology Control of Copolymer Thin Films by Nanoparticles". Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-135862.
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Diblock-Copolymers (DBCs), created by covalently joining two chemically distinct polymer blocks, spontaneously form various nanoscale morphologies such as lamellae, cylinders, spheres, etc. due to the chemical incompatibility of its constituent blocks. This effect is called microphase separation in the literature. Because of this self-organizing property DBCs find applications in many areas e.g. in creating selective membranes, and in polymer based modern electronic devices like organic photovoltaics where the internal morphology plays an important role in determining the performance of the device. Many such modern devices are based on thin film technologies and uses copolymer nanocomposites as it exhibits advantageous electrical, optical, and mechanical properties. Also, DBC can direct the spatial distribution of nanoparticles (NPs) in the polymer matrix via microphase separation. Generally, two types of NPs are distinguished with respect to their monomer affinity: selective NPs which prefer one component of DBC, and non-selective NPs which interact equally with both components of DBC. In this work, using molecular dynamics simulations and analytical calculations, we explore the effect of adding both types of NP in the copolymer matrix considering a thin film (or confined) geometry. We consider a cylinder forming DBC melt confined by purely repulsive walls in slit geometry and study the behavior of the system upon adding non-selective NPs. Two models of non-selective interactions between the monomers and NPs are applied, i.e repulsive and weakly attractive interactions (athermal and thermal cases respectively). Spatial distribution of NPs in the copolymer matrix is sensitive to the NP-monomer interaction behavior. We focus on the thermal case and discuss, in particular, the following points: (1) role of diblock and polymer-wall interfaces, (2) spatial distribution of NPs, and (3) NP segregation and uptake behavior by the copolymer film. The uptake of NPs by the copolymer film in the thermal case displays a non-monotonic dependence on temperature which can be explained qualitatively using a mean-field model. In general, addition of non-selective NPs do not affect the copolymer morphology and the NPs are preferentially localized at the interface between microphase domains. Morphological transitions are observed when adding selective NPs to the copolymer matrix. By varying the amount of selective NPs and diblock composition we systematically explore the various structures formed by the nanocomposites under confinement and constructed the corresponding phase diagram in diblock composition and NP concentration. We also discuss the NP induced orientation transition of lamellar structure and study the stability of lamellar phases formed by the nanocomposites. To study the commensurability and wetting transition of horizontally oriented lamellar phase formed by the nanocomposites we have developed a mean field model based on the strong segregation theory. Our model predicts that it is possible to reduce the frustration in a film of fixed thickness by properly tuning the NP-monomer interaction strength. Furthermore, the model predicts a discontinuous transition between the non-wetted phase (where a dense NP layer is present in the polymer-substrate interface) and wetted phase (where the substrate is covered by polymers). Finally, we extend our study to non-equilibrium where we apply a shear flow field to copolymer thin films. Here, we study the flow behavior, lamellae deformation and change of pair-wise interaction energy, and macroscopic response like kinetic friction coefficient and viscosity of the copolymer thin film with and without NPsLösungen von Diblock-Copolymeren (DBC), welche durch die kovalente Bindung zweier chemisch unterschiedlicher linearer Polymerblöcke entstehen, können spontan mikroskopische Strukturen ausbilden, welche je nach dem Grad der chemischen Kompatibiliät der Blöcke beispielsweise lamellen-, zylinder- oder kugelartige Formen zeigen. Dieses Phänomen wird meist als Mikrophasenseparation bezeichnet. Aufgrund dieser selbstorganisierenden Eigenschaft finden DBCs Anwendungen in vielen Bereichen der Forschung und der Industrie. Beispielsweise zur Erzeugung selektiver Membranen oder in moderner polymerbasierter Elektronik, wie organischen Solarzellen, wo die innere Struktur eine wichtige Rolle spielt um die Leistungsfähigkeit zu erhöhen. Viele moderne Geräte basieren auf der Technologie dünner Schichten und nutzen Copolymer-Nanokomposite um elektrische, optische oder mechanische Eigenschaften zu verbessern. In Folge der Mikrophasenseparation kann man mit Hilfe von DBC die räumliche Verteilung von Nanopartikeln (NP) in der Polymermatrix kontrollieren. Man unterscheidet im Allgemeinen zwischen zwei Arten von NP: selektive NP, welche eine der beiden Komponenten der DBC bevorzugen und nicht-selektive NP, welche mit beiden Komponenten gleichartig wechselwirken. In der vorliegenden Arbeit nutzen wir molekulardynamische Simulationen und analytische Rechnungen um den Eigenschaften zu studieren, welche eine Zugabe von selektiven und nicht-selektiven NP auf eine dünnschichtige Copolymermatrix hat. Wir betrachten eine zylinderformende Schmelze aus DBC, welche in einem dünnen Film, zwischen zwei harten Wänden eingeschränkt ist, und untersuchen das Verhalten des Systems unter Zugabe nicht-selektiver NP. Zwei Modelle nicht-selektiver Wechselwirkungen werden angenommen: ausschließlich repulsive (athermische) Wechselwirkungen und schwach anziehende (thermische) Wechselwirkungen. Die räumliche Verteilung der NP ist abhängig von dem jeweiligen Wechselwirkungsverhalten. Wir konzentrieren uns hierbei auf den thermischen Fall und diskutieren speziell folgende Schwerpunkte: (1.) die Rolle der sich ausbildenden Grenzschichten, (2.) die räumliche Verteilung der NP und (3.) die Abscheidung der NP, sowie die Aufnahmefähigkeit derselben durch die Polymermatrix. Im thermische Fall zeigt die Aufnahme der NP durch die Copolymerschicht eine nicht-monotone Abhängigkeit von der Temperatur, was mit Hilfe eines Mean-Field Modells erklärt werden kann. Die Zugabe nicht-selektiver NP hat keinen Einfluss auf die Struktur der Copolymermatrix und die NP werden vorzugsweise an der Grenzschicht der jeweiligen Mikrophasen gefunden. Im Gegensatz dazu kann man durch die Zugabe selektiver NP eine Strukturveränderung in der Copolymermatrix feststellen. Durch Veränderung der Menge der NP und der Zusammensetzung der DBC können wir systematisch unterschiedliche Strukturen des räumlich eingeschränkten Nanokomposits erzeugen und ein entsprechendes Phasendiagram bezüglich der NP Konzentration und der DBC Zusammensetzung erstellen. Wir untersuchen auch die durch NP induzierte Orientierung der Lamellenstruktur und analysieren ihre Stabilität. Um den sogenannten Kommensurabilitäts- und Benetzungsübergang in horizontal orientierten Lamellenstrukturen zu untersuchen haben wir ein Mean-Field Modell entwickelt, welches auf der Annahme der 'starken Segregation' basiert. Unser Modell macht die Vorhersage, dass es möglich ist die Frustration in einem Kompositfilm zu reduzieren, indem man die NP-Monomer-Wechselwirkung entsprechend anpasst. Zusätzlich sagt das Modell einen diskontinuierlichen Übergang zwischen der unbenetzten Phase (Ausbildung einer dichten NP Konzentration an der Polymer-Substrat Grenzschicht) und der benetzten Phase (das Substrat ist ausschließlich vom Polymerkomposit bedeckt) voraus. Abschließend weiten wir unsere Untersuchungen auf Nicht-Gleichgewichtszustände aus und induzieren durch Scherung der Substratwände einen Strömungprofil im Kompositfilm. Dabei analysieren wir das Strömungsverhalten, die Lamellendeformation und die Änderung der paarweisen Wechselwirkungsenergie. Wir untersuchen auch makroskopische Größen, wie den kinetischen Reibungskoeffizienten und die Viskosität, je in An- und Abwesenheit von Nanopartikeln
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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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Brandt, Erik G. "Molecular Dynamics Simulations of Fluid Lipid Membranes". Doctoral thesis, KTH, Teoretisk biologisk fysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-42586.
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Lipid molecules form thin biological membranes that envelop all living cells, and behave as two-dimensional liquid sheets immersed in bulk water. The interactions of such biomembranes with their environment lay the foundation of a plethora of biological processes rooted in the mesoscopic domain - length scales of 1-1000 nm and time scales of 1-1000 ns. Research in this intermediate regime has for a long time been out of reach for conventional experiments, but breakthroughs in computer simulation methods and scattering experimental techniques have made it possible to directly probe static and dynamic properties of biomembranes on these scales. Biomembranes are soft, with a relatively low energy cost of bending, and are thereby influenced by random, thermal fluctuations of individual molecules. Molecular dynamics simulations show how in-plane (density fluctuations) and out-of-plane (undulations) motions are intertwined in the bilayer in the mesoscopic domain. By novel methods, the fluctuation spectra of lipid bilayers can be calculated withdirect Fourier analysis. The interpretation of the fluctuation spectra reveals a picture where density fluctuations and undulations are most pronounced on different length scales, but coalesce in the mesoscopic regime. This analysis has significant consequences for comparison of simulation data to experiments. These new methods merge the molecular fluctuations on small wavelengths, with continuum fluctuations of the elastic membrane sheet on large wavelengths, allowing electron density profiles (EDP) and area per lipid to be extracted from simulations with high accuracy. Molecular dynamics simulations also provide insight on the small-wavelength dynamics of lipid membranes. Rapidly decaying density fluctuations can be described as propagating sound waves in the framework of linearized hydrodynamics, but there is a slow, dispersive, contribution that needs to be described by a stretched exponential over a broad range of length- and time scales - recent experiments suggest that this behavior can prevail even on micrometer length scales. The origin of this behavior is discussed in the context of fluctuations of the bilayer interface and the molecular structure of the bilayer itself. Connections to recent neutron scattering experiments are highlighted.QC 20111014
Modelling of biological membranes
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Holland, David M. "Nano-scale computational fluid dynamics with molecular dynamics pre-simulations". Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/72851/.
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A procedure for using Molecular Dynamics (MD) simulations to provide essential fl uid and interface properties for subsequent use in Computational Fluid Dynamics (CFD) calculations of nano-scale fluid fl ows is presented. The MD presimulations enable an equation of state, constitutive relations, and boundary conditions to be obtained for any given fl uid/solid combination, in a form that can be conveniently implemented within an otherwise conventional Navier-Stokes solver. The results presented demonstrate that these enhanced CFD simulations are capable of providing good fl ow field results in a range of complex geometries at the nano-scale. Comparison for validation is with full-scale MD simulations here, but the computational cost of the enhanced CFD is negligible in comparison with the MD. It is shown that this enhanced CFD can predict unsteady nano-scale ows in non-trivial geometries. A converging-diverging nano-scale channel is modelled where the fl uid fl ow is driven by a time-varying body force. The time-dependent mass fl ow rate predicted by the enhanced CFD agrees well with a MD simulation of the same configuration. Conventional CFD predictions of the same case are wholly inadequate. It is demonstrated that accurate predictions can be obtained in geometries that are more complex than the planar MD pre-simulation geometry that provides the nano-scale fl uid properties. The robustness of the enhanced CFD is tested by application to water fl ow along a (15,15) carbon nanotube (CNT) and it is found that useful fl ow information can be obtained. The enhnaced CFD model is applied as a design optimisation tool on a bifurcating two-dimensional channel, with the target of maximising mass fl ow rate for a fixed total volume and applied pressure. At macro scales the optimised geometry agrees well with Murray's law for optimal branching of vascular networks; however, at the nano-scale, the optimum result deviates from Murray's law, and a corrected equation is presented. However, it is found that as the mass flow rate increases through the channel high pressure losses occur at the junction of the network. These high pressure losses also have an impact on the optimal design of a network.
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Granero-Fernandez, Emanuel. "Fluides supercritiques et solvants biosourcés : propriétés physicochimiques des systèmes expansés par du CO2". Thesis, Toulouse, INPT, 2018. http://oatao.univ-toulouse.fr/23928/1/Granero%20Fernandez_Emanuel.pdf.
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Les objectifs environnementaux (COP21) visant à réduire les émissions de gaz à effet de serre et l'impact de l'industrie sur la nature, font face au défi de la demande croissante d'énergie et de produits. Les procédés chimiques sont les premiers en cause lorsqu’ils mettent en œuvre des solvants. L'ingénierie des solvants est une solution innovante qui vise à trouver des milieux alternatifs bénins possédant les propriétés de solvant adaptés pour chaque étape du procédé.Dans cette perspective, nous avons étudié les Liquides expansés par un gaz (LEGs), qui sont desliquides dont le volume augmente sous l’effet d’un gaz dissous sous pression. En particulier, le CO2 peut être utilisé comme agent d'expansion pour obtenir des liquides expansés par du CO2(LECs), combinant les avantages du CO2 et du solvant. La phase expansée peut contenir des concentrations élevées de CO2, jusqu'à 80%, selon le solvant, ce qui conduit à une réduction du besoin du solvant organique, mais aussi à des changements des propriétés physicochimiques et de transport de la nouvelle phase expansée. On peut de plus moduler ces propriétés par la pression et la température, d'une manière réversible, et améliorer la séparation des produits. Dans cette étude, différents solvants biosourcés ont été utilisés pour obtenir des systèmes expansés par du CO2, tels que les acétates d'alkyle, les carbonates organiques, les méthoxybenzènes, etc.La connaissance des équilibres de phase, des propriétés de solvatation et de transport est essentielle pour concevoir des processus qui exploitent le comportement particulier de ces systèmes biphasiques. Deux approches principales ont été utilisées pour caractériser ces systèmes. Dans un premier temps, des mesures ont été effectuées dans une cellule à haute pression et à volume variable pour évaluer la polarité au travers du paramètre Kamlet-Taft (KT) *(dipolarité / polarisabilité) dans les solvants expansés par du CO2 sous des pressions allant jusqu'à 30 MPa. La technique utilisée a été la spectroscopie UV-Vis suivant le déplacement hypsochromique du Rouge de Nile, une sonde solvatochromique déjà utilisée pour obtenir les paramètres KT dans des solvants purs. De plus, des mesures d'équilibre vapeur-liquide (ELV) ont été effectuées pour obtenir la composition de la phase expansée à différentes pressions et températures afin de comprendre la solvatation du CO2 dans les solvants organiques et de fournir des informations manquantes dans la littérature. En deuxième lieu, dans une approche plus théorique, les données ELV ont été utilisées pour calculer numériquement d'autres propriétés telles que la densité et la viscosité. Des équations d'état et des simulations par dynamique moléculaire (DM) ont été utilisées ; ces dernières donnant de meilleurs résultats dans un mode prédictif de la masse volumique et permettant de suivre les positions moléculaires au cours du temps, qui peut être liée à de nombreuses propriétés, y compris la viscosité étudiée ici. Ces calculs ont été effectués en utilisant un champ de force de type Amber adapté. Les résultats obtenus dans l’ensemble complètent les données de la littérature existante et apportent de nouvelles informations sur les propriétés des LEGs. Par exemple, le comportement non linéaire de l'expansion volumétrique, vérifié après les déterminations de masse volumique sur les simulations DM à l'équilibre, est une clé dans la compréhension des interactions soluté-solvant ; ainsi que les valeurs KT * obtenues qui confirment la large gamme de polarité couverte par ces systèmes.Enfin, certains systèmes expansés par du CO2 ont été utilisés pour produire des nanoparticules de TiO2 pour panneaux solaires, améliorant leur surface spécifique et donc leur efficacité en tant que semi-conducteurs ; et d’autres ont été appliqués à un processus d'activation enzymatique entraînant une augmentation significative du taux de conversion
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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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Smith, Edward. "On the coupling of molecular dynamics to continuum computational fluid dynamics". Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/15610.
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Molecular dynamics (MD) is a discrete modelling technique that is used to capture the nanoscale motion of molecules. MD can be used to accurately simulate a range of physical problems where the continuum assumption breaks down. Examples include surface interaction, complex molecules, local phase changes, shock waves or the contact line between fluids. However, beyond very small systems and timescales (μm and msec), MD is prohibitively expensive. Continuum computational fluid dynamics (CFD), on the other hand, is easily capable of simulating scales of engineering interest, (m and s). However, CFD is unable to capture micro-scale effects vital for many modern engineering fields, such as nanofluidics, tribology, nano-electronics and integrated circuit development. This work details the development of a set of techniques that combine the advantages of both continuum and molecular modelling methodologies, allowing the study of cases beyond the range of either technique alone. The present work is split into both computational and theoretical developments. The computational aspect involves the development of a new high-performance MD code, as well as a coupler (CPL) library to link it to a continuum solver. The MD code is fully verified, has similar performance to existing MD software and allows simulation of a wide range of cases. The CPL library is a robust, flexible and language independent API and the source code has been made freely available under the GNU GPL v3 license. Both MD and CPL codes are developed to allow very large scale simulation on high performance computing (HPC) facilities. The theoretical aspect includes the development of a rigorous mathematical framework and its application to develop novel coupling methodologies. The mathematical framework allows a discrete molecular system to be expressed in terms of the control volume (CV) formulation from continuum fluid dynamics. A discrete form of Reynolds’ transport theorem, is thus obtained, allowing both molecular and continuum systems to be expressed in a consistent manner. This results in a number of important insights into the molecular definition of stress. This CV framework allows mathematical operations to be localised to a control volume in space. It is ideally suited to apply coupling constraints to a region in space. To link the CFD and MD solvers in a rigorous and physically consistent manner, the CV framework is combined with the variational principles of classical mechanics. The result is a unification of a number of existing forms used in the coupling literature and a rigorous derivation of a new and more general coupling scheme.
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Meyer, Nadège. "Simulation numérique de la viscosité de liquides : effets des paramètres d'interaction, de la température et de la pression sous conditions ambiantes et extrêmes". Thesis, Université de Lorraine, 2017. http://www.theses.fr/2017LORR0293/document.
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Ce travail est consacré à l'étude de la viscosité de cisaillement par simulation numérique de dynamique moléculaire classique à l'équilibre avec une attention particulière à l'influence des hautes pressions sur cette propriété. La viscosité est obtenue à partir des trajectoires générées par ces simulations et en appliquant la formule de Green-Kubo. Un large panel de systèmes a été étudié, allant de fluides atomiques purs à un liquide moléculaire, en passant par des mélanges binaires. En premier lieu, nous nous sommes focalisés sur les métaux alcalins. La conclusion majeure de cette étude est que la viscosité des alcalins a un comportement universel sur une large plage du diagramme de phases. Par ailleurs, sur cet intervalle, la relation universelle que nous avons proposée permet de prédire la valeur de la viscosité de n'importe quel élément avec une incertitude inférieure à 10%. La validité de la relation de Stokes-Einstein, reliant le coefficient d'autodiffusion à la viscosité, a également été vérifiée. Une étude systématique a ensuite été menée sur des mélanges modèles de type Lennard-Jones an de tester l'influence des paramètres d'interaction sur le comportement de la viscosité. Une estimation théorique basée sur le modèle de fluide effectif pur a été proposée. D'autre part, la relation de Stokes-Einstein a été étendue aux mélanges avec succès. Ces observations ont été confrontées aux cas de deux alliages réels : K-Cs et Li-Bi. Pour finir, une étude préliminaire a été entreprise sur l'eau en modélisant les interactions par deux potentiels : SPC/E, non polarisable, et BK3, polarisable. L'effet de l'introduction de la polarisabilité sur le calcul de la viscosité a été étudié. La validité des relations de Stokes-Einstein et de Stokes-Einstein-Debye, faisant intervenir la rotation de la molécule, a été évaluée à très haute pressionThis work is devoted to the study of the shear viscosity by numerical simulation of equilibrium classical molecular dynamics with a particular attention to the influence of high pressures on this property. From trajectories generated by these simulations and using the Grenn-Kubo formula, the viscosity is obtained. A broad range of systems has been studied, covering from pure atomic fluids to a molecular liquid, as well as binary mixtures. First, we focused on alkali metals. The main outcome of this study is that the viscosity of these metals has a universal behavior over a wide range of phase diagram. Furthermore, over this interval, the universal relation that we have proposed permits the prediction of the viscosity value of any elements with an uncertainty lower than 10%. The validity of the Stokes-Einstein relation, connecting the self-diffusion coefficient and the viscosity, has also been verified. Then, a systematic study has been carried out on model mixtures of Lennard-Jones fluids to test the influence of interaction parameters on the viscosity behavior. A theoretical estimation based on the effective one-component fluid model has been proposed. Moreover, the Stokes-Einstein relation has been successfully extended to mixtures. These observations have been compared with two real alloys: K-Cs and Li-Bi. Lastly, a preliminary study on water has been undertaken by modeling the interactions with two models: SPC/E, non-polarizable and BK3, polarizable. The effect of the introduction of the polarizability on the viscosity has been studied. The validity of Stokes-Einstein and Stokes-Einstein-Debye, involving the rotation of the molecule, has been evaluated under very high pressure
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Favero, Frank Wilson. "Solvatação de alcaloides em fluidos supercriticos por simulação de dinamica molecular". [s.n.], 2006. http://repositorio.unicamp.br/jspui/handle/REPOSIP/248870.
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Orientador: Munir Salomão SkafTese (doutorado) - Universidade Estadual de Campinas, Instituto de Química
Made available in DSpace on 2018-08-08T16:04:54Z (GMT). No. of bitstreams: 1 Favero_FrankWilson_D.pdf: 4593221 bytes, checksum: 814b6567e6e2d0a7222d5f62cf803e1e (MD5) Previous issue date: 2006
Resumo: Foram realizados estudos por Simulações de Dinâmica Molecular em sistemas formados por alcalóides em CO2 supercrítico para determinarmos suas propriedades estruturais e dinâmicas. Os alcalóides estudados foram as xantinas (cafeína, teofilina e teobromina) e os alcalóides indólicos (voacangina e coronaridina), todas substãncias de grande interesse da indústria farmacêutica e/ou de alimentos. Detalhes da estrutura de solvatação em torno do soluto foram obtidos através de mapas de contornos onde a escala de cores representa a densidade local em relação ao valor médio da densidade no "bulk". Os mapas mostraram uma distribuição não homogênea do solvente com concentrações em regiões específica como nos planos dos anéis e nas carbonilas das moléculas. Os resultados dos coeficientes de difusão do solvente puro e do sistema cafeína/CO2 reproduziram muito bem os valores experimentais. É conhecido que a adição de pequenas quantidades de co-solventes polares amplia o poder de solubilização do CO2. Estudamos como a inclusão do co-solvente etanol à mistura afeta as propriedades de estrutura e dinâmicas dos sistemas. Observamos uma ampliação das interações soluto-solventes com a formação de ligações de hidrogênio, uma solvatação preferencial do soluto pelo co-solvente. As dinâmicas dos solutos tornaram-se mais lentas com a inclusão do co-solvente.
Abstract: Molecular Dynamics Simulation of systems formed by alkaloids in supercritical CO2 have been performed in order to determine their structural and dynamic properties. The studied alkaloids are the xanthines (caffeine, theophylline, and theobromine) and indole alkaloids (voacangine and coronaridine), substances of great interest of the pharmaceutical and foods industry. Details of the solvation structure around the solute were obtained by means of density maps representing the local density in relation to the average value of the density in bulk. The maps show an inhomogeneous distribution solvent with concentrations in specific regions such as above end below the planar rings and carbonyl groups of the molecules. The simulations results for the diffusion coefficients of pure solvent and the caffeine/CO2 system reproduce the experimental values very well. It is known that the addition of small amounts of polar co-solvent increases the power of CO2 solubilization. We investigated the effects of co-solvent ethanol to the systems structural and dynamical properties. We observe a magnification of the solute-solvent interactions with the formation of hydrogen bonding and the preferential solvation by the co-solvent. The dynamics of the solute become slower upon addition of the co-solvent.
Doutorado
Físico-Química
Doutor em Ciências
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Hall, Christopher David. "Neutron diffraction and molecular dynamics studies of fluid halocarbons". Thesis, University of Liverpool, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316495.
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Manias, Evangelos D. "Nanorheology of strongly confined molecular fluids a compter simulation study /". [S.l. : [Groningen] : s.n.] ; [University Library Groningen] [Host], 1995. http://irs.ub.rug.nl/ppn/142099473.
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Adair, Kenneth Valloyd. "Diffusive, reactive and orientational dynamics of molecular systems using molecular Fourier imaging correlation spectroscopy /". view abstract or download file of text, 2006. http://proquest.umi.com/pqdweb?did=1251854551&sid=1&Fmt=2&clientId=11238&RQT=309&VName=PQD.
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Thesis (Ph. D.)--University of Oregon, 2006.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 103-108). Also available for download via the World Wide Web; free to University of Oregon users.
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Thomas, Jason Christopher. "Prediction of Fluid Viscosity Through Transient Molecular Dynamic Simulations". Diss., CLICK HERE for online access, 2009. http://contentdm.lib.byu.edu/ETD/image/etd3312.pdf.
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Macpherson, Graham Bruce. "Molecular dynamics simulation in arbitrary geometries for nanoscale fluid mechanics". Thesis, University of Strathclyde, 2008. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=23483.
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Simulations of nanoscale systems where fluid mechanics plays an important role are required to help design and understand nano-devices and biological systems. A simulation method which hybridises molecular dynamics (MD) and continuum computational fluid dynamics (CFD) is demonstrated to be able to accurately represent the relevant physical phenomena and be computationally tractable. An MD code has been written to perform MD simulations in systems where the geometry is described by a mesh of unstructured arbitrary polyhedral cells that have been spatially decomposed into irregular portions for parallel processing. The MD code that has been developed may be used for simulations on its own, or may serve as the MD component of a hybrid method. The code has been implemented using OpenFOAM, an open source C++ CFD toolbox (www.openfoam.org) . Two key enabling components are described in detail. 1) Parallel generation of initial configurations of molecules in arbitrary geometries. 2) Calculation of intermolecular pair forces, including between molecules that lie on mesh portions assigned to different, and possibly non-neighbouring processors. To calculate intermolecular forces, the spatial relationship of mesh cells is calculated once at the start of the simulation and only the molecules contained in cells that have part of their surface closer than a cut-off distance are required to interact. Interprocessor force calculations are carried out by creating local copies of molecules from other processors in a layer around the processor in question. The process of creating these copied molecules is described in detail. A case study of flow in a realistic nanoscale mixing channel, where the geometry is drawn and meshed using engineering CAD tools, is simulated to demonstrate the capabilities of the code for complex simulations.
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Fried, Jeremy. "Numerical Simulation of Viscous Flow: A Study of Molecular Dynamics and Computational Fluid Dynamics". Thesis, Virginia Tech, 2007. http://hdl.handle.net/10919/34661.
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Molecular dynamics (MD) and computational fluid dynamics (CFD) allowresearchers to study fluid dynamics from two very different standpoints. From a microscopic standpoint, molecular dynamics uses Newton's second law of motion to simulate the interatomic behavior of individual atoms, using statistical mechanics as a tool for analysis. In contrast, CFD describes the motion of a fluid from a macroscopic level using the transport of mass, momentum, and energy of a system as a model.
This thesis investigates both MD and CFD as a viable means of studying viscous flow on a nanometer scale. Specifically, we investigate a pressure-driven Poiseuille flow. The results of the MD simulations are processed using software we created to measure velocity, density, and pressure. The CFD simulations are run on numerical software that implements the MacCormack method for the Navier-Stokes equations. Additionally, the CFD simulations incorporate a local definition of viscosity, which is usually uncharacteristic of this simulation method. Based on the results of the simulations, we point out similarities and differences in the obtained steady-state solutions.Master of Science
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Taddese, Tseden. "Thermodynamics and dynamics of polymers at fluid interfaces". Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/thermodynamics-and-dynamics-ofpolymers-at-fluid-interfaces(27166765-7d8b-405f-90d2-7f2489a200ca).html.
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The aim of this thesis is to study the structural and thermodynamical properties of polymers at liquid/liquid interfaces by means of multiscale molecular dynamics simulations. This thesis is presented in alternative format, and the results, consisting of three journal articles, are divided into two main parts. The first part of the thesis looks at the structural and dynamical changes as well as the thermodynamic stability of polymers of varying topology (linear and star-shaped) at interfaces by performing molecular dynamics simulations on model systems. It was found that homopolymers are attracted to the interface in both good and poor solvent conditions making them a surface active molecule, despite not being amphiphilic. In most cases changing polymer topology had only a minor effect on the desorption free energy. A noticeable dependence on polymer topology is only seen for relatively high molecular weight polymers at the interface. Examining separately the enthalpic and entropic components of the desorption free energy suggests that its largest contribution is the decrease in the interfacial free energy caused by the adsorption of the polymer at the interface. Furthermore, we propose a simple method to qualitatively predict the trend of the interfacial free energy as a function of the polymer molecular weight. In terms of the dynamics of a linear polymer, the scaling behaviour of the polymer confined between two liquids did not follow that predicted for polymers adsorbed onsolid or soft surfaces such as lipid bilayers. Additionally, the results show that in the diffusive regime the polymer behaves like in bulk solution following the Zimm model and with the hydrodynamic interactions dominating its dynamics. Further simulations carried out when the liquid interface is sandwiched between two solid walls show that when the confinement is a few times larger than the blob size the Rouse dynamics is recovered. The second part of the thesis focuses on optimizing the MARTINI coarse-grained (CG) Model, which retains certain chemical properties of molecules, to reproduce solubility of polymers, in specific polyethylene oxide (PEO), in both polar and non-polar solvents. Performing molecular dynamics simulations using this CG model will then enable us to study the properties PEO in octanol/water and hexane/water systems with increased length and timescales not accessible by atomistic simulations. The MARTINI CG method (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812) is based on developing the optimal Lennard-Jones parameters to reproduce the partition free energy between water (polar solvent) and octanol (apolar solvent). Here we test the MARTINI CG method when modelling the partitioning properties of PEO, with increasing molecular weight between solvents of different polarity by comparing the results with atomistic simulation. We show that using simply the free energy of transfer from water to octanol to obtain the force parameters does not guarantee the transferability of the model to other solvents. Instead one needs to match the solvation (or hydration) free energies to ensure that the polymer has the correct polarity. We propose a simple method to select the Lennard-Jones parameter to match the solvation free energies for different beads. We also show that, even when the partition coefficient of the monomer is correct, even for modestly high molecular weight of the polymer the predicted partitioning properties could be wrong.
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Kenyon, A. J. "Surfaces and flows : a study of the molecular dynamics of liquids". Thesis, University of Sussex, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.305385.
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Houston, Peter Henry Robert. "On the behaviour of nanoscale fluid samples far from equilibrium". Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312120.
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Kobsch, Anaïs. "Behavior of feldspars during the Giant Impact". Thesis, Lyon, 2020. http://www.theses.fr/2020LYSEN026.
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L’hypothèse majeure pour la formation de la Lune est celle d’un Impact Géant entre deux planètes en formation, généralement appelées Théïa et Gaïa. L’agglomération du disque de débris résultant aurait ensuite formé la Lune. Cependant aucune des simulations d’impacts ne permet de reproduire totalement les observations du système Terre-Lune actuel. Une solution à ce problème pourrait être d’améliorer notre compréhension des propriétés des différents minéraux, non seulement à hautes pressions et hautes températures (typiques des impacts), mais aussi à basses pressions et hautes températures (typiques de l’état du disque dans l’espace). Comme les expériences en laboratoire ne permettent pas d’atteindre ces dernières conditions, nous réalisons ici des expériences numériques. Nous travaillons sur les feldspaths, les minéraux les plus abondants dans les croûtes lunaire et terrestre. Il existe une multitude de compositions différentes de feldspaths, ici nous nous limitons aux trois compositions extrêmes idéales : NaAlSi3O8, KAlSi3O8 et CaAl2Si2O8. Au moyen d’un ensemble de codes informatiques appelé VASP® nous obtenons de nombreuses données sur les trois feldspaths pour des températures allant d’environ 2000 à 20 000°C et des masses volumiques entre 0.5 et 6 g.cm−3. Les codes du « package » UMD développés pendant ces trois années au sein de l’équipe permettent l’analyse de ces données. Ces expériences numériques permettent de construire un diagramme de phases indicatif pour chacun des feldspaths étudiés. Nous avons visuellement identifié les conditions de pressions et températures pour lesquelles le liquide se vaporise (des bulles de gaz apparaissent). Ce gaz semble être constitué majoritairement d’atomes libres Na et K, mais aussi de petites molécules comme SiO, SiO2 ou O2. Nous avons également estimé la température critique. En dessous de cette température il est possible de voir un changement de phase liquide-gaz, mais au-dessus nous trouvons un fluide unique appelé fluide supercritique. Cette température est estimée entre 5250°C et 5750°C pour KAlSi3O8, entre 6250°C et 6750°C pour NaAlSi3O8 et entre 7250°C et 7750°C pour CaAl2Si2O8. Les propriétés des feldspaths à très hautes pressions (jusqu’à 4 000 000 de fois la pression atmosphérique) et températures (jusqu’à 20 000°C) nous permettent d’estimer l’état physique qu’une croûte planétaire composée de feldspaths pourrait avoir lors d’impacts météoritiques. Lorsque l’impact se produit sur une croûte froide (entre le zéro absolu et les conditions atmosphériques classiques) il pourrait au maximum faire fondre la croûte. Au contraire, lorsque l’impact a lieu sur une croûte chaude voire fondue (2200°C et plus) il pourrait transformer toute la croûte en fluide supercritique. Si c’était bien le cas de l’Impact Géant qui a formé la Lune, alors ce fluide supercritique ainsi créé pourrait permettre de résoudre bien des problèmes de composition chimique que les simulations d’Impact Géant présententThe impact of a planet in formation with the proto-Earth, also known as the Giant Impact, is now the main hypothesis for the Moon formation. Nevertheless, there are still discrepancies between the impact simulations and the observations of the current Earth-Moon system. To improve their models, geophysicists need a better understanding of geological materials not only at high pressures and high temperatures, typical of impacts, but also at low pressures and high temperatures, typical of the debris disc that follows the impact. Since this latter region cannot be reached by experiments we use here ab-initio molecular dynamics simulations. We work on feldspars, with formula (Ca,K,Na)(Al,Si)4O8, as they represent the major mineral component of the crust of terrestrial bodies. Using the VASP® code for numerical experiments and the home-made UMD package for post-processing, we obtain structural, transport and thermodynamic data on a wide range of temperatures (2000–7000 K) and densities (0.5–6 g.cm−3). The three feldspar end-members display a critical density between 0.4 and 0.9 g.cm−3 and critical temperatures as follows: 5000 K < TK < 5500 K, 6000 K < TNa < 6500 K and 7000 K < TCa < 7500 K. At low densities and below the critical temperatures, we can identify the start of gas bubble nucleation. The vaporization is incongruent, the gas is mostly made of free Na or K and of SiO, SiO2 or O2 molecules. There is an O2 degassing of the fluids above 4000 K at all densities. Our study at very high temperatures and pressures tells us that impacts in a cold crust would at most melt the crust, whereas impacts in a hot crust or in a magma ocean would completely bring the crust into supercritical state
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Mi, Xiaobing, i 密小兵. "Modeling of flows at nano scale". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31245857.
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Asproulis, N. "Hybrid molecular and continuum fluid dynamics models for micro and nanofluidic flows". Thesis, Cranfield University, 2009. http://dspace.lib.cranfield.ac.uk/handle/1826/6966.
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From molecules to living organisms and from atoms to planets a variety of physical phe-
nomena operate at different temporal and spatial scales. Understanding the nature of those
phenomena is crucial for advancing new technologies in many disciplines. In micro and
nanofluidics as the operational dimensions are downsized to smaller scales the surface-to-
volume ratio increases and the surface phenomena become dominant. Numerical modelling
is the key for obtaining a better insight into the processes involved. The Achilles heel of
fine grain microscopic numerical simulations is their computational cost. Simulating a
multiscale phenomenon with an accurate microscopic description is extremely demand-
ing computationally. On the contrary, simulations of multiscale phenomena based only on
macroscopic descriptions cannot fully capture the physics of the multiscale systems. In
order to confront this dilemma multiscale frameworks, called hybrid codes, have been de-
veloped to couple the microscopic and macroscopic description of a system and to facilitate
the exchange of information.
The aim of this research project is to establish and implement a robust hybrid molecular-
continuum method for micro- and nano-scale fluid flows. Towards that direction a hybrid
multiscale method named as Point Wise Coupling (PWC) has been developed. PWC aims
to circumvent the limitations of the existing hybrid continuum/atomistic approaches and
deliver a modular and applicable methodology. In the PWC, the whole domain is covered
with the macroscopic solver and the microscale model enters as a local refinement. Ad-
ditionally, numerical techniques based on neural networks are employed to minimise the
cost of the molecular solver and reduce the outcomes’ variability induced by the fluctuating
nature of the atomistic data.
Molecular studies have been performed (i) to obtain a better insight of the interfacial
phenomena in the solid/liquid interfaces, and (ii) to study the parametrisation of the molec-
ular models and mapping of atomistic information to hybrid frameworks. Specifically, the
impact of parameters, such as surface roughness and stiffness, to slip process is studied.
PWC framework has been employed to study a number of fundamental test cases in-
cluding Poiseuille flow of polymeric fluids, isothermal slip Couette flow and slip Couette
flow with heat transfer. Attention is drawn to the boundary condition transfer from the
continuum solver to the atomistic description. In the performed hybrid studies the effects
of the numerical optimisation techniques (linear interpolation, neural networks) to simu-
lations’ accuracy, stability and efficiency are studied. The outcomes of the simulations
suggest that the neural networks scheme enhance the simulation’s efficiency by minimising
the number of atomistic simulations and at the same time act as a smoothing operator for
reducing the oscillations’ strength of the atomistic outputs.
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Liu, Jiangping. "Prediction of Fluid Dielectric Constants". BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2787.
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The dielectric constant or relative static permittivity of a material represents the capacitance of the material relative to a vacuum and is important in many industrial applications. Nevertheless, accurate experimental values are often unavailable and current prediction methods lack accuracy and are often unreliable. A new QSPR (quantitative structure-property relation) correlation of dielectric constant for pure organic chemicals is developed and tested. The average absolute percent error is expected to be less than 3% when applied to hydrocarbons and non-polar compounds and less than 18% when applied to polar compounds with dielectric constant values ranging from 1.0 to 50.0. A local composition model is developed for mixture dielectric constants based on the Nonrandom-Two-Liquid (NRTL) model commonly used for correlating activity coefficients in vapor-liquid equilibrium data regression. It is predictive in that no mixture dielectric constant data are used and there are no adjustable parameters. Predictions made on 16 binary and six ternary systems at various compositions and temperatures compare favorably to extant correlations data that require experimental values to fit an adjustable parameter in the mixing rule and are significantly improved over values predicted by Oster's equation that also has no adjustable parameters. In addition, molecular dynamics (MD) simulations provide an alternative to analytic relations. Results suggest that MD simulations require very accurate force field models, particularly with respect to the charge distribution within the molecules, to yield accurate pure chemical values of dielectric constant, but with the development of more accurate pure chemical force fields, it appears that mixture simulations of any number of components are likely possible. Using MD simulations, the impact of different portions of the force field on the calculated dielectric constant were examined. The results obtained suggest that rotational polarization arising from the permanent dipole moments makes the dominant contribution to dielectric constant. Changes in the dipole moment due to angle bending and bond stretching (distortion polarization) have less impact on dielectric constant than rotational polarization due to permanent dipole alignment, with angle bending being more significant than bond stretching.
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Patwary, Md Zillur R. "Clay Fluid Interactions in Montmorillonite Swelling Clays: A Molecular Dynamics and Experimental Study". Thesis, North Dakota State University, 2012. https://hdl.handle.net/10365/26757.
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Swelling clays cause tremendous amounts of damage to infrastructure. For the effective prevention of detrimental effects of these clays, and to optimize the beneficial properties for industrial applications it is necessary to clearly understand the fundamental mechanisms of swelling of clays. In this study, we studied the effect of fluid polarity on swelling and flow properties of swelling clays using molecular modeling and experimental technique for bridging the molecular level phenomenon of these clays with microstructure change, particle breakdown and macro scale swelling and flow properties. A wide range of fluids (Dielectric Constant 110 to 2.4) were used, those are also commonly present in landfill leachates. We were able to tie the properties of swelling clays at different length scales. Then, we simulated the solvation of clay sheets, studied the effect of discrete charge distribution, contribution of edge charges on swelling clays and discussed some fundamental assumptions associated with double layer theories.Department of Civil Engineering, North Dakota State University
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DI, PASQUALE NICODEMO. "MULTISCALE SIMULATION OF POLYMER NANOPARTICLES PRECIPITATION FOR PHARMACEUTICAL APPLICATIONS". Doctoral thesis, Politecnico di Torino, 2012. http://hdl.handle.net/11583/2506098.
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This work focuses on the development and use of a multiscale computational
tool for the simulation of the process of precipitation of polymeric nanoparticles
in micro-mixers. This process, as will be shown through the rest of the thesis,
is not very easy to model with single scale model (i.e., Computational Fluid Dy-
namics, Population Balances, Molecular Dynamics). The main reason stands in
the complex behaviour of the system investigated (the polymer); the behaviour at
atomistic scale influences the macro-scale. With micro-scale (which is equivalent
in our notation to the atomistic scale) we refer to all the phenomena occurring at
length-scales of nanometres (1 nm = 10−9 m) and time-scales of picoseconds
(1 ps = 10−12 s), whereas with macroscale we intend all the phenomena occur-
ring at length-scale of meters and at time-scale of seconds. There are different
models used to describes these (apparently) uncorrelated phenomena. Computa-
tional Fluid Dynamics (CFD) which describes at the macroscale the motion of
a fluid in a given domain often coupled with Population Balance Model (PBM)
to describe the presence of a dispersed colloidal phase, and Molecular Dynamics
(MD) which describes the motion of a collection of atoms in an interval of time.
The coupling of these methods in a unique description of the problem is called
multiscale modelling, a research area which has raised much interests in the last
few years. In this work, precipitation of nanoparticles occurs in a micromixer, is
investigated trough CFD-PBM, whilst the precipitation process is described by
extracting some information from MD simulations, hence, coupling these differ-
ent models in one description. The thesis is structured as follows:
1. The First Chapter is an introduction to the investigated problem. A brief
description of the use of polymer nanoparticles in the pharmaceutical in-
dustry is given, with the current state of the art. A brief overview of the
different production processes and devices used will be also given
2. The Second Chapter in intended to give all the theoretical background re-
quired for the understanding of the subsequent chapters. Starting from
the very beginning, the governing equations for the generic N-body prob-
lem are derived together with the description of the theoretical tools for
the molecular dynamics. By using the Boltzmann Equation we show how
to move from a description of the problem a the micro-scale (here repre-
sented by the MD) to a description of the problem at the macro-scale (rep-
resented by the CFD). The introduction of the Boltzmann equation (and the
mesoscale) is also useful since the PBM is a kinetic equation very similar
to the Boltzmann equation
3. The Third Chapter involves the description of the CFD model of the micro-
mixer used in this study. The polymeric nanoparticles precipitation model
is presented along with its intrinsic limitations highlighting the need of a
more fundamental approach
4. In the Fourth Chapter we discuss the improvement of the CFD model by
developing a nucleation theory adequate to the description of the polymer
particle formation. The parameters appearing in this theory are estimated
by using the standard full atoms MD simulations. Eventually the nucle-
ation theory is integrated into the CFD-PBM and used to simulate the entire
process
5. The Fifth Chapter is devoted to the extension of the MD framework. In
fact, in order to further investigate the polymer particle formation process,
larger systems, involving many polymeric chains have to be described.
This requires some form of partial coarse-graining, resulting in hybrid
atomistic/coarse-grained model. The framework to do this is in this chapter
described, showing how the model allows to speed up the simulation by ne-
glecting some Degrees of Freedom of the original problem but maintaining
the necessary details where needed
6. In the last Chapter some conclusions from the simulations presented are
drawn.
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Wittmann, Jan-Hubert [Verfasser]. "Simulation in Nucleation Research - From Molecular- to Computational Fluid Dynamics / Jan-Hubert Wittmann". München : Verlag Dr. Hut, 2015. http://d-nb.info/1074063759/34.
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Ritos, Konstantinos. "Water flow at the nanoscale : a computational molecular and fluid dynamcis investigation". Thesis, University of Strathclyde, 2014. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=24387.
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A complete understanding of the most common and abundant fluid on Earth, water, has challenged the scientific community since the dawn of science. Nanoscale confinement and flow through nanotubes show counter-intuitive behaviour and produce interesting new phenomena. Experimental studies of water flow at the nanoscale report diverse results because measurement devices still struggle to provide the necessary accuracy. Molecular Dynamics (MD) simulations can instead provide molecular detail and a plethora of information. The main disadvantage of the method is space and time restraints on the simulated problems. To overcome this, hybrid multiscale methods that combine MD with macroscopic equations have been recently developed. This thesis investigates water flow at the nanoscale, over free surfaces and in nanotube membranes, using MD, multiscale methods and macroscopic hydrodynamic equations. Initially, water nanodroplets on static and moving surfaces of different hydrophilicity are studied here with the developed MD solver. The findings, contrary to macroscopic observations, suggest that the dynamic contact angle of water nanodroplets on graphite is independent of the capillary number. Then, a new method is firstly presented here in order to measure the average molecular orientation of water and highlight any type of anisotropy. For the first time, biaxial ordering of water molecules close to the nanotube walls is observed. It is also found that static electric fields can control the flow rate through them (e.g. a 2 V/nm electric field increases the flow rate by more than 300% for the same pressure difference). The effect of the wall material on water flow is also investigated. The accuracy of a flow enhancement prediction model originally suggested by Mattia et al. [1] is tested, giving satisfactory results for nanotube membranes of small thickness. Finally, results from hybrid multiscale simulations are presented in this thesis, showing perfect agreement with pure MD simulations. The same multiscale method is used for the first time to simulate water flow through a millimeter thick membrane with a pore diameter smaller than 2 nm. All the results presented in this thesis contribute towards the better understanding of water flow at the nanoscale. In parallel this thesis provides a number of computational tools and methods that will help in future studies as well as in the design and simulation of nanoscale fluid devices.
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Chia, Chung Lim. "Classical and ReaxFF molecular dynamics simulations of fuel additives at the solid-fluid interface". Thesis, University of Manchester, 2019. https://www.research.manchester.ac.uk/portal/en/theses/classical-and-reaxff-molecular-dynamics-simulations-of-fuel-additives-at-the-solidfluid-interface(a1a5cb5d-3283-4ebc-9ef1-b44aac16821b).html.
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In the automotive industry, a kind of fuel additives, known as surfactant, is used to protect metallic surfaces. Its efficiency strongly depends on factors such as temperature, solvent properties and the presence of other surfactants in the system. In this thesis, both classical and ReaxFF molecular dynamics (MD) simulations are used in studying the impacts of these factors on the adsorption of organic surfactants at the fluid-solid interface. Firstly, a classical MD simulation study of competitive adsorption is carried out on a multi-functional phenol and amine surfactant model with ethanol at the oil/iron oxide interface. As the concentration of ethanol increases, the ethanol molecules effectively compete for the adsorption sites on the iron oxide surface. This observation concurs with the experimental findings of similar oil/iron oxide systems. Unlike most MD interfacial studies, ReaxFF MD uses a fully flexible and polarizable solid surface. The second part of the thesis includes a study on the effect of polarity of organic molecules on the structure of iron oxide using ReaxFF-based MD simulations. The simulation results suggest that care must be taken when parameterising empirical and transferable force fields because the fixed charges on a solid slab may not be a perfect representation of the real system, especially when the solid is in contact with polar compounds. Lastly, but not the least, missing ReaxFF interaction parameters for Fe/N have been developed to simulate the adsorption of amine based surfactant on iron oxide. The parameterisation of the force field is done by fitting these interaction parameters to a set of quantum mechanical data involving iron-based clusters. These newly developed parameters are able to capture chemisorption and proton transfer between hexadecylamine and iron oxide.
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Tang, Jing Ph D. Massachusetts Institute of Technology. "Single molecule DNA dynamics in micro- and nano-fluidic devices". Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/62739.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2011."October 2010." Cataloged from PDF version of thesis.
Includes bibliographical references (p. 140-147).
Rapid genome characterization is one of the grand challenges of genome science today. Although the complete sequences of certain representative human genomes have been determined, genomes from a much larger number of individuals are yet to be studied in order to fully understand genome diversity and genetic diseases. While current state-of-the-art sequencing technologies are limited by the large timescale and cost required to analyze a single sample, an alternative strategy termed DNA mapping has recently received considerable attention. Unlike sequencing which produces single-base resolution, DNA mapping resolves coarse-scale (~kbp) information of the sequence, which is much faster and cheaper to obtain, but still sufficient to discern genomic differences among individuals within a given species. Advances in fluorescence microscopy have allowed the possibility to directly map a single DNA molecule. This concept, though straightforward, faces a major challenge that the entropic tendency of polymeric DNA to adopt a coiled conformation must be overcome so as to optically determine the position of specific sequences of interest on the DNA backbone. The ability to control and manipulate the conformation of single DNA molecules, especially, to stretch them into a linear format in a consistent and uniform manner, is thus crucial to the performance of such mapping devices. The focus of this thesis is to develop a reliable single DNA stretching device that can be used in single molecule DNA mapping, and to experimentally probe the fundamental physics that govern DNA deformation. In the aspect of device design, the strategy we pursue is the use of an elongational electric field with a stagnation point generated in the center of a cross-slot or T channel to stretch DNA molecules. The good compatibility of electric field with small channel dimensions allows us to use micro- or nano-fabricated channels with height on the order of or smaller than the natural size of DNA to keep the molecule always in focus, a feature desirable for any mapping applications. The presence of the stagnation point allows the possibility to dynamically trap and stretch single DNA molecules. This trapping capability ensures uniform stretching within a sample ensemble, and also allows prolonged imaging time to obtain accurate detection results. We primarily investigate the effects of channel height on the stretching process, specifically, we seek the possibility of utilizing slit-like nanoconfinement to aid DNA stretching. Although extensive previous studies have demonstrated that geometric confinement of DNA can substantially alter the conformation and dynamics of these molecules at equilibrium, no direct studies of this non-equilibrium stretching process in confinement exist prior to the work presented in this thesis. We find that slit-like confinement indeed facilitates DNA stretching by reducing the deformation Abstract rate required to achieve a certain extension. However, due to the fact that the steric interactions between the DNA and the confining walls vanish at large extensions, highly stretched DNA under confinement behaves qualitatively similar to unconfined DNA except with screened hydrodynamic interactions, and a new time scale arises that should be used to describe the large change in extension with applied deformation rate. In a consecutive study, we examine the low-extension stretching process and observe a strongly modified coil-stretch transition characterized by two distinct critical deformation rates for DNA in confinement, different from the unconfined case where a single critical deformation rate exists. With kinetic theory modeling, we demonstrate that the two-stage coilstretch transition in confinement is induced by a modified spring force law, which is essentially related to the extension-dependent steric interactions between DNA and the confining walls. We also study aspects of the equilibrium conformation and dynamics of DNA in slit-like confinement in order to provide insight into regimes where existing studies show inconsistent results. We use both experiments and simulations to demonstrate that the in-plane radius of gyration and the 3D radius of gyration of DNA behaves differently in weak confinement. In strong confinement, we do not identify any evident change in the scalings of equilibrium size, diffusivity, and longest relaxation time of the DNA with channel height from the de Gennes regime to the Odijk regime. Although the transition between the de Gennes and Odijk regimes in slit-like confinement still remains an open question, our finding adds more experimental evidence to the side of a continuous transition. The impact of this thesis will be two-fold. We design a DNA stretching device that is readily applicable to single molecule DNA mapping and establish guidelines for the effective operation of the device. Our fundamental results regarding both the equilibrium and non-equilibrium dynamics of DNA molecules in slit-like confinement will serve as a solid basis for both the design of future devices aiming to exploit confinement to manipulate biopolymers, and more complicated studies of confined polymer physics.
by Jing Tang.
Ph.D.
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Nixon, Grant Ian. "Entropic trapping and polymer dynamics in static, quasi-periodic arrays of obstacles in two dimensional media". Thesis, University of Ottawa (Canada), 2003. http://hdl.handle.net/10393/26307.
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Using the bond fluctuation algorithm of Carmesin and Kremer (Carmesin and Kremer 1988), we investigate the static and dynamic properties of self-avoiding linear polymers embedded in static, two-dimensional (d=2), quasi-periodic arrays of obstacles with entropic traps.
The phenomenon of polymer collapse, the closely related enrichment and depletion of polymer configurations, the conformational relaxation, and the diffusive behaviour are all investigated within the framework of the lattice Monte Carlo method. Several distinct dynamical regimes are encountered: the (obstacle-free) Rouse-like regime (obstacle sub-array concentration c=0), the reptation regime for chains in perfectly periodic obstacle sub-arrays (c=1), and, in the presence of disorder and entropic traps (0<c<1), the anomalous regimes where the scaling properties differ from those predicted by the Rouse and reptation theories.
Prior to the onset of normal diffusion, even systems characterized by very slight disorder (i.e., the existence of random isolated void spaces) are shown to lead to long, transient, subdiffusive regimes where the mean square displacement of the centre of mass scales as RCM 2∼D*tbeta where 0.5<beta<1 is the anomalous diffusion exponent and D* is the anomalous diffusion coefficient.
In such disordered systems, conformational relaxation is shown to be coupled with centre of mass subdiffusion, resulting in long, time-stretched, exponential relaxation of the Rouse coordinates, viz. exp.[-(t/tau) alpha]. The stretching exponents 0.5<alpha<1 are shown to be closely related to the anomalous diffusion exponents beta and where the alpha, for a given chain, are shown to decrease with increasing mode number and with strong disorder.
The molecular size-dependence of the steady-state diffusion coefficient, as well as that of the conformational relaxation time, is shown to be greatest when the concentration of obstacles is large and when that of the voids is non-vanishing (c ≲ 1). Thus, the dynamical scaling in entropic trapping systems is non-monotonic with respect to the concentration of obstacles. Polymer reptation dynamics thus appears to be intrinsically unstable with respect to static disordered systems of obstacles.
Having demonstrated the coupling of centre of mass subdiffusion and conformational relaxation, we introduce a new relaxation length scale, lambda=(2dD*t alpha)1/2, that is more appropriate for characterizing disordered systems than is the ubiquitous radius of gyration used in both the Rouse and reptation theories. However, lambda could not be distinguished from the radius of gyration in terms of the molecular size scaling given the uncertainty in our data.
Finally, having proposed a theoretical dynamic model of entropic trapping for dilute polymer solutions in embedded mesoscopic voids, we investigate the effect of polymer solution concentration on the dynamics for both monodisperse and polydisperse polymer solutions. New, unexplored dynamical behaviours are manifest as the conformational and translational entropies compete to minimize the system free energy.
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Almahmoud, Omar H. M. "Design Optimization of Functionalized Silica-Polymer Nanocomposite through Finite Element and Molecular Dynamics Modeling". Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1707245/.
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This dissertation focuses on studying membrane air dehumidification for a membrane moisture exchanger in a membrane heat pump system. The study has two parts: an optimization of membrane moisture exchanger for air dehumidification in the macroscale, and diffusion of water vapor in polymer nanocomposites membrane for humid air dehumidification in the nanoscale. In the first part of the research, the mass transport of water vapor molecules through hydrophilic silica nanochannel chains in hydrophobic polyurethane matrix was studied by simulations and experiments for different membrane moisture exchanger design configurations. The mass transport across the polymer nanocomposite membrane occurs with the diffusion of moist air water vapor molecules in the membrane moisture exchanger in a membrane heat pump air conditioning system for air dehumidification purposes. The hydrophobic polyurethane matrix containing the hydrophilic silica nanochannel chains membrane is responsible for transporting water vapor molecules from the feed side to the permeate side of the membrane without allowing air molecules to pass through.In the second part of the research, diffusion analysis of the polymer nanocomposite membrane were performed in the nanoscale for the polymer nanocomposite membrane. The diffusion phenomena through the polymer, the polymer nanocomposite without modifying the silica surfaces, and the polymer nanocomposite with two different silica modified surfaces were studied in order to obtain the highest water vapor removal through the membrane. Different membrane moisture exchanger configurations for optimal water vapor removal were compared to get the desired membrane moisture exchanger design using the finite element method (FEM) with the COMSOL Multiphysics software package. The prediction of mass transport through different membrane configurations can be done by obtaining the mass flux value for each configuration. An experimental setup of one membrane moisture exchanger design was introduced to verify the simulation results. Also, for different membrane structures, permeability was measured according to the ASTM E-96 method. The prediction of water vapor diffusion through the polymer nanocomposite was studied by molecular dynamics simulation with the MAPS 4.3 and LAMMPS software packages. As a new nanocomposite material used in air dehumidification application, water vapor diffusivity through Silica-Polyurethane nanocomposite membranes was measured by the random movement of water vapor molecules through the formed nanochannels in the nanocomposite. For the diffusivity value, the Einstein's relationship was employed for the movement of each single water vapor molecule during the simulation time for all suggested membranes. The results of the proposed research will contribute to enhancing the energy efficiency of air conditioning systems by choosing the membrane moisture exchanger configuration which maximizes water vapor removal while, at the same time, enhancing the silica surfaces with the desired surface modifier that will maximize diffusion through the membrane itself.