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Molecular structure and dynamics of liquid water : Simulations complementing experimentsSchlesinger, Daniel January 2015 (has links)
Water is abundant on earth and in the atmosphere and the most crucial liquid for life as we know it. It has been subject to rather intense research since more than a century and still holds secrets about its molecular structure and dynamics, particularly in the supercooled state, i. e. the metastable liquid below its melting point. This thesis is concerned with different aspects of water and is written from a theoretical perspective. Simulation techniques are used to study structures and processes on the molecular level and to interpret experimental results. The evaporation kinetics of tiny water droplets is investigated in simulations with focus on the cooling process associated with evaporation. The temperature evolution of nanometer-sized droplets evaporating in vacuum is well described by the Knudsen theory of evaporation. The principle of evaporative cooling is used in experiments to rapidly cool water droplets to extremely low temperatures where water transforms into a highly structured low-density liquid in a continuous and accelerated fashion. For water at ambient conditions, a structural standard is established in form of a high precision radial distribution function as a result of x-ray diffraction experiments and simulations. Recent data even reveal intermediate range molecular correlations to distances of up to 17 Å in the bulk liquid. The barium fluoride (111) crystal surface has been suggested to be a template for ice formation because its surface lattice parameter almost coincides with that of the basal plane of hexagonal ice. Instead, water at the interface shows structural signatures of a high-density liquid at ambient and even at supercooled conditions. Inelastic neutron scattering experiments have shown a feature in the vibrational spectra of supercooled confined and protein hydration water which is connected to the so-called Boson peak of amorphous materials. We find a similar feature in simulations of bulk supercooled water and its emergence is associated with the transformation into a low-density liquid upon cooling. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Manuscript.</p>
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Freezing Supercooled Water Nanodroplets near ~225 K through Homogeneous and Heterogeneous Ice NucleationAmaya, Andrew J. January 2017 (has links)
No description available.
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X-ray scattering and spectroscopy of supercooled water and iceSellberg, Jonas A. January 2014 (has links)
This thesis presents experimental studies of water and ice at near-atmospheric pressures using intense x-rays only accessible at synchrotrons and free-electron lasers. In particular, it focuses on the deeply supercooled, metastable state and its implications on ice nucleation. The local structure of the liquid phase was studied by x-ray scattering over a wide temperature range extending from 339 K down to 227 K. In order to be able to study the deeply supercooled liquid, micron-sized water droplets were evaporatively cooled in vacuum and probed by ultrashort x-ray pulses. This is to date the lowest temperature at which measurements of the structure have been performed on bulk liquid water cooled from room temperature. Upon deep supercooling, the structure evolved toward that of a low-density liquid with local tetrahedral coordination. At ~230 K, where the low-density liquid structure started to dominate, the number of droplets containing ice nuclei increased rapidly. The estimated nucleation rate suggests that there is a “fragile-to-strong” transition in the dynamics of the liquid below 230 K, and its implications on water structure are discussed. Similarly, the electronic structure of deeply supercooled water was studied by x-ray emission spectroscopy down to 222 K, but the spectral changes expected from the structural transformation remained absent and explanations are discussed. At high fluence, the non-linear dependence of the x-ray emission yield indicated that there were high valence hole densities created during the x-ray pulse length due to Auger cascades, resulting in reabsorption of the x-ray emission. Finally, the hydrogen-bonded network in water was studied by x-ray absorption spectroscopy and compared to various ices. It was found that the pre-edge absorption cross-section, which is associated with distorted hydrogen bonds, could be minimized for crystalline ice grown on a hydrophobic BaF2(111) surface with low concentration of nucleation centers. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript. Paper 6: Manuscript.</p>
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Structure, Dynamics and Thermodynamics of Liquid Water : Insights from Molecular SimulationsWikfeldt, Kjartan Thor January 2011 (has links)
Water is a complex liquid with many unusual properties. Our understanding of its physical, chemical and biological properties is greatly advanced after a century of dedicated research but there are still many unresolved questions. If answered, they could have important long-term consequences for practical applications ranging from drug design to water purification. This thesis presents results on the structure, dynamics and thermodynamics of liquid water. The focus is on theoretical simulations applied to interpret experimental data from mainly x-ray and neutron scattering and spectroscopy techniques. The structural sensitivity of x-ray and neutron diffraction is investigated using reverse Monte Carlo simulations and information on the pair-correlation functions of water is derived. A new method for structure modeling of computationally demanding data sets is presented and used to resolve an inconsistency between experimental extended x-ray absorption fine-structure and diffraction data regarding oxygen-oxygen pair-correlations. Small-angle x-ray scattering data are modeled using large-scale classical molecular dynamics simulations, and the observed enhanced scattering at supercooled temperatures is connected to the presence of a Widom line emanating from a liquid-liquid critical point in the deeply supercooled high pressure regime. An investigation of inherent structures reveals an underlying structural bimodality in the simulations connected to disordered high-density and ordered low-density molecules, providing a clearer interpretation of experimental small-angle scattering data. Dynamical anomalies in supercooled water observed in inelastic neutron scattering experiments, manifested by low-frequency collective excitations resembling a boson peak, are investigated and found to be connected to the thermodynamically defined Widom line. Finally, x-ray absorption spectra are calculated for simulated water structures using density functional theory. An approximation of intra-molecular zero-point vibrational effects is found to significantly improve the relative spectral intensities but a structural investigation indicates that the classical simulations underestimate the amount of broken hydrogen bonds. / Vatten är en komplex vätska med flera ovanliga egenskaper. Vår förståelse av dess fysiska, kemiska och biologiska egenskaper har utvecklats mycket sedan systematiska vetenskapliga studier började genomföras för mer än ett sekel sedan, men många viktiga frågor är fortfarande obesvarade. En ökad förståelse skulle på sikt kunna leda till framsteg inom viktiga områden så som medicinutveckling och vattenrening. Denna avhandling presenterar resultat kring vattnets struktur, dynamik och termodynamik. Fokusen ligger på teoretiska simuleringar som använts för att tolka experimentella data från huvudsakligen röntgen- och neutronspridning samt spektroskopier. Den strukturella känsligheten i röntgen- och neutrondiffraktionsdata undersöks via reverse Monte Carlo metoden och information om de partiella parkorrelationsfunktionerna erhålls. En ny metod för strukturmodellering av beräkningsintensiva data presenteras och används för att lösa en motsägelse mellan experimentell diffraktion och EXAFS angående syre- syre parkorrelationsfunktionen. Data från röntgensmåvinkelspridning modelleras med storskaliga klassiska molekyldynamiksimuleringar, och den observerade förhöjda småvinkelspridningen vid underkylda temperaturer kopplas till existensen av en Widomlinje härrörande från en vätske- vätske kritisk punkt i det djupt underkylda området vid höga tryck. En undersökning av inherenta strukturer i simuleringarna påvisar en underliggande strukturell bimodalitet mellan molekyler i oordnade högdensitetsregioner respektive ordnade lågdensitetsregioner, vilket ger en tydligare tolkning av den experimentella småvinkelspridningen. Dynamiska anomalier i underkylt vatten som har observerats i inelastisk neutronspridning, speciellt förekomsten av lågfrekventa excitationer som liknar en bosontopp, undersöks och kopplas till den termodynamiskt definierade Widomlinjen. Slutligen presenteras densitetsfunktionalberäkningar av röntgenabsorptionsspektra för simulerade vattenstrukturer. En approximation av intramolekylära nollpunktsvibrationseffekter förbättrar relativa intensiteteri spektrumen avsevärt, men en strukturanalys visar att klassiska simuleringar av vatten underskattar andelen brutna vätebindningar. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 6: Submitted. Paper 7: Submitted. Paper 8: Manuscript. Paper 9: Submitted.
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Multiscale experimental and numerical study of the structure and the dynamics of water confined in clay minerals / Étude multi-échelles expérimentale et numérique de la structure et de la dynamique de l’eau confinée dans les argilesGuillaud, Emmanuel 10 July 2017 (has links)
Les argiles sont des minéraux complexes présentant une porosité multi-échelles et une aptitude à gonfler sous atmosphère humide. Ces matériaux ont diverses applications en catalyse, dans le stockage des déchets, dans le bâtiment… Pourtant, les propriétés de l'eau confinées sont encore mal comprises, notamment en raison de la complexité de l'eau elle-même. Le but de ce travail est, en utilisant principalement les simulations moléculaires et les spectrométries vibrationnelles, de comprendre la structure et la dynamique de l'eau confinée dans les argiles.Afin d'évaluer la précision des modèles numériques pour décrire l'eau confinée dans les argiles, et pour comprendre l'origine de ses propriétés structurales et dynamiques, un large part de ce travail est consacrée aux briques constitutives de l'argile : l'eau pure, l'eau interfaciale et l'eau salée. A ce titre, on étudie les propriétés viscoélastiques de l'eau du domaine surfondu jusqu'à la température d'ébullition par dynamique moléculaire classique. On analyse aussi les propriétés de frottement près d'une surface type, et la précision des approches ab initio et des modèles de sels.Dans une seconde partie, on confronte ces résultats aux propriétés de l'eau confinée dans les argiles à basse température et à température ambiante, expérimentalement et numériquement. Les expériences consistent en des mesures exhaustives par spectrométrie d'absorption dans l'infrarouge moyen et lointain, tandis que les calculs sont des simulations de dynamique moléculaire classique. En particulier, on s'intéresse à l'existence de transitions de phases induites par le confinement ou les variations de température / Clay are complex minerals with a multiscale porosity and a remarkable ability to swell under humid atmosphere. These materials have many applications in catalysis, waste management, construction industry... However, the properties of confined water are still not fully understood, due in particular to the complexity of water itself. The aim of this work is, using mainly molecular simulations and vibrational spectroscopy, to understand the structure and the dynamics of water confined in clay minerals. To evaluate the accuracy of numerical models to describe water confined in clay minerals, and to understand the origin of its structural and dynamical properties, a large part of the work was devoted to the building blocks of clays: pure bulk water, water at the surface of a solid, and salt water. To this extent, the viscoelastic properties of water from the deeply supercooled regime to the boiling temperature were investigated using classical molecular dynamics. The evolution of the friction properties of water on a prototypical solid surface was also analyzed, and the accuracy of ab initio approaches and empirical salt models was studied.In a second part, those results were confronted to the properties of water confined in clay minerals at low and room temperature, studied both experimentally and numerically. Experimental work consisted mostly in extensive far- and -mid infrared absorption spectrometry measurements, whereas numerical work mainly consisted in empirical molecular dynamics simulations. Especially, the existence of confinement- or temperature-induced phase transitions of confined water was investigated
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EFFECT OF REVERSIBLE CROSSLINKS ON NANOSTRUCTURE AND PROPERTIES OF SUPRAMOLECULAR HYDROGELSWang, Chao 12 October 2018 (has links)
No description available.
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Investigating the influence of water in lysozyme structure and dynamics using FT-IR and XRDYousif, Rafat January 2019 (has links)
Water is “the matrix of life” for its fascinating properties. The well-known simple water molecule consists of one oxygen atom and two hydrogen atoms, covering most of planet earth’ssurface. It is the most studied element in science; however, its properties are still not fully understood. Another essential building block of life is proteins, which manifest naturally in aqueous environments. The protein activity is controlled by the protein folding process that is dependent on the surrounding environment. It is hypothesized that the hydrogen bond network of water plays an important role in the folding process. Here, we investigate the protein lysozyme in liquid water as well as in the crystalline state ice Ih, exploring various temperatures, using FT-IR and XRD. Our main finding is that a transition occurs at approximately T=210 K, indicative of the hypothesised protein dynamic “glass” transitionobserved by previous studies in supercooled water at similar temperatures.
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Polimorfismo líquido e efeito hidrofóbico através de modelos simplificados / Liquid polymorphism and hydrophobic effect through simplified modelsGuisoni, Nara Cristina 13 December 2002 (has links)
Desenvolvemos dois modelos estatísticos para água, nos quais diferentes aspectos de sua estrutura são considerados. O modelo geométrico permite diferentes números de coordenação. Em uma aproximação de campo médio mostramos que sob pressão o modelo apresenta linha de coexistência entre fases de baixa e alta densidade, e ponto crítico. A entropia das ligações de hidrogênio tem papel fundamental na definição da inclinação da linha de coexistência. O comportamento do modelo pode estar realcionado como segundo ponto crítico da água super resfriada e com transições líquido-líquido em geral.O modelo da água quadrada é uma versão térmica do modelo do gelo, no qual considera-se a direcionalidade das ligações de hidrogênio. O modelo foi estudado na rede de Bethe e através de simulações de Monte Carlo em três situações diferentes: para a água pura e na presença de solutos polares e apolares. A água quadrada pura não apresenta transição de fase. No modelo para solvente com solutos apolares, medidas de frequência relativa de ligações e do tempo de correlação mostram que o modelo apresenta estruturação da camada de hidratação. Medidas de correlação temporal no modelo de Ising mostram comportamento oposto. Em um estudo preliminar para uma solução com solutos que realizam ligações de hidrogênio não conseguimos encontrar diagramas de coexistência com círculo fechado, para o conjunto de parâmetros utilizados, possivelmente devido à ausência de buracos. / We have developed two statistical models for water in which different features of water structure are considered. In the geometrical model different coordination numbers are present and the model allows for translational disorder. A mean-field treatment shows that under pressure the model exhibits phases of different densities and a coexistence line ending in a critical point. Entropy of the hydrogen network plays an essential role in defining the slope of the coexistence line. The model behavior might be related with the second critical point in supercooled water and to liquid-liquid transitions in general. The square water model is a thermal version of the ice model, and takes into account the directionality of the hydrogen bonds. The model was studied on a Bethe lattice and through Monte Carlo simulations, for three different situations: as pure water and in the presence of polar and apolar solutes. Pure square water does not present a phase transition. In the presence of apolar solutes, first shell square water presents ordering, as shown from comparison of relative frequency of bonds, as well as from study of time correlations. The latter was shown to present opposite behavior in case of an Ising system. In a preliminary study for a solution of hydrogen bonding solutes we were unable to find a closed loop for the sets of parameters chosen. Vacancies might need to be included.
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Electronically coarse grained molecular model of waterCipcigan, Flaviu Serban January 2017 (has links)
Electronic coarse graining is a technique improving the predictive power of molecular dynamics simulations by representing electrons via a quantum harmonic oscillator. This construction, known as a Quantum Drude Oscillator, provides all molecular long-range responses by uniting many-body dispersion, polarisation and cross interactions to all orders. To demonstrate the predictive power of electronic coarse graining and provide insights into the physics of water, a molecular model of water based on Quantum Drude Oscillators is developed. The model is parametrised to the properties of an isolated molecule and a single cut through the dimer energy surface. Such a parametrisation makes the condensed phase properties of the model a prediction rather than a fitting target. These properties are studied in four environments via two-temperature adiabatic path integral molecular dynamics: a proton ordered ice, the liquid{vapour interface, supercritical and supercooled water. In all these environments, the model predicts a condensed phase in excellent agreement with experiment, showing impressive transferability. It predicts correct densities and pressures in liquid water from 220 K to 647 K, and a correct temperature of maximum density. Furthermore, it predicts the surface tension, the liquid-vapour critical point, density of ice II, and radial distribution functions across all conditions studied. The model also provides insight into the relationship between the molecular structure of water and its condensed phase properties. An asymmetry between donor and acceptor hydrogen bonds is identified as the molecular scale mechanism responsible for the surface orientation of water molecules. The dipole moment is identified as a molecular scale signature of liquid-like and gas-like regions in supercritical water. Finally, a link between the coordination number and the anomalous thermal expansion of the second coordination shell is also presented.
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Polimorfismo líquido e efeito hidrofóbico através de modelos simplificados / Liquid polymorphism and hydrophobic effect through simplified modelsNara Cristina Guisoni 13 December 2002 (has links)
Desenvolvemos dois modelos estatísticos para água, nos quais diferentes aspectos de sua estrutura são considerados. O modelo geométrico permite diferentes números de coordenação. Em uma aproximação de campo médio mostramos que sob pressão o modelo apresenta linha de coexistência entre fases de baixa e alta densidade, e ponto crítico. A entropia das ligações de hidrogênio tem papel fundamental na definição da inclinação da linha de coexistência. O comportamento do modelo pode estar realcionado como segundo ponto crítico da água super resfriada e com transições líquido-líquido em geral.O modelo da água quadrada é uma versão térmica do modelo do gelo, no qual considera-se a direcionalidade das ligações de hidrogênio. O modelo foi estudado na rede de Bethe e através de simulações de Monte Carlo em três situações diferentes: para a água pura e na presença de solutos polares e apolares. A água quadrada pura não apresenta transição de fase. No modelo para solvente com solutos apolares, medidas de frequência relativa de ligações e do tempo de correlação mostram que o modelo apresenta estruturação da camada de hidratação. Medidas de correlação temporal no modelo de Ising mostram comportamento oposto. Em um estudo preliminar para uma solução com solutos que realizam ligações de hidrogênio não conseguimos encontrar diagramas de coexistência com círculo fechado, para o conjunto de parâmetros utilizados, possivelmente devido à ausência de buracos. / We have developed two statistical models for water in which different features of water structure are considered. In the geometrical model different coordination numbers are present and the model allows for translational disorder. A mean-field treatment shows that under pressure the model exhibits phases of different densities and a coexistence line ending in a critical point. Entropy of the hydrogen network plays an essential role in defining the slope of the coexistence line. The model behavior might be related with the second critical point in supercooled water and to liquid-liquid transitions in general. The square water model is a thermal version of the ice model, and takes into account the directionality of the hydrogen bonds. The model was studied on a Bethe lattice and through Monte Carlo simulations, for three different situations: as pure water and in the presence of polar and apolar solutes. Pure square water does not present a phase transition. In the presence of apolar solutes, first shell square water presents ordering, as shown from comparison of relative frequency of bonds, as well as from study of time correlations. The latter was shown to present opposite behavior in case of an Ising system. In a preliminary study for a solution of hydrogen bonding solutes we were unable to find a closed loop for the sets of parameters chosen. Vacancies might need to be included.
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