Water is the most common solvent for most biological reactions, therefore it is vital that we fully understand water and all its properties. The complex hydrogen bonding network that water forms can influence protein-protein and protein-substrate interactions and can slow protein conformational shifts. Here, I examine an important property of water known as energetic roughness. The network of interactions between individual water molecules affect the energy landscape of proteins by altering the underlying energetic roughness. I have attributed this roughness to the making and breaking of hydrogen bonds as the network of hydrogen bonds constantly adopts new conformations. Through a novel computational approach I have analyzed five prominent water models and have determined their inherent roughness to be between 0.43 and 0.62 kcal/mol.

The city of Melbourne in Victoria, Australia has been recognised as having high quality drinking water, but like other urban cities in the world, its growing population means increasing water demand. Melbourne is also already on its eight year of dry climatic conditions and is currently experiencing a drought that forced water authorities to impose water restrictions after 20 years of unrestricted supply. The current drought, dwindling supplies and possible impact of climate change highlight the importance of making better use of this precious resource. The Water Resources Strategy has been developed for Melbourne, which serve as the basis for the Victorian Government to set per capita consumption reduction targets of 15%, 25% and 30% by 2010, 2015 and 2020 respectively. The strategy was developed to ensure a continuation of a safe, reliable and cost effective water supply that is environmentally sustainable in the long term. This is in recognition that population growth and water consumption will eventually require additional supplies of water (Water Resources Strategy Committee for the Melbourne Area 2002). One of the key findings of the National Land and Water Resources Audit's Australian Water Resources Assessment 2000 is the lack of detailed knowledge about the end use (Australian Water Association 2001). The

Water is a fundamental part of life as we know it, and by that also a fundamental for biology, chemistry, and parts of physics. Understanding how water behaves and interacts is key in many fields of all these three branches of science. Numerical simulation using molecular dynamics can aid in building insight in the behavior and interactions of water. In this thesis molecular dynamics is used to simulate common rigid 3 point water models to see how well they replicate certain physical and chemical properties as functions of temperature. This is done with molecular dynamics program GROMACS which offers a complete set of tools to run simulations and analyze results. Everything has been automated to work with a python script and a file of input parameters. Most of the models follow the same trends and are valid within a limited temperature range. / Vatten är en av de fundamentala byggstenarna för liv, därmed är det även fundamentalt för biologi, kemi och delar av fysiken. Att förstå hur vatten beter sig och interagerar är en stor fråga inom dessa tre grenar av vetenskap. Med molekyldynamik går det att utföra numeriska simuleringar som kan användas som hjälpmedel för att bygga en djupare förståelse för riktigt vatten. I den här uppsatsen så har molekyldynamik använts till att simulera vanliga rigida 3 punkts parametiseringar av vatten för att se hur bra de kan replikera vissa egenskaper som funktioner av temperatur. Simuleringen är gjord med hjälp av molekyldynamik programet GROMACS som ger en fullständig uppsättning verktyg för att simulera och analysera molekylsystem. Alla simuleringar och analys är automatiserat med ett pythonprogram och en fil för parametrar. De allra flesta modeller följer liknande trender och är giltiga inom små temperaturintervall.

La Structuration des molécules d’eau à l’interface eau/vapeur d’eau fait l’objet de l’intérêt scientifique depuis des années. La plupart des études sont focalisées sur le bulk d’eau mais des études plus détaillées sur l’eau de surface sont nécessaires. De plus, les interfaces avec les alcanes sont intéressantes d’un point de vue biologique et industriel. Puisque pour des applications biologiques et industrielles les interfaces eau/air et eau/huile possèdent des médiateurs amphiphiles, l’influence d’une monocouche de tensioactif sur la structuration de la surface de l’eau mérite aussi une attention particulière.Dans cette thèse, plusieurs modèles atomistiques d’eau ont été sélectionnés. Des simulations de dynamique moléculaire classique ont été réalisées à 298K pour le bulk d’eau, des systèmes eau/vapeur d’eau et eau/alcane (C5-C9), ainsi que des systèmes eau/DLPC/vapeur d’eau et eau/DLPC/octane (DLPC : dilauroyl phosphatidylcholine). Plusieurs propriétés structurelles, ainsi que les moments dipolaires, la tension de surface et les liaisons hydrogène, du bulk d’eau et des couches de surface d’eau ont été examinées grâce à la fonction de distribution radiale et les diagrammes de Voronoi. L’objectif a été d’estimer l’impact de l’incorporation de la polarisabilité sur les propriétés de l’eau et de sélectionner un modèle optimal (qualité/temps de calcul) pour leur description, ainsi que d’enrichir les données existantes sur la structuration de l’eau à l’interface.Cette étude aborde la structuration de l’eau du bulk et de la surface à l’interface avec la vapeur d’eau ou des alcanes. Un des objectifs de ce travail a été d’évaluer la reproductibilité des données expérimentales en utilisant différents modèles et de s’assurer pour quelles propriétés l’utilisation d’un modèle polarisable est critique. De simples modèles polarisables basés sur les oscillateurs de Drude ont été testés afin de limiter le temps de calcul. Pour le bulk d’eau et les systèmes eau/vapeur d’eau, les modèles TIP4P, SWM4-NDP et COS/G2 ont été les plus performants. Dans la mesure où le modèle TIP4P produit des résultats commensurables avec les modèles polarisables, il a été utilisé pour la simulation des interfaces eau/alcanes (C5-C9). Les molécules à la surface sont organisées de manière plus compacte et moins ordonnée. Cette diminution de l’ordre est principalement due aux liaisons hydrogène qui sont deux fois plus nombreuses dans le bulk qu’en surface. Les analyses de Voronoi ont montré que la coordination tétraédrique n’est pas si claire et que des polyèdres plus complexes sont formés. Les couches de surfaces trouvées s’avèrent être formées de 2 sous-couches, interne et externe, avec des polarités inégales orientées de manières opposées, définissant des zones de charges résiduelles à l’interface.En plus des systèmes avec un contact direct entre l’eau et le fluide apolaire, des interfaces comportant des monocouches de lipides ont été modélisées. La compacité de l’eau de surface, déjà renforcée par la présence d’alcanes, a été augmentée davantage par l’introduction de lipide. Néanmoins, l’orientation de l’eau a été changée et la polarité de la surface inversée, équilibrée par les têtes lipidiques au lieu des sous-couches externes diffuses.Les résultats principaux de cette thèse de doctorat sont les suivants:1. Il a été montré que l’utilisation de modèles d’eau polarisable n’est pas nécessaire pour une évaluation correcte d’un certain nombre de propriétés, mais elle est critique pour les moments dipolaires et la tension de surface.2. Pour la première fois une analyse structurelle a été réalisée en utilisant les diagrammes de Voronoi et un ensemble de modèles d’eau démontrant la différence entre propriétés de l’eau liquide en bulk et en surface.3. Considérant le nombre limité de données existantes, l’étude d’une monocouche de DLPC solide condensée à l’interface eau/vapeur et eau/octane en utilisant différents modèles d’eau a été une contribution originale. / The structuring of water molecules at the water/vapour interface is an object of scientific interest for decades. Most of the existing theoretical studies are focused on bulk water but there is still need of a more detailed research on surface water. In addition, interfaces with alkanes are interesting as being instructive from both biological and industrial perspectives. Since in both bio- and industrial applications water/air and water/oil interfaces are mediated by amphiphiles, the role of a surfactant monolayer on surface water structuring deserves more attention as well.In the present Ph. D. thesis several atomistic water models were chosen and classical molecular dynamics simulations were carried out on bulk water, water/vapour and water/alkane (from pentane to nonane) systems, as well as on water/DLPC/vapour and water/DLPC/octane models, DLPC being dilauroyl phosphatidylcholine. In all cases the temperature was kept at 298 K. Several structural properties of bulk and surface water layers were examined by means of radial distribution functions and Voronoi diagrams. Dipole moments, surface tension and hydrogen bonding were tackled too. The objective was to estimate the impact of accounting for polarisability on the water properties of interest and to select a cost-efficient water model for describing them, as well as to add new data to the existing knowledge about interfacial water structuring.The study addresses the water structuring in bulk and surfacial water at the interface with vapour or alkanes of different chain length. One of the aims of the work was to assess the reproducibility of experimental data using an assortment of polarisable and non-polarisable water models and to check for which properties the utilisation of polarisable models is critical. Simple polarisable models based on Drude oscillators were tested in order to keep the computational costs low. For bulk water and water/vapour systems the models TIP4P, SWM4-NDP and COS/G2 performed the best. Since the TIP4P model produced results commeasurable with the polarisable ones, it was used predominantly further on to simulate water/alkane (C5-C9) interface and to quantify the structural parameters of water obtained from RDFs and Voronoi analyses. The molecules in this layer are organised in a more compact and less ordered manner. The ordering is owed mainly to hydrogen bonds which are twice as many in the bulk compared to the surface. The analysis of the Voronoi diagrams showed that the tetrahedral coordination was blurred and more complex polyhedra were formed. The surface layer was found to consist of two sublayers, inner and outer, with oppositely oriented unequal polarity, defining areas of residual charges at the interface.In addition to the systems with direct contact between water and non-polar fluids, interfaces mediated by lipid monolayers were modelled. The monolayer was meant to seam together the two phases. The compactness of the surfacial water, which was enhanced by the presence of alkanes, was tightened further by the lipid introduction. However, the water orientation was changed and the surfacial polarity was inverted, balanced by the lipid heads instead of the diffuse outer sublayer.The main contributions of the Ph.D. thesis are as follows:1. It is shown that the usage of a polarisable water model is not necessary for correct evaluation of a number of properties, but is critical for characteristics such as dipole moments and surface tension.2. For the first time a structural analysis has been made using Voronoi diagrams and an assortment of water models which demonstrates the difference between bulk and surfacial characteristics of liquid water.3. An original contribution is the study of a solid-condensed DLPC monolayer at the water/vapour interface utilising different water models and at the interface of water/octane, considering the limited experimental data available.

Understanding the connection of surface waters to ground-water systems is important when evaluating potential water resources. In the past surface waters and ground-water have been viewed as two different sources of water but more commonly now they are viewed as one connected resource (Winter et al, 1998). The nature of connection between surface and ground-waters varies depending on climatic and geologic settings, as well as anthropogenic influences such as ground-water pumping and manipulation of river flows by dams. This thesis takes advantage of daily stage changes in the Deerfield River to investigate surface water interactions with ground-water in Charlemont, MA. Two dimensional transient numerical models are constructed to simulate ground-water response to river stage changes. These models are coupled to hypothetical mass transport models to investigate mixing mechanisms of conservative solutes under varying hydraulic scenarios. These simulations support the hypothesis that daily stage fluctuations cause a pumping mechanism which drives solutes into ground-water systems adjacent to a river at rates higher then normal flow conditions, or even under certain flood conditions. Riverbed pore-water temperature responses to diurnal temperature fluctuations are measured at two sites along the Deerfield River exposed to the same daily stage changes caused by dams. Temperature and stage data are collected at two sites with differing geologic settings. These data are used to calibrate simple two dimensional models of ground-water flow and heat transport to site specific riverbed hydraulic conductivities. It is suggested that due to the differing depositional environments of the two field sites, hydraulic conductivity of riverbed materials differ, which affects the exchange flux between surface water and ground-water. Understanding the exchange between surface and ground waters under varying hydraulic and geologic conditions is vital to characterizing local water resources and determining ecosystems health.

Le modèle de couche mince intégré sur l'épaisseur, Saint-Venant, utilisé classiquement pour simuler la propagation de laves torrentielles et coulées boueuses, repose sur plusieurs approximations concernant la forme des profils de vitesse en zones non-uniformes. Il est pourtant nécessaire d'utiliser ce type de modélisation, comme outil d'aide à la gestion des risques liés aux laves torrentielles. Nous proposons d'éprouver ses hypothèses, en observant une zone fortement non-uniforme, le front de coulées à surface libre et le champ de vitesse à l'intérieur de cette zone.En améliorant notre connaissance de l'évolution de la forme des profils de vitesse (de la dynamique interne) au front de coulées, nous cherchons à améliorer les modèles de couche mince. Cette thèse porte donc sur l'étude de la dynamique interne au front d'écoulements à surface libre de fluides newtoniens et viscoplastiques.Nous avons utilisé le dispositif du canal à fond mobile qui permet de générer des coulées stationnaires dans le référentiel de l'observateur au moyen d'un fond mobile remontant vers l'amont. Nous avons réalisé un travail technique sur ce canal et sur l'analyse des images pour pouvoir mesurer les champs de vitesse à haute résolution spatiale aux fronts de coulées à surface libre de fluides viscoplastiques. L'étude des fluides newtoniens a aussi été réalisée afin de valider les modèles et éprouver le dispositif expérimental.Nous avons comparé les résultats expérimentaux aux solutions théoriques de deux modèles de couche mince adaptés à la rhéologie de Herschel-Bulkley : le modèle classique de la lubrification, à la base du modèle de Saint-Venant et un modèle consistant à l'ordre 1 développé dans cette thèse. Le modèle consistant d'ordre 1 est la somme du modèle à l'ordre 0 (la lubrification) et de termes correctifs qui proviennent des contraintes normales et des termes d'inertie. Dans le cadre de notre configuration du fond mobile remontant vers l'amont, il est possible de déduire la forme du front en cherchant une solution de type onde progressive, sans passer par un modèle intégré dans l'épaisseur.Pour les fluides viscoplastiques, la structure classique du profil de vitesse, avec une zone cisaillée surmontée d'un plug non cisaillé est bien reconnaissable sur nos profils de vitesse en zone uniforme, et en zone faiblement variée. Mais à l'approche du front, cependant, la vitesse de surface augmente, les profils de vitesse expérimentaux deviennent cisaillés sur toute l'épaisseur, conduisant à la disparition du plug à proximité de la ligne de front.Le modèle de lubrification prédit l’existence d'un plug dans le front jusqu'à la ligne de contact, ce qui n'est pas observé expérimentalement. La vitesse de surface du modèle de lubrification augmente à l'approche du front, mais est largement sous-estimée par rapport à la vitesse de surface mesurée. Les vitesses de surface prédites par le modèle d'ordre 1 augmentent plus drastiquement au front, en meilleur accord avec les mesures que le modèle de lubrification. Pour certaines configurations expérimentales l'accord est même très bon. Remarquablement, le cisaillement des profils de vitesse à l'approche du front, observé expérimentalement, est aussi prédit par le modèle d'ordre 1.Les profils de vitesse présentent donc une évolution au front de coulées viscoplastiques en contradiction avec les hypothèses du modèle de Saint-Venant. Le modèle consistant d'ordre 1 permet d'améliorer les prédictions. Un modèle intégré dans l'épaisseur de type Saint-Venant basé sur les développements consistants d'ordre 1 est alors calculé, car il constitue l'étape nécessaire avant d'être intégré dans un outil de simulation opérationnel. / A depth-averaged model based on the thin-layer assumption, called Saint-Venant (Shallow-Water), is classically used to simulate the propagation and the spreading of debris and mud flows. It is based on several approximations concerning the shape of the velocity profile in non-uniform zones. We propose to test these hypotheses, examining a strongly non-uniform zone, the front of free-surface viscoplastic flows and the velocity field within this zone. By improving our knowledge about the internal dynamics in the front zone, we seek to improve the thin-layer models. This thesis therefore focuses on the study of the internal dynamics within the front of viscoplatic free-surface flows.We used the moving conveyor belt to generate stationary flows. We carried out a technical work on this set-up, and specific analysis of images obtained from the high-speed camera, in order to be able to measure velocity fields with a high resolution. The study of a Newtonian fluid was also carried out in order to validate the lubrication model and the experimental device.We compared experimental results to theoretical solutions of two thin-layer models taking into account the Herschel-Bulkley rheology: the classical model of lubrication, which is at the base of Saint-Venant model, and a consistent first-order model specifically developed in this thesis.The first-order model is equal to the zero-order model (lubrication), plus corrective terms derived from the normal stresses and inertia terms.In this study, for the purpose of comparison with our experimental results, we are interested in travelling-wave solutions. We are able to solve the shape of the front without using a depth-averaged model.Far from the front, experimental velocity profiles clearly display the characteristic 2-layer structure predicted by the lubrication solution, with constant values close to the free-surface (plug) and a sheared layer underneath. Closer to surge tip, the shape of experimental longitudinal velocity profilesthen begins to differ from the theoretical prediction. The 2-layer structure tends to disappear, and the profiles display shear across the whole depth ofthe flow. In this tip region, surface velocity also appears to increase faster than its theoretical counterpart. Surface velocity predicted by the first-order model increase more drastically in the tip region, in better agreement with the measurements than the lubrication model. The first-order model predicts a sheared velocity profile when approaching the front, as observed experimentally.The consistent first-order model then provides better predictions about internal dynamics than lubrication model. A depth-integrated model like Saint-Venant, based on consistent first-order developments is then calculated, as a first step before being integrated into an operational simulation tool.

Atomistic modeling and simulation methods enable a modern molecular approach to bio-medical research. Issues addressed range from structure-function relationships to structure-based drug design. The ability of these methods to address biologically relevant problems is largely determined by their accurate treatment of electrostatic interactions in the target biomolecular structure. In practical molecular simulations, the electrostatic charge density of molecules is approximated by an arrangement of fractional "point charges" throughout the molecule. While chemically intuitive and straightforward in technical implementation, models based exclusively on atom-centered charge placement, a major workhorse of the biomolecular simulations, do not necessarily provide a sufficiently detailed description of the molecular electrostatic potentials for small systems, and can become prohibitively expensive for large systems with thousands to millions of atoms. In this work, we propose a rigorous and generally applicable approach, Optimal Point Charge Approximation (OPCA), for approximating electrostatic charge distributions of biomolecules with a small number of point charges to best represent the underlying electrostatic potential, regardless of the distance to the charge distribution. OPCA places a given number of point charges so that the lowest order multipole moments of the reference charge distribution are optimally reproduced. We provide a general framework for calculating OPCAs to any order, and introduce closed-form analytical expressions for the 1-charge, 2-charge and 3-charge OPCA. We demonstrate the advantage of OPCA by applying it to a wide range of biomolecules of varied sizes. We use the concept of OPCA to develop a different, novel approach of constructing accurate and simple point charge water models. The proposed approach permits a virtually exhaustive search for optimal model parameters in the sub-space most relevant to electrostatic properties of the water molecule in liquid phase. A novel rigid 4-point Optimal Point Charge (OPC) water model constructed based on the new approach is substantially more accurate than commonly used models in terms of bulk water properties, and delivers critical accuracy improvement in practical atomistic simulations, such as RNA simulations, protein folding, protein-ligand binding and small molecule hydration. We also apply our new approach to construct a 3-point version of the Optimal Point Charge water model, referred to as OPC3. OPCA can be employed to represent large charge distributions with only a few point charges. We use this capability of OPCA to develop a multi-scale, yet fully atomistic, generalized Born approach (GB-HCPO) that can deliver up to 2 orders of magnitude speedup compared to the reference MD simulation. As a practical demonstration, we exploit the new multi-scale approach to gain insight into the structure of million-atom 30-nm chromatin fiber. Our results suggest important structural details consistent with experiment: the linker DNA fills the core region and the H3 histone tails interact with the linker DNA. OPC, OPC3 and GB-HCPO are implemented in AMBER molecular dynamics software package. / Ph. D.

Ce travail s'inscrit dans l'étude mathématique d'écoulements de fluides environnementaux. Nous en abordons deux aspects, à travers deux contextes distincts d'application.En lien avec la simulation des écoulements en milieux poreux, on s'intéresse dans une première partie à la discrétisation d'opérateurs de diffusion anisotropes hétérogènes par des méthodes de volumes finis sur des maillages généraux. Dans le but d'obtenir des solutions approchées qui respectent les bornes physiques des modèles, notre attention se porte sur la conservation du principe du maximum pour les opérateurs elliptiques. Nous présentons des mécanismes généraux permettant de corriger tout schéma volumes finis afin de garantir un principe du maximum discret tout en préservant certaines de ses propriétés principales. On étudie en particulier les propriétés de coercivité et de convergence des schémas corrigés.La deuxième partie est consacrée à la construction de modèles approchés pour la propagation des vagues en eaux peu profondes et sur des topographies irrégulières. A cet effet, nous proposons tout d'abord une adaptation de la démarche d'étude classique à des écoulements bidimensionnels sur des topographies polygonales. Dans un cadre plus général, nous développons ensuite une démarche formelle qui débouche sur des alternatives non locales à quelques modèles classiques (équations de Saint-Venant, équations de Serre, système de Boussinesq). Ces nouveaux modèles contiennent des termes régularisants pour les contributions du fond. / This work investigates two research questions associated with environmental flows and their mathematical modeling.The first part is devoted to the development of finite volume methods for anisotropic and heterogeneous diffusion operators arising in models of porous media flows. To ensure that the approximate solutions lie within physical bounds, we aim at maintaining a discrete analogous of the maximum principle for elliptic operators. Starting from any given cell-centered finite volume scheme, we present a general approach to devise non-linear corrections providing a discrete maximum principle while retaining some main properties of the scheme. In particular, we study the coercivity and convergence properties of the modified schemes.The second part of this work focuses on the derivation of approximate models for shallow water wave propagation over rough topographies. In the particular case of one-dimensional polygonal bottom profiles, we first propose an adaptation of the usual derivation method using complex analysis tools. We then develop a formal approach to account for more general topographies. We propose nonlocal alternatives to some classical models (namely Saint-Venant equations, Serre equations and Boussinesq system). All these alternative models only involve smoothing contributions of the bottom.

This thesis deals with several aspects of the structure and dynamics of water molecules confined in nanoscopic pores. Water molecules confined in hydrophobic nanocavities exhibit unusual structural and dynamic properties. Confining walls of single-wall carbon nanotubes (SWCNTs) promote strong inter-water hydrogen bonding which in turn leads to several novel structural, dynamic and thermodynamic features not found in bulk water. Confined water molecules form ordered hydrogen-bonded networks, exhibit exceptionally high flow rates as compared to conventional flow in pipes, allow fast proton conduction and exhibit various other anomalous properties. Proteins are known to exploit some of the properties of confined water to perform certain physiological functions. Various properties of confined water can also be exploited in the design of nanofludic devices such as those for desalination and flow sensors. In addition, water molecules confined in SWCNTs and near graphene sheets serve as model systems to study various effects of confinement on the properties of liquids. In this thesis, we present the results of detailed molecular dynamics simulation studies of confined water molecules. In chapter 1, we summarize the findings of existing simulations and experimental studies of bulk and confined water molecules. We also highlight the significance of studying the structure and dynamics of confined water molecules in biological and biotechnological applications. Chapter 2 provides a brief ac-count of the methods and techniques used to perform the simulations described in subsequent chapters of the thesis. We also present a brief overview of the methods used to extract physical properties of water molecules from simulation data, with emphasis on the Two Phase Thermodynamics (2PT) method which we have used to compute the entropy of confined and bulk water molecules. In chapter 3, we discuss the thermodynamics of water entry in SWCNTs of various diameters. Experiments and computer simulations demonstrate that water spontaneously fills the interior of a carbon nanotube. Given the hydrophobic nature of the interior of carbon nanotubes and the strong confinement produced by narrow nanotubes, the spontaneous entry of water molecules in the pores of such nanotubes is surprising. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed Two Phase Thermodynamics (2PT) method to compute translational and rotational entropies of water molecules confined in SWCNTs and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with those of bulk water shows significant shifts in the positions of spectral peaks that are directly related to the tube radius. These peaks are experimentally accessible and can be used to characterize water dynamics from spectroscopy experiments. We have also computed the free-energy transfer when a bulk water molecule enters a SWCNT for various temperatures and carbon-water interactions. We show that for reduced carbon-oxygen interaction, the free energy transfer is unfavourable and the SWCNT remains unoccupied for significant periods of time. As the temperature is increased, the free energy of confined water becomes unfavourable and reduced occupancy of water is observed. Bulk water exhibits many anomalous properties. No single water model is able to reproduce all properties of bulk water. Different empirical water models have been developed to reproduce different properties of water. In chapter 4, a comparative study of the structure, dynamics and thermodynamic proper-ties of water molecules confined in narrow SWCNTs, obtained from simulations using several water models including polarizable ones, is presented. We show that the inclusion of polarizability quantitatively affects the nature of hydro-gen bonding which governs different properties of water molecules. The SPC/E water model is shown to reproduce results in close agreement with those from polarizable water models with much less computational cost. In chapter 5, we report results obtained from simulations of the properties of water confined in the space between two planar surfaces. We consider three cases: two graphene surfaces, two Boron Nitride (BN) surfaces and one graphene and one BN surface. This is the first detailed study of the behaviour of water near extended BN surfaces. We show that the hydrophilic nature of the BN surface leads to several interesting effects on the dynamics of water molecules near it. We have observed a change in the activation energy, extracted from the temperature dependence of the translational and rotational dynamics, near 280K. This change in activation energy coincides with a change in the structure of the confined sheet of water, indicated by a sudden change in energy. We have also found signatures of glassy dynamics at low temperatures for all three cases, the glassy effects being the strongest for water molecules confined between two BN sheets. These results are similar to those of earlier studies in which novel phases of water have been found for water molecules confined between other surfaces at high pressure. In chapter 6, we have described our observation of a novel phenomenon exhibited by water molecules flowing through a SWCNT under a pressure gradient. We have shown that the flow induces changes in the orientation of the water molecules flowing through the nanotube. In particular, the dipole moments of the water molecules inside the nanotube get aligned along the axis of the nanotube under the effect of the flow. With increasing flow velocities, the net dipole moment first increases and eventually saturates to a constant value. This behaviour is similar to the Langevin theory of paramagnetism with the flow velocity acting as an effective aligning field. Preferential entry of water molecules with dipole moments pointing inward is shown to be the main cause of this effect. This observation provides a way to control the dipolar alignment of water molecules inside nano-channels, with possible applications in nanofluidic devices. Chapter 7 contains a summary of our main results and a few concluding re-marks.