The aim of this dissertation is to investigate self-assembled structures and the phase diagram of amphiphilic molecules of diverse geometric shapes using a number of different computer simulation methods. The semi-realistic coarse-grained model, used extensively for simulation of polymers and surfactant molecules, is adopted in an off-lattice approach to study how the geometric structure of amphiphiles affects the aggregation properties. The results of simulations show that the model system behavior is consistent with theoretical predictions, experiments and lattice simulation models. We demonstrate that by modifying the geometry of the molecules, self-assembled aggregates are altered in a way close to theoretical predictions. In several two and three dimensional off-lattice Brownian Dynamics simulations, the influence of the shape of the amphiphilic molecules on the size and form of the aggregates is studied systematically. Model phospholipid molecules, with two hydrophobic chains connected to one hydrophilic head group, are simulated and the formation of stable bilayers is observed. In addition, (practically very important) mixtures of amphiphiles with diverse structures are studied under different mixing ratios and molecular structures. We find that in several systems, with Poisson distributed chain lengths, the effect on the aggregation distribution is negligible compared to that of the pure amphiphilic system with the mean length of the Poisson distribution. The phase diagrams of different amphiphilic molecular structures are investigated in separate simulations by employing the Gibbs Ensemble Monte Carlo method with an implemented configurational-bias technique. The computer simulations of the above mentioned amphiphilic systems are done in an area where physics, biology and chemistry are closely connected and advances in applications require the use of new theoretical, experimental and simulation methods for a better understanding of their self-assembling properties. Obtained simulation results demonstrate the connection between the structure of amphiphilic molecules and the properties of their thermodynamically stable aggregates and thus build a foundation for many applications of the remarkable phenomena of amphiphilic self-assembly in the area of nanotechnology.

It is commonly known that water plays a crucial role in many natural and industrial processes. One of these processes is the formation of water trees, and the subsequent breakdown of polyethylene used for high voltage cable insulation purposes. It has been shown that the mechanism for water molecules diffusing through amorphous polyethylene includes the formation of small water clusters. Gibbs Ensemble Monte Carlo molecular simulations has been performed to study the clustering of vapour phase water under vapour - liquid equilibrium conditions at temperatures ranging from 300 K to 600 K. The increase in vapour density with increasing temperature leads to a radical increase in the fraction of molecules belonging to clusters with two or more water molecules. It is also seen that the size of the clusters increases with temperature. The topologies of the smaller clusters, up to pentamers, have also been studied. A structural transition is observed from a large percentage with cyclic topology, which is the minimum energy configuration, at lower temperatures to predominantly linear clusters, favoured by entropic effects, at higher temperatures. Similar water properties have been obseved in simulations where the vapour phase has been replaced with a hydrocarbon rich phase ( n-alkanes and polyethylene ). Application of an external electric field to the polymer system reduces the water solubility and affects the water structure. A dramatic increase in water solubility in the hydrocarbon phase is observed when two oppositely charged ions are introduced in the hydrocarbon. The structure of the water have changed from several small clusters to a single large cluster with a rod-like shape. The cluster is extremely stable during the simulation. Application of an external electric field may enhance or reduce the effect of the ions depending on the direction of the field. Based on these observations is an alternative mechanism for water tree propagation proposed.

Noble gas partitioning between supercritical CO2-H2O phases can be used to monitor Carbon Capture and Storage (CCS) sites and their natural analogues. However, in order for viable application, noble gas partitioning within these environments must be well constrained. Present estimates of partition coefficient for these systems are taken from the low pressure pure noble gas-water experiments of Crovetto et al. and Smith (Crovetto et al., 1982; Smith, 1985). The effect a supercritical CO2 phase may have on noble gas partitioning is assumed negligible, although this has not been empirically verified. In this work this assumption of noble gas behaviour within a supercritical CO2-H2O binary phase system is evaluated using a combined approach of experiment and simulation. Using a specially commissioned high pressure system at the British Geological Survey paired CO2 and H2O samples were collected from noble gas-enriched systems at pressures and temperatures ranging between 90 – 140 bar and 323.15 – 373.15 K. These were analysed for their noble gas content using a quadrupole mass spectrometer system developed specifically for this project. By comparing the relative concentrations of noble gases in each phase partition coefficients were defined for the experimental conditions. These were compared to their low pressure analogues. At higher CO2 densities all noble gases expressed a significant deviation from predicted partition coefficients. At the highest density (656 kg/m3) helium values decreased by -54% (i.e. reduced solubility within CO2) while argon, krypton and xenon values increased by 76%, 106% and 291% respectively. These deviations are due to supercritical CO2 acting as a polar solvent, the solvation power of which increases as a function of density. Polarisation is induced in each noble gas within this solvent based on their respective polarisabilities. Hence xenon, krypton and argon become more easily solvated as a function of CO2 density while solvating helium becomes harder. These deviation trends are well described using a second order polynomial. This fit defines a deviation coefficient which can be used to adapt low pressure partition coefficients to allow accurate predictions of partitioning within highly dense CO2 phases. Concurrently a Gibbs Ensemble Monte Carlo (GEMC) molecular model was iteratively developed to reproduce noble gas behaviour within these experimental systems. By optimising noble gas-water interactions a pure noble gas-water system was constructed for each noble gas at low pressure which replicated published partition coefficients. These optimised interactions were subsequently applied to low pressure CO2-H2O systems where partition coefficients were derived by calculating excess chemical potentials of noble gases in each phase. Again a good agreement was observed with published values. When the model was applied to the experimental conditions however, a poor agreement with the experimental values was observed. Instead simulated values replicated the low pressure Crovetto et al. and Smith datasets (Crovetto et al., 1982; Smith, 1985). This was due to no CO2-noble gas polarisation terms being included in the current iteration of the model. By including this within the model in the future a full reconciliation between the datasets is expected.

Third phase formation is an undesirable phenomenon during the PUREX process, which is a continuous liquid-liquid extraction approach for the reprocessing of uranium and plutonium from spent nuclear fuel. When third phase formation occurs, the organic extraction solution splits into two layers. The light upper layer, which is commonly named the light organic phase, contains a lower concentration of metal ions, tri-n-butyl phosphate (TBP) and nitric acids but is rich in the organic diluent. The heavy lower layer, which is commonly named the third phase, contains high concentrations of metal ions, TBP and nitric acids. As the third phase contains high concentrations of the uranium and plutonium complexes it can thus cause processing and safety concerns. Therefore, a comprehensive understanding of the mechanism of third phase formation is needed so as to improve the PUREX flowsheet. To investigate third phase formation through molecular simulations, one should first obtain reliable molecular models. A refined model for TBP, which uses a new set of partial charges generated from our density functional theory calculations, was proposed in this study. To compare its performance with other available TBP models, molecular dynamics simulations were conducted to calculate the thermodynamic properties, transport properties and the microscopic structures of liquid TBP, TBP/water mixtures and TBP/n-alkane mixtures. To our knowledge, it is only TBP model that has been validated to show a good prediction of the microscopic structure of systems that consist of both hydrophobic and hydrophilic species. This thesis also presents evidence that the light-organic/third phase transition in the TBP/n-dodecane/HNO3/H2O systems, which is relevant to the PUREX process, is an unusual transition between two isotropic, bi-continuous micro-emulsion phases. The light-organic /third phase coexistence was first observed using Gibbs Ensemble Monte Carlo (GEMC) simulations and then validated through Gibbs free energy calculations. Snapshots from the simulations as well as the cluster analysis of the light organic and third phases reveal structures akin to bi-continuous micro-emulsion phases, where the polar species reside within a mesh whose surface consists of amphiphilic TBP molecules. The non-polar n-dodecane molecules are outside this mesh. The large-scale structural differences between the two phases lie solely in the dimensions of the mesh. To our knowledge, the observation of the light-organic/third phase coexistence through simulation approaches and a phase transition of this nature have not previously been reported. Finally, this thesis presents evidence that the microscopic structure of the light organic phase of the Zr(IV)/TBP/n-octane/HNO3/H2O system, which is also related to the PUREX process, is different from that of the common hypothesis, where such system is consisted of large ellipsoidal reverse micelles. Snapshots from simulations, hydrogen bonding analysis and cluster analysis showed that the Zr4+, nitrate, TBP and H2O form extended aggregated networks. Thus, as above, we observe a bi-continuous structure but this time with embedded local clusters centred around the Zr4+ ions. The local clusters were found to consist primarily of Zr(NO3)4·3TBP complexes. This finding provides a new view of the structure of the Zr(IV)/TBP/n-octane/HNO3/H2O system.

Electric double layer capacitors (EDLCs) are an important class of electrical energy storage devices which store energy in the form of electric double layers. The charging mechanism is highly reversible physical adsorption of ions into the porous electrodes, which empower these devices to show a remarkable power performance (15kW/kg) and greater life expectancy (> 1 million cycles). However, they store a small amount of energy (5Wh/kg) when compared with batteries. Optimization of the performance of EDLCs based on porous activated carbons is highly challenging due to complex charging process prevailing in the Nano pores of electrodes. Molecular simulations provide information at the molecular scale which in turn can be used to develop insights that can explain experimental results and design improved EDLCs. The conventional approach to simulate EDLCs places both the electrodes and electrolyte region in a single simulation box. With present day computers, however, this one-box method limits us to system sizes of the order of nanometres whereas the size of a typical EDLC is at least of the order of micrometres. To overcome this system size limitation, a Gibbs-ensemble based Monte Carlo (MC) method was recently developed, where the electrodes are simulated in a separate simulation boxes and each box is subjected to periodic boundary conditions in all the three directions. This allows us to eliminate the electrode-electrolyte interface. The simulation of the bulk electrolyte is avoided through the use of the grand canonical ensemble. The electrode atoms in the electrode are maintained at an equal constant electric potential likewise the case in a pure conductor with the use of the constant voltage ensemble. In this thesis, the Gibbs-ensemble based MC simulations are performed for an EDLC consisting of porous electrodes. The simulations are performed with aqueous electrolytes of type MX and DX2 (where M=Na+, K+; D=Ca+2; X=Cl , F ) for a wide variety of operating conditions. The water is modelled as a continuum background with a dielectric constant value of 30. The electrodes are silicon carbide-derived carbon, whose microstructure generated from reverse MC technique, is used in the simulations. The results from these simulations help us understand the charge storage mechanism, the effect of size and valence of ions on the performance of nonporous carbon based EDLCs when the hydration effects are indignant. The thesis first demonstrates the presence of finite size effects in the simulations performed with the one-box method for KCl electrolyte. The capacitance (ratio of the charged stored on the positive electrode to the voltage applied) values obtained for KCl electrolyte with the one-box method are significantly higher than the corresponding values obtained from the Gibbs-ensemble method. This shows the presence of finite size effects in the one-box method simulations and justices the use of the Gibbs-ensemble based method in our simulations. The fundamental characteristics of aqueous electrolytes in the EDLC are analyzed with the simulation results for KCl electrolyte. In agreement with experiments and modern mean held theory, the capacitance monotonically decreases with voltage (bell-shaped curve) due to overcrowding of ions near the electrode surface. The charge storage mechanism in both the electrodes is mainly a combination of countering (ions oppositely charged to that of the electrode) adsorption and ion exchange, where coins (ions identically charged to that of the electrode) are replaced with countering. However, at higher voltages, the mechanism is predominantly counter ion adsorption because of the scarcity of coins in the electrodes. The mechanism is preferentially more ion exchange for the positive electrode because of its relatively bulky countering, Cl . The shifting of mechanism towards counter ion adsorption at higher voltages and preferential ion exchange process for the positive electrode are in qualitative agreement with the recent experimental results. The constraint of equal electric potential on all the electrode atoms of the amorphous electrode in the simulations resulted in a non-uniform average charge distribution on the electrodes. It shows that the Gibbs-ensemble simulation approach can account for the polarization effects which arises due to a complex topology of the electrodes. In agreement with earlier experiments and simulation studies, the local structure analyses of the electrodes shows that the highly conned ions store charge more efficiently. On the application of voltage difference between the electrodes, the electrolyte ions move towards higher degree of con ned regions of the electrodes indicating the charging process involves local rearrangement and rescuing of electrolyte ions. The thesis also discusses the effect of temperature and bulk concentration on the performance of EDLCs. The Gibbs-ensemble based simulations are performed for the EDLC with varying temperature and bulk concentration for the KCl electrolyte independently. In agreement with the Guo -Chapman theory and experiments, the capacitance decreases with the temperature and increases with the bulk concentration. This is because the concentration of countering in the electrodes decreases with an increase in the temperature but increases with an increase in the bulk concentration. Lastly, the effect of ion size and valency on the performance of EDLCs is analyzed. The capacitance monotonically decreases with voltage (bell-shaped curve) for all the electrolytes, except for NaF, where a maximum is observed at a non-zero finite voltage (camel-shaped curve). The capacitances of NaCl and NaF are greater than that for KCl and KF, respectively. This is because the smaller Na+ ions have more accessibility to narrow con ned regions, where the charge storage efficiency is high. As expected, the capacitance for CaCl2 and CaF2 are highest among their monovalent counterparts, NaCl and KCl; NaF and KF, respectively. This is attributed to the relatively smaller double layer thickness of the bivalent Ca+2 ions. Interestingly, at higher voltages, the capacitance for the bivalent electrolytes approaches the capacitance for the monovalent electrolytes because the concentration of Ca+2 ions in the negative electrode increases sluggishly with voltage due to a strong electrostatic repulsion between Ca+2 ions.

La simulación molecular presenta la ventaja de ofrecer un marco teórico importante para predecir propiedades termodinámicas y de transporte de fluidos con aplicaciones industriales. En este trabajo, se explotó está ventaja para predecir el equilibrio líquido vapor de agua, compuestos aromáticos y sus mezclas a condiciones tanto sub- como supercríticas. Se realizó una comparación de diferentes potenciales intermoleculares conocidos mediante el cálculo de propiedades termodinámicas de sistemas puros que sirvió de punto de partida para llevar a cabo una optimización de parámetros transferibles para un potencial intermolecular de agua y compuestos aromáticos. En el caso de agua, se llevo a cabo el análisis y evaluación de propiedades termodinámicas de un modelo simple de agua. En este modelo, las contribuciones electrostáticas se aproximan mediante interacciones de corto alcance en vez de las típicas fuerzas de Coulomb de largo alcance. En general, se han encontrado grandes desviaciones con respecto a los datos experimentales, tal como un valor de temperatura crítica de 360K, valor 50% alejado del valor experimental. Debido a que estos resultados nos indican la importancia de incluir las fuerzas de Coulomb en el modelo molecular empleado para reproducir correctamente las propiedades de agua, el trabajo de investigación se ha enfocado en la optimización de los parámetros de los potenciales TIP4P y SPC/E. Los resultados obtenidos muestran que es posible encontrar una mejor aproximación al punto crítico experimental a partir de la optimización del modelo SPC/E. Sin embargo, el buen acuerdo con los experimentos del modelo original a condiciones ambiente se pierde usando los parámetros del modelo optimizado. Por otro lado, la estimación de propiedades de compuestos aromáticos esta de acuerdo con los datos experimentales permitiendo la reproducción de la densidad de líquido saturado, presión de saturación y entalpía de vaporización para compuestos puros. Finalmente, en el caso de mezclas se ha aplicado el conjunto de parámetros obtenidos para aromáticos. Las propiedades termodinámicas de la mezcla binaria aromático-aromático y aromático agua son analizadas en un amplio rango de temperaturas y presiones. Las desviaciones encontradas entre los valores calculados y los experimentales sugieren aplicar un mejor método de optimización para sistemas puros o por otro lado, promover un potencial de interacción intermolecular más sofisticado. Las estimaciones a condiciones cercanas al punto crítico están en buen acuerdo con los datos experimentales. / La simulació molecular presenta l'avantatge d'oferir un marc teòric important per a cercar propietats termodinàmiques i de transport de fluids amb aplicacions industrials. En aquest treball es va explotar aquesta avantatge per predir l'equilibri líquid vapor d'aigua, components aromàtics i les seves mescles, tant a condicions sub com supercrítiques. Es va realitzar una comparació de diferents potencials intermoleculars, coneguts mitjançant el càlcul de propietats termodinàmiques de sistemes purs, que ha servit de punt de sortida per portar a terme una optimització de paràmetres transferibles per a un potencial intermolecular de propietats termodinàmiques d'un model simple d'aigua. En aquest model, les contribucions electrostàtiques s'aproximen mitjançant interaccions de curt abast en lloc de les típiques forces de Coulomb de llarg abast. En general, s'ha trobat grans desviacions respecte a les dades experimentals, tal com un valor de temperatura crítica de 360K, valor 50% allunyat del valor experimental. Degut a que aquests resultats ens indiquen la importància d'incloure les forces de Coulomb en el model molecular emprat per reproduir correctament les propietats d'aigua, el treball d'investigació s'ha enfocat en l'optimització dels paràmetres dels potencials TIP4P i SPC/E. Els resultats obtinguts mostren que és possible trobar una millor aproximació al punt crític experimental a partir de l'optimització del model SPC/E. No obstant, el bon acord amb els experiments del model original a condicions ambientals es perden usant els paràmetres del model optimitzat. Per altre banda, l'estimació de propietats de compostos aromàtics esta d'acord amb les dades experimentals permetent la reproducció de la densitat de líquid saturat, pressió de saturació i entalpia de vaporització per a compostos purs mitjançant el potencial AUA-Aromátics proposat. Finalment, en el cas de mescles s'ha aplicat el conjunt de paràmetres obtinguts per aromàtics. Les propietats termodinàmiques de la mescla binària aromàtic-aromàtic i aromàtic-aigua són analitzades en un ample rang de temperatures i pressions. Les desviacions trobades entre els valors calculats i els experimentals suggereixen aplicar un millor mètode d'optimització per a sistemes purs o, per altre banda, promoure un potencial d'interacció intermolecular més sofisticat. Les estimacions en condicions properes al punt crític tenen un bon acord amb les dades experimentals. / Molecular simulation presents the advantage of providing a unified theoretical framework to model fluid properties for industrial applications. In this work we exploit this advantage to predict thermodynamic properties of pure water and aromatics and their mixtures at sub- and supercritical conditions. A comprehensive comparison of different intermolecular potentials has been carried out in order to analyze model predictions for pure component properties. In addition, an optimization of transferable parameters has been performed for an intermolecular potential for aromatics and water. In the case of water, an analysis and evaluation of the thermodynamic properties of a simple model has been performed. In this model, the electrostatic contributions are approximated by short-range interactions instead of the typical long-range Coulombic forces. On the whole, we found huge deviations with experimental data, such as a critical temperature value of 360K, 50% far away from the experimental value. Since, these calculations indicate the importance of including the electrostatic contribution in order to correctly model water, we also focus on reproducing critical properties from an optimization of the well known TIP4P and SPC/E water model parameters. Results obtained show that a better approximation to the critical point prediction is possible from the optimization of the SPC/E parameters, however, the good agreement with experiments for the original model at room conditions vanishes using the optimized parameters. On the other hand, thermodynamic property estimations of aromatic molecules are in good agreement with experimental data and we are able to reproduce saturation liquid densities, saturation pressures, vaporization enthalpies and liquid structure for pure compounds. Finally, in the case of mixtures, we applied the optimized set of parameters obtained for aromatics. The thermodynamic properties of binary aromatic-aromatic and aromatic water mixtures are analyzed over a wide range of temperatures and pressures. Deviations between the predicted and experimental values are found at low temperatures and high densities suggesting that a better optimization process needs to be performed for the pure systems or a more sophisticated intermolecular interaction potential is needed. Nevertheless, the estimations close to critical conditions are in good agreement with experimental data.