Elastic bag model for molecular dynamics simulations of liquids and solutions and studies of solution properties of ionic liquids

This thesis mainly focuses on a fluctuating elastic boundary (FEB) model, a non-periodic boundary model, and solution properties of ionic liquids. The FEB model is developed to study the dynamics of the localized process in solutions and other condensed phase systems. In the FEB model a flexible boundary which consists of particles connected by spring is used to confine the simulated system that mimics the effects of the bulk solvent. This alleviates the need for periodic boundary conditions, and allows for a reduction in the number of solvent molecules that need to be included in the simulation. The FEB model allows for volume and density fluctuations characteristic of the bulk system, and the shape of the boundary fluctuates during the course of the simulation to adapt to the configuration fluctuations of the explicit solute-solvent system inside. The method is applied to the simulation of a Lennard-Jones model of liquid argon. Various structural and dynamical quantities are computed and compared with those obtained from conventional periodic boundary simulations. The agreement between the two is excellent in most cases, thus validating the viability of the FEB method. We extend this model to the simulation of bulk water and solvated alanine dipeptide. Both the confining potential and boundary particle interaction functions are modified to prevent the leakage of the solute-solvent system through the boundary. A broad spectrum of structural and dynamic properties of liquid water are computed and compared with those obtained from conventional periodic boundary condition simulations. The applicability of the model to biomolecular simulations is investigated through the analysis of conformational population distribution of solvated alanine dipeptide. In most cases we find remarkable agreement between the two simulation approaches. When super-critical CO2 is dissolved in an ionic liquid its partial molar volume is much smaller than that observed in most other solvents. In this thesis we explore in atomistic detail and explain in an intuitive way the peculiar volumetric behavior experimentally observed when supercritical CO2 is dissolved in 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim+] [ PF-6 ]).