| Molecular dynamics (MD) simulations of classical fluids have led to a revolution in our understanding of the equilibrium and non-equilibrium properties of fluids. In this thesis we have used MD method on fluids confined by membranes to study an equilibrium thermodynamic problem (solubility of gases in liquids) and a dynamic problem (permeation of gas in biomembranes). A simulation system with a selective permeable membrane in it to mimic a real experiment was developed. When investigating gas solubilities, the MD method, intermolecular NMR (Nuclear Magnetic Resonance) chemical shifts were used to fine tune intermolecular potentials. Modification of the exponential-6 potential model for solute-solvent interaction resulted in leading to better agreement with experimental chemical shift values, which in turn improved estimates of Xe solubility, and oxygen solubilities. In our studies on gas permeation, by reducing the degrees of freedom and employing suitable potentials, direct insight into collective phenomena in biological membranes at longer time and length scales were provided. Coarse-grained DPPC bilayer was parameterized to mimic its fundamental structural properties, which made it possible to study the permeation process of small molecules such as Xe, O2 and CO2 through lipid bilayers. |
