Molecular dynamics (MD) simulation studies were considered in this study in the fields of phosphonium based ionic liquids (PBILs) and heterogeneous (solid/liquid) zeolite systems. A new generation of ionic liquids (ILs) called phase-separable ionic liquids (PSILs) are able to dissolve cellulose and lignin, a necessary step, for conversion of biomass to fuels and chemicals with co-solvents and are immiscible with water or saline solutions. Molecular simulations on these systems will provide insights of phase behavior and dissolution phenomenon. The knowledge of interfacial phase behavior of ionic liquids/solvent systems is critical for materials discovery for designing efficient dissolution processes. Transition zone from miscible to immiscible behavior was observed for alkyl chain lengths varying from 6 to 8. Emulsion phase was observed for [P8888]+ ion. Result from molecular dynamics (MD) simulations shows excellent agreement with experimental data for both chloride and acetate anions. These contributions will be helpful in modeling PBILs system for cellulose dissolution, liquid-liquid extraction and biomass studies. Another important aspect in biofuel conversion is glucose isomerization step using zeolites. Zeolites are crystalline solids that have wide applications in industrial areas for its hydrocarbon conversion, adsorption of molecules. In this study, we report MD simulation studies on glucose solution diffusion into zeolite structure as a function of temperature and pressure. Development of united-atom force field for PBILs, for phosphonium cation with anions of chloride and acetate, is considered in this study. Force field parameterization was considered for these ionic liquids with a variation of alkyl chain length in phosphonium ion with chloride and acetate anions. Performance of force field parameters was analyzed by calculating properties such as density and viscosity at various temperature and compared with available experimental data. Efficient algorithm techniques were developed in molecular simulations that will reduce computational load in calculating non-bonded interactions. We introduce theory of local sample (TLS) in calculating non-bonded interactions acting on atoms. Another algorithmic improvement in MD simulations is calculating force acting on atoms based on previous time steps, that achieves up to 50 % reduction in computational time