Porous media are used in a wide variety of separation processes, notably including differential adsorption of gases and ion exchange into crystalline materials containing a negatively-charged framework with accessible charge-balancing cations in the pore spaces. Molecular simulations are a particularly useful tool for studying the behavior of these systems due to their allowance for study of molecular-level interactions, and they are also attractive for the study of systems involving materials that are hazardous or difficult to synthesize. In the first phase of this study, Monte Carlo simulation techniques are applied to the study of adsorption and cation siting in Keggin ion type materials. These materials had been characterized experimentally as candidates for application toradioactive waste remediation. New force fields had been developed to model their behavior, and this study applied grand canonical and replica exchange Monte Carlo simulations to verify the performance of the new force fields and to obtainadditional insight into the behavior of the systems. The adsorption isotherms and cation sites are shown to be in good agreement with experiment, confirming that the force fields and methods used to obtain them may be applied to future study of similar systems. In the second phase of this study, fractional component Monte Carlo simulation techniques are applied to the study of single-component and ternary adsorption of nitrogen, oxygen, and water into sodium faujasite type X zeolites. Type Xzeolites are used in commercial air separation processes, where a pre-treatment step is required to remove most of the water from the feed gas. Due to difficulty of modeling the ternary system, it has not been extensively studied. This studyapplies the fractional component Monte Carlo method to obtain single-component and ternary adsorption isotherms. Although nitrogen dsorption is found to be in good agreement with previous experimental results, significant deficiencies arefound in water adsorption at lower partial pressures. These issues are further characterized and recommendations are presented for future study to improve modeling of low-pressure water adsorption. In the final phase of this study, a new statistical mechanical ensemble is developed,denoted the ion exchange ensemble, and the corresponding move acceptance probabilities for Monte Carlo simulation in this ensemble. The exchange of cesium for sodium in titanosilicate (TS) and niobium-substituted titanosilicate (Nb-TS) are studied using the Monte Carlo simulation in the ion exchange ensemble. Thispair of materials is of particular interest for the treatment of radioactive tank wastes at the Department of Energy Savannah River Site. The ion exchange simulations are found to exchange cesium for sodium, but significant issues areobserved with the performance and results of the simulations. The results from the simulations are analyzed to obtain insight into the behavior of the materials and an understanding of how ion exchange simulations may be conducted moreeffectively in the future.