Molecular dynamics simulations are an increasingly valuable tool to biochemical researchers: advances in computational power have expanded the range of biomolecules that can be simulated, and parameters describing these interactions are increasingly accurate. Despite substantial progress in force field parameterization, recent simulations of protein molecules using state-of-the-art, fixed-charge force fields revealed that the interactions among and within protein molecules can be too favorable, resulting in unrealistic aggregation or structural collapse of the proteins being simulated. To understand why these protein-protein interactions are so over-stabilized, I first assessed the ability of simulation force fields to represent accurately the interactions of individual amino acids, employing an osmotic pressure simulation apparatus that enabled direct comparison with experiment. Surprisingly, simulations of most of the amino acids resulted in behavior that was in strong agreement with experiment. A number of amino acids, however—notably those that contain hydroxyl groups and those that carry a formal charge—interacted in ways that were clearly inaccurate. Additionally, some commonly-used force fields failed to accurately represent the interactions of amino acids in a consistent manner. By further investigating the interactions of the functional groups of these amino acids, I was able not only to determine some of the root causes of individual amino acid inaccuracies, but also to implement simple modifications that brought the interactions of these small molecules and amino acids in stronger accord with experiment. These studies have highlighted some of the shortcomings in popular simulation force fields, and have proposed useful modifications to address them. Still, there is additional work that must be—and is being—conducted in order to correctly model the interaction behavior of proteins in simulation.

Over the past centuries, a number of process routes for extraction of metal values from an ore or other resources have been developed. These can generally be classifiedinto pyrometallurgical, hydrometallurgical or electrometallurgical routes. In the caseof the latter two processes, the reaction medium consists of liquid phase electrolytesthat can be aqueous, non-aqueous as well as molten salts. The present dissertationpresents the work carried out with two aspects of the above-mentioned electrolytes.First part is about the electrolyte solutions, which can be used in solvent extractionrelevant to many hydrometallurgical or chemical engineering processes; the secondpart is about the molten salts, which is often used in the electrometallurgical processesfor production of a variety of many kinds of metals or alloys, especially those that arehighly reactive.In the first part of this thesis, the focus is given to the thermodynamics ofelectrolyte solutions. Since the non-ideality of high concentration solution is not wellsolved, a modified three-characteristic-parameter correlation model is proposed,which can calculate the thermodynamic properties of high concentration electrolytesolutions accurately. Model parameters for hundreds of systems are obtained foraqueous as well as non-aqueous solutions. Moreover, a new predictive method tocalculate the freezing point depression, boiling point elevation and vaporizationenthalpy of electrolyte solutions is also proposed. This method has been shown to be agood first approximation for the prediction of these properties.In the second part, a process towards the extraction of metal values from slags,low-grade ores and other oxidic materials such as spent refractories using molten saltsis presented. Firstly, this process is developed for the recovery of Cr, Fe values fromEAF slag as well as chromite ore by using NaCl-KCl salt mixtures in the laboratoryscale. The slags were allowed to react with molten salt mixtures. This extraction stepwas found to be very encouraging in the case of Cr and Fe present in the slags. Byelectrolysis of the molten salt phase, Fe-Cr alloy was found to be deposited on thecathode surface. The method is expected to be applicable even in the case of V, Mnand Mo in the waste slags.Secondly, this process was extended to the extraction of copper/iron from copperore including oxidic and sulfide ores under controlled oxygen partial pressures.Copper or Cu/Fe mixtures could be found on the cathode surface along with theemission of elemental sulphur that was condensed in the cooler regions of the reactor.Thus, the new process offers a potential environmentally friendly process routereducing SO2 emissions.Furthermore, the cyclic voltammetric studies of metal ions(Cr, Fe, Cu, Mg, Mn)in (CaCl2-)NaCl-KCl salt melt were performed to understand the mechanisms, such asthe deposition potential, electrode reactions and diffusion coefficients, etc. In addition,another method using a direct electro-deoxidation concept(FFC Cambridge method),was also investigated for the electrolysis of copper sulfide. Sintered solid porouspellets of copper sulfide Cu2S and Cu2S/FeS were electrolyzed to elemental Cu, S andCu, Fe, S respectively in molten CaCl2-NaCl at 800oC under the protection of Argongas. This direct electrolysis of the sulfide to copper with the emission of elementalsulfur also offers an attractive green process route for the treatment of copper ore. / QC 20100714