Structure factors obtained from small-angle neutron or X-ray scattering experiments (SANS and SAXS) provide ensemble average information about aggregate size and potentially shape using relatively simplified models (e.g., Baxter sticky sphere ) While lowtemperature X-ray crystallography may trap representative conformational states, gathering adequate statistics or accessing higher-temperature conformations inhibits quantitative understanding. Atomistic molecular simulations (i.e. molecular dynamics) can sample the conformational ensemble, yet when monomeric units have high degrees of freedom they generate a huge amount of high-dimensional complex data. Under these circumstances, Markov state models (MSMs) are an as yet under-utilized tool to analyze simulation trajectories and provide a way to understand the conformational free energy landscape and its dependence upon solution conditions. MSMs are perhaps best known for their application to elucidate structural transitions in protein folding. The workflow relies heavily upon the extraction of low dimensional features that are responsible for the kinetic event of interest. For events occurring in the solution phase, the solvent is often neglected because it complicates the analysis and its role in large amplitude protein motions can be thought of as a continuum effect. In contrast to protein simulations, atomistic simulations of microemulsions involve many independent amphiphiles in the phase space and the solvation environment cannot be generalized due to large variations in individual solvation environments. Water-in-oil microemulsions are an attractive platform for studying the influence of local solvent interactions upon amphiphihle conformation; in this case the concentration of polar solutes/solvent is limited, which in turn allows for the identification of key interactions that influence the conformational energy landscape. In such systems, surface active amphiphiles surround a polar-core comprised of water and acid along with the analyte of interest (generally a metal ion) to form reversemicelle-like aggregates. "Solvation" at this level derives primarily from direct hydrogen bonding interactions instead of the continuous properties of the polar solvent.