Using Molecular Dynamics, we simulate detailed All-Atom models of (at the time) unsynthesized polythiophene derivatives with oligoethylene glycol side chains under the stimulus of an applied electric field to evaluate their ionic conduction properties. The originally proposed chemistry (P3MEET) has an oxygen atom in the side chain bonded directly to the polythiophene backbone which is identified as detrimental to the ionic mobility as the mobility of that oxygen is hampered by the covalent bond to the backbone. The simple insertion of a single methylene group between this oxygen and the backbone (P3MEEMT) leads to a near five-fold improvement in the ionic conductivity as observed in our simulations. Results from these studies informed experimental collaborators leading to experimental evidence verifying the accuracy of our initial predictions. We continue by examining more chemistries which take the three oxygens in the side chain of P3MEEMT and goes through every permutation of replacing any number of the oxygens with a methylene group. The results of this study show that the main factors that are in competition are the tendency to reduce the oxygen concentration to reduce the average number of oxygens that coordinate a given ion and the percolation of solvation sites. While a reduced number of coordinating oxygens is beneficial as it becomes easier to escape that trap, it also correlates to an increased distance between solvation sites. This weakened percolation of solvation sites increases the energetic barrier as the ion needs to make a longer jump between sites. This competition is observed only in the amorphous domain because the crystalline domain has a regular arrangement of side chains which automatically creates a percolated network of nearby solvation sites, masking this issue. We use generic coarse-grained (CG) models which can represent many different polymers to study networks of semi-flexible block copolymer chains (D-LCE) which exhibit a saw-tooth tensile response when subjected to a strain field. A simulated synthesis shows the synthetic viability of these networks which leads to an exploration of the block architecture and segregation strength of the chains to elucidate new behaviors or improved properties in the deformation mechanics. These studies show that this class of materials has promise and should be studied. To aid experimentalists in finding a chemistry for these systems, we have developed a methodology to begin the process of inverse coarse graining (ICG) which aims to find a molecule whose physics/behavior fits well onto the physics/behavior of a CG model of interest. Outside of our studies, generic CG models which don’t represent a specific chemistry are used extensively to scan design spaces in search of novel behaviors/properties. As such, the ICG process is critical if computer simulations using generic CG models are to inform experimentalists. We also present a method for calculating the free energy of polymer self-assembly into different mesophases. A guiding field approach is used to take a system of athermal chains in the isotropic phase and assembly them in into the target mesophase which circumvents the often problematic first-order transition that is seen in polymer self-assembly. Using this approach the phase behavior or rod-coil block copolymers is studied as well as the statistical mechanical origins for differences in the phase behavior of two nearly identical molecules who only vary in the their architecture.