Implementation of directed self-assembly (DSA) of block copolymers (BCPs) introduces a series of engineering challenges that have not been completely addressed in previous block copolymer and lithography studies. One of the required innovations for further DSA development and implementation is the accurate simulation of specific block copolymer chemistries and their interactions with interfaces. Many of the BCP simulation tools developed so far have limitations or difficulty in terms of matching many of the common issues found in experimental BCP systems such as polydispersity and different statistical segment lengths. One of the potentially most important issues is the fact that real BCPs often have block energy and/or density asymmetry, meaning that each block has a different homopolymer density and/or cohesive energy density (CED). A simulation of BCP behavior and DSA processes based on molecular dynamics (MD) of coarse-grained polymer chains has been developed that can independently parameterize and control the density and CED of each block to more accurately match the asymmetry found in experimental BCPs. This model was used to study the effect of block asymmetry on the order-disorder transition (ODT), domain scaling, and self-assembly of thin films of BCPs. BCPs whose blocks each have a different density show deviations from the mean-field ODT coexistence curve, exhibiting an order-disorder transition or co-existence curve that is asymmetric with shifts and tilts in the direction of majority highest density block. This impact of density and cohesive energy differences diblock copolymers on their phase behavior can explain some of the unexpected shapes found experimentally in BCP ODT curves. Asymmetry in the BCP block energy or density does not appear to have a significant effect on domain scaling behavior compared to the mean-field estimates. Self-assembly of thin films of BCPs with mismatches in CED shows significant deviations in the expected morphologies from ones simulated using equivalent densities and cohesive energy densities. The lowest CED block has a strong propensity to segregate to and wet the free interface at the top of the film because it has the lowest energy penalty for the loss of interactions with other chains at the free surface relative to the bulk. This gives rise to an effective skinning of the film by the lowest CED block for almost the entire potential range of underlayer compositions and film thicknesses. Such materials will be extremely difficult to successfully pattern transfer for a lithographically useful process because they will not form vertically aligned morphologies through the entire film thickness. This CED mismatch also gives rise to a large number of non-bulk morphologies and deviations from bulk behavior including changing vertical-to-horizontal morphologies through film depth, compression and expansion of domain sizes to match film thickness dimensions, and island and hole formation among others. Increasing the ΧN value can potentially suppress some of these non-idealities due to CED asymmetry, but the required ΧN to overcome these issues will differ from polymer to polymer depending on the magnitude of the CED asymmetry.