| Molecular dynamics (MD) simulations offer researchers a high resolution window into the atomic world. Though far from perfect, they provide researchers with a direct method for probing molecular scale processes. We have used MD to address a range of questions which span three fundamentally different topics. First, we used MD to elucidate the native state energy landscape of a small globular protein. We are able to identify a subset of direct and water-mediated contacts which may be responsible for sculpting this landscape. Next, we turn to the topic of chromatin, specifically, nucleosomal electrostatics. Using a combination of all-atom simulations and Poisson-Boltzmann calculations we are able to observe and explain counterion condensation levels and distribution patterns around the nucleosome core particle. Additionally, our results reveal the significant solvent accessibility of the core particle. Finally, we use all-atom simulations to examine small, artificial, coiled-coil peptides under development for use in light harvesting antennae. Photosensitive chromophores can be tethered to these peptides at a range of sites, and we observe that the choice of these sites plays an important role in regulating energy transfer. In addition, the flexibility of the tethers imbues the chromophores with a large amount of conformational freedom, making their dynamics important for regulating energy transfer. |
