Element Software Enabling Millisecond-scale Biomolecular Dynamics

The goal of this proposed research is to develop an open software framework to enable multi- millisecond dynamic simulations of peptides and peptidomimetic polymers. This will be achieved by implementing a parallel discontinuous molecular dynamics (DMD) package, developing a suite of DMD interaction potentials, and providing tools for translating continuous atomistic models into DMD models. Although there are many coarse-grained potentials and codes available to simulate large biomolecular systems, the longest times scales that can typically be accessed are on the order of tens of microseconds, and most are unable to predict the formation of structures such as fibrils in a reasonable time frame. Our tools will allow the scientific/engineering community to study long time-scale phenomena such as biopolymer folding, aggregation, and fibril formation. The code will be tested by volunteer users and validated both by comparison with literature results, and an experimental case study on peptoid-based inhibition of antibody aggregation.