Large-Scale Simulations of Protein Self-Assembly

Despite steady advances in computing methodology and in the accuracy of all-atom force fields, large scale simulations of biological self-assembly processes still defy the current capabilities of computer simulation. However, with simplified models it is sometimes possible to extract the important physics on the relevant time and length scales. Here we present results of our efforts to simulate the nucleation of protein crystals on the Titan supercomputer, employing large-scale simulations of rigid protein models to form the experimentally observed crystal structure. It has been hypothesized that biological crystallization occurs non-classically via an intermediate of a liquid droplet, to overcome the large barriers to nucleation via critical fluctuations. Using a model with an artificially tunable specificity, we test this hypothesis. We outline how more powerful simulations of biological self-assembly can be achieved on upcoming pre-exascale architectures using HOOMD-blue with support for NVLINK node-local communication.