A Model of Thermally Activated Molecular Transport: Implementation in a Massive FPGA Cluster

Abstract

In this paper, a massively parallel implementation of Boltzmann’s thermally activated molecular transport model is presented. This models allows taking into account potential energy barriers in molecular simulations and thus modeling thermally activated diffusion processes in liquids. The model is implemented as an extension to the basic Dynamic Lattice Liquid (DLL) algorithm on ARUZ, a massively parallel FPGA-based simulator located at BioNanoPark Lodz. The advantage of this approach is that it does not use any exponentiation operations, minimizing resource usage and allowing one to perform simulations containing up to 4,608,000 nodes.