Simulation of diffusion in dense molecular systems on ARUZ – Massively-parallel FPGA-based machine

In this paper, the implementation of a molecular diffusion model named Dynamic Lattice Liquid (DLL) is discussed. Two algorithms, sequential and parallel, implementing this model are examined. The presented theoretical considerations indicate some limitations of the sequential approach. The proposed parallel algorithm overcomes these limitations, but it requires dedicated hardware. An example of such hardware, the FPGA-based HPC system named ARUZ, is presented.