Molecular Simulations Using Boltzmann’s Thermally Activated Diffusion - Implementation on ARUZ – Massively-parallel FPGA-based Machine

Abstract

ARUZ (Analizator Rzeczywistych Układów Złożonych, Analyser of Real Complex Systems) is a massively parallel FPGA-based simulator located at BioNanoPark Lodz. This machine has been designed to reflect the Dynamic Lattice Liquid (DLL) algorithm in hardware. In this paper, FPGA implementation details are presented for DLL functionality extension. This extension allows taking into account potential energy barriers in molecular simulations performed on ARUZ and thus modeling thermally-activated diffusion processes in liquids.