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

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 i...

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Bibliographic Details
Published in:Electronics (Basel) 2023-03, Vol.12 (5), p.1198
Main Authors: Jabłoński, Grzegorz, Amrozik, Piotr, Hałagan, Krzysztof
Format: Article
Language:English
Subjects:
Algorithms
Diffusion
Diffusion barriers
Digital integrated circuits
Energy
Equilibrium
Equilibrium (Physics)
Field programmable gate arrays
Molecular dynamics
Polymerization
Potential energy
Simulation
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Summary: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.
ISSN:2079-9292
2079-9292
DOI:10.3390/electronics12051198