Distributed Simulations of DNA Multi-strand Dynamics

Frankie Spencer, Usman Sanwal, Usman Sanwal, Eugen Czeizler, Eugen Czeizler

2022

Abstract

In a recent study, Spencer et al. 2021, we have proposed a computational modeling framework for DNA multi-strand dynamics implemented using the agent- and rule-based modeling methodology. While this modeling methodology allows for compact representations for systems with large numbers of different species and complexes, such as the case of self-assembly systems, one of its main drawbacks concerns its scalability. Since each agent is individually represented and modeled in the system, the framework becomes slow when dealing with tens- and hundreds of thousands of individual components. In this study we introduce a method to parallelize the computational modeling process by distributing it over several CPU’s. We show that such multi-thread models remain equivalent to their sequential counterpart, while the speedup of the computational process can reach even a one-fold increase.

Paper Citation

in Harvard Style

Spencer F., Sanwal U. and Czeizler E. (2022). Distributed Simulations of DNA Multi-strand Dynamics. In Proceedings of the 12th International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH, ISBN 978-989-758-578-4, pages 234-243. DOI: 10.5220/0011266400003274

in Bibtex Style

@conference{simultech22,
author={Frankie Spencer and Usman Sanwal and Eugen Czeizler},
title={Distributed Simulations of DNA Multi-strand Dynamics},
booktitle={Proceedings of the 12th International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,},
year={2022},
pages={234-243},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0011266400003274},
isbn={978-989-758-578-4},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,
TI - Distributed Simulations of DNA Multi-strand Dynamics
SN - 978-989-758-578-4
AU - Spencer F.
AU - Sanwal U.
AU - Czeizler E.
PY - 2022
SP - 234
EP - 243
DO - 10.5220/0011266400003274