A Scalable Parallel Framework for Multicellular Communication in Bacterial Quorum Sensing

Abstract

Certain species of bacteria are capable of communicating through a mechanism called Quorum Sensing (QS) wherein they release and sense signaling molecules, called autoinducers, to and from the environment. Despite stochastic fluctuations, bacteria gradually achieve coordinated gene expression through QS, which in turn, help them better adapt to environmental adversities. Existing sequential approaches for modeling information exchange via QS for large cell populations are time and computational resource intensive, because the advancement in simulation time becomes significantly slower with the increase in molecular concentration. This paper presents a scalable parallel framework for modeling multicellular communication. Simulations show that our framework accurately models the molecular concentration dynamics of QS system, yielding better speed-up and CPU utilization than the existing sequential model that uses the exact Gillespie algorithm. We also discuss how our framework accommodates evolving population due to cell birth, death and heterogeneity due to noise. Furthermore, we analyze the performance of our framework vis-á-vis the effects of its data sampling interval and Gillespie computation time. Finally, we validate the scalability of the proposed framework by modeling population size up to 2000 bacterial cells.

Meeting Name

11th International Conference on Bio-Inspired Information and Communications Technologies, BICT (2019: Mar. 13-14, Pittsburgh, PA)

Department(s)

Chemical and Biochemical Engineering

Second Department

Computer Science

Research Center/Lab(s)

Intelligent Systems Center

Second Research Center/Lab

Center for High Performance Computing Research

Keywords and Phrases

Autoinducer; Gillespie; Multicellular system; Noise analysis; Population evolution; Quorum Sensing; Scalability

International Standard Book Number (ISBN)

978-303024201-5

International Standard Serial Number (ISSN)

1867-8211; 1867-822X

Document Type

Article - Conference proceedings

Document Version

Citation

File Type

text

Language(s)

English

Rights

© 2019 ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, All rights reserved.

Publication Date

14 Mar 2019

Link to Full Text

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