BMX: Biological modelling and interface exchange

Journal Article · 27 July 2023 · Scientific Reports

DOI: https://doi.org/10.1038/s41598-023-39150-1 · OSTI ID:1992973

Palmer, Bruce J.; Almgren, Ann S.; Johnson, Connah G. M.; Myers, Andrew T.; Cannon, William R.

Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AC02-05CH11231; AC05-76RL01830
• OSTI ID: 1992973
• Report Number(s): PNNL-SA-189605; 12235; PII: 39150
• Journal Information: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 13; ISSN 2045-2322
• Publisher: Nature Publishing GroupCopyright Statement
• Country of Publication: United Kingdom
• Language: English