From Microbes to Machines: Harnessing the multiscale organization of microbial communities for energy-efficient natural computing.

Oral-In-person  · Withdrawn

Abstract

Computing faces a growing energy challenge, driven by the end of Moore’s law and the increasing demands of energy-intensive data centers. In contrast, nature has evolved efficient analog systems, such as microbial communities, that process environmental "inputs," perform computations, and generate actionable "outputs" at minimal energy cost. Microbes, with their complex multiscale organization offer a promising avenue for developing energy-efficient natural computing systems by harnessing Microbe's adaptive and self-organizing properties.

This talk explores the potential of microbial communities to transform energy-efficient computing by serving as analog platforms for solving complex computational problems. We consider a range of modelling approaches to capture the spatio-temporal behavior of microbial communities and view microbial communities as a reservoir computing platform.  By leveraging multiscale insights and the intrinsic capabilities of these systems, we aim to uncover innovative strategies for sustainable, bio-inspired computing and deepen our understanding of nature’s mechanisms for efficient information processing in energy-limited environments.

Publication: Johnson, C. G. M., Johnson, Z., Mackey, L. S. et al. Multi-Omics Reveals Temporal Scales of Carbon Metabolism in Synechococcus Elongatus PCC 7942 Under Light Disturbance. PRX Life, 3, (2025). https://doi.org/10.1103/l2dp-kw2t
Palmer, B.J., Almgren, A.S., Johnson, C.G.M. et al. BMX: Biological modelling and interface exchange. Sci Rep 13, 12235 (2023). https://doi.org/10.1038/s41598-023-39150-1

Bohm Agostini, N., Johnson, C., Cannon, W., and Tumeo, A. ChemComp: A Compilation Framework for Computing with Chemical Reaction Networks. In Proceedings of the 30th Asia and South Pacific Design Automation Conference (ASPDAC '25), (2025). https://doi.org/10.1145/3658617.3703315

Johnson, C. G. M., Fletcher, A. G., Soyer, O. S. ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks, GigaScience, 11, (2022). https://doi.org/10.1093/gigascience/giac051

Johnson, C. G. M., Bohm Agostini, N., Cannon, W. R., Tumeo, A. Computing with a Chemical Reservoir, 2024 IEEE International Conference on Rebooting Computing (ICRC), (2024). https://doi.org/10.1109/ICRC64395.2024.10937022

Palmer, B.J., Johnson, C.G.M., Almgren, A.S. et al. Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi. Phys. Rev. E, 112, (2025). https://doi.org/10.1103/xbjp-zqj1

Presenters

  • Connah Johnson

    • Pacific Northwest Natl Lab

Authors

  • Connah Johnson

    • Pacific Northwest Natl Lab