Joe Larkin

Lab Website

Current Research

Throughout evolutionary history, life has explored the laws of physics, creating remarkable new strategies to perpetuate itself. Our group seeks to understand how these strategies arise, using microbial populations as a model. We are interested in how the physical and chemical environment influences microbes, and how these microbes in turn engineer that very environment. In particular, we study how bacterial biofilms change their local conditions by producing extracellular matrix and how cell-to-cell signals drive such behaviors. We probe theoretical models of these phenomena with the goal of building toward an emergent understanding of living matter.

Our group also has specific interest in how electrophysiology influences the behavior of bacteria, including through cell-to-cell communication, and control of both metabolism and gene expression.

To investigate these problems, we use time-lapse imaging and custom experimental devices to observe and probe microbial behaviors in space and time.

Selected Publications

• Brooks C, Yao M, McCool JT, Gillman A, Süel GM, Mugler A, and Larkin JW, “Computational model of fractal interface formation in bacterial biofilms”, Physical Review E, 10.1103/2zm9-r3qs (2025).
• Mulder OJ, Peters Kostman M, Almodaimegh A, Edge MD*, and Larkin JW*, “An agent-based model of metabolic signaling oscillations in Bacillus subtilis biofilms”, PLOS Computational Biology, 10.1371/journal.pcbi.1013746 (2025).
  • Featured on the cover.
• Incandela JT, Hu K, Joshi P, Rosenstin JK, and Larkin JW, “Non-optical, label-free electrical capacitance imaging of microorganisms”, mBio, 10.1128/mbio.01676-25 (2025).
• Abdelatty M, Incandela J, Hu K, Joshi P, Larkin JW, Reda S, and Rosenstein JK, “Electrical Capacitance Tomography of Cell Cultures on a CMOS Microelectrode Array“, IEEE Transactions on Biomedical Circuits and Systems, 10.1109/TBCAS.2024.3415360 (2024).
• Hu K, Incandela J, Lian X, Larkin JW, Rosenstein JK, “A 13.1 mm2 512 x 256 Multimodal CMOS Array for Spatiochemical Imaging of Bacterial Biofilms”, 10.1109/CICC53496.2022.9772787, IEEE CICC (2022). 
• Yang C*, Bialecka-Fornal M.*, Weatherwax C, Larkin JW, Prindle A, Liu J, Garcia-Ojalvo J, Süel GM, “Encoding membrane potential-based memory within a microbial community“, Cell Systems, 10, 417-423 (2020). 
• Larkin J, Zhai XL, Kikuchi K, Redford SE, Prindle A, Liu J, Greenfield S, Walczak AM, Garcia-Ojalvo J, Mugler A, and Süel G, “Signal Percolation within a Bacterial Community”, Cell Syst. 7: 1-9. (2018)