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College of Liberal Arts and Sciences University of Florida

Emrah ŞIMŞEK

Emrah-Simsek

Assistant Professor

PhD, Emory University (2019) esimsek@ufl.edu Office: 2368 352.392.3233 ŞIMŞEK Lab Research Group: Biological Physics

Research Focus

We investigate how bacteria respond to environmental changes—such as nutrient shifts, antibiotic exposure, and mobility constraints—across scales from single cells to communities of many interacting populations. Our research is primarily experimental, and we regularly employ mechanistic physical models to interpret and predict these responses. We also plan to increasingly leverage machine learning to tackle problems that are difficult to model or solve mechanistically, yet have key observables that are straightforward to measure. Why it matters? Understanding how bacteria respond to environmental changes is crucial for addressing challenges in health (such as the antibiotic resistance crisis), ecology, and biotechnology. By combining experiments, physical models, and emerging machine learning approaches, our research aims to reveal fundamental principles underlying these responses, including stochasticity, collective dynamics, and adaptation, which could be relevant across living systems.

Selected Publications

“Spatial proximity dictates bacterial competition and expansion in microbial communities”, E. ŞIMŞEK*, C.A. Villalobos, K. Sahu, Z. Zhou, N. Luo, D. Lee, H.R. Ma, D.J. Anderson, C.T. Lee, and L. You*, Nature Communications 16, 10885 (2025); * corresponding authors A ‘rich-get-richer’ mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria, E. ŞIMŞEK, K. Kim, J. Lu, A. Silver, N. Luo, C.T. Lee, and L. You, Mol Syst Biol 20: 880 – 897 (2024) (also see an insightful commentary by Prof. Kyle R. Allison) The collapse of cooperation during range expansion of Pseudomonas aeruginosa, N. Luo#, J. Lu#, E. ŞIMŞEK#, A. Silver, Y. Yao, X. Ouyang, S.A. West, and L. You, Nature Microbiology 9: 1220–1230 (2024); # equal contribution Power-law tail in lag-time distribution underlies bacterial persistence, E. ŞIMŞEK and M. Kim, PNAS 116 (36) 17635-17640 (2019) Complete list of publications.