Thomas M. Gaul

Ph.D. Student in Biomedical Science (Systems Biology)
University of Connecticut Health Center

Location: Farmington, Connecticut
Email: gaul@uchc.edu
Google Scholar: Thomas M. Gaul
Bluesky: @tomgaul.bsky.social
Gitlab: tgaul
Github: ThomasGaul

About Me

I am a Ph.D. student in Biomedical Science at UConn Health, with a concentration in Systems Biology. I am a member of Dr. Eran Agmon's Vivarium Lab working on two projects: (i) modelling antibiotic response in E. coli; and (ii) predicting viability outcomes in a fluid mechanical model of protocells. I graduated with a B.S. in Cognitive Science from Indiana University Bloomington, working in Dr. Randall Beer's Computational Neuroethology Lab. Here you will find a list of my publications and information about my research. In the future, I might also post thoughts that do not quite fit into a paper or on subjects unrelated to my research.

My overall research goal is to develop a mathematical theory of biological organization and how it relates to behaviour and viability. Biologists are increasingly recognizing the importance of self-organization and material turnover in understanding how cells work, as well as the central role of cells as the basic unit of biology. However, we do not yet have a precise notion of what it means for a cell to die, and so we cannot predict such outcomes in a theoretically consistent way. What is needed is a theory of biological organization that describes organisms as a certain kind of dynamic pattern, independent of its physical instantiations or its lineage. In this way, we can say that an organism dies when its organization is no longer realized -- the difficulty comes in defining what that organization is mathematically.

To this end, I work on simulating simple protocells in a Lattice Boltzmann model, a common tool in fluid mechanics research. This provides a more tractable model system for which rigorous theory can be developed. This work will lay a theoretical foundation from which we can begin to understand the viability of real and engineered cells more precisely.

I carried out similar work on a simpler model for my Senior Honors thesis, where I extended previous work by Dr. Beer on biological organization in the Game of Life cellular automaton to a generalization called Larger than Life, and then to a continuum limit called RealLife.

Other interests of mine include mathematical approaches in other sciences, epistemology, philosophy of science, open-source software, and Computer Algebra Systems.

Feel free to reach out through any of the contacts listed above.