Publications

"I was an embarrassment to the department when they did research assessment exercises.
A message would go round the department: 'Please give a list of your recent publications.'
And I would send back a statement: 'None.'"
-Peter Higgs

A list of my publications

1. Confinement-induced accumulation and de-mixing of microscopic active-passive mixtures, S Williams, R Jeanneret, I Tuval, M Polin, Nature Communications volume 13, Article number: 4776 (2022).
   URL: https://www.nature.com/articles/s41467-022-32520-9

2.  Identifiability, Sensitivity, and Genetic Algorithms in Bacterial Biofilm Selection Models, S Williams, D Cheam, M K Nishiguchi, S S Sindi, S Khatri, E M Rutter, Bulletin of Mathematical Biology 88(7), 132 (2026).
   URL: https://doi.org/10.1007/s11538-026-01693-5 

3. Exaiptasia diaphana core microbiome members are lost under climate change conditions despite host thermal tolerance, K M Muffett, S Williams, S MacVittie, M J W Schwiesow, Su A Mendoza, Sa A Mendoza, H Hatch-West, E M Sogin, Nature Communications (2026).
   URL:  https://doi.org/10.1038/s41467-026-79034-2 

4. Thermal Stress Disrupts Symbiotic Fluid Dynamics in Bobtail Squid, S Williams, K A Ruiz, E Heath-Heckman, E M Rutter, S Khatri, Journal of the Royal Society Interface 23(240), 20251136 (2026).
   URL: https://doi.org/10.1098/rsif.2025.1136 

A list of my publications, in prep and ongoing project

1. Controlling passive particle distributions in mixed systems through active scattering events, S Williams, S Khatri, M Polin.

2. Exploring the impacts of squid breathing dynamics on bacterial symbiont acquisition, S Williams, K A Ruiz, E Heath-Heckman, E M Rutter, S Khatri. 

3. Modeling and identifiability in size-structured populations of Exaiptasia diaphana, S Williams, K M Muffett, S S Sindi, E M Sogin, S Khatri, E M Rutter.

4. Deep learning measures the timing of strobilation in Cassiopea from daily photographs, S Williams, K M Muffett.

Open source code

[1] https://github.com/StephWilleniams/BiofilmModelAnalysis - A number of model analysis tools applied to analyse synthetic biofilm data. Includes a custom Julia module for practical identifiability, Sobol sensitivity analysis, and basic Genetic algorithms.

[2] https://github.com/StephWilleniams/SquidInternalFlows - A set of fluid dynamics models used to simulate the motion of particles in a 2D approximation to the bobtail squid's internal cavity. These models can be simulated using Sobol sensitivity analysis across a range of conditions to determine impacts on particle motion through the space.

[3] https://github.com/StephWilleniams/ActivePassiveConfinement - Simulation code for mixed active-passive particle systems in confinement, from my work on how swimming microalgae redistribute passive particles.