Shawn D. Ryan, PhD

Publications: Chronological Order or By Subject

Full CV

Mathematical Biology: Collective Behavior/Self-Organization

• “Boundary accumulations of active rods in microchannels with elliptical cross-section” C. Brown, S. D. Ryan, M. Potomkin, In Revision (2024). Preprint
•  “Toe Twitch or Not Toe Twitch: A Frog Pursuit Model” C. Gibson, S. D. Ryan, Submitted (2024).
• “Walk This Way: Modeling Foraging Ant Dynamics in Multiple Food Source Environments” S. Hartman, S. D. Ryan, B. Karamched, Journal for Mathematical Biology,  89(41) (2024).
• “Agent-based modeling of nuclear chromosome ensemble identifies determinants of homolog pairing during meiosis“ A. Chriss, G. V. Börner, S. D. Ryan, PLoS Computational Biology 20(5) e1011416 (2024). Preprint on BioRx
• “Fluid-Structure Interaction Modelling of Neighboring Tubes with Primary Cilium Analysis” N. Zekaj, S. D. Ryan, and A. Resnick Mathematical Biosciences and Engineering, 20(2) 3677-3699 (2023).

• “The Space Between Us: Modeling Spatial Heterogeneity in Synthetic Microbial Consortia Dynamics” R. Godin, B. Karamched, and S. D. Ryan Biophysical Reports, 2(4) 100085 (2022).

• “Heterogeneous Bacterial Swarms with Mixed Lengths” S. Peled, S. D. Ryan, S. Heidenreich, M. Bar, G. Ariel, A. Be’er Phys. Rev. E, 103 032413(2021). Preprint: arXiv Preprint

• “Macroscopic model for foraging ant dynamics” S. D. Ryan, In Preparation, (2021).

• “Motor Protein Transport Along Inhomogeneous Microtubules” S. D. Ryan, Z. McCarthy, M. Potomkin, Bulletin of Mathematical Biology 83(9):1-29, (2021). Preprint

• “Role of hydrodynamic interactions in chemotaxis of bacterial populations” S. D. Ryan, Physical Biology,17 016003 (2020).
  • Press: Featured Article on Phys. Biology Homepage Dec. 2019 – Feb. 2020

• “Model for Ant/Crab Interactions on Christmas Island, N. Baumgartner, S. D. Ryan, Mathematical Biosciences, 330 108486 (2020).

• “Collective dynamics of two-dimensional swimming bacteria: Experiments and models” G. Ariel, M. Sidortsov, S. D. Ryan, S. Heidenreich, M. Bar, and A. Be’er, Phys. Rev. E, 98 032415 (2018).

• “The effect of randomness on the distribution of multiple Ginzburg-Landau vortices pinned by small holes” L. Berlyand, V. Mityushev, S. D. Ryan, IMA Journal of Applied Mathematics, 83(6) 977-1006 (2018).

• “Anomalous fluctuations in the orientation and velocity of swarming bacteria” S. D. Ryan, G. Ariel, A. Be’er, Biophysical Journal, 111(1) 247-255 (2016).

• “Effective rheological properties in semidilute bacterial suspensions” M. Potomkin, S. D. Ryan, L. Berlyand, Bulletin of Mathematical Biology,

• “A Model for Collective Dynamics in Ant Raids” S. D. Ryan, Journal of Mathematical Biology, 72(6) 1579-1606 (2016).

• “Effective Properties and Collective Dynamics in Bacterial Suspensions” S. D. Ryan, Ph. D. Dissertation, (2014).

• “Correlation properties of collective motion in bacterial suspensions” S. D. Ryan, A. Sokolov, L. Berlyand, and I. S. Aranson, New Journal of Physics, 15 105021, (2013).
  • Chosen as a “Highlight of 2013” for Soft Matter and Biophysics

• “A Kinetic Model for Semi-Dilute Bacterial Suspensions”. S. D. Ryan, L. Berlyand, B. M. Haines, and D. Karpeev, SIAM Multiscale Modeling and Simulation, 11(4), 1176-1196, (2013).

• “Viscosity of bacterial suspensions: Hydrodynamic interactions and self-induced noise” S. D. Ryan, B. M. Haines, L. Berlyand, F. Ziebert, and I. S. Aranson Rapid Communication to Phys. Rev. E 83 050904(R) (2011).

Mathematical Biology: Biomedicine

• “Pulsatile Flow Through Idealized Renal Tubules: Fluid-Structure Interaction and Dynamic Pathologies” N. Praljak, S. D. Ryan, A. Resnick Accepted to Mathematical Biosciences and Engineering, 17(2) 1787-1807 (2020).

Mathematical Biology: Bacterial Cross-Contamination

• “Spatial cross-contamination profiles: Effect of water reuse on dynamics of Campylobacter and E. coli during poultry chilling” D. Munther, S. D. Ryan, C. Kothapalli, N. Zekaj, Submitted (2024).
• “Spatial characterizations of bacterial dynamics for food safety: Modeling for shared water processing environments” D. Munther, S. D. Ryan, C. Kothapalli, N. Zekaj, Accepted to Applied Mathematical Modeling, (2024). Preprint on BioRxiv
• “Optimal Strategy for Limiting Cross-Contamination in Poultry Chilling Process” S. D. Ryan, D. Munther, In Preparation, (2019).

• “An individual-carcass model for quantifying bacterial cross-contamination in an industrial three-stage poultry scalding tank” Z. McCarthy, B. Smith, A. Fazil, J. Wu, S. D. Ryan, D. Munther, Journal of Food Engineering, 252 142-153 (2019).

• “pH dependent C. jejuni thermal inactivation models and application to poultry scalding” Z. McCarthy, B. Smith, A. Fazil, J. Wu, S. D. Ryan, D. Munther, Journal of Food Engineering, 223 1-9 (2018).

• “Individual based modeling and analysis of pathogen levels in poultry chilling process” Z. McCarthy, B. Smith, A. Fazil, J. Wu, S. D. Ryan, D. Munther, Mathematical Biosciences, 294 172-180 (2017).

• “Mechanisms of bacterial contamination in poultry chill tanks” Z. McCarthy, D. Munther, S. D. Ryan, J. Wu, Technical Report for the Public Health Agency of Canada (PHAC), (2017).

Materials Science

• “Influence of PEG on the Clustering of Active Janus Colloid” M. Kalil, N. Baumgartner, M. Issa, S. D. Ryan, C. Wirth Colloids and Surfaces A: Physicochemical and Engineering Aspects 627, 127191 (2021). Preprint: arXiv

• “Charged Nanoparticles Quench the Propulsion of Active Janus Colloids” M. Issa, N. Baumgartner, M. Kalil, S. D. Ryan, C. Wirth, ACS Omega, 4(8) 13034-13041 (2019).

• “The effect of randomness on the distribution of multiple Ginzburg-Landau vortices pinned by small holes” L. Berlyand, V. Mityushev, S. D. Ryan, IMA Journal of Applied Mathematics, (2018).

• “Optimal Shape of Water Towers” A. Sulak, S. D. Ryan, SIAM Undergraduate Research Journal (SIURO), 10 233-247 (2017).

• “A finite volume method for computing flow induced orientation of nematic liquid crystals” S. D. Ryan, G. Richards, X. Zheng, P. Palffy-Muhoray, Molecular Crystals and Liquid Crystals (MCLC), 647(1) 207-215 (2017).

• “Curvature-driven foam coarsening on a sphere: A computer simulation” S. D. Ryan, X. Zheng, P. Palffy-Muhoray, Physical Review E, 93 053301 (2016). Preprint.
  • Press: Phys. Rev. E Kalediscope (best aesthetic images)

• “Rayleigh Approximation for ground states of the Bose and Coulomb glasses” S. D. Ryan, V. Mityushev, V. M. Vinokur, L. Berlyand, Scientific Reports: Nature Publishing Group, 5 7821 (2015).
  • Press: Mathematical approach provides a new step in resolving mystery of glass

• “Buckling of a Graphene Sheet Perpendicular to a Rigid Substrate” S. D. Ryan, D. Golovaty, and J. P. Wilber, International Journal of Solids and Structures 49 3681-3692, (2012).

• “Bifurcation and Boundary Layer Analysis for Graphene Sheets” S. D. Ryan, Master of Science Thesis, Ohiolink, The University of Akron (2009).

• “A Buckling Problem For Graphene Sheets” J. Gallagher, Y. Milman, S. Ryan, D. Golovaty, P. Wilber, and A. Buldum in the “Proceedings of the 11th International Congress on Continuum Modeling of Discrete Systems”, Les Presses de l’Ecole des Mines de Paris (2007).

Miscellaneous

• “A Clinical Mathematical Model Estimating Postoperative Urine Output in Children Underwent Cardiopulmonary Bypass for Congenital Heart Surgery” O. Baloglu, S. D. Ryan, A. M. Onder, D. Rosen, C. J. Mullett, and D. Munther J. Pediatric Intensive Care, (2022).

• “Reconciling chord length distributions and area distributions for fields of fractal cumulus clouds” N. Barron, S. D. Ryan, T. Heus, Atmospheres 11(8) 824 (2020).

• “An OER Approach to Linear Algebra” S. D. Ryan and T. M. Nawalaniec PRIMUS, 721-737 (2022).

• • “The contributions of shear and turbulence to cloud overlap for cumulus clouds” A. Sulak, B. Calabrase, S. D. Ryan, T. Heus, Journal of Geophysical Research: Atmospheres 125 (2020). Preprint