Publications – Ryan, Shawn D.

Publications: Chronological Order or By Subject

Full CV

In Preparation:

47. “Face Your Fears: Ant Colony Competition Modeling” S. Guha, S. D. Ryan, B. Karamched, In Preparation, (2025).
46. “Contamination Dynamics of Active Rods in Long Micro-channels” J. Palos, C. Brown, M. Potomkin, S. D. Ryan, In Preparation, (2025).
45. “PAA Efficacy and Decay Kinetics in Poultry Processing Under Chiller Conditions” V. Ciluveru, J. Simon, J. Boulter-Bitzer, S. D. Ryan, C. Kothapalli, D. S. Munther, In Preparation, (2025)
44. “Macroscopic model for foraging ant dynamics” S. D. Ryan, In Preparation, (2025).

Submitted / Under Revision:

43. “Modeling Multi-Phase Growth in Cyanobacterial Harmful Algal Blooms” A. Brown, D. Munther, S. D. Ryan, Submitted (2025).
42. “Boundary accumulations of active rods in 3D microchannels with elliptical cross-section” C. Brown, S. D. Ryan, M. Potomkin, Submitted (2025). Preprint
41. “Toe Twitch or Not Toe Twitch: A Frog Pursuit Model” C. Gibson, S. D. Ryan, In Revision (2025).

Published / Accepted:

40. “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, Accepted to Food and Bioproducts Processing (2025).
39. “Spatial characterizations of bacterial dynamics for food safety: Modeling for shared water processing environments” D. Munther, S. D. Ryan, C. Kothapalli, N. Zekaj, Applied Mathematical Modeling 139, 115818 (2025). Preprint on BioRxiv
38. “Walk This Way: Modeling Foraging Ant Dynamics in Multiple Food Source Environments” S. Hartman, S. D. Ryan, B. R. Karamched, Journal of Mathematical Biology 89(41) (2024). Preprint on BioRxiv
37. “External Validation of a Clinical Mathematical Model Estimating Postoperative Urine Output Following Cardiac Surgery in Children” O. Baloglu*, B. S. Marino, S. Q. Latifi, A. Morca, D. S. Munther, S. D. Ryan, J. Pediatric Nephrology 1-6, (2024).
36. “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 BioRxiv
35. “Book Review: Mathematical Modeling in Biology: A Research Methods Approach“ S. D. Ryan SIREV: SIAM Review, Editor: A. T. Layton, 66(4): 795-805 (2024).
34. “Noninvasive cardiac output monitoring in congenital heart disease” A. Tandon, S. Bhattacharya, O. T. Inan, J. Lasa, S. Latifi, N. Lu, B. Marino, A. Morca, D. Munther, S. D. Ryan, O. Baloglu, Current Treatment Options in Pediatrics (2023).
33. “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).

32. “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).

31. “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).

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

29. “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

28. “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

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

26. “Interaction of red crabs with yellow crazy ants during migration on Christmas Island”, N. Baumgartner, S. D. Ryan, Mathematical Biosciences, 330 108486 (2020).

25. “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
24. “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).
23. “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

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

21. “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).

20. “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).

19. “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).

18. “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).

17. “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).

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

15. “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).

14. “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).

13. “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).

12. “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).

11. “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)

10. “Effective rheological properties in semidilute bacterial suspensions” M. Potomkin, S. D. Ryan, L. Berlyand, Bulletin of Mathematical Biology,
78(3) 580-615 (2016).

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

8. “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

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

6. “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

5. “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).

4. “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).

3. “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).
2. “Bifurcation and Boundary Layer Analysis for Graphene Sheets” S. D. Ryan, Master of Science Thesis, Ohiolink, The University of Akron (2009).
1. “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).