Submitted manuscripts

— Microbes can affect the likelihood of regime shifts and alternative stable states in coral reefs. Amy A Briggs, Scott A McKinley, and Craig Osenberg. Submitted February, 2024.

— Dendrogram of mixing measures: Learning latent hierarchy and model selection for finite mixture models. Dat Do, Linh Do, Scott A McKinley, Jonathan Terhorst, and XuanLong Nguyen. Submitted February, 2024.

— Minimal mechanisms of microtubule length distributions in living cells. Anna C Nelson, Melissa M Rolls, Maria-Veronica Ciocanel, and Scott A McKinley. Submitted November 2023.

— Inferring stochastic rates from heterogeneous snapshots of particle positions. Christopher E Miles, Fangyuan Ding, Richard B Lehoucq, and Scott A McKinley. Submitted October, 2023.

— Extreme Statistics and Significance Thresholds for Maximally Persistent Topological Features.  Scott A McKinley and Maria-Veronica Ciocanel. Submitted August, 2022.

Published Articles

(38) Palmitate-mediated disruption of the endoplasmic reticulum decreases intracellular vesicle motility. Nathan T Rayens, Keisha J Cook, Scott A McKinley, and Christine K Payne. Biophysical Journal. Vol 122, No 7, pgs 1355-1363. (2023)

(37) Transport of lysosomes decreases in the perinuclear region: Insights from chagepoint analysis.
Nathan T Rayens, Keisha J Cook, Scott A McKinley, Christine K Payne. Biophysical Journal. Vol 121, No 7, pgs 1205-1218 (2022)

(36) On the Hölder regularity of a linear stochastic partial-integro-differential equation with memory. ( pdf )
Scott A McKinley and Hung D Nguyen. Journal of Fourier Analysis and Its Applications. Vol 28, No 13. (2022)

(35) A change point analysis protocol for comparing intracellular transport by different molecular motor combinations. ( pdf )
Melanie A. Jensen, Qingzhou Feng, William O. Hancock, and Scott A McKinley. Mathematical Biosciences and Engineering. Vol 18, No 6, pgs 8962 -- 8996. (2021)

(34) Leaf economics of early- and late-successional plants. ( pdf supp )
Jeremy W. Lichstein, Brandon Peterson, Jessica Langebrake, and Scott A McKinley. The American Naturalist. Vol 198 No 3. (2021)

(33) Topological Data Analysis Approaches to Uncovering the Timing of Ring Structure Onset in Filamentous Networks ( pdf )
Maria-Veronica Ciocanel, Riley Juenemann, Adriana T. Dawes & Scott A. McKinley. Bulletin of Mathematical Biology. Vol 83, No 21. (2021)

 (32) Renewal Reward Perspective on Linear Switching Diffusion Systems in Models of Intracellular Transport ( pdf )
Maria-Veronica Ciocanel, John Fricks, Peter R. Kramer & Scott A. McKinley. Bulletin of Mathematical Biology. Vol 82, No 10. (2020)

(31) The Generalized Langevin Equation With Power-Law Memory in a Nonlinear Potential Well ( pdf )
Nathan Glatt-Holtz, David P Herzog, Scott A McKinley, and Hung D Nguyen, Nonlinearity. Vol. 33, No 6, pgs 2820-2852 (2020)

(30) Antibody-mediated Immobilization of Virions in Mucus ( pdf )
Melanie A Jensen, Ying-Ying Wang, Samuel K Lai, M Gregory Forest, Scott A McKinley. Bulletin of Mathematical Biology. Vol. 81, No 10, pgs 4069-4099 (2019)

(29) Anomalous Diffusion and the Generalized Langevin Equation ( pdf )
Scott A McKinley and Hung D Nguyen, SIAM Journal on Mathematical Analysis. Vol 50, No 5, pgs 5119-5160. (2018)

(28) Reconstructing Complex Fluid Properties from the Behavior of Fluctuating Immersed Particles. ( pdf )
Christel Hohenegger and Scott A McKinley. SIAM Journal on Applied Mathematics. Vol 78 No 4, pgs 2200-2226 (2018)

(27) Assessing the Impact of Electrostatic Drag on Processive Molecular Motor Transport. ( pdf )
J Darby Smith and Scott A McKinley, Bulletin of Mathematical Biology. Vol 80 No 8, pgs 2088-2123. (2018)

(26) Continuum Approximation of Invasion Probabilities ( pdf )
Rebecca K Borchering and Scott A McKinley, Multiscale Modeling and Simulation. Vol 16 No 2, pgs 551-582. (2018)

(25) ZMapp Reinforces the Airway Mucosal Barrier Against Ebola Virus
Bing Yang, Alison Schaefer, Ying-Ying Wang, Justin McCallen, Phoebe Lee, Jay M Newby, Harendra Arora, Priya A Kumar, Larry Zeitlin, Kevin J Whaley, Scott A McKinley, William A Fischer II, Dimple Harit, Samuel K Lai. Journal of Infectious Diseases. Vol 218 No 6, pgs 901-910. (2018)

(24) Landscape configuration drives persistent spatial patterns of occupant distributions. ( pdf )
Elizabeth A Hamman, Scott A McKinley, Adrien C Stier, Craig W Osenberg. Theoretical Ecology. Vol 11 No 1 pgs 111-127. (2018)

(23) Geometric ergodicity of two-dimensional Hamiltonian systems with a Lennard–Jones-like repulsive potential. ( pdf )
Ben Cooke, David P Herzog, Jonathan C Mattingly, Scott A McKinley, Scott C Schmidler. Communications in Mathematical Sciences. Vol 15 No 7, pgs 1987-2025 (2017)

(22) Resource-driven encounters among consumers and implications for the spread of infectious disease. ( pdf )
Rebecca K Borchering, Steven E Bellan, Jason M Floyd, Juliet RC Pulliam, and Scott A McKinley. The Journal of the Royal Society - Interface. Vol 14 No 135: 20170555. (2017)

(21) Fluid–particle dynamics for passive tracers advected by a thermally fluctuating viscoelastic medium. ( pdf )
Christel Hohenegger and Scott A McKinley. Journal of Computational Physics. Vol 340 pgs 688-711. (2017)

(20) The Evolutionary Trade-off between Stem Cell Niche Size, Aging, and Tumorigenesis ( pdf )
Vincent L Cannataro, Scott A McKinley, and Colette M St Mary. Evolutionary Applications. Vol 10 No 6, pgs 590-602. (2017)

(19) Model comparison for single particle tracking in biological fluids. ( pdf )
Martin Lysy, Natesh S. Pillai, David B. Hill, M. Gregory Forest, John Mellnik, Paula Vasquez and Scott A McKinley. Journal of the American Statistical Association. Vol 111 No 56 (2016)

(18) Maximum Likelihood Estimation for Single Particle, Passive Microrheology Data with Drift ( pdf )
John Mellnik, Martin Lysy, Paula Vasquez, Natesh Pillai, David B Hill, Jeremy A Cribb, Scott A McKinley and M Gregory Forest. Journal of Rheology. 60, 379 (2016)

(17) The Implications of Small Stem Cell Niche Sizes and the Distribution of Fitness Effects of New Mutations in Aging and Tumorigenesis ( pdf )
Vincent L Cannataro, Scott A McKinley and Colette St Mary. Evolutionary Applications. 9 (4) pgs 565-582. (2016)

(16) Using computational modeling to optimize the design of antibodies that trap viruses in mucus (pdf)
Timothy Wessler, Alex Chen, Scott A McKinley, Richard Cone, M Gregory Forest and Samuel K Lai.  ACS Infectious Disease 2 (1) pgs 82-92 (2016)

(15) Minimizing biases associated with tracking analysis of submicron particles in heterogeneous biological fluids (pdf)
Ying-Ying Wang, Kenetta L Nunn, Dimple Harit, Scott A McKinley, and Samuel K. Lai.
Journal of Controlled Release.Vol 220, Part A, pgs 37-43 (2015)

(14) Modeling of Virion Collisions in Cervicovaginal Mucus Reveals Limits on Agglutination as the Protective Mechanism of Secretory Immunoglobulin A (pdf)
Alex Chen, Scott A McKinley, Feng Shi, Simi Wang, Peter J Mucha, Dimple Harit, M Gregory Forest, and Samuel K Lai. PLoS ONE 10(7): e0131351. doi:10.1371/journal.pone.0131351 (2015)

(13)  Micro-heterogeneity metrics for diffusion in soft matter
John Mellnik, Paula A Vazquez, Scott A McKinley, Jacob Witten, David B Hill, M Gregory Forest. Soft Matter. 10 (39) 7781-7796. (2014)

(12) Hidden semi-Markov models reveal multiphasic movement of the endangered Florida panther
Madelon Van de Kirk, David P Onorato, Marc A Criffield, Benjamin M Bolker, Ben C Augustine, Scott A McKinley, Madan K Oli. Journal of Animal Ecology. Vol 84 No 2, 576-585. (2014)

(11) Modeling Neutralization Kinetics of HIV by Broadly Neutralizing Monoclonal Antibodies in Genital Secretions Coating the Cervicovaginal Mucosa. (pdf, supplemental)
Scott A McKinley, Alex Chen, Feng Shi, Simi Wang, Peter J Mucha, M Gregory Forest, Samuel K Lai. PLoS ONE 9(6): e100598. (2014) doi:10.1371/journal.pone.0100598

(10) A flexible simulation platform to quantify and manage emergency department crowding (pdf)
Joshua E Hurwitz, Jo Ann Lee, Kenneth K Lopiano, Scott A McKinley, James Keesling and Joseph A Tyndall. BMC Medical Informatics and Decision Making. Vol 15 No 50 (2014)

(9)  Transient Antibody-Mucin Interactions Produce a Dynamic Molecular Shield against Viral Invasion. (pdf)
Alex Chen, Scott A McKinley, Simi Wang, Feng Shi, Peter J. Mucha, M. Gregory Forest, & Samuel K Lai. Biophysical Journal, 106(9), 2028–2036. doi:10.1016/j.bpj.2014.02.038 (2014)

(8) A Biophysical Basis for Mucus Solids Concentration as a Candidate Biomarker for Airways Disease. (pdf)
David B. Hill, Paula A. Vasquez, John Mellnik, Scott A McKinley, Aaron Vose, Frank Mu, Ashley G Henderson, Scott H. Donaldson, Neil E. Alexis, Richard C. Boucher and M. Gregory Forest. PLoS ONE, 9(2), e87681. doi:10.1371/journal.pone.0087681  (2014).

(7) Sensory Information and Encounter Rates of Interacting Species. (pdf, supplemental)
Andrew M Hein, Scott A McKinley. PLoS Computational Biology 9(8): e1003178. 2013.

(6) Geometric ergodicity of a bead-spring system forced by a stochastic Stokes fluid. (pdf)
Jonathan C Mattingly, Scott A McKinley, Natesh S Pillai. Stochastic Processes and Their Applications 122 (12) 3953-3979, 2012.

(5) Sensing and Decision-Making in Random Search. (pdf)
Andrew M Hein, Scott A McKinley. Proceedings of the National Academy of Sciences. 109 (30) 12070-12074, 2012.

(4) Statistical Challenges in Microrheology. (pdf)
Gustavo Didier, Scott A McKinley, David B Hill, John Fricks. Journal of Time Series Analysis (33) 5 724-743, 2012.

(3) Asymptotic Analysis of Microtubule-based Transport by Multiple Identical Molecular Motors. (pdf)
Scott A McKinley, Avanti Athreya, John Fricks, Peter R Kramer. Journal of Theoretical Biology, Vol 305, July 21, 2012.

(2)  A Stochastic Compartmental Model for Fast Axonal Transport. (pdf)
Lea Popovic, Scott A McKinley and Michael C. Reed. SIAM Journal on Applied Mathematics, 71 (4) 2011.

(1) Transient Anomalous Diffusion of Tracer Particles in Soft Matter. (pdf)
Scott A McKinley, Lingxing Yao and M Gregory Forest.  Journal of Rheology, 53 (6) 2009.

Technical reports

-- Particle Sensitivity Analyses. ( pdf )
Stephen D Bond, Brian C Franke, Richard C Lehoucq, and Scott A McKinley.
Technical report for Sandia National Laboratories, SAND2020-9871. (2020)

-- Anomalous Diffusion of Distinguished Particles in Bead-Spring Systems.
Scott A McKinley. arXiv:0911.4293