### Submitted manuscripts — [_Inequality and Mobility in a Minimal Model for Evolving Income Distributions_](https://arxiv.org/abs/2503.17375). Scott A McKinley and Gary A Hoover. Submitted, March 2025. — _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. — *[Change-in-velocity detection for multidimensional data.](https://arxiv.org/abs/2510.27150)* Linh Do, Dat Do, Keisha J. Cook, Yitao Shen, Scott A. McKinley. Submitted Summer 2026. — [_Dendrogram of mixing measures: Hierarchical clustering and model selection for finite mixture models_](https://arxiv.org/abs/2403.01684)_._ Dat Do, Linh Do, Scott A McKinley, Jonathan Terhorst, and XuanLong Nguyen. Submitted February, 2024. — _Extreme Statistics and Significance Thresholds for Maximally Persistent Topological Features._  Scott A McKinley and Maria-Veronica Ciocanel. Submitted August, 2022. ### Published and Accepted Articles (45) [_Source identification via pathwise gradient estimation_](https://arxiv.org/abs/2505.18205). ([pdf](https://arxiv.org/pdf/2505.18205)) Richard B. Lehoucq, Scott A. McKinley, Petr Plecháč. [arXiv2505.18205](https://arxiv.org/abs/2505.18205) Accepted and to appear in SIAM Applied Math, Fall 2026. (44) [_Nucleation feedback can drive establishment and maintenance of biased microtubule polarity in neurites_](https://www.sciencedirect.com/science/article/pii/S0025556425001646?via%3Dihub)_._ Hannah G Scanlon, Gibarni Mahata, Anna C Nelson, **Scott A McKinley**, Melissa M Rolls, Maria-Veronica Ciocanel. Vol 389 pg 109538. (43) [_DNA tensiometer reveals catch-bond detachment kinetics of kinesin-1, -2 and -3_](https://www.biorxiv.org/content/10.1101/2024.12.03.626575v2.abstract). Crystal R Noell, Tzu-Chen Ma, Rui Jiang, **Scott A McKinley**, William O Hancock. Accepted and to appear in _eLife._ (42) [_Emergent microtubule properties in a model of filament turnover and nucleation_.](https://www.sciencedirect.com/science/article/pii/S0022519325002206?dgcid=coauthor) Anna C Nelson, **Scott A McKinley**, Melissa M Rolls, Maria-Veronica Ciocanel. Journal of Theoretical Biology. Vol 616 pg 112254 (2025). (41) [_Considering experimental frame rates and robust segmentation analysis of piecewise-linear microparticle trajectories_](https://www.aimspress.com/article/doi/10.3934/mbe.2025095)_._ Keisha J Cook, Nathan Rayens, Linh Do, Christine K Payne, **Scott A McKinley**. _Mathematical Biosciences and Engineering_. Vol 22, No 10, pgs 2595-2626. (2025) (40) [_Minimal mechanisms of microtubule length distributions in living cells_](https://link.springer.com/article/10.1007/s11538-024-01279-z)_._ Anna C Nelson, Melissa M Rolls, Maria-Veronica Ciocanel, and Scott A McKinley. _Bulletin of Mathematical Biology_. Vol 86, No 58, pgs 1-33. (2024) (39) [_Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions_](https://link.springer.com/article/10.1007/s11538-024-01301-4)_._ Christopher E Miles, **Scott A McKinley**, Fangyuan Ding, Richard B Lehoucq. _Bulletin of Mathematical Biology._ Vol 86, No 74, pgs 1-31. (2024) ( [pdf](https://scott-a-mckinley.net/s/2024-Miles-McKinley-Snapshot-Inference.pdf) ) (38) [_Palmitate-mediated disruption of the endoplasmic reticulum decreases intracellular vesicle motility._](https://www.cell.com/biophysj/fulltext/S0006-3495\(23\)00154-6) 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._](https://www.sciencedirect.com/science/article/abs/pii/S0006349522001564) 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._](https://link.springer.com/article/10.1007/s00041-022-09911-z) ( [pdf](https://randommathdotnet.files.wordpress.com/2022/03/2022-nguyen-mckinley-jfa.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._](https://www.aimspress.com/article/doi/10.3934/mbe.2021442?viewType=HTML) ( [pdf](https://randommathdotnet.files.wordpress.com/2022/03/2021-jensen-mbe-changepoints.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._](https://www.journals.uchicago.edu/doi/10.1086/715453) 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_](https://link.springer.com/article/10.1007/s11538-020-00847-3) 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_](https://link.springer.com/article/10.1007/s11538-020-00797-w) 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_](https://arxiv.org/abs/1804.00202)  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_](https://link.springer.com/article/10.1007/s11538-019-00653-6)  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_](https://epubs.siam.org/doi/abs/10.1137/17M115517X) **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_](https://epubs-siam-org.libproxy.tulane.edu/doi/abs/10.1137/17M1131660)_._ 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_](https://link.springer.com/article/10.1007%2Fs11538-018-0448-9)_._  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_](https://epubs.siam.org/doi/abs/10.1137/17M1155259) 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_](https://academic.oup.com/jid/article-abstract/218/6/901/4983045) 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_](https://link.springer.com/article/10.1007%2Fs12080-017-0352-1)_._ 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_](http://intlpress.com/site/pub/pages/journals/items/cms/content/vols/0015/0007/a010/index.html)_._ 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._](http://rsif.royalsocietypublishing.org/content/14/135/20170555)  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_](http://www.sciencedirect.com/science/article/pii/S0021999117302541)_._ 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_](http://onlinelibrary.wiley.com/doi/10.1111/eva.12476/full) 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_](http://www.tandfonline.com/doi/full/10.1080/01621459.2016.1158716).  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_](http://scitation.aip.org/content/sor/journal/jor2/60/3/10.1122/1.4943988)  John Mellnik, Martin Lysy, Paula Vasquez, Natesh Pillai, David B Hill, Jeremy A Cribb, **Scott A McKinley** and M Gregory Forest. [_Journal of Rheology_](http://scitation.aip.org/content/sor/journal/jor2)_._ 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_](http://onlinelibrary.wiley.com/doi/10.1111/eva.12361/abstract)  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_](http://pubs.acs.org/doi/abs/10.1021/acsinfecdis.5b00108)  Timothy Wessler, Alex Chen, **Scott A McKinley**, Richard Cone, M Gregory Forest and Samuel K Lai.  [_ACS Infectious Disease_](http://pubs.acs.org/journal/aidcbc) 2 (1) pgs 82-92 (2016) (15) [_Minimizing biases associated with tracking analysis of submicron particles in heterogeneous biological fluids_](http://www.sciencedirect.com/science/article/pii/S0168365915301905)  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_](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131351) 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_](http://pubs.rsc.org/en/content/articlelanding/2014/sm/c4sm00676c#!divAbstract) 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_](http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12290/abstract) 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_.](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0100598)  **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_](http://www.biomedcentral.com/1472-6947/14/50)  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_.](http://www.sciencedirect.com/science/article/pii/S0006349514003348)  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_](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0087681)_._ 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_](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003178)_._ 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._](http://www.sciencedirect.com/science/article/pii/S0304414912001548)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_](http://www.pnas.org/content/109/30/12070)_._  Andrew M Hein, **Scott A McKinley**. _Proceedings of the National Academy of Sciences_. 109 (30) 12070-12074, 2012. (4) [_Statistical Challenges in Microrheology._](http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9892.2012.00792.x/abstract) 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._](http://www.sciencedirect.com/science/article/pii/S0022519312001671)  **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_.](http://epubs.siam.org/siap/resource/1/smjmap/v71/i4/p1531_s1?isAuthorized=no)  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._](http://www.journalofrheology.org/resource/1/jorhd2/v53/i6/p1487_s1)  **Scott A McKinley,** Lingxing Yao and M Gregory Forest.  _Journal of Rheology_, 53 (6) 2009. #### **Technical reports** -- _Particle Sensitivity Analyses._ ( [pdf](https://randommathdotnet.files.wordpress.com/2021/04/2020-sand2020-9871.pdf "2020 SAND2020-9871") ) 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. _](http://arxiv.org/abs/0911.4293)**Scott A McKinley**. arXiv:0911.4293