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Published and accepted articles

(21) Fluid–particle dynamics for passive tracers advected by a thermally fluctuating viscoelastic medium.pdf )
Christel Hohenegger and Scott A McKinleyJournal 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. Accepted. (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. Available online Oct 20 (2014)

(11) Modeling Neutralization Kinetics of HIV by Broadly Neutralizing Monoclonal Antibodies in Genital Secretions Coating the Cervicovaginal Mucosa. (pdfsupplemental)
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. (pdfsupplemental)
Andrew M Hein, Scott A McKinleyPLoS 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.

Submitted articles and technical reports

Spatial patterns of symbionts arising from propagule redirection
Elizabeth A Hamman, Craig W Osenberg, Scott A McKinley, and Adrian C Stier. Submitted and in review. (2015)

Resource-Driven Encounters and the Induction of Disease Among Consumers (pdf)
Rebecca K Borchering, Steve E Bellan, Jason M Flynn, Juliet RC Pulliam, Scott A McKinley. Submitted and in first revision (2016).

— Reconstructing Complex Fluid Properties from the Behavior of Fluctuating Immersed Particles. ( pdf )
Christel Hohenegger and Scott A McKinleySubmitted and in review (2017).

— Anomalous Diffusion of Distinguished Particles in Bead-Spring Systems.

Scott A McKinley. arXiv:0911.4293