Publication List

E. Korunova, V. Sikirzhystki, J.L. Twiss, P.A. Vasquez, and M. Shtutman. “Single Particle Tracking of Genetically Encoded Nanoparticles: Optimizing Expression for Cytoplasmic Diffusion Studies.” Biophysical Journal, 2025. https://doi.org/10.1016/j.bpj.2025.05.025.  PDF

V. Chebotaeva, A. Srinivasan, and P.A. Vasquez. “Differentiating Contact with Symptomatic and Asymptomatic Infectious Individuals in a SEIR Epidemic Model.” Bulletin of Mathematical Biology 87(3): 38, 2025. https://doi.org/10.1007/s11538-025-01416-2.  PDF

A. Kokkanti, A. Atanasiu, D. Kolbin, D. Adalsteinsson, K. Bloom and P.A. Vasquez. “TopoLoop: A new tool for chromatin loop detection in live cells via single-particle tracking.” The Journal of Chemical Physics, 161(20), 204105, 2024. https://doi.org/10.1063/5.0236090.  PDF

P.A. Vasquez. “Multiscale Modeling of Viscoelastic Fluids.” Notices of The American Mathematical Society, 71(8), 2024. https://doi.org/10.1090/noti3001.  PDF

C.T. Hann, S.F. Ramage, H. Negi, C. Bequette, P.A. Vasquez and J. Stratmann. “Dephosphorylation of the MAP kinases MPK6 and MPK3 fine-tunes responses to wounding and herbivory in Arabidopsis.” Plant Science, 339, 111962, 2024. https://doi.org/10.1016/j.plantsci.2023.111962.  PDF

M. Cromer and P.A. Vasquez. “Macro-Micro Coupled Simulations of Dilute Viscoelastic Fluids”. Applied Sciences, 13(22), 12265, 2023. https://doi.org/10.3390/app132212265.  PDF

P.A. Vasquez, B. Walker, K. Bloom, D. Kolbin,  N. Caughman, R. Freeman, M. Lysy, C. Hult, K.A. Newhall, M. Papanikolas, C. Edelmaier, and M.F. Forest. “The power of weak, transient interactions across biology: A paradigm of emergent behavior.” Physica D: Nonlinear Phenomena, 454, 133866, 2023. https://doi.org/10.1016/j.physd.2023.133866.  PDF

V. Chebotaeva, P.A. Vasquez. “Erlang-Distributed SEIR Epidemic Models with Cross-Diffusion.” Mathematics, 11, 2167, 2023. https://doi.org/10.3390/math11092167.  PDF

Medved, R. Davis, and P.A. Vasquez. "Understanding Fluid Dynamics from Langevin and Fokker–Planck Equations." Fluids 5(1), 40, 2020. https://doi.org/10.3390/fluids5010040. PDF

H. Kim, J. L. Bauer, P.A. Vasquez and E.M. Furst. “Structural coarsening of magnetic ellipsoid particle suspensions driven in toggled fields.” Journal of Physics D: Applied Physics, 52(18), 184002, 2019. https://doi.org/10.1088/1361-6463/ab062f.  PDF

Hult, D. Adalsteinsson, P.A. Vasquez, J. Lawrimore, M. Bennett, A. York, D. Cook, E. Yeh, M.G. Forest, and K. Bloom. “Enrichment of dynamic chromosomal crosslinks drive phase separation of the nucleolus.” Nucleic Acids Research, 45(19), 11159-11173, 2017. https://doi.org/10.1093/nar/gkx741. PDF

J. Lawrimore, T.M. Barry, R.M. Barry, A.C. York, B. Friedman, D.M. Cook, K. Akialis, J. Tyler, P.A. Vasquez, E. Yeh, and K. Bloom. "Microtubule dynamics drive enhanced chromatin motion and mobilize telomeres in response to DNA damage." Molecular Biology of the Cell, 28(12), 1701-1711, 2017. https://doi.org/10.1091/mbc.e16-12-0846. PDF

P.A. Vasquez, C. Hult, D. Adalsteinsson, J. Lawrimore, M.G. Forest, and K. Bloom. "Entropy gives rise to topologically associating domains." Nucleic acids research, 44(12), 5540–5549, 2016. https://doi.org/10.1093/nar/gkw510. PDF

M. Lysy, N.S. Pillai, D.B. Hill, M.G. Forest, J. Mellnik, P.A. Vasquez, and S.A. McKinley. "Model comparison and assessment for single particle tracking in biological fluids." Journal of the American Statistical Association 111(516),1413-1426, 2016. https://doi.org/10.1080/01621459.2016.1158716.  PDF

P.A. Vasquez, Y. Jin, E. Palmer, D.B. Hill, and G. Forest, “Modeling and Simulation of Mucus Flow in Human Bronchial Epithelial Cell Cultures – Part I: Idealized Axisymmetric Swirling Flow.” PLoS Comput Biol, 12(8), e1004872, 2016. https://doi.org/10.1371/journal.pcbi.1004872.  PDF

J. Mellnik, M. Lysy, P.A. Vasquez, N.S. Pillai, D.B. Hill, J. Cribb, S.A. McKinley, and M.G. Forest. "Maximum likelihood estimation for single particle, passive microrheology data with drift." Journal of Rheology, 60(3), 379-392, 2016. https://doi.org/10.1122/1.4943988.  PDF

P.A. Vasquez and M.G. Forest. "Complex Fluids and Soft Structures in the Human Body," Invited Chapter for Complex Fluids in Biological Systems: Experiment, Theory, and Computation, Springer Series on Biological and Medical Physics, Biomedical Engineering, Saverio Spagnolie, Editor (2015). https://doi.org/10.1007/978-1-4939-2065-5_2.

J. G. Lawrimore, P.A. Vasquez, M. Falvo, R. Taylor II, L. Vicci, E. Yeh, M.G. Forest, K. Bloom, “DNA loops generate intracentromere tension in mitosis.” The Journal of Cell Biology, 210(4), 553-64, 2015. https://doi.org/10.1083/jcb.201502046.  PDF

Y. Zhu, L.H. Abdullah, S.P. Doyle, K. Nguyen, C. Ribeiro, P.A. Vasquez, M.G. Forest, M.I. Lethem, B.F. Dickey, and C.W. Davis, “Baseline Goblet Cell Mucin Secretion in the Airways Exceeds Stimulated Secretion over Extended Time Periods, and is Sensitive to Shear Stress and Intracellular Mucin Stores.” PloS one, 10(5), e0127267, 2015. https://doi.org/10.1371/journal.pone.0127267.  PDF

P.A. Vasquez, K. Bloom, “Polymer models of interphase chromosomes.” Nucleus, 5(5), 0-1, 2014. https://doi.org/10.4161/nucl.36275.  PDF

J.W. Swan, P.A. Vasquez, and E. M. Furst, “Buckling instability of self-assembled colloidal columns.” Physical Review Letters, 113(13), 138301, 2014. http://dx.doi.org/10.1103/PhysRevLett.113.138301.  PDF

J. Mellnik, P.A. Vasquez, S.A. McKinley, J. Witten, D.B. Hill, and M.G. Forest, “Micro-heterogeneity metrics for diffusion in soft matter.” Soft matter, 10(39), 7781-7796, 2014. https://doi.org/10.1039/C4SM00676C.  PDF

D.B. Hill, P.A. Vasquez, J. Mellnik, S.A. McKinley, A. Vose, F. Mu, A.G. Henderson, S.H. Donaldson, N.E. Alexis, R.C. Boucher and M.G. Forest, “A Biophysical Basis for Mucus Solids Concentration as a Candidate Biomarker for Airways Disease.” PloS one, 9(2), e8768, 2014. https://doi.org/10.1371/journal.pone.0087681.  PDF

J.A. Cribb, P.A. Vasquez*, P. Moore, S. Norris, S. Shah, M.G. Forest, and R. Superfine, “Nonlinear Signatures of Entangled Polymer Solutions in Active Microbead Rheology.” Journal of Rheology, 57(4), 1247-1264, 2013. https://doi.org/10.1122/1.4811477. PDF

P.A. Vasquez, Y. Jin, K. Vuong, D.B. Hill and M.G. Forest, “A New Twist on Stokes’ Second Problem: Partial Penetration of Nonlinearity in Sheared Viscoelastic Layers.” Journal of Non-Newtonian Fluid Mechanics, 196, 36-50, 2013. https://doi.org/10.1016/j.jnnfm.2012.12.016. PDF

A.D. Stephens, R.A. Haggerty, P.A. Vasquez, L. Vicci, C.E. Snider, F. Shi, C. Quammen, C. Mullins, J. Haase, R.M. Taylor II, J.S. Verdaasdonk, M.R. Falvo, Y. Jin, M.G. Forest, K. Bloom, “Pericentric chromatin loops function as a nonlinear spring in mitotic force balance.“ The Journal of Cell Biology, 193(7), 1167-1180, 2013. https://doi.org/10.1083/jcb.201208163. PDF

J.S. Verdaasdonk, P.A. Vasquez, R.M. Barry, T. Barry, S. Goodwin, M.G. Forest, K. Bloom, “Centromere tethering confines chromosome domains.” Molecular Cell, 52(6), 819-831, 2013. http://dx.doi.org/10.1016/j.molcel.2013.10.021.  PDF

A.D. Stephens, C.E. Snider, J. Haase, R.A. Haggerty, P.A. Vasquez, M.G. Forest, K. Bloom, “Individual pericentromeres display coordinated motion and stretching in the yeast spindle.“ The Journal of Cell Biology, 203(3), 407-416, 2013. https://doi.org/10.1083/jcb.201307104.  PDF

J.W. Swan, P.A. Vasquez, P.A. Whitson, E.M. Fincke, K. Wakata, S.H. Magnus, F.D. Winne, M.R. Barratt, .H. Agui J, R.D. Green, N.R. Hall, D.Y. Bohman, C.T. Bunnell, A.P. Gast, E.M. Furst, “Multi-scale kinetics of a field-directed colloidal phase transition.” Proceedings of the National Academy of Sciences, 109, 16023-16028, 2012. https://doi.org/10.1073/pnas.1206915109.  PDF

C.J. Pipe, N.J. Kim, P.A. Vasquez, L.P. Cook, and G.H. McKinley, “Wormlike Micellar Solutions II: Comparison Between Experimental Data and Scission Model Predictions.” Journal of Rheology, 54(4), 881-913, 2010. https://doi.org/10.1122/1.3439729.  PDF

M.W. Liberatore, F. Nettesheim, P.A. Vasquez, M.E. Helgeson, N.J. Wagner, E.W. Kaler, L.P. Cook, L. Porcar, and Y.T. Hu, “Microstructure and Shear Rheology of Entangled Wormlike Micelles in Solution.” Journal of Rheology 53(2), 441-458, 2009.  https://doi.org/10.1122/1.3072077.  PDF

M.E. Helgeson, P.A. Vasquez, E.W. Kaler and N.J. Wagner, “Constitutive modeling and spatially-resolved structure of cetyltrimethylammonium bromide wormlike micelles through the shear banding transition.” Journal of Rheology, 53(3), 727-756, 2009. https://doi.org/10.1122/1.3089579.  PDF

L. Zhou, P.A. Vasquez, G.H. McKinley and L.P. Cook, “Modeling the Inhomogeneous Response and Formation of Shear Bands in Steady and Transient Flows of Entangled Liquids.” Journal of Rheology, 52(2), 591- 623, 2008.  https://doi.org/10.1122/1.2829769.  PDF

P.A. Vasquez, L.P. Cook, and G.H. McKinley, “A network scission model for wormlike micellar solutions: I. Model formulation and viscometric flow predictions.” Journal of Non-Newtonian Fluid Mechanics, 144(2-3), 122-139, 2007.  https://doi.org/10.1016/j.jnnfm.2007.03.007.  PDF