Publication List
|
|
|
|
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 |