Aaron Fogelson
- 90. 'Kinetic model of two monomer polymerization', (with
Anna C. Nelson and James P. Keener), Physical Review E, 2020,
accepted.
- 89. 'A mathematical model of coagulation under flow identifies
factor V as a modifier of thrombin generation in hemophilia A'
(with Kathryn G. Link, Michael T. Stobb, Matthew G. Sorrells,
Maria Bortot Katherine Ruegg, Marilyn J. Manco-Johnson, Jorge A. Di
Paola, Suzanne S. Sindi, Karin Leiderman, Keith B. Neeves)
Journal of Thrombosis and Hemostasis, 2020, 18, 306-317.
- 88.'Electrodiffusion-mediated swelling of a two-phase gel
model of gastric mucus', (with Owen L. Lewis and James P. Keener), Gels, 2018, 4, 76, doi:10.3390/gels4030076..
- 87.'A local and global sensitivity analysis of a mathematical
model of coagulation and platelet deposition under flow', (with
Kathryn G Link, Michael T Stobb, Jorge A Di Poala, Keith B Neeves,
Suzanne S Sindi, Karin Leiderman), PLoS One, 2018,
https://doi.org/10.1371/journal.pone.0200917.
- 86.'Hyperviscosity-Based Stabilization for Radial Basis Function-Finite
Difference (RBF-FD) Discretizations of Advection-Diffusion
Equations', (with Varun Shankar), Journal of Computational
Physics, 2018, 372, 616-639.
- 85.'Robust Node Generation for Meshfree Discretizations
on Irregular Domains and Surfaces', (with Varun Shankar and Robert
M. Kirby), SIAM Journal on Scicentific Computing, 2018, 40, A2584-2608.
- 84.'A Physics-based Model for Maintenance of the pH Gradient in the
Gastric Mucus Layer', (with Owen Lewis and James P. Keener),
American Journal of Physiology, Gastrointestinal and Liver
Physiology, 2017, 313, G599-G612.
- 83.'Molecular and Physical Mechanisms of Fibrinolysis and
Thrombolysis from Mathematical Modeling and Experiments', (with
Brittany E. Bannish, Irina N. Chernysh, James P. Keener, John W. Weisel), Scientific Reports, 2017, 7(1):6914.
doi: 10.1038/s41598-017-06383-w.
- 82.'A two-phase mixture model of platelet aggregation', (with
Jian Du), Mathematical Biology and Medicine, 2018, 35, 225-256.
- 81.'A microfluidic model of hemostasis sensitive to platelet
function and coagulation', (with R.M. Schoeman, K. Rana, N. Danes,
M. Lehmann, J.A. Di Paola, K. Leiderman, K.B. Neeves), Cellular
and Molecular Bioengineering, 2017, 10, 3-15.
- 80.'Elevated hematocrit promotes arterial thrombosis', (with
Bethany L. Walton, Marcus Lehmann, Tyler Skorczewski, Joan
D. Beckman, Lori A. Holle, Jeremy A. Cribb, Micah J. Mooberry,
Adam R. Wufsus, Brian C. Cooley, Jonathan W. Homeister, Michael
R. Falvo, Keith B. Neeves, Alisa S. Wolberg Blood, 2017, 129, 2537-2546.
- 79.'A model of venous thrombosis initiation' of platelets in
flowing blood', (with Priscilla Elizondo),
Biophysical Journal, 2016, 111, 2722-2734.
- 78.'Functional assay of antiplatelet drugs based on margination
of platelets in flowing blood', (with Colin D. Eichinger and
Vladimir Hlady), Biointerphases, 2016, 11, 029805.
- 77.'Synergy Between Tissue Factor and
Factor XIa in Initiating Coagulation', (with Karin Leiderman,
William Chang, and Mikhail Ovanesov),
Arteriosclerosis, Thrombosis, and Vascular Biology,
2016, 36, 2334-2345.
- 76.'Eulerian-Lagrangian Treatment of Non-dilute
Two-phase Gels', (with Victor Camacho and James P. Keener),
SIAM Journal on Applied Mathematics,
2016, 76, 341-367.
- 75.'Augmenting the Immersed Boundary Method with Radial Basis Functions (RBFs) for the
modeling of platelets in hemodynamic flows', (with Varun Shankar, Grady B. Wright, and Robert M. Kirby),
International Journal of Numerical Methods for Fluids,
2015, 79, 536-557.
- 74.'A Framework for Exploring the Post-gelation Behavior of Ziff and
Stell's Polymerization Models', (with James P. Keener),
SIAM Journal on Applied Mathematics, 2015, 75, 1346-68.
- 73.'MARS: An analytic framework of interface tracking via mapping and
adjusting regular semi-algebraic sets', (with Qinghai Zhang),
SIAM Journal on Numerical Analysis, 2016, 54, 530-560.
- 72.'A Radial Basis Function (RBF)-Finite Difference (FD) Method for Diffusion and
Reaction-Diffusion Equations on Surfaces', (with Varun Shankar,
Grady B. Wright and Robert M. Kirby),
Journal of Scientific Computings, 2016, 63, 745-768.
- 71.'Fluid Mechanics of Blood Clotting', (with Keith Neeves),
Annual Review of Fluid Mechanics, 2015, 47, 377-403.
- 70.'An Overview of Mathematical Modeling of Thrombus Formation Under
Flow', (with Karin Leiderman), Thrombosis Research, 2014,
133 Suppl 1, 512-14.
- 69.'Fourth-order interface tracking by an improved polygonal area
mapping (iPAM) method', (with Qinghai Zhang), SIAM Journal of
Scientific Computing, 2014, 36, A2369-A2400.
-
68.'A Radial Basis Function (RBF)-Finite Difference Method for the Simulation of
Reaction-Diffusion Equations on Stationary Platelets within the Augmented Forcing Method', (with
Varun Shankar, Grady B. Wright, and Robert M. Kirby)
International Journal of Numerical Methods for Fluids,
2014, 75, 1-22.
-
67.'The role of factor VIII and factor VIIa bypass treatment in modulating the
dynamics of thrombin and fibrin generation under flow', (with
A.A. Onasoga, K. Leiderman, M. Wang, M.U. Manco-Johnson, J.A. DiPaola, K.B. Neeves
PLOS One, 2013, 8(11), e75732.
-
66.'Multi-bond Models for Platelet Adhesion and Cohesion', (with Tyler
Skorczewski and Boyce Griffith),
Contemporary Mathematics, 2014, 628, 149-173.
-
65.'An Immersed Boundary Method for Two-fluid Mixtures', (with Jian Du
and Robert D. Guy),
Journal of Computational Physics, 2014, 262, 231-243.
-
64.'Platelet Motion near a Vessel Wall or Thrombus Surface in Two-dimensional Whole Blood
Simulations', (with Tyler Skorczewski and Lindsay Crowl Erickson),
Biophysical Journal, 2013, 104(8), 1764-72.
-
63.'An Interface-capturing Regularization Method for Solving the
Equations for Two-fluid Mixtures', (with Jian Du, Robert D. Guy,
Grady B. Wright, and James P. Keener),
Communications in Computational Physics, 2013, 14(5), 1322-1346.
-
62.'The Effect of Divalent vs. Monovalent ions on the Swelling of
Mucin-like Polyelectrolyte Gels: Governing Equations and Equilibrium
Analysis', (with Sarthok Sircar and James P. Keener),
Journal of Chemical Physics, 2013, 138, 014901.
-
61.'The Influence of Hindered Transport on the Development of Platelet
Thrombi Under Flow', (with Karin Leiderman),
Bulletin of Mathematical Biologyy, 2013, 75, 1255-1283.
-
60.'Modeling Fibrinolysis: A 3-Dimensional Stochastic Multiscale Model', (with
Brittany E. Bannish and James P. Keener),
Mathematical Medicine and Biology, 2014, 31, 17-44.
-
59.'Modeling Fibrinolysis: 1-Dimensional Continuum Models', (with
Brittany E. Bannish, James P. Keener, Michael Woodbury, and John W. Weisel),
Mathematical Medicine and Biology, 2014, 31, 45-64.
-
58.'A Study of Different Modeling Choices For Simulating Platelets Within the Immersed Boundary
Method' , (with Varun Shankar, Grady B. Wright and Robert M. Kirby),
Applied Numerical Mathematics, 2013, 63, 58-77.
-
57.'Low Reynolds-number Swimming in Viscous Two-Phase Fluids' , (with
Jian Du, James P. Keener, and Robert D. Guy),
Physical Review E, 2012, 85, 036304.
-
56.'Blood Clot Formation Under Flow: The Importance of Factor XI on Thrombin Production Depends Strongly on
Platelet Count' , (with Yasmeen H. Hussain and Karin Leiderman),
Biophysical Journal, 2012, 102, 10-18.
-
55.'A high-resolution finite-difference method for simulating two-fluid, viscoelastic
gel dynamics' , (with Grady B. Wright, Robert D. Guy, Jian Du),
Journal of Non-Newtonian Fluid Mechanics, 2011, 166, 1137-1157.
-
54.'Simulations of Chemical Transport and Reaction in a Suspension of Cells I: An Augmented Forcing Point Method for the
Stationary Case' , (with Linxing Yao),
International Journal of Numerical Methods for Fluids, 2011, DOI 0.1002/fld.2661.
-
53.'Mathematical Modeling of Blood Clotting' , Encyclopedia of Applied and Computational Mathematics, accepted.
-
52.'The Influence of the Standard Free Energy on Swelling Kinetics of Gels' , (with James P. Keener and Sarthok Sircar),
Physical Review E, 2011, 83, 041802.
-
51.'Kinetics of Swelling Gels' , (with James P. Keener and Sarthok Sircar),
SIAM Journal on Applied Mathematics, 2011, 71, 854-875.
-
50.'Analysis of Mechanisms for Platelet Near-wall Excess Under
Arterial Blood Flow Conditions' , (with Lindsay M. Crowl),
Journal of Fluid Mechanics, 2011, 676, 348-375.
-
49.'Toward an understanding of fibrin branching structure' , (with
James P. Keener),
Physical Review E, 2010, 81, 051922.
-
48.'Grow with the Flow: A spatial-temporal model of
coagulation and platelet deposition under flow' , (with Karin Leiderman),
Mathematical Medicine and Biology, 2011, 28, 47-84.
-
47.'A Cartesian Grid Method for Two-Phase Gel Dynamics on Irregular
Domains' , (with Jian Du),
International Journal for Numerical Methods in Fluids, 2011,
67, 1799-1817.
-
46.'Computational Model of Whole Blood Exhibiting Lateral
Platelet Motion Induced by Red Blood Cells' , (with Lindsay
M. Crowl),
International Journal for Numerical Methods in Biomedical Engineering, 2010,
26, 471-487.
-
45.'A Parallel Computatational Method for
Simulating Two-Phase Gel Dynamics' , (with Jian Du),
International Journal for Numerical Methods in Fluids, 2009,
60, 633-649.
-
44. 'An Efficient and Robust Method for Simulating Two-Phase Gel
Dynamics', (with Grady Wright and Robert Guy), SIAM
J. Sci. Comput., 2008, 30, 2535-2565.
-
43. 'The Effects of Spatial Inhomogeneities on Flow Through
the Endothelial Surface Layer, J. Theor. Biol.,
(with Karin Leiderman and Laura Miller), 2008, 252, 313-325.
-
42. 'A Comparison of Implicit Solvers for the Immersed Boundary
Equations', (with Elijah Newren, Robert Guy, and Robert
M. Kirby), Computer Methods in Applied Mechanics and
Engineering , 2008, 197, 2290-2304.
-
41.'A Wave-Propagation Algorithm for Viscoelastic Fluids
with Spatially and Temporally Varying Properties', (with Robert Guy),
Computer Methods in
Applied Mechanics and Engineering , 2008, 197, 2250-2264.
-
40. 'Immersed-Boundary-Based Models of Intravascular
Platelet Aggregation', (with Robert Guy), Computer Methods in
Applied Mechanics and Engineering , 2008, 197, 2087-2104.
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39. 'Cell-based Models of Blood Clotting', in Single Cell
Based Models in Biology and Medicine, A. Anderson, M. Chaplain,
and K. Rejniak (eds), Birkhauser, 2007.
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38. 'Unconditionally stable discretizations of the Immersed
Boundary Method', (with E. Newren, R. Guy and R. M. Kirby),
Journal of Computational Physics, 222(2007), 702-719.
-
37. 'Fibrin gel formation in a shear flow', (with R. Guy and
J. Keener), Mathematical Medicine and Biology, 24(2007),
111-130.
-
36. `Coagulation under flow: The influence of flow-mediated
transport on the initiation and inhibition of coagulation',
(with Nessy Tania), Pathophyiology of Haemostasis and
Thrombosis, 34, (2005), 91-108.
-
35. Stability of Approximate Projection Methods on
Cell-Centered Grids, (with Robert D. Guy), Journal of
Computational Physics, 203, (2005), 517-538.
-
34. `Platelet-Wall Interactions in Continuum Models of Platelet
Aggregation: Formulation and Numerical Solution', (with Robert
D. Guy), Mathematical Medicine and Biology, 21, (2004),
293-334.
-
33. `Computational Modeling of Blood Clotting: Coagulation and
Three-dimensional Platelet Aggregation', (with Haoyu Yu and Andrew
Kuharsky), Polymer and Cell Dynamics: Multicsale Modeling and
Numerical Simulations, Alt et al (Editors), Birkhaeuser-Verlag, Basel,
2003.
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32. `A Mathematical Study of Volume Shifts and Ionic Concentration Changes
During Ischemia and Hypoxia', (with Chung-Seon Yi, James Keener, and Charles
Peskin), J. Theor. Biol., 220, 2002, 83-106..
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31. `IBIS: Immersed Boundary and Interface Software Users Guide', (with David
Eyre), http://www.math.utah.edu/IBIS
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30. `IBIS: Immersed Boundary and Interface Software Package', (with David Eyre),
http://www.math.utah.edu/IBIS
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29. `Computational Engineering and Science Program at the University of Utah',
(with Carleton DeTar, Christopher R. Johnson, and Christopher A. Sikorski),
Proceedings of the 2001 International CES conference, San Francisco, May,
2001.
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28. `Probabilistic Modeling of Platelet Aggregation: Effects of Activation
Time and Receptor Occupancy', (with Robert D. Guy), J. Theor. Biol.,
219, (2002), 33-53.
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27. `Surface-mediated Control of Blood Coagulation: The Role of Binding Site
Densities and Platelet Deposition', (with Andrew Kuharsky), Biophysical
J., 80, (2001), 1050-1074.
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26. `Immersed Interface Methods for Neumann and Related Problems in Two and
Three Dimensions', (with James Keener),
SIAM J. Sci. Comput., 22,
(2000), 1630-1654.
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25. `Computational Methods for Continuum Models of Platelet Aggregation', (with
Nien-Tzu Wang), J. Comput. Phys., 151, (1999), 649-675.
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24. `Functional geometry of ciliated tentacular arrays in active suspension
feeders' (with David Eyre and Daniel Grunbaum), J. Exp. Biol., 201,
(1998), 2575-2589.
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23. `Membrane Binding-site Density Can Modulate Activation Thresholds in Enzyme
Systems', (with Andrew Kuharsky), J. Theor. Biol., 193, (1998),
1-18.
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22. `Modeling Biofilm Processes Using the Immersed Boundary Method', (with
Robert Dillon, Lisa Fauci, and Donald Gaver), J. Comput. Phys.,(129)(1996),
57-73.
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21. `Platelet Dense Granule Centralization and the Persistence of ADP Secretion'
(with Nien-Tzu Wang), Amer. Jrl. Physiology, (270) (Heart Circ.
Physiol. 39): H1131-H1140,(1996)
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20. `Expansion Behavior of Filtration Media', Technical Report to EIMCO Process
Equipment Company, November, 1994.
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19. `Optimal Smoothing in Function-transport Particle Methods for Diffusion
Problems' (with Robert Dillon), J. Comput. Phys.,(109)(1993), 155-163.
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18. `Activation Waves in a Model of Platelet Aggregation: Existence of Solutions
and Stability of Travelling Fronts' (with Victor Moll), Jrl. Math. Biol.,
(31)(1993), 675-701.
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17. `Truncated Newton Methods and the Modeling of Complex Immersed Elastic
Structures' (with Lisa Fauci), Comm. Pure Appld. Math., (46)(1993),
787-818.
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16. `Continuum Models of Platelet Aggregation: Mechanical Properties and Chemically-induced
Phase Transitions,' Fluid Dynamics in Biology, (A.Y. Cheer and C.P.
van Dam, Eds.), Contemporary Mathematics Series, American Mathematical
Society, Providence, RI, 1993.
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15. `Activation Waves and Threshold Phenomena in Platelet Aggregation' (with
Victor Moll), Partial Differential Equations (J.Weiner and J.Hale,
Eds.) Longman Scientific and Technical, Essex, England, 1992.
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14. `Continuum Models of Platelet Aggregation: Formulation and Mechanical Properties',
SIAM JAM, 52(1992), 1089-1110.
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13. `Particle-Method Solution of Two-Dimensional Convection-Diffusion Equations',
J. Comput. Phys., 100(1992), 1-16.
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12. `TNPACK - A Truncated Newton Minimization Package for Large-Scale Problems:
II. Implementation Examples' (with Tamar Schlick), ACM TOMS, 18(1992),
71-111.
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11. `TNPACK - A Truncated Newton Minimization Package for Large-Scale Problems:
I. Algorithm and Usage' (with Tamar Schlick). This is both a paper and
a software package, ACM TOMS, 18(1992), 46-70.
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10. `A Fast Numerical Method for Solving the Three-dimensional Stokes' Equations
in the Presence of Suspended Particles,' (with Charles S. Peskin), J.
Comput. Phys., 79(1988), 50-69.
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9. `Mathematical Models in Physiology' (with C. Peskin, D. McQueen, D. Tranchina,
H.M. Lacker and R. Novick), Proc. of Conference on Technological Advances
in Models for Biomedical Research (EMBS/IEEE), Boston, Nov. 1987.
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8. `Numerical Solution of the 3D Stokes' Equations in the Presence of Suspended
Particles,' (with Charles S. Peskin), Proceedings of the SIAM Multiphase
Flow Workshop, Leesburg, VA June 1986.
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7. `Can Presynaptic Depolarization Release Transmitter Without Calcium Influx?'
(with R. S. Zucker and L. Lando), J. Physiol., Paris, 81(1986),
237-245.
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6. `Relationship Between Transmitter Release and Presynaptic Calcium Influx
When Calcium Enters Through Discrete Channels,' (with Robert S. Zucker),
Proc. Nat. Acad. Sci., 83(1986), 3032-3036.
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5. `Mathematical and Computational Aspects of Blood Clotting,' Proceedings
of the 11th IMACS World Congress, Oslo, Norway, 1985.
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4. `Presynaptic Calcium Diffusion from Various Arrays of Single Channels:
Implications for Transmitter Release and Synaptic Facilitation,' (with
Robert S. Zucker), Biophysical J., 48(1985), 1003-1017.
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3. `A Mathematical Model and Numerical Study of Platelet Aggregation During
Blood Clotting,' Lectures in Applied Mathematics, 22, Large-scale Computations
in Fluid Mechanics, Proc. of the 15th AMS-SIAM Summer Seminar on Applied
Math., Scripps Institute of Oceanography, 1983, Vol. 1, pp. 119-148, American
Mathematical Society, Providence, RI, 1985.
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2. `A Mathematical Model and Numerical Method for Studying Platelet Adhesion
and Aggregation During Blood Clotting,' J. Comput. Phys., 56(1984),
111-134.
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1. `A Mathematical Model and Numerical Method for Studying Platelet Adhesion
and Aggregation in the Early Stages of Blood Clotting,' Ph.D. thesis, New
York University, 1982.