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.
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.
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.
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..
31. `IBIS: Immersed Boundary and Interface Software Users Guide', (with David Eyre), http://www.math.utah.edu/IBIS
30. `IBIS: Immersed Boundary and Interface Software Package', (with David Eyre), http://www.math.utah.edu/IBIS
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.
28. `Probabilistic Modeling of Platelet Aggregation: Effects of Activation Time and Receptor Occupancy', (with Robert D. Guy), J. Theor. Biol., 219, (2002), 33-53.
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.
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.
25. `Computational Methods for Continuum Models of Platelet Aggregation', (with Nien-Tzu Wang), J. Comput. Phys., 151, (1999), 649-675.
24. `Functional geometry of ciliated tentacular arrays in active suspension feeders' (with David Eyre and Daniel Grunbaum), J. Exp. Biol., 201, (1998), 2575-2589.
23. `Membrane Binding-site Density Can Modulate Activation Thresholds in Enzyme Systems', (with Andrew Kuharsky), J. Theor. Biol., 193, (1998), 1-18.
22. `Modeling Biofilm Processes Using the Immersed Boundary Method', (with Robert Dillon, Lisa Fauci, and Donald Gaver), J. Comput. Phys.,(129)(1996), 57-73.
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)
20. `Expansion Behavior of Filtration Media', Technical Report to EIMCO Process Equipment Company, November, 1994.
19. `Optimal Smoothing in Function-transport Particle Methods for Diffusion Problems' (with Robert Dillon), J. Comput. Phys.,(109)(1993), 155-163.
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.
17. `Truncated Newton Methods and the Modeling of Complex Immersed Elastic Structures' (with Lisa Fauci), Comm. Pure Appld. Math., (46)(1993), 787-818.
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.
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.
14. `Continuum Models of Platelet Aggregation: Formulation and Mechanical Properties', SIAM JAM, 52(1992), 1089-1110.
13. `Particle-Method Solution of Two-Dimensional Convection-Diffusion Equations', J. Comput. Phys., 100(1992), 1-16.
12. `TNPACK - A Truncated Newton Minimization Package for Large-Scale Problems: II. Implementation Examples' (with Tamar Schlick), ACM TOMS, 18(1992), 71-111.
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.
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.
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.
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.
7. `Can Presynaptic Depolarization Release Transmitter Without Calcium Influx?' (with R. S. Zucker and L. Lando), J. Physiol., Paris, 81(1986), 237-245.
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.
5. `Mathematical and Computational Aspects of Blood Clotting,' Proceedings of the 11th IMACS World Congress, Oslo, Norway, 1985.
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.
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.
2. `A Mathematical Model and Numerical Method for Studying Platelet Adhesion and Aggregation During Blood Clotting,' J. Comput. Phys., 56(1984), 111-134.
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.