mypapers

Aaron Fogelson

45. 'An Efficient and Robust Method for Simulating Two-Phase Gel Dynamics', (with Grady Wright and Robert Guy), SIAM J. Sci. Comput., under revision.
44. 'The Effects of Spatial Inhomogeneities on Flow Through the Endothelial Surface Layer, J. Theor. Biol., (with Karin Leiderman and Laura Miller), under revision.
43. '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 , 2007, to appear.
42.'A Wave-Propagation Algorithm for Viscoelastic Fluids with Spatially and Temporally Varying Properties', (with Robert Guy), Computer Methods in Applied Mechanics and Engineering , 2007, to appear.
41. 'Immersed-Boundary-Based Models of Intravascular Platelet Aggregation', (with Robert Guy), Computer Methods in Applied Mechanics and Engineering , 2007, to appear.
40. '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.
39. 'A Re-examination of Molecular Bond Breaking Under Dynamic Forcing', (with N. Hancock, J. Keener, R. Litvinov, and J. Weisel), under revision.
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.