Aaron Fogelson

45. 'An Efficient and Robust Method for Simulating TwoPhase 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 WavePropagation Algorithm for Viscoelastic Fluids
with Spatially and Temporally Varying Properties', (with Robert Guy),
Computer Methods in
Applied Mechanics and Engineering , 2007, to appear.

41. 'ImmersedBoundaryBased Models of Intravascular
Platelet Aggregation', (with Robert Guy), Computer Methods in
Applied Mechanics and Engineering , 2007, to appear.

40. 'Cellbased 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 Reexamination 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), 702719.

37. 'Fibrin gel formation in a shear flow', (with R. Guy and
J. Keener), Mathematical Medicine and Biology, 24(2007),
111130.

36. `Coagulation under flow: The influence of flowmediated
transport on the initiation and inhibition of coagulation',
(with Nessy Tania), Pathophyiology of Haemostasis and
Thrombosis, 34, (2005), 91108.

35. Stability of Approximate Projection Methods on
CellCentered Grids, (with Robert D. Guy), Journal of
Computational Physics, 203, (2005), 517538.

34. `PlateletWall Interactions in Continuum Models of Platelet
Aggregation: Formulation and Numerical Solution', (with Robert
D. Guy), Mathematical Medicine and Biology, 21, (2004),
293334.

33. `Computational Modeling of Blood Clotting: Coagulation and
Threedimensional Platelet Aggregation', (with Haoyu Yu and Andrew
Kuharsky), Polymer and Cell Dynamics: Multicsale Modeling and
Numerical Simulations, Alt et al (Editors), BirkhaeuserVerlag, Basel,
2003.

32. `A Mathematical Study of Volume Shifts and Ionic Concentration Changes
During Ischemia and Hypoxia', (with ChungSeon Yi, James Keener, and Charles
Peskin), J. Theor. Biol., 220, 2002, 83106..

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), 3353.

27. `Surfacemediated Control of Blood Coagulation: The Role of Binding Site
Densities and Platelet Deposition', (with Andrew Kuharsky), Biophysical
J., 80, (2001), 10501074.

26. `Immersed Interface Methods for Neumann and Related Problems in Two and
Three Dimensions', (with James Keener),
SIAM J. Sci. Comput., 22,
(2000), 16301654.

25. `Computational Methods for Continuum Models of Platelet Aggregation', (with
NienTzu Wang), J. Comput. Phys., 151, (1999), 649675.

24. `Functional geometry of ciliated tentacular arrays in active suspension
feeders' (with David Eyre and Daniel Grunbaum), J. Exp. Biol., 201,
(1998), 25752589.

23. `Membrane Bindingsite Density Can Modulate Activation Thresholds in Enzyme
Systems', (with Andrew Kuharsky), J. Theor. Biol., 193, (1998),
118.

22. `Modeling Biofilm Processes Using the Immersed Boundary Method', (with
Robert Dillon, Lisa Fauci, and Donald Gaver), J. Comput. Phys.,(129)(1996),
5773.

21. `Platelet Dense Granule Centralization and the Persistence of ADP Secretion'
(with NienTzu Wang), Amer. Jrl. Physiology, (270) (Heart Circ.
Physiol. 39): H1131H1140,(1996)

20. `Expansion Behavior of Filtration Media', Technical Report to EIMCO Process
Equipment Company, November, 1994.

19. `Optimal Smoothing in Functiontransport Particle Methods for Diffusion
Problems' (with Robert Dillon), J. Comput. Phys.,(109)(1993), 155163.

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), 675701.

17. `Truncated Newton Methods and the Modeling of Complex Immersed Elastic
Structures' (with Lisa Fauci), Comm. Pure Appld. Math., (46)(1993),
787818.

16. `Continuum Models of Platelet Aggregation: Mechanical Properties and Chemicallyinduced
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), 10891110.

13. `ParticleMethod Solution of TwoDimensional ConvectionDiffusion Equations',
J. Comput. Phys., 100(1992), 116.

12. `TNPACK  A Truncated Newton Minimization Package for LargeScale Problems:
II. Implementation Examples' (with Tamar Schlick), ACM TOMS, 18(1992),
71111.

11. `TNPACK  A Truncated Newton Minimization Package for LargeScale Problems:
I. Algorithm and Usage' (with Tamar Schlick). This is both a paper and
a software package, ACM TOMS, 18(1992), 4670.

10. `A Fast Numerical Method for Solving the Threedimensional Stokes' Equations
in the Presence of Suspended Particles,' (with Charles S. Peskin), J.
Comput. Phys., 79(1988), 5069.

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),
237245.

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), 30323036.

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), 10031017.

3. `A Mathematical Model and Numerical Study of Platelet Aggregation During
Blood Clotting,' Lectures in Applied Mathematics, 22, Largescale Computations
in Fluid Mechanics, Proc. of the 15th AMSSIAM Summer Seminar on Applied
Math., Scripps Institute of Oceanography, 1983, Vol. 1, pp. 119148, 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),
111134.
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.