Computational approaches to studying thrombus development

Arteriosclerosis, Thrombosis, and Vascular Biology

Volumn 31, Issue 3, 2011, Pages 500-505

  Xu, Zhiliang ^a   Kamocka, Malgorzata ^b   Alber, Mark ^a,b   Rosen, Elliot D ^b  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

blood coagulation; blood flow; coagulation; computational model; platelets; stochastic multiscale model; thrombosis; thrombus development

Indexed keywords

FIBRIN;

ARTICLE; BLOOD CLOTTING; BLOOD FLOW; HEMOSTASIS; MATHEMATICAL MODEL; MONTE CARLO METHOD; ORDINARY DIFFERENTIAL EQUATION; PRIORITY JOURNAL; SHEAR RATE; SIGNAL TRANSDUCTION; SIMULATION; STOKESIAN DYNAMICS; THROMBOCYTE ACTIVATION; THROMBOCYTE ADHESION; THROMBOGENESIS; THROMBOSIS; VOIGT MODEL;

ANIMALS; BLOOD COAGULATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; FIBRIN; FIBRINOGEN; HUMANS; KINETICS; MODELS, CARDIOVASCULAR; PLATELET ACTIVATION; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP; THROMBOSIS;

EID: 79952179443     PISSN: 10795642     EISSN: None     Source Type: Journal    
DOI: 10.1161/ATVBAHA.110.213397     Document Type: Article

References (43)

1. Mann KG. Thrombin formation. Chest. 2003;124(suppl 3):4S-10S. (Pubitemid 37128430)
2. Brass LF, Stalker TJ, Zhu L, Woulfe DS. Signal transduction during platelet plug formation. In: Michelson AD, ed. Platelets, 2nd ed. Amsterdam: Elsevier; 2007;319-346.
3. Westrick RJ, Winn ME, Eitzman DT. Murine models of vascular thrombosis. Arterioscler Thromb Vasc Biol. 2007;27:2079-2093.
4. Hogan KA, Weiler H, Lord ST. Mouse models in coagulation. Thromb Haemost. 2002;87:563-574. (Pubitemid 34308430)
5. Lambert MP, Sachais BS, Kowalska MA. Chemokines and thrombogenicity. Thromb Haemost. 2007;97:722-729. (Pubitemid 46779957)
6. Hockin M, Jones K, Mann KG. A model for the stoichiometric regulation of blood coagulation. J Biol Chem. 2002;277:18322-18333. (Pubitemid 34952376)
7. Purvis JE, Chatterjee MS, Brass LF, Diamond SL. A molecular signaling model of platelet phosphoinositide and calcium regulation during homeostasis and P2Y1 activation. Blood. 2008;112:4069-4079.
8. Weisel JW, Nagaswami C. Computer modeling of fibrin polymerization kinetics correlated with electron microscope and turbidity observations: clot structure and assembly are kinetically controlled. Biophys J. 1992; 63:111-128.
9. Lawson JH, Kalafatis M, Stram S, Mann KG. A model for the tissue factor pathway to thrombin: I: an empirical study. J Biol Chem. 1994; 269:23357-23366. (Pubitemid 24283329)
10. Jones KC, Mann KG. A model for the tissue factor pathway to thrombin: II: a mathematical simulation. J Biol Chem. 1994;269: 23367-23373. (Pubitemid 24283330)
11. Lo K, Denney WS, Diamond SL. Stochastic modeling of blood coagulation initiation. Pathophysiol Haemost Thromb. 2005;34:80-90.
12. Kuharsky AL, Fogelson AL. Surface-mediated control of blood coagulation: the role of binding site densities and platelet deposition. Biophys J. 2001;80:1050-1074. (Pubitemid 32182136)
13. Fogelson AL, Tania N. Coagulation under flow: the influence of flowmediated transport on the initiation and inhibition of coagulation. Pathophysiol Haemost Thromb. 2005;34:91-108.
14. Bungay SD, Gentry PA, Gentry RD. A mathematical model of lipidmediated thrombin generation. Math Med Biol. 2003;20:105-129.
15. Luan D, Zai M, Varner JD. Computationally derived points of fragility of a human cascade are consistent with current therapeutic strategies. PLoS Comput Biol. 2007;3:1347-1359. (Pubitemid 47196175)
16. Yang Z, Mochalkin I, Doolittle RF. A model of fibrin formation based on crystal structures of fibrinogen and fibrin fragments complexed with synthetic peptides. Proc Natl Acad Sci U S A. 2000;97: 14156-14161. (Pubitemid 32016546)
17. Fogelson AL, Keener JP. Toward an understanding of fibrin branching structure. Phys Rev E Stat Nonlin Soft Matter Phys. 2010;81:051922.
18. Ziff RM. Kinetics of polymerization. J Stat Phys. 1980;23:241-263.
19. Ziff RM, Stell G. Kinetics of polymer gelation. J Chem Phys. 1980;73: 3492-3499.
20. Purvis JE, Radhakrishnan R, Diamond SL. Steady-state kinetic modeling constrains cellular resting states and dynamic behavior. PLoS Comput Biol. 2009;5:1-9.
21. Chatterjee MS, Purvis JE, Brass LF, Diamond SL. Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli. Nat Biotechnol. 2010;28:727-732.
22. Nesbitt WS, Westein E, Tovar-Lopez FJ, Tolouei E, Mitchell A, Fu J, Carberry J, Fouras A, Jackson SP. A shear gradient-dependent platelet aggregation mechanism drives thrombus formation. Nat Med. 2009;15: 665-675.
23. Gibbins JM. Platelet adhesion signalling and the regulation of thrombus formation. J Cell Sci. 2004;117:3415-3425. (Pubitemid 39206382)
24. Mori D, Yano K, Tsubota K, Ishikawa T, Wada S, Yamaguchi T. Simulation of platelet adhesion and aggregation regulated by fibrinogen and von Willebrand factor. Thromb Haemost. 2008;99:108-115.
25. Mody NA, King MR. Platelet adhesive dynamics: part I: characterization of platelet hydrodynamic collisions and wall effects. Biophys J. 2008;95: 2539-2555.
26. Mody NA, King MR. Platelet adhesive dynamics part II: high shearinduced transient aggregation via GPIba-vWF-GPIba bridging. Biophys J. 2008;95:2556-2574.
27. Mody NA, King MR. Three-dimensional simulations of a platelet-shaped spheroid near a wall in shear flow. Phys Fluids. 2005;17:113302-113301-113302- 12.
28. Mody NA, Lomakin O, Doggett TA, Diacovo TG, King MR. Mechanics of transient platelet adhesion to von Willebrand factor under flow. Biophys J. 2005;88:1432-1443. (Pubitemid 40975970)
29. Lobanov AI, Starozhilova TK. The effect of convective flows on blood coagulation processes. Pathophysiol Haemost Thromb. 2005; 34:121-134.
30. Anand M, Rajagopal K, Rajagopal KR. A model for the formation and lysis of blood clots. Pathophysiol Haemost Thromb. 2005;34: 109-120.
31. Wang J, Slattery MJ, Hoskins MH, Liang S, Dong C, Du Q. Monte Carlo simulation of heterotypic cell aggregation in nonlinear shear flow. Math Biosci Eng. 2006;3:683-696.
32. Laurenzi IJ, Diamond SL. Monte Carlo simulation of the heterotypic aggregation kinetics of platelets and neutrophils. Biophys J. 1999;77: 1733-1746. (Pubitemid 29407344)
33. Pivkin IV, Richardson PD, Karniadakis G. Blood flow velocity effects and role of activation delay time on growth and form of platelet thrombi. Proc Natl Acad Sci U S A. 2006;103:17164-17169. (Pubitemid 44788940)
34. Begent N, Born GV. Growth rate in vivo of platelet thrombi, produced by iontophoresis of ADP, as a function of mean blood flow velocity. Nature. 1970;227:926-930.
35. Fogelson AL, Guy RD. Immersed-boundary-type models of intravascular platelet aggregation Comput Methods. Appl Mech Eng. 2008;197: 2087-2104. (Pubitemid 351509247)
36. Xu Z, Chen N, Kamocka MM, Rosen ED, Alber MS. Multiscale model of thrombus development. J R Soc Interface. 2008;5:705-722.
37. Xu Z, Chen N, Shadden S, Marsden JE, Kamocka MM, Rosen ED, Alber MS. Study of blood flow impact on growth of thrombi using a multiscale model. Soft Matter. 2009;5:769-779.
38. Xu Z, Lioi J, Mu J, Kamocka MM, Liu X, Chen DZ, Rosen ED, Alber MS. A multiscale model of venous thrombus formation with surface-mediated control of blood coagulation cascade. Biophys J. 2010;98:1723-1732.
39. Xu Z, Mu J, Liu X, Kamocka MM, Rosen ED, Chen DZ, Alber MS. Combined experimental and simulation study of blood clot formation. In: Mota M, ed. Proceedings of the 2009 IEEE Toronto International Conference- Science and Technology for Humanity TIC-STH. Piscataway, NJ: Institute of Electrical and Electronics Engineers, 2009:357-362.
40. Alber M, Chen N, Glimm T, Lushnikov P. Two-dimensional multiscale model of cell motion in a chemotactic field. In: Anderson ARA, Chaplain MAJ, Rejniak KA, eds. Single Cell Based Models in Biology and Medicine. Basel, Switzerland: Birkhauser-Verlag; 2007;53-76.
41. Glazier JA, Graner F. Simulation of the differential adhesion driven rearrangement of biological cells. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993;47:2128-2154.
42. Graner FMC, Glazier JA. Simulation of biological cell sorting using a two-dimensional extended Potts model. Phys Rev Lett. 1992;69: 2013-2016.
43. Leiderman K, Fogelson AL. Grow with the flow: a spatial-temporal model of platelet deposition and blood coagulation under flow. [published online ahead of print May 3, 2010] Math Med Biol. doi: 10.1093/ imammb/dqq005