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Systems Biology

The Diamond laboratory has worked on a variety of numerical problems motivated by reaction-transport processes in cardiovascular biology:

  • Moving front systems in eroding biopolymers
  • Two-body hydrodynamic collisions
  • Heterotypic aggregation-fragmentation processes
  • Stochastic kinetics during platelet and neutrophil adhesion
  • Stochastic kinetics of blood coagulation
  • P2Y1 - Phosphoinositides Model
  • Platelet-Plasma Clotting Model
  • Pairwise Agonist Scanning
  • LKMC for reactive platelet flow and deposition



1. 1996

Anand S, Diamond SL. Computer simulation of systemic circulation and clot lysis dynamics during thrombolytic therapy that accounts for inner clot transport and reaction. Circulation 1996; 94 (4): 763-774


Vaidya DS, Nitsche JM, Diamond SL, Kofke DA. Convection-diffusion of solutes in media with piecewise constant transport properties. Chemical Engineering Science 1996; 51 (24): 5299-5312


Vaidya DS, Nitsche JM, Diamond SL, Kofke DA. Convection-diffusion of solutes in dynamic media. Adsorption-Journal of the International Adsorption Society 1996; 3 (1): 41-54

4. 1997

Tandon P, Diamond SL. Hydrodynamic effects and receptor interactions of platelets and their aggregates in linear shear flow. Biophys J 1997; 73 (5): 2819-2835


Vaidya DS, Diamond SL, Nitsche JM, Kofke DA. Potential for use of liquid crystals as dynamically tunable electrophoretic media. Aiche Journal 1997; 43 (5): 1366-1368


Vaidya DS, Nitsche JM, Diamond SL, Kofke DA. Perturbation solution to the convection-diffusion equation with moving fronts. Aiche Journal 1997; 43 (3): 631-644

7. 1998

Tandon P, Diamond SL. Kinetics of beta2-integrin and L-selectin bonding during neutrophil aggregation in shear flow. Biophys J 1998; 75 (6): 3163-3178

8. 1999

Laurenzi IJ, Diamond SL. Monte Carlo simulation of the heterotypic aggregation kinetics of platelets and neutrophils. Biophys J 1999; 77 (3): 1733-1746

9. 2002

Laurenzi IJ, Bartels JD, Diamond SL. A general algorithm for exact simulation of multicomponent aggregation processes. Journal of Computational Physics 2002; 177 (2): 418-449

10. 2003

Doggett TA, Girdhar G, Lawshe A, Miller JL, Laurenzi IJ, Diamond SL, Diacovo TG. Alterations in the intrinsic properties of the GPIb?-VWF tether bond define the kinetics of the platelet-type von Willebrand disease mutation, Gly233Val. Blood 2003; 102 (1): 152-160


Laurenzi IJ, Diamond SL. Kinetics of random aggregation-fragmentation processes with multiple components. Phys Rev E Stat Nonlin Soft Matter Phys 2003; 67 (5 Pt 1): 051103

12. 2005

Lo K, Denney WS, Diamond SL. Stochastic modeling of blood coagulation initiation. Pathophysiol Haemost Thromb 2005; 34 (2-3): 80-90

13. 2008

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 (10): 4069-4079

14. 2009

Diamond SL. Systems biology to predict blood function. J Thromb Haemost 2009; 7 Suppl 1 : 177-180


Flamm MH, Diamond SL, Sinno T. Lattice kinetic Monte Carlo simulations of convective-diffusive systems. J Chem Phys 2009; 130 (9): 094904


Purvis JE, Radhakrishnan R, Diamond SL. Steady-state kinetic modeling constrains cellular resting states and dynamic behavior. PLoS Comput Biol 2009; 5 (3): e1000298

17. 2010

Chatterjee MS, Denney WS, Jing HY, Diamond SL. Systems Biology of Coagulation Initiation: Kinetics of Thrombin Generation in Resting and Activated Human Blood. Plos Computational Biology 2010; 6 : 9


Chatterjee MS, Purvis JE, Brass LF, Diamond SL. Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli. Nat Biotechnol 2010; 28 (7): 727-732


Neeves KB, Illing DA, Diamond SL. Thrombin flux and wall shear rate regulate fibrin fiber deposition state during polymerization under flow. Biophys J 2010; 98 (7): 1344-1352

20. 2011

Colace T, Falls E, Zheng XL, Diamond SL. Analysis of morphology of platelet aggregates formed on collagen under laminar blood flow. Ann Biomed Eng 2011; 39 (2): 922-929


Flamm MH, Sinno T, Diamond SL. Simulation of aggregating particles in complex flows by the lattice kinetic Monte Carlo method. J Chem Phys 2011; 134 (3): 034905

22. 2012

Flamm MH, Colace TV, Chatterjee MS, Jing H, Zhou S, Jaeger D, Brass LF, Sinno T, Diamond SL. Multiscale prediction of patient-specific platelet function under flow. Blood 2012; 120 (1): 190-198


Flamm MH, Diamond SL. Multiscale systems biology and physics of thrombosis under flow. Ann Biomed Eng 2012; 40 (11): 2355-2364


King MR, Diamond SL. Multiscale systems biology: a special issue devoted to understanding biology and medicine across multiple scales. Ann Biomed Eng 2012; 40 (11): 2293-2294


Muthard RW, Diamond SL. Blood clots are rapidly assembled hemodynamic sensors: flow arrest triggers intraluminal thrombus contraction. Arterioscler Thromb Vasc Biol 2012; 32 (12): 2938-2945


Welsh JD, Colace TV, Muthard RW, Stalker TJ, Brass LF, Diamond SL. Platelet-targeting sensor reveals thrombin gradients within blood clots forming in microfluidic assays and in mouse. J Thromb Haemost 2012; :

27. 2013

Diamond SL, Purvis J, Chatterjee M, Flamm MH. Systems biology of platelet-vessel wall interactions. Front Physiol 2013; 4 : 229


Stalker TJ, Traxler EA, Wu J, Wannemacher KM, Cermignano SL, Voronov R, Diamond SL, Brass LF. Hierarchical organization in the hemostatic response and its relationship to the platelet-signaling network. Blood 2013; 121 (10): 1875-1885


Voronov RS, Stalker TJ, Brass LF, Diamond SL. Simulation of intrathrombus fluid and solute transport using in vivo clot structures with single platelet resolution. Ann Biomed Eng 2013; 41 (6): 1297-1307



spacer Institute of Medicine & Engineering (IME) spacer|spacer Biotech spacer|spacer BE spacer|spacer CBE spacer|spacer EMTM spacer|spacer Penn Center for Molecular Discovery spacer|spacer Blood Systems Biology spacer

    Institute for Medicine & Engineering (IME)
    3340 Smith Walk
    1020 Vagelos Research Laboratories
    University of Pennsylvania
    Philadelphia, PA 19104-6383
    Lab No.: (215) 573-5704
    Fax: (215) 573-7227