Biomedical Multiscale Microfluidic Modeling

  1. Y. Deng, D. P. Papageorgiou, X. Li, N. Perakakis, C. S. Mantzoros, M. Dao, G. E. Karniadakis, Quantifying Fibrinogen-Dependent Aggregation of Red Blood Cells in Type 2 Diabetes Mellitus, Biophysical Journal, Volume 119, Issue 5, 1, 2020.
  2. K. Sampani, H. Li, X. Zheng, D. Papageorgiou, M. O. Bernabeu, W. Fickweiler, L. P. Aiello; G. Karniadakis, J. K. Sun, Computational fluid dynamics (CFD) estimation of thrombus formation in diabetic retinal microaneurysms (MAs), Investigative Ophthalmology & Visual Science June 2020, Vol. 61, 5023, Issue 7, June 2020.
  3. Y. Wang, Z. Li, J. Ouyang, G. E. Karniadakis, Controlled release of entrapped nanoparticles from thermoresponsive hydrogels with tunable network characteristics, Royal Society of Chemistry, DOI: 10.1039/D0SM00207K, April 2020.
  4. X Zheng, A Yazdani, H Li, JD Humphrey, GE Karniadakis, A three-dimensional phase-field model for multiscale modeling of thrombus biomechanics in blood vessels, PLoS Computational Biology 16 (4), e1007709, 2020.
  5. K. Kim, C. Kim, G.E. Karniadakis, E.K. Lee, J. Kozak, “Density-dependent finite system-size effects in equilibrium molecular dynamics estimation of shear viscosity: Hydrodynamics and configurational study”, The Journal of Chemical Physics (Vol. 151, Issue 10), 2019.
  6. L.Lu, Z. Li, H. Li, X. Li, P.G. Vekilov, G.E. Karniadakis, “Quantitive prediction of erythrocyte sickling for the development of advanced sickle cell therapies”, Science Advances 5 (8), eaax3905, 2019.
  7. M. Yin, A. Yazdani, G.E. Karniadakis, “One-dimensional modeling of fractional flow reserve in coronary artery disease: Uncertainty quantification and Bayesian optimization”, Computer Methods in Applied Mechanics and Engineering, 2019.
  8. K.S. Kim, M.H Han, C. Kim, Z. Li, G.E. Karniadakis, E.K. Lee, “Nature of intrinsic uncertainties in equilibrium molecular dynamics estimation of shear viscosity for simple and complex fluids”, The Journal of Chemical Physics 149 (4), 044510, 2019.
  9. K. Zhang, Z. Li, M. Maxey, S. Chen, G.E. Karniadakis, “Self-cleaning of hydrophobic rough surfaces by coalescence-induced wetting transition.” Langmuir 35 (6), 2431-2442, 2019
  10. Y. Deng, D.P. Papageorgiou, H.Y Chang, S.Z. Abidi, X. Li, M. Dao, G.E. Karniadakis, “Quantifying shear-induced deformation and detachment of individual adherent sickle red blood cells”, Biophysical Journal 116 (2), 360-371, 2019.
  11. Y. Wang, Z. Li, J. Xu, C. Yang, G.E. Karniadakis, “Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces.” Soft Matter 15 (8), 1747-1757, 2019.
  12. H. Li, L. Lu, X. Li, P. A. Buffet, M. Dao, G. E. Karniadakis, S. Suresh, “Mechanics of diseased red blood cells in human spleen and consequences for hereditary blood disorders.” PNAS 2018,201806501; DOI:10.1073/pnas.1806501115.
  13. D. P. Papageorgiou, S. Z. Albidi, H.U. Chang, X. Li, G. J. Kato, G. E. Karniadakis, S. Suresh, M. Dao, “Simultaneous polymerization and adhesion under hypoxia in sickle cell disease.” PNAS 2018,201807405; DOI:10.1073/pnas.1807405115
  14. Y. Yu, F. F. Bargos, H. You, M. L. Parks, M. L. Bittencourt, G. E. Karniadakis, “A partioned coupling framework for peridynamics and classical theory: Analysis and simulations.” Comput. Methdos Appl. Mech. Engrg. 2018
  15. H. Li, J. Tang, t. T. Chu, R. Naidu, L. Lu, R. Chandramohanadas, M. Dao, G. E. Karniadakis, “Cytoskeleton Remodeling Induces Membrane Stiffness and Stability Changes of Maturing Reticulocytes.” Biophys. J. 114, 2014-2023, 2018.
  16. A. Yazdani, H. Li, M. R. Bersi, P. DiAchille, J. Insley, J. D. Humphrey, G. E. Karniadakis, “Data-driven Modeling of Hemodynamics and its Role on Thrombus Size and Shape in Aortic Dissections.” Scientific Reports, 8:2515, 2018.
  17. Z. Li, X. Bian, Y. H. Tang, G. E. Karniadakis, “A dissipative particle dynamics method for arbitrarily complex geometries.”  J. Comp. Phys. 355: 534-547, 2018.
  18. D. P. Papageorgiou, S. Z. Abidi, H.-Y. Chang, X. J. Li, G. J. Kato, G. E. Karniadakis, M. Dao, and S. Suresh, “Simultaneous polymerization and adhesion under hypoxia in sickle cell anemia.” P.N.A.S. U.S.A. 2018, in revision.
  19. H. Li, L. Lu, X. Li, P. Buffet, M. Dao, G. E. Karniadakis, and S. Suresh, “Mechanics of diseased red blood cells in human spleen and consequences for hereditary blood disorders.” P.N.A.S. U.S.A. 2018, in revision.
  20. X. Li, H. Li, H.-Y. Chang, G. Lykotrafitis, and G. E. Karniadakis, “Computational biomechanics of human red blood cells in hematological disorders.” J. Biomech. Eng. 139, 020804, 2017.
  21. Y. Yoshimoto, Z. Li, L. Kinefuchi and G.E. Karniadakis. “Construction of non-Markovian coarse-grained models employing the Mori-Zwanzig formalism and iterative Boltzmann inversion.” J. Chem. Phys. 147: 244110. 2017.  (Selected as Editor’s Pick featured article).
  22. L. Lu, H Li, X. Bian, X. Li, G.E. Karniadakis, “Mesoscopic adaptive resolution scheme: toward understanding of interactions between sickle cell fibers.” Biophys. J. (COVER).113(1):48-59. 2017.
  23. Y. Tang, L. Lu, H. Li, C. Evangelinos, L. Grinberg, V. Sachdeva, G. E. Karniadakis, “OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution.” Biophys. J. 112:2030-2037, 2017.
  24. A. L. Blumers, Y. H. Tang, Z. Li, X. Li, G. E. Karniadakis, “GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics.” Comp. Phys. Comm. 2017.
  25. M. Deng, W. Pan, G. E. Karniadakis, “Anisotropic single-particle dissipative particle dynamics model.” J. Comp. Phys. 336; 481-491, 2017.
  26. H.-Y. Chang, X. Li, and G. E. Karniadakis*, “Modeling of biomechanics and biorheology of red blood cells in type-2 diabetes mellitus.” Biophys. J. 113, 481-490, 2017. (BJ Highlighted Article)
  27. X. Li, E. Du, M. Dao, S. Suresh, and G. E. Karniadakis, “Patient-specific modeling of individual sickle cell behavior under transient hypoxia.” PLOS Comput. Biol. 13, e1005426, 2017. (Highlighted on Biophysical Society Blog).
  28. X. Li, M. Dao, G. Lykotrafitis, and G. E. Karniadakis, “Biomechanics and biorheology of red blood cells in sickle cell anemia.” J. Biomech. 50, 34-41, 2017.(Quarterly Most-downloaded Articles, as of June 2017)
  29. A. Yazdani, H. Li, J. D. Humphrey, G. E. Karniadakis, “A General Shear-Dependent Model for Thrombus Formation.” PLoS Comput. Biol. 13(1): e1005291, 2017. doi:10.1371/journal.pcbi.1005291.
  30. Z. Li, H. S. Lee, E. Darve, G. E. Karniadakis, “Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts.” J. Chem. Phys. 146, 2017. DOI:10.1063/1.4973347
  31. H. Lei, X. Yang, Z. Li, G. E. Karniadakis, “Systematic parameter inference in stochastic mesoscopic modeling.” J. Comput. Phys. 330, 571-593, 2017. doi:10.1016j.jcp.2016.10.029.
  32. H. Chang, X. Li, H. Li, G. E. Karniadakis, “MD/DPD Multiscale framework for predicting morphology and stresses of red blood cells in health and disease.” PLOS Comp. Bio. 2016 DOI:10.1371/journal.pcbi.1005173.
  33. X. Bian, M. Deng, Y.H. Tang and G.E. Karniadakis, “Analysis of hydrodynamic fluctuations in heterogeneous adjacent multidomains in shear flow.” Phys. Rev. E. 93(3), 033312, 2016.
  34. X. Bian, C. Kim and G.E. Karniadakis, “111 years of Brownian motion.” Soft Matter, 12, 6331-6346, 2016.
  35. P. Perdikaris, L. Grinberg, G. E. Karniadakis. “Multiscale modeling and simulation of brain blood flow.” Phys. Fluids. 28(2), 2016.
  36. A. Yazdani, M. Deng, B. Caswell and G.E. Karniadakis, “Flow in complex domains simulated by Dissipative Particle Dynamics driven by geometry-specific body-forces.” J. Comp. Phys. 305, 906-920, 2016.
  37. A. Witthoft, A. Yazdani, Z. Peng, C. Bellini, J.D. Humphrey and G.E. Karniadakis, “A discrete particle model of a multi-layered fiber-reinforced arterial wall.” J. Roy. Soc. Interface, 13, 20150964, 2016.
  38. A. Yazdani and G.E. Karniadakis, “Sub-cellular modeling of platelet transport in blood flow through microchannels with constriction.” Soft Matter, 12, 4339, 2016.
  39. X.J. Li, E. Du, H. Lei, Y.-H. Tang, M. Dao, S. Suresh and G.E. Karniadakis, “Patient-specific modeling and predicting blood viscosity in sickle -cell anemia.” Interface Focus, 6, 20150065, DOI: 10.1098/rsfs.2015.0065 2016.
  40. Y.-H. Tang, Z. Li, X.J. Li, M.G. Deng and G.E. Karniadakis, “Non-equilibrium dynamics of vesicles and micelles by self-assembly of block copolymers with double thermoresponsivity.” Macromolecules, 59, 2895-2903, 2016.
  41. A. Yazdani, X. J. Li, G. E. Karniadakis, “Dynamic and rheological properties of soft biological cell suspensions.” Rheol Acta. 55(6), 433-449, 2016. DOI 10.1007/s00397-015-0869-4.
  42. L. Lu, X.J. Li, P.G. Vekilov and G.E. Karniadakis, “Probing the twisted structure of sickle hemoglobin fibers via particle simulations.” Biophys. J. 110, 2085-2093, 2016.
  43. X. Bian, Z. Li and G.E. Karniadakis, “Multi-resolution flow simulations by smoothed particle hydrodynamics via domain decomposition.” J. Comput. Phys. 297, 131-155, 2015.
  44. C. Kim and G.E. Karniadakis, “Brownian motion of a Rayleigh Particle Confined in a Channel: A Generalized Langevin Equation Approach.” J. of Stat Phys. 158(5), 1100-1125, 2015.
  45. X. Bian, Z. Li, M. Deng and G.E. Karniadakis, “Fluctuating hydrodynamics in periodic domains and heterogeneous adjacent multidomains: Thermal equilibrium.” Phys. Rev. E. 92(5), 053302, 2015.
  46. Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis, “Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems,” J. Chem. Phys., 143, 014101, 2015.
  47. M. K. Rausch, G. E. Karniadakis, J. D. Humphrey, “Modeling Soft Tissue Damage and Failure Using a Combined Particle/Continuum Approach.” Biomech Model Mechanobiol. 2016. DOI 10.1007/s10237-016-0814-1.
  48. Z. Li, X. Bian, X. Yang, G. E. Karniadakis, “A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization.” J.  Chem. Physics. 145, 044102, 2016. doi.org/10.1063/1.4959121.
  49. P. Perdikaris, L. Grinberg, G. E. Karniadakis, “An effective fractal-tree closure model for simulating blood flow in large arterial networks.” Ann. Biomed. Eng. 1-11, 2015.
  50. Z. Li, X. Bian, X. Li and G.E. Karniadakis, “Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.”J. Chem. Phys. 143, 243128, 2015.
  51. Z. Li, Y-H. Tang, X. Li and G.E. Karniadakis, “Mesoscale modeling of phase transition dynamics of thermoresponsive polymers.” Chem. Commun. 51, 11038-11040, 2015.
  52. K. Lykov, X. Li, H. Lei, I.V. Pivkin and G.E. Karniadakis, “Inflow/outflow boundary conditions for particle-based blood flow simulations: Application to arterial bifurcations and trees.” PLOS Comput. Biol. 11(8): e1004410, 2015.
  53. M. Deng, L. Grinberg, B. Caswell and G.E. Karniadakis, “Effects of thermal noise on the transitional dynamics of an inextensible elastic filament in stagnation flow.” Soft Matter, 11, 4962-4972, 2015.
  54. M. Deng and G.E. Karniadakis, “Electrostatic correlations near charged planar surfaces.” J. Chem. Phys. 141, 094703, 2014.
  55. P. Perdikaris, G. E. Karniadakis, “Fractional-order viscoelasticity in one-dimensional blood flow models.” Ann. Biomed. End. 42 1012-1023, 2014.
  56. Z. Li, X. Bian, B. Caswell, G. E. Karniadakis, “Construction of dissipative particle dynamics models for complex fluids via the Mori-Zwannzig formulation.” Soft Matter. 2014, DOI: 10.1039/C4SM01387E.
  57. C. Kim, G. E. Karniadakis, “Time correlation functions of Brownian motion and evaluation of friction coefficent in the near-Brownian-limt regime.” Multiscale Model. Simul. 12(1), 225-258, 2014.
  58. Z. Li, Y-H. Tang, H. Lei, B. Caswell, G. E. Karniadakis, “Energy-conserving dissipative particle dynamics with temperature-dependent properties.” J. Comput. Phys. 265, 113-127, 2014.
  59. M. Deng, G. E. Karniadakis, “Electrostatic correlations near charged planar surfaces.” J. Chemical Physics, 141, 094703, 2014.
  60. X. Li, Z. Peng, H. Lei*, M. Dao and G.E. Karniadakis, “Probing red cell mechanics, rheology and dynamics with a two-component multiscale model.” Phil. Trans. Royal Society A. 372, 20130389, 2014.
  61. D. Fedosov*, M. Dao, G.E. Karniadakis and S. Suresh, “Computational biorheology of human blood flow in health and disease.” Ann. Biomed. Engin. 42:368-387, 2014.
  62. X. Li, Y.-H. Tang*, H. J. Liang, and G.E. Karniadakis, “Large-scale dissipative particle dynamics simulations of self-assembled amphiphilic systems.” Chem. Commun. 50, 8306-8308. 2014.
  63. M. Deng* and G.E. Karniadakis, “Coarse-grained modeling of protein unfolding dynamics.” Multiscale Model. Simul. 12, 109-118, 2014.
  64. A. Witthoft*, J.A. Filosa and G.E. Karniadakis, “Potassium buffering in the neurovascular unit: Models and sensitivity analysis.” Biophys. J. 105(9), 2046-2054, 2013.
  65. Z. Peng, X. Li, I. Pivkin, M. Dao, G.E. Karniadakis, and S. Suresh “Lipid bi-layer and cytoskeletal interactions in a red blood cell.” P.N.A.S. 110(33):13356-61, 2013.
  66. X. Li, P. Vlahovska and G.E. Karniadakis, Continuum-and particle-based modeling of shapes and dynamics of red cells in health and disease”, Soft Matter, 9:28-37, 2013.
  67. H. Lei*, B. Caswell and G.E. Karniadakis, “Blood flow in small tubes: Quantifying the transition to the non-Newtonian regime.” J. Fluid Mech. 722:214-239, 2013.
  68. H. Lei* and G.E. Karniadakis, “Probing vasoocclusion phenomena in sickle cell anemia via mesoscopic simulations.” P.N.A.S. 110(28):11326-30, 2013.
  69. L. Grinberg, D.A. Fedosov and G.E. Karniadakis, “Parallel multiscale simulations of a brain aneurysm.” J. Comp. Phys., 244, 131-147, 2013.
  70. C. Kim, G. E. Karniadakis, “Microscopic theory of Brownian motion revisited: The Rayleigh model.” Physical Review E. 87, 032129, 2013.
  71. D.A. Steinman et al., “Variability of Computational Fluid Dynamics Solutions for pressure and flow in a giant aneurysm: The ASME 2012 Summer Bioengineering Conference CFD Challenge.” J. Biomech. Engin. 135(2):021016­, 2013
  72. X. Li, A. Popel, G. E. Karniadakis, “Blood-plasma separation in Y-shaped bifurcating microfluidic channels: A dissipative particle dynamics simulation study.” Phys. Bio. 9, 026010, 2012.
  73. H. Lei, G. E. Karniadakis, “Quantifying the rheological and hemodynamic characteristics of sickle cell anemia.” J. Biophys.  102, 185-194, 2012.
  74. H. Lei, G. E. Karniadakis, “Predicting the morphology of sickle red blood cells using coarse-grained models of intracellular aligned hemoglobin polymers.” Soft Matter. 8, 4507-4516, 2012.
  75. M. Deng, X. Li, H. Liang, B. Caswell, G. E. Karniadakis, “Simulation and modeling of slip flow over surface grafted with polymer brushes and alycocalyx fibers.” J. Fluid Mech. 711, 192-211, 2012.
  76. X. Li, B. Caswell, G. E. Karniadakis, “Effect of chain chirality on self-assembly of sickle hemoglobin.” J. Biophys. 103, 1130-1140, 2012.
  77. D. Fedosov, W. Pan, B. Caswell, G. E. Karniadakis, “Predicting human blood viscosity in silico.” PNAS. 108(29), 11772-11777, 2011.
  78. D. Fedosov, B. Caswell, G. E. Karniadakis, “Wall shear stress-based method for adhesive dynamics of red blood cells in malaria.”  J. Biophys. 100, 2084-2093, 2011.
  79. D. Fedosov, H. Lei, B. Caswell, S. Suresh, G. E. Karniadakis, “Multiscale modeling of red blood cell mechanics and blood flow in malaria.” PLOS Comput. Bio. 7(12), e1002270, 2011.
  80. W. Pan*, D. Fedosov*, B. Caswell, and G.E. Karniadakis, “Predicting dynamics and rheology of blood flow: A comparative study of multiscale and low-dimensional models of red blood cells.” Microvas. Res. 82(2), 163-170, 2011.
  81. H. Lei, D. A. Fedosov, G. E. Karnidakis, “Time-dependent and outflow boundary conditions for Dissipative Particle Dynamics.” J. Comput. Phys. 230, 3765-3779, 2011.
  82. M. Arienti, W. Pan*, X. Li, and G.E. Karniadakis, “Many-body dissipative particle dynamics simulation of liquid/vapor and liquid/solid interactions.” J. Chem. Phys. 134, 204114, 2011.
  83. D. Fedosov*, B. Caswell, S. Suresh and G.E. Karniadakis, “Quantifying the biophysical characteristics of Plasmododium-­falciparum-parasitized red blood cells in microcirculation.” P.N.A.S. 108, 35-39, 2011.
  84. D. Quinn, I. Pivkin, S.Y. Yong, K.-H. Chiam, M. Dao, G.E. Karniadakis and S. Suresh, “Combined simulation and experimental study of large deformation of red blood cells in microfluidic systems.” Ann. Biomed. Engin. 39(3), 1041-1050, 2011.
  85. L. Grinberg* and G.E. Karniadakis, “Extrapolation-based acceleration of iterative solvers: Application to simulation of 3D flows.” Commun. Comput. Phys. 9, 607-626, 2011.
  86. D. Fedosov, B. Caswell, G. E. Karniadakis, “Steady shear rheometry of DPD models of polymer fluids in reverse Poiseuille flow.” J. Chem. Phys. 132, 144103, 2010.
  87. X. Luo, A. Beskok, G. E. Karniadakis, “Modeling electrokinetic flows by the smoothed profile method.” J. Comp. Phys. 229, 3828-3847, 2010.
  88. T. Anor, L. Grinberg*, H. Baek, M. Jayraman, J.R. Madsen and G.E. Karniadakis, “Modeling of blood flow in arterial trees.” Wiley Interdiscip. Rev. Syst. Biol. Med. 2(5), 612-623, 2010.
  89. L. Grinberg*, E. Cheever*, T. Anor, J.R. Madsen and G.E. Karniadakis, “Modeling blood flow circulation in intracranial arterial networks: A comparative 3D/1D simulation study.” Ann. Biomed. Engin. 39, 297-309, 2010.
  90. H. Baek*, M.V. Jayaraman, P.D. Richardson and G.E. Karniadakis, “Flow instability and wall shear stress variation in intracranial aneurysms.” J. R. Soc. Interface. 7(47), 967-988, 2010.
  91. D. Fedosov*, B. Caswell, A. Popel and G.E. Karniadakis, “Blood flow and cell-free layer in microvessels.” Microcircu­lation, 17(8), 615-628, 2010.
  92. W. Pan*, B. Caswell and G.E. Karniadakis, “A low-dimensional model for the red blood cell.” Soft Matter. 6, 4366-4376, 2010.
  93. D. Fedosov*, B. Caswell and G.E. Karniadakis, “Systematic coarse-graining of spectrin-level red blood cell models.” Comput. Methods Appl. Mech. Engin. 199(29-32): doi:10.1016/j.cma.2010.02.001. 2010.
  94. D. Fedosov*, B. Caswell and G.E. Karniadakis, “A multiscale red blood cell model with accurate mechanics, rheology and dynamics.” Biophys. J. 98, 1-11, 2010.
  95. H. Lei, B. Caswell, G. E. Karniadakis, “Direct construction of mesoscopic models from microscopic simulations.” Phys. Rev. E. 81, 026704, 2010.
  96. W. Pan, B. Caswell, G. E. Karniadakis, “Rheology, Microstructure and Migration in Brownian Colloidal Suspensions.” Langmuir. 26(1), 133-142, 2010.
  97. H. Baek*, M.V. Jayaraman and G.E. Karniadakis, “Wall shear stress and pressure distribution on aneurysms and infundibulae in the posterior communicating artery bifurcation.” Ann. Biomed. Engin. 37(12), 2469-2487, 2009.
  98. I. Pivkin*, P. Richardson and G.E. Karniadakis, “Effect of red blood cells on platelet aggregation.” IEEE Engineering in Medicine & Biology Magazine, 28(2), 32-37, March-April 2009.
  99. L. Grinberg*, A. Yakhot and G.E. Karniadakis, “Analyzing transient turbulence in a stenosed artery by Proper Or­thogonal Decomposition.” Ann. Biomed. Engin. 37(1), 2200-2217, 2009.
  100. X. Li, I. Pivkin*, H. Liang and G.E. Karniadakis, “Shape transformations of membrane vesicles from amphiphilic triblock copolymers: A Dissipative Particle Dynamics simulation study.” Macromolecules, 42, 3195-3200, 2009.
  101. J. Foo*, S. Sindi and G.E. Karniadakis, “Multi-element probabilistic collocation for sensitivity analysis in cellular signaling networks.” IET Systems Biology, 3 (4), 239-254, 2009.
  102. D. Fedosov, G. E. Karniadakis, “Triple-decker: Interfacing atomistic-mesocopic-continuum flow regimes.” J. Comp. Phys. 228, 1157-1171, 2009.
  103. L. Grinberg*, T. Anor, E. Cheeve, J. R. Madsen and G. E. Karniadakis, “Simulation of the Human Intracranial Arterial Tree.” Phil. Trans. R. Soc. A. 367, 2371-2386, 2009.
  104. L. Grinberg*, T. Anor, J.R. Madsen, A. Yakhot and G.E. Karniadakis, “Large-Scale Simulation of the Human Arterial Tree.” Clin. Exp. Pharmacol. Physiol. 36(2):194-205, 2009.
  105. D. Fedosov, G. E. Karniadakis, B. Caswell, “DPD simulation of depletion layer and polymer migration in micro- and nano-channels for dilute polymer solutions.” J. Chem. Phys. 128, 144903, 2008.
  106. W. Pan, I. V. Pivkin, G. E. Karniadakis, “Single-particle hydrodynamics in DPD: A new formulation.” Europhysics Letters. 84(1), 10012, 2008.
  107. W. Pan, D.Fedosov, G. E. Karniadakis, “Hydrodynamic interactions for single dissipative-particle-dynamics particles and their clusters and filaments.” Phys. Rev. E. 78, 046706, 2008.
  108. L. Grinberg* and G.E. Karniadakis, “Outflow boundary conditions for arterial networks with multiple outlets.” Ann. Biomed. Engin. 36 (9), 1496-1514, 2008.
  109. I. Pivkin* and G.E. Karniadakis, “Accurate coarse-grained modeling of red blood cells.” Phys. Rev. Lett. 101(11), 118105, 2008.
  110. D. Fedosov, I. V. Pivkin, G. E. Karniadakis, “Velocity limit in DPD simulations of wall-bounded flows.” J. Comp. Phys. 227(4), 2540-2559, Feb. 2008.
  111. E. Climent, K. Yeo, M. Maxey, G. E. Karniadakis, ”Dynamic self-assembly of spinning particles.” J. Fluids Engin. 129, 379-387, April 2007.
  112. A. Yakhot, T. Amor and G.E. Karniadakis, “A reconstruction method for gappy and noisy arterial flow data.” IEEE Transactions on Medical Imaging, 26(12), 1681-1697, 2007.
  113. V. Symeonidis, G. E. Karniadakis, B. Caswell, ”Schmidt number effects in simulation of polymer dissipative particle dynamics.” J. Chem. Phys. 125, 184902, 2006.
  114. I. Pivkin*, P.D. Richardson and G.E. Karniadakis, “Blood flow velocity effects and role of activation delay time on growth and form of platelet thrombi.” P.N.A.S. 103(46), 17164, 2006.
  115. P.D. Richardson, I. Pivkin*, G.E. Karniadakis, and D.H. Laidlaw “Blood flow at arterial branches: Complexities to resolve at the angioplasty suite.” Lecture Notes in Computer Science, 3993, 538-545, 2006.
  116. I. Pivkin* and G.E. Karniadakis, “Controlling density fluctuations in wall-bounded dissipative particle dynamics sys­tems.” Phys. Rev. Lett. 96(20), 206001, 2006.
  117. I. Pivkin* and G.E. Karniadakis, “Coarse-graining limits in open and wall-bounded DPD systems.” J. Chem. Phys. 124, 184101, 2006.
  118. V. Symeonidis, G. E. Karniadakis, ”A family of time-staggered schemes for integrating hybrid DPD models for polymers: Algorithms and applications.” J. Comp. Phys. 218, 82-101, 2006.
  119. D. Liu, M. Maxey, G. E. Karniadakis, ”Simulations of dynamic self-assembly in confined microgeometries.” J. Micromech. Microeng. 15(12), 2298-2308, 2005.
  120. E. Keaveny, I. Pivkin, M. Maxey, G. E. Karniadakis, ”A comparative study between dissipative particle dynamics and molecular dynamics for simple- and complex-geometry flows.” J. Chem. Phys. 123, 104107, 2005.
  121. J. Xu, S. Dong, M. Maxey, G. E. Karniadakis, ”Wall slippage effect in microbubble drag reduction.” 2nd International Symposium on Seawater Drag Reduction, Busan, Korea, May 23-26, 2005.
  122. V. Symeonidis*, G.E. Karniadakis and B. Caswell, “Dissipative particle dynamics simulations of polymer chains: Scaling laws and shearing response compared to DNA experiments.” Phys. Rev. Lett, 95, 076001, 2005.
  123. I. Pivkin*, P.D. Richardson, D.H. Laidlaw and G.E. Karniadakis, “Combined effects of pulsatile flow and dynamic curvature on wall shear stress in a coronary artery bifurcation model.” J. Biomech. 38, 1283-1290, 2005.
  124. I. Pivkin* and G.E. Karniadakis, “A new method to impose no-slip boundary conditions in dissipative particle dynam­ics.” J. Comp. Phys. 207, 114-128, 2005.
  125. V. Symeonidis*, G.E. Karniadakis and B. Caswell, “A seamless approach to multiscale complex fluid simulation.” Comput. Sci. Engin. 7, 39-46, May/June 2005.
  126. M. Maxey, D. Liu, S. Dong, G. E. Karniadakis, ”New advances in force-coupled method from micro to macro.” Proceeding of IUTAM Symposium: Computational Approaches to Disperse Multiphase Flow, Argonne, IL, Oct. 2004.
  127. M. Maxey, D. Liu, G. E. Karniadakis, E. Climent, ”Self-assembled particle structures for microflow systems.” International Conference on Multiphase Flow, Yokohama, Japan, May 30 – June 4 2004.
  128. D. Liu, M. Maxey, G. E. Karniadakis, ”Modeling and optimization of colloidal micro-pumps.” J. Micromech. Microeng. 14, 567-575, 2004.
  129. E. Climent, M. Maxey, G. E. Karniadakis, “Dynamics of self-assembled chaining in magnetorehological fluids.” Langmuir, 20(2), 507-513, 2004.
  130. D. Liu, M. Maxey, G. E. Karniadakis, ”FCM-spectral element method for simulating colloidal micro-devices.” 2nd MIT Conference on Computational Fluid and Solid Mechanics edited by K. J. Bathe, June 17-20, 2003.
  131. D. Liu, M. Maxey, G. E. Karniadakis, ”Simulation and optimization of colloidal micro-pumps.” NanoTech 2003 Conference, San Francisco, CA, Feb. 23-27 2003.
  132. D. Liu, M. Maxey, G. E. Karniadakis, ”A fast method for particulate microflows.” J. Microelectromechanical Systems, 11(6), 691-702, 2002.
  133. G. E. Karniadakis, A. Beskok, ”Microflows: Fundamentals and Simulation.” Springer, 2001. (Note: first textbook/monograph in this field).
  134. D. Liu, M. Maxey, G. E. Karniadakis, ”A fast algorithm for particulate micro-flows in complex geometries.” 2001 ASME International Mechanical Engineering Congress, New York,  NY, Nov. 11-16, 2001.
  135. G. Lin, G. E. Karniadakis, ”High-order modeling of micro-pulsed plasma thrusters.” AIAA 2002-2872, 3rd AIAA Theoretical Fluid Mechanics Meeting, St. Louis, Missouri, June 24-26 2002.
  136. R. M. Kirby, G. E. Karniadakis, O. Mikulchenko, K. Mayaram, ”Integrated simulation for MEMS: Coupling flow-structure-thermal-electrical domains.” Ch. 5, The MEMS Handbook, CRC Press, ISBN:084930077-0
  137. R. M. Kirby, G. E. Karniadakis, O. Mikulchenko, K. Mayaram, ”An integrated simulator for coupled domain problems in MEMS.” J. Microelectromechan. Systems, 10(3), 379-399, 2001.
  138. A. Beskok, G. E. Karniadakis, ”A model for flows in channels, pipes and ducts at micro- and nano-scales.” J. Microscale Thermophys. Engin. 3, 43-77, 1999.
  139. H. F. Liu, N. Gatsonis, A. Beskok, G. E. Karniadakis, “Simulation models for rarefied flow past a sphere in a pipe.” Proc. 21st Symposium on Rarefied Gas Dynamics, France, 1998.
  140. A. Beskok, G. E. Karniadakis, ”Modeling separation in rarefied gas flows.” AIAA 97-1783, 4th AIAA Shear Flow Conference, Snowmass Village, CO, 1997.
  141. A. Beskok, G. E. Karniadakis,  W. Trimmer, ”Rarefaction and compressibility effects in gas microflows.” J. Fluids Engin. 118, 448, 1996.
  142. A. Beskok, W. Trimmer, G. E. Karniadakis, ”Rarefaction, compressibility and thermal creep effects for gas microflows.” ASME Annual Winter Meeting,  San Francisco, CA, Nov. 1995.
  143. S. J. Sherwin, G. E. Karniadakis, S. A. Orszag, ”Numerical simulation of the ion etching process.” J. Comp. Phys. 110, 373, 1994.
  144. A. Beskok, G. E. Karniadakis, ”Simulation of heat and momentum transfer in complex micro-geometries.” J. Thermophys. Heat Transfer. 8(4) 647, 1994.
  145. S. J. Sherwin, E. Barough, G. E. Karniadakis, S. A. Orszag, ”Modeling of multilayer etching processes.” J. Vacuum Sci. Tech. 11, 1310, 1993.
  146. A. Beskok, G. E. Karniadakis, ”Simulation of heat and momentum transfer in complex micro-geometries.” AIAA 93-3269, 1st Shear Flow Conference, Orlando, FL, 1993.
  147. S. J. Sherwin, E. Barough, S. A. Orszag,  G. E. Karniadakis, ”Application of an ENO scheme to simulate the ion etching process.” Proc. Fourth Int. Conf. on Hyperb. Problems, Taormina, Italy, April, 1992.
  148. A. Beskok, G. E. Karniadakis, ”Simulation of slip-flows in complex micro-geometries.” Proc. ASME, Winter Annual Meeting, Anaheim, CA, 1992.
  149. M.K. Sharp, R. D. Kamm, A.H. Shapiro, E. Kimmel & G.E. Karniadakis, “Dispersion in a curved tube during oscillatory flow.” J. Fluid Mech. 223, 537, 1991.
  150. E. Barough, B. Bradie, U. Hollerbach, G. E. Karniadakis, S. A. Orszag, ”Comprehensive 3-D notching simulator with non-planar substrates.” Proc. on Optical/Laser Microlithography.  3, 334, SPIE, 1990.