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Biomedical/Multiscale/Microfluidic Modeling

Biomedical/Multiscale/Microfluidic Modeling

  1. 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." Biophysical Journal,  2017, 112:2030-2037.
  2. A.L. Blumers, Y.H. Tang, Z. Li, X. Li, G.E. Karniadakis, "GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics." Computer Physics Communications, 2017, http://dx.doi.org/10.1016/j.cpc.2017.03.016.
  3. M. Deng, W. Pan, G.E. Karniadakis, "Anisotropic single-particle dissipative particle dynamics model." J. Comp. Phys.  2017, 336; 481-491
  4. X. Li, M. Dao, G. Lykotrafitis, G.E. Karniadakis, "Biomechanics and biorheology of red blood cells in sickle cell anemia." J. Biomechanics, 2017, 50, 34-41.  doi.org/10.1016/j.jbiomech.2016.11.022
  5. 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.
  6. 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. 2017, 146, DOI:10.1063/1.4973347
  7. X. Li, M. Dao, G. Lykotrafitis,  G.E. Karniadakis, "Biomechanics and biorheology of red blood cells in sickle cell anemia." J. Biomechanics, 2016, In press DOI:10.1016/j.jbiomech.2016.11.022
  8. 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 Computational Biology, 2016 DOI:10.1371/journal.pcbi.1005173. 
  9. 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.
  10. P. Perdikaris, L. Grinberg and G. E. Karniadakis. "Multiscale modeling and simulation of brain blood flow." Phys. Fluids, vol 28(2), 2016.
  11. A. Yazdani, X.J. Li and G.E. Karniadakis, “Dynamic and rheological properties of soft biological cell suspensions," Rheol Acta, 55(6), 433-449, DOI 10.1007/s00397-015-0869-4, 2016. 
  12. 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
  13. 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." The Journal of Chemical Physics, 145, 044102, 2016.  doi.org/10.1063/1.4959121
  14. P. Perdikaris, L. Grinberg and G. E. Karniadakis, "An effective fractal-tree closure model for simulating blood flow in large arterial networks." Ann. Biomed. Eng., 1-11, 2015.
  15. P. Perdikaris, and G. E. Karniadakis, "Fractional-order viscoelasticity in one-dimensional blood flow models." Ann. Biomed. End., 42"1012-1023, 2014.
  16. Z. Li, X. Bian, B. Caswell and G.E. Karniadakis, "Construction of dissipative particle dynamics models for complex fluids via the Mori-Zwannzig formulation." Soft Matter 2014, DOI: 10.1039/C4SM01387E.

  17. C. Kim and 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.

  18. Z. Li, Y-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis, "Energy-conserving dissipative particle dynamics with temperature-dependent properties," J. Comput. Phys., 265, 113-127, 2014.

  19. M. Deng and G.E. Karniadakis, "Electrostatic correlations near charged planar surfaces," J. Chemial Physics, 141, 094703, 2014.

  20. C. Kim and G.E. Karniadakis, "Microscopic theory of Brownian motion revisited: The Rayleigh model," Physical Review E, 87, 032129, 2013.

  21. X. Li, A. Popel and G.E. Karniadakis, "Blood-plasma separation in Y-shaped bifurcating microfluidic channels: A dissipative particle dynamics simulation study," Physical Biology, 9, 026010, 2012.

  22. H. Lei and G.E. Karniadakis, "Quantifying the rheological and hemodynamic characteristics of sickle cell anemia," Biophysical Journal, 102, 185-194, 2012.

  23. H. Lei and 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.

  24. M. Deng, X. Li, H. Liang, B. Caswell and 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.

  25. X. Li, B. Caswell and G.E. Karniadakis, "Effect of chain chirality on self-assembly of sickle hemoglobin," Biophysical Journal, 103, 1130-1140, 2012.

  26. D. Fedosov, W. Pan, B. Caswell and G.E. Karniadakis, "Predicting human blood viscosity in silico, PNAS, 108(29), 11772-11777, 2011.

  27. D. Fedosov, B. Caswell and G.E. Karniadakis, "Wall shear stress-based method for adhesive dynamics of red blood cells in malaria, Biophysical Journal, 100, 2084-2093, 2011.

  28. D. Fedosov, H. Lei, B. Caswell, S. Suresh and G.E. Karniadakis, "Multiscale modeling of blood flow in malaria," PLOS Comput. Bio., 7(12), e1002270, 2011.

  29. H. Lei, D.A. Fedosov and G.E. Karnidakis, "Time-dependent and outflow boundary conditions for Dissipative Particle Dynmics," J. Comput. Phys., 230, 3765-3779, 2011.

  30. D. Fedosov, B. Caswell and G.E. Karniadakis, "Steady shear rheometry of DPD models of polymer fluids in reverse Poiseuille flow," J. Chem. Phys., 132, 144103, 2010.
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  32. X. Luo, A. Beskok, G.E. Karniadakis, "Modeling electrokinetic flows by the smoothed profile method," J. Comp. Phys, 229, 3828-3847, 2010.

     

  33. H. Lei, B. Caswell and G.E. Karniadakis, "Direct construction of mesoscopic models from microscopic simulations," Phys. Rev. E, 81, 026704, 2010.

     

  34. W. Pan, B. Caswell and G.E. Karniadakis, "Rheology, Microstructure and Migration in Brownian Colloidal Suspensions," Langmuir, 26(1), 133-142, 2010.

     

  35. D. Fedosov and G.E. Karniadakis, "Triple-decker: Interfacing atomistic-mesocopic-continuum flow regimes," J. Comp. Phys., 228, 1157-1171, 2009.

     

  36. D. Fedosov, G.E. Karniadakis and 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.

     

  37. W. Pan, I.V. Pivkin and G.E. Karniadakis, "Single-particle hydrodynamics in DPD: A new formulation," Europhysics Letters, 84(1), 10012, 2008.

     

  38. W. Pan, D.A. Fedosov and G.E. Karniadakis, "Hydrodynamic interactions for single dissipative-particle-dynamics particles and their clusters and filaments,'' Phys. Rev. E., 78, 046706, 2008.

     

  39. W. Pan, I.V. Pivkin and G.E. Karniadakis, "Single-particle hydrodynamics in DPD: A new formulation," EPL, 84, 10012, doi: 10.1209/0295-5075/84/10112, 2008.

     

  40. D.A. Fedosov, I.V. Pivkin and G.E. Karniadakis, "Velocity limit in DPD simulations of wall-bounded flows," J. Comp. Phys. 227(4), 2540-2559, Feb. 2008.

     

  41. V. Symeonidis, G.E. Karniadakis and B. Caswell, ''Schmidt number effects in simulation of polymer dissipative particle dynamics,'' J. Chem. Phys., 125, 184902, 2006.

     

  42. E. Climent, K. Yeo, M. Maxey and G.E. Karniadakis, ''Dynamic self-assembly of spinning particles,'' J. Fluids Engin. 129, 379-387, April 2007.

     

  43. V. Symeonidis and G.E. Karniadakis, ''A family of time-staggered schemes for integrating hybrid DPD models for polymers: Algorithms and applications,'' J. Comp. Phys. vol. 218, 82-101, 2006.

     

  44. D. Liu, M.R. Maxey and G.E. Karniadakis, ''Simulations of dynamic self-assembly in confined microgeometries,'' J. Micromech. Microeng. 15(12), 2298-2308, 2005.

     

  45. E. Keaveny, I. Pivkin, M.R. Maxey and G.E. Karniadakis, ''A comparative study between dissipative particle dynamics and molecular dynamics for simple- and complex-geometry flows,'' J. Chem. Phys. vol 123, 104107, 2005.

     

  46. J. Xu, S. Dong, M.R. Maxey and G.E. Karniadakis, ''Wall slippage effect in microbubble drag reduction,'' 2nd International Symposium on Seawater Drag Reduction, Busan, Korea, May 23-26, 2005.

     

  47. M.R. Maxey, D. Liu, S. Dong and G.E. Karniadakis, ''New advances in force-coupled method from micro to macro,'' Proceeding of IUTAM Symposium: Computational Approaches to Disperse Multiphase Flow, Argonne, Illinois, October 2004.

     

  48. M.R. Maxey, D. Liu, G.E. Karniadakis and E. Climent, ''Self-assembled particle structures for microflow systems,'' International Conference on Multiphase Flow, Yokohama, Japan, May 30 - June 4 2004.

     

  49. D. Liu, M.R. Maxey and G.E. Karniadakis, ''Modeling and optimization of colloidal micro-pumps,'' J. Micromech. Microeng., 14, 567-575, 2004.

     

  50. E. Climent, M.R. Maxey and G.E. Karniadakis, "Dynamics of self-assembled chaining in magnetorehological fluids," Langmuir, 20(2), 507-513, 2004.

     

  51. D. Liu, M.R. Maxey and G.E. Karniadakis, ''FCM-spectral element method for simulating colloidal micro-devices,'' 2nd MIT Conference on Computational Fluid and Solid Mechanics Solid Mechanics edited by K.J. Bathe, June 17-20 2003.

     

  52. D. Liu, M.R. Maxey and G.E. Karniadakis, ''Simulation and optimization of colloidal micro-pumps,'' NanoTech 2003 Conference, February 23-27 2003, San Francisco, CA.

     

  53. D. Liu, M.R. Maxey and G.E. Karniadakis, ''A fast method for particulate microflows,'' J. Microelectromechanical Systems, 11(6), 691-702, 2002.

     

  54. G.E. Karniadakis and A. Beskok, ''Microflows: Fundamentals and Simulation," Springer, 2001. (first textbook/monograph in this field).

     

  55. D. Liu, M.R. Maxey and G.E. Karniadakis, ''A fast algorithm for particulate micro-flows in complex geometries,'' 2001 ASME International Mechanical Engineering Congress, November 11-16 2001, New York.

     

  56. G. Lin and G.E. Karniadakis, ''High-order modeling of micro-pulsed plasma thrusters,'' AIAA 2002-2872, 3rd AIAA Theoretical Fluid Mechanics Meeting, June 24-26 2002, St. Louis, Missouri.

     

  57. R.M. Kirby, G.E. Karniadakis, O. Mikulchenko and K. Mayaram, ''Integrated simulation for MEMS: Coupling flow-structure-thermal-electrical domains,'' Chapter 5, The MEMS Handbook, CRC Press, ISBN:084930077-0

     

  58. R.M. Kirby, G.E. Karniadakis, O. Mikulchenko and K. Mayaram, ''An integrated simulator for coupled domain problems in MEMS,'' J. Microelectromechanical Systems, vol. 10(3), pp. 379-399, 2001.

     

  59. A. Beskok and G.E. Karniadakis, ''A model for flows in channels, pipes and ducts at micro- and nano-scales,'' J. Microscale Thermophysical Engineering, vol. 3, pp. 43-77, 1999.

     

  60. H.F. Liu, N. Gatsonis, A. Beskok and G.E. Karniadakis, "Simulation models for rarefied flow past a sphere in a pipe,'' Proc. 21st Symposium on Rarefied Gas Dynamics, France, 1998.

     

  61. A. Beskok and G.E. Karniadakis, ''Modeling separation in rarefied gas flows,'' AIAA 97-1783, 4th AIAA Shear Flow Conference, Snowmass Village, CO, 1997.

     

  62. A. Beskok, G.E. Karniadakis and W. Trimmer, ''Rarefaction and compressibility effects in gas microflows,'' J. Fluids Engineering, vol. 118, p. 448, 1996.

     

  63. A. Beskok, W. Trimmer and G.E. Karniadakis, ''Rarefaction, compressibility and thermal creep effects for gas microflows,'' ASME Annual Winter Meeting, November 1995, San Francisco, CA.

     

  64. S.J. Sherwin, G.E. Karniadakis and S.A. Orszag, ''Numerical simulation of the ion etching process,'' J. Comp. Phys., vol. 110, p. 373, 1994.

     

  65. A. Beskok and G.E. Karniadakis, ''Simulation of heat and momentum transfer in complex micro-geometries,'' J. Thermophys. and Heat Transfer, vol. 8, no. 4, p. 647, 1994.

     

  66. S.J. Sherwin, E. Barough, G.E. Karniadakis and S.A. Orszag, ''Modeling of multilayer etching processes,'' J. of Vacuum Science and Technology, vol. 11, p. 1310, 1993.

     

  67. A. Beskok and G.E. Karniadakis, ''Simulation of heat and momentum transfer in complex micro-geometries,'' AIAA 93-3269, 1st Shear Flow Conference, Orlando, 1993.

     

  68. S.J. Sherwin, E. Barough, S.A. Orszag and 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.

     

  69. A. Beskok and G.E. Karniadakis, ''Simulation of slip-flows in complex micro-geometries,'' Proc. ASME, Winter Annual Meeting, Anaheim, CA, 1992.

     

  70. E. Barough, B. Bradie, U. Hollerbach, G.E. Karniadakis and S.A. Orszag, ''Comprehensive 3-D notching simulator with non-planar substrates,'' Proc. on Optical/Laser Microlithography, vol. 3, p. 334, SPIE, 1990.