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Computational Biology

  1. L. Lu, X. Li, P.G. Vekilov and G.E. Karniadakis, "Probing the twisted structure of sickle hemoglobin fibers via a particle simulation," Biophysical Journal, 110, 2085-1093, 2016, DOI: 10.1016/j.bpj.2016.04.002

  2. A. Yazdani and G.E. Karniadakis, "Sub-cellular modelig of platelet transport in blood flow through microchannels with constriction," Soft Matter, DOI: 10.1039/c6sm00154h, 2016

  3. Y-H. Tang, Z. Li, X. Li and G.E. Karniadakis, "Non-equilibrium dynamics of vesicles and miscelles by self-assembly of block copolymers with double thermorespnsivity," Macromolecules, 49, 2895-2903, DOI: 10.1021/acs.macromol.6b00365.
    pub.acs.org/Macromolecules

  4. A. Witthoft, A. Yazdani, Z. Peng, C. Bellini, J.D. Humphrey and G.E. Karniadakis, "A discrete mesoscopic particle model fo the mechanids of a mli-constituent arterial wall," Interface, 13, 20150964, 2015, DOI: 1098/rsif.2015.0964
  5. 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 Computational Biology, DOI:10.1371/journal.pcbi.1004410, August 28, 2015.

  6. 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, DOI: 10.1039/C4SM02395A, 2015.

  7. D.A. Fedosov, M. Dao, G.E. Karniadakis and S.Suresh, "Computational biorheology of human blood flow in health and disease," Annals of Biomedical Engineering, 42(2), 368-387,  February 2014.

  8. M. Deng and G.E. Karniadakis, "Coarse-grained modeling of protein unfolding dynamics," Multiscale Model. Simul. 12(1), 109-118, 2014.

  9. P. Perdikaris and G.E. Karniadakis, "Fractional-order viscoelasticity in one-dimensional blood flow models," Annals of Biomedical Engineering,  DOI: 10.1007/s10439-014-0970-3, 2014.

  10. Z.L. Peng, X.J. Li, I.V. Pivkin, M. Dao, G.E. Karniadakis and S. Suresh, "Lipid-bilayer and cytoskeletal interactions in a red blood cell," Proc. Natl. Acad. Sci, USA, 110, 13356-13361, 2013.

  11. H. Lei and G.E. Karniadakis, "Probing vaso-occlusion phenomena in sickle cell anemia via mesoscopic simulations," PNAS, 110(28) 11326-11330, 2013.

  12. A. Witthoft, J.A. Filosa and G.E. Karniadakis, "Potassium buffering in the neurovascular unit: Models and sensitivity analysis," Biophysical Journal, 105, 2046-2054, 2013.

  14. X. Li, P. Vlahovska and G.E. Karniadakis, "Continuum- and particle-based modeling of shapes and dynamics of red blood cells in health and disease,", Soft Matter, 9, 28-37, 2013.

  15. L. Grinberg, D. Fedosov and G.E. Karniadakis, "Parallel multiscale simulations of a brain aneurysm," J. Comp. Phys., 244, 131-147, 2013.

  16. H. Lei, D. Fedosov, B. Caswell and G.E. Karniadakis, "Blood flow in small tubes: Quantifying the transition to the non-Newtonian regime," J. Fluid Mechanics, 722, 214-239, 2013.

  17. A. Witthoft and G.E. Karniadakis, "A bidrectional model for communication in the neurovascular unit," Journal of Theoretical Biology, 311, 80-93, 2012.

  18. 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," Microvasular Journal, 82, 163-170, 2011.

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

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

  21. D.J. Quinn, I. Pivkin, S.Y. Wong, 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., Annls of Biomedical Eng., 39(3), 041-1050, 2011.

  22. D.A. Fedosov, B. Caswell, S. Suresh and G.E. Karniadakis, "Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation, " PNAS 108(1), 35-39, 2011.

  23. 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, " Annals of Biomedical Engineering, 39(1), 297-309, DOI:10.1007/s10439-010-0132-1, 2011.

  24. 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," Annals of Biomedical Engineering, 39(1), 297-309, 2011.

  25. D. Fedosov, B. Caswell, A. Popel and G.E. Karniadakis, "Blood flow and cell-free layer in microvessels," Microcirculation," 17(8), 615-628, 2010.

  26. T. Anor, L. Grinberg, H. Baek, M. Jayraman, J.R. Madsen and G.E. Karniadakis, "Modeling of blood flow in arterial trees," Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2, 612-623, 2010.

  27. D. Fedosov, B. Caswell and G.E. Karniadakis, "Systematic coarse-graining of spectrin-level red blood cell models," Computer Methods in Applied Mechanics and Engineering, 199, 1937-1948, 2010.

  28. W. Pan, B. Caswell, G.E. Karniadakis, "A low-dimensional model for the red blood cell," Soft Matter, 6, 4366-4376, DOI: 10.10391.C0SM00183j, 2010.

  29. D. Fedosov, B. Caswell and G.E. Karniadakis, "A multiscale red blood cell model with accurate mechanics, rheology and dynamics, Biophysical Journal, 98(10), 2215-2225, 2010.

  30. 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, 967-988, doi: 10.1098/rsif.2009.0476, 2010.

  31. D. Fedosov, B. Caswell and G.E. Karniadakis, "Coarse-grained red blood cell model with accurate mechanical properties, rheology and dynamics, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Minneapolis, MN, September 2-6 2009.

  32. 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," Annals of Biomedical Engineering, 37(12), 2469-2487, 2009.

  33. L. Grinberg, T. Anor, J.R. Madsen and G.E. Karniadakis, "Simulation of the human intracranial arterial tree," Philosophical Transactions of the Royal Society A,' 367, 2371-2386, 2009.

  34. I. Pivkin, P. Richardson and G.E. Karniadakis, "Effect of red blood cells on platelet aggregation," IEEE Engineering in Medicine and Biology Magazine, 28(2), 32-32, March-April 2009.

  35. L. Grinberg, A. Yakhot and G.K. Karniadakis, "Analyzing transient turbulence in a stenosed carotid artery by proper orthogonal decomposition," Annals of Biomedical Engineering, 37(11), 2200-2217, 2009.

  36. H. Baek, M. Jayaraman and G.E. Karniadakis, "Wall stress and pressure distribution on aneurysms and infundibulae in the posterior communicating artery bifurcation," Annals of Biomedical Engineering, 37(12), 2469-2487, 2009.

  37. X. Li, I.V. Pivkin, H. Liang and G.E. Karniadakis, "Shape transformation of membrane vesicles from amphiphilic triblock copolymers: A dissipative particle dynamics simulation study," Macromolecules, 42(8), 3195-3200, DOI: 10.1021/ma9000918, 2009.

  38. L. Grinberg, T. Anor, J.R. Madsen and G.E. Karniadakis, "Simulation of the human intracranial arterial tree," Philosophical Transactions of the Royal Society, 367(1896), 2371-2386, 2009.

  39. I.V. Pivkin, P.D. Richardson and G.E. Karniadakis, "Effect of red blood cells on platelet aggregation," IEEE Engineering in Medicine and Biology Magazine, vol. 28(2), 32-37, Digital Object Identifier 10.1109/MEMB.2009.931788, March/April 2009.

  40. L. Grinberg, T. Anor, J.R. Madsen, A. Yakhot and G.E. Karniadakis, "Large-scale simulation of the human arterial tree, Clinical and Experimental Pharmacology and Physiology, 36, 194-205, 2009.

  41. L. Grinberg and G.E. Karniadakis, "A scalable domain decomposition method for ultra-parallel arterial flow simulation, Commun. Comput. Phys., 4(5), 1151-1169, November 2008.

  42. L. Grinberg and G.E. Karniadakis, "Outflow boundary conditions for arterial networks," Annals of Biomedical Engineering, 36)9), 1496-1514, September 2008.

  43. I. Pivkin and G.E. Karniadakis, "Accurate coarse-grained modeling of red blood cells," Phys. Rev. Letts. 101, 118105, 2008.

  44. H. Baek, M.V. Jayaraman, G.E. Karniadakis, "Blood flow in the supraclinoid internal carotid artery and the effect of the posterior communication artery bifurcation," SBC 2008-192055, ASME Summer Bioengineering Conference, June 25-29, 2008.

  45. A. Yakhot, T. Anor and G.E. Karniadakis, ''A reconstruction method for gappy and noisy arterial flow data,'' IEEE Trans. Med. Imag. (to appear in vol 26) 2007.

  46. I. Pivkin, P. Richardson and G.E. Karniadakis, ''Blood flow velocity effects and role of activation delay time on growth and form of platelet thrombi,'' PNAS, 103, 17164-17169, 2006.

  47. I. Pivkin and G.E. Karniadakis, ''Controlling density fluctuations in wall bounded DPD systems,'' Phys. Rev. Letts. 96(20) 206001-1 - 20600-4, 2006.

  48. S. Dong, J. Insley, N.T. Karonis, M. Papka, J. Binns and G.E. Karniadakis, ''Simulating and visualizing the human arterial system on the TeraGrid,'' Future Generation Computer Systems, The International Journal of Grid Computing: Theory, Methods and Applications, vol. 22, 1011-1017, 2006.

  49. I. Pivkin and G. E. Karniadakis ''Coarse-graining limits in open and wall-bounded dissipative particle dynamics systems,'' J. Chem. Phys., 124, 184101, 2006.

  50. S. Dong, N.T. Karonis, G.E. Karniadakis, ''Grid solutions for biological and physical cross-site simulations on the TeraGrid,'' In Proceedings of 20th IEEE International Parallel and Distributed Processing Symposium (IPDPS'06), Rhodes Island, Greece, April 2006.

  51. B. Boghosian, P. Coveney, S. Dong, L. Finn, S. Jha, G.E. Karniadakis and N.T. Karonis, ''Nektar, SPICE and Vortonics: Using Federated Grids for Large Scale Scientific Applications,'' Workshop on Challenges of Large Applications in Distributed Environments (CLADE), in conjunction with 15th International Symposium on High Performance Distributed Computing (HPDC-15), Paris, France, June 2006.

  52. G.E. Karniadakis, A. Beskok and N. Aluru, "Microflows and Nanoflows: Fundamentals and Simulation, Springer 2005.

  53. 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. Letts. vol. 95, article number: 076001, 2005.

  54. I. Pivkin, P. Richardson, D.H. Laidlaw and G.E. Karniadakis, ''Combined effects of pulsatile flow and dynamic curvature on wall shear stress in coronary artery bifurcation model, J. of Biomechanics, vol. 38, pp. 1283-1290, 2005.

  55. I. Pivkin and G.E. Karniadakis, ''A new method to impose no-slip boundary conditions in dissipative particles,'' J. Comp. Phys., vol. 207, pp. 114-128, 2005.

  56. V. Symeonidis, G.E. Karniadakis and B. Caswell, ''A seamless approach to multiscale complex fluid simulation,'' Computing in Science and Engineering, 39-46, May/June 2005.

  57. I. Pivkin, E. Hueso, R. Weinstein, D.H. Laidlaw, S. Swartz and G.E. Karniadakis, ''Simulation and visualization of airflow around bat wings during flight,'' International Conference on Computational Science (2), pp. 689-694, 2005.

  58. E. Hueso, I. Pivkin, S. Swartz, D.H. Laidlaw, G.E. Karniadakis and K. Breuer, "Visualization of vortices in simulated airflow around bat wings during flight," IEEE Visualization , 2004.

  59. J.S. Sobel, A.S. Forsberg, D.H. Laidlaw, R.C. Zeleznik, D.F. Keefe, I. Pivkin, G.E. Karniadakis, P. Richardson and S. Swartz, ''Particle flurries: synoptic 3D pulsatile flow visualization,'' IEEE Computer Graphics and Applications, March/April, 24(2), 76-85, 2004.

  60. I. Pivkin, P. Richardson and G.E. Karniadakis, ''Simulation of mural platelet aggregation,'' In BMES 2004 Annual Fall Meeting, Philadelphia, PA, October 2004.

  61. I. Pivkin, D.H. Laidlaw, P. Richardson and G.E. Karniadakis, ''Moving meshes and flow simulations in coronary arteries,'' Proceedings of the 8th International Conference on Numerical Grid Generation in Computational Field Simulations, p. 467, Honolulu, Hawaii, June 2002.

  62. J. Sobel, A.S. Forsberg, P. Richardson, D.H. Laidlaw, D.F. Keefe, I. Pivkin and G.E. Karniadakis, ''Arterial flows seen in virtual reality,'' Proceedings of the 21st Southern Biomedical Engineering Conference, pp. 349-350, 2002.

  63. A. Forsberg, R.M. Kirby, D.H. Laidlaw, G.E. Karniadakis, A. van Dam and J. Elion, ''Immersive virtual reality for visualizing flow through an artery,'' Proc. IEEE Visualization 2000, Salt Lake City, UT, October 2000.

  64. M.K. Sharp, R. D. Kamm, A.H. Shapiro, E. Kimmel and G.E. Karniadakis, ''Dispersion in a curved tube during oscillatory flow,'' J. Fluid Mech., vol. 223, p. 537, 1991.

 

next up previous
Next: About this document ... Up: pubs Previous: Heat Transfer
George Karniadakis 2009-12-14