Computational Biology

1. 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.

2. 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.

3. 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 Oject Identifier 10.1109/MEMB.2009.931788, March/April 2009.

4. 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.

5. 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.

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

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

8. 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.

9. 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.

10. 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.

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

12. 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.

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

14. 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.

15. 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.

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

17. 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.

18. 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.

19. 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.

20. 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.

21. 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.

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

23. 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.

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

25. 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.

26. 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.

27. 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.

28. 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.