Stanford Mechanics and Computation

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Major Publications

Preprints

  1. Cecka, C., and E. Darve. "Fourier Based Fast Multipole Method for the Helmholtz Equation." J. Comp. Phys., 2009.

PhD thesis

Darve, E. "Méthodes multipôles rapides: résolution des équations de Maxwell par formulations intégrales." June 17th 1999.

Book chapters

  1. Darve, E. "Thermodynamic integration using constrained and unconstrained dynamics." In Free Energy Calculations: Theory and Applications in Chemistry and Biology, edited by C. Chipot and A. Pohorille, 119–170. 2007. Pre-print copy.

Peer-reviewed journal articles

  1. Fong, W., and E. Darve. "The Black-Box Fast Multipole Method." J. Comp. Phys., 228, no. 23 (2009): 8712-8725.
  2. Darve, E., J. Solomon, and A. Kia. "Computing Generalized Langevin Equations and Generalized Fokker-Planck Equations." Proceedings of the National Academy of Sciences, 27 (2009): 10884-10889.
  3. Petersen, D. A., L. Song, K. Stokbro, H. H. B. Sørensen, P. C. Hansen, S. Skelboe, and E. Darve. "A Hybrid Method for the Parallel Computation of Green’s Functions." J. Comp. Phys. 228, no. 14 (2009): 5020-5039.
  4. Kim, D., and E. Darve. "High ionic strength electroosmotic flows in uncharged hydrophobic nanochannels." J. Coll. Interf. Sci. 330, no. 1 (2009): 194-200.
  5. Elsen, E., P. LeGresley, and E. Darve. "Large calculation of the flow over a hypersonic vehicle using a GPU." J. Comp. Phys. 227, no. 24 (2008): 10148-10161
  6. Li, S., S. Ahmed, G. Klimeck, and E. Darve. "Computing entries of the inverse of a sparse matrix using the FIND algorithm." J. Comp. Phys. 227, no. 22 (2008): 9408-9427
  7. Fong, W., E. Darve, and A. Lew. "Stability of asynchronous variational integrators." J. Comp. Phys. 227, no. 18 (2008): 8367-8394.
  8. Darve, E., D. Rodríguez-Gómez, and A. Pohorille. "Adaptive biasing force method for scalar and vector free energy calculations." J. Chem. Phys. 128, no. 14 (2008): 144120.
  9. Kia, A., D. Kim, and E. Darve. "Fast electrostatic force calculation on parallel computer clusters." J. Comp. Phys. 227, no. 19 (2007): 8551-8567.
  10. Li, S., S. Ahmed, and E. Darve. "Fast inverse using nested dissection for NEGF." J. Comput. Electron. 6 (2007): 187-190.
  11. Kim, D. and E. Darve. "Molecular dynamics simulation of electroosmotic flows in rough wall nanochannels." Phys. Rev. E 73 (2006): 051203.
  12. Saintillan, D., E.S.G. Shaqfeh, and E. Darve. "Effect of flexibility on the shear-induced migration of short-chain polymers in parabolic channel flow." J. Fluid Mech. 557 (2006): 297-306.
  13. Saintillan, D., E. Darve, and E.S.G. Shaqfeh. "Hydrodynamic interactions in the induced-charge electrophoresis of colloidal rod dispersions." J. Fluid Mech. 563 (2006): 223-259.
  14. Saintillan, D., E.S.G. Shaqfeh, and E. Darve. "The effect of stratification on the wave number selection in the instability of sedimenting spheroids." Phys. Fluids 18 (2006): 121503.
  15. Saintillan, D., E.S.G. Shaqfeh, and E. Darve. "Stabilization of a suspension of sedimenting rods by induced-charge electrophoresis." Phys. Fluids 18 (2006): 121701.
  16. Saintillan, D., E.S.G. Shaqfeh, and E. Darve. "The growth of concentration fluctuations in dilute dispersions of orientable and deformable particles under sedimentation." J. Fluid Mech. 553 (2006): 347-388.
  17. Saintillan, D., E. Darve, and E.S.G. Shaqfeh. "A smooth particle-mesh Ewald algorithm for Stokes flow simulations: the sedimentation of fibers." Phys. Fluids 17 (2005): 033301.
  18. Darve, E., and P. Havé. "A fast multipole method for Maxwell equations stable at all frequencies." Phil. Trans. R. Soc. Lond. A 362 (2004): 1-27.
  19. Rodríguez-Gómez, D., E. Darve, and A. Pohorille. "Assessing the efficiency of free energy calculation methods." J. Chem. Phys. 120 (2004): 3563–3578.
  20. Darve, E., and P. Havé. "Efficient fast multipole method for low-frequency scattering." J. Comp. Phys. 197 (2003): 341-363.
  21. Darve, E., M. Wilson, and A. Pohorille. "Calculating free energies using scaled force molecular dynamics algorithm." Mol. Sim. 28 (2002): 113–144.
  22. Darve, E., and A. Pohorille. "Calculating free energies using average force." J. Chem. Phys. 115 (2001): 9169-9183.
  23. Darve, E. "The fast multipole method: numerical implementation." J. Comp. Phys. 160 (2000): 195-240.
  24. Darve, E. "The fast multipole method (I): error analysis and asymptotic complexity." SIAM Num. Anal. 38 (2000): 98-128.
  25. Darve, E. "Fast-multipole: a mathematical study (abridged version)." Comptes Rendus Acad. Sci. Ser. I-Math. 325, no. 9 (1997): 1037-1042.

Other publications and reports

  1. Elsen, E., V. Vishal, M. Houston, V. Pande, P. Hanrahan, and E. Darve. "N-Body Simulations on GPUs". arXiv database, 0706.3060 (June 2007).
  2. Erez, M., J. H. Ahn, A. Garg, W. J. Dally, and E. Darve. "Analysis and Performance Results of a Molecular Modeling Application on Merrimac." Proceedings of the International Conference for High Performance Computing, Networking and Storage Conference (SC2004), November 2004:563-572.
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