Stanford Mechanics and Computation

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Contents

Seminars and talks

  1. Badi' Abdul-Wahid, Ronan Costaouec, Eric Darve, Michelle Feng, Jesus Izaguirre, "Computing Reaction Rates Using Macro-states," 9th AIMS Conference on Dynamical Systems, Differential Equations and Applications, Orlando, Florida, USA, July 1-5, 2012.

Major Publications

Preprints

  1. Cecka, C., and E. Darve. "Fourier Based Fast Multipole Method for the Helmholtz Equation." SIAM Num. Anal., 2010.
  2. Cecka, C., A. Lew, and E. Darve. "Assembly and Solution of Finite Element Methods on Graphics Processors." Int. J. Numer. Meth. Eng., accepted, 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. Cecka, C., A. Lew, and E. Darve. "Introduction to assembly of finite element methods on graphics processors." IOP Conf. Ser.: Mater. Sci. Eng., 10, no. 1 (2010): 012009
  2. Létourneau, P-D, C. Cecka, and E. Darve. "Generalized fast multipole method." IOP Conf. Ser.: Mater. Sci. Eng., 10, no. 1 (2010): 012230
  3. Fong, W., and E. Darve. "The Black-Box Fast Multipole Method." J. Comp. Phys., 228, no. 23 (2009): 8712-8725.
  4. 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.
  5. 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.
  6. Kim, D., and E. Darve. "High ionic strength electroosmotic flows in uncharged hydrophobic nanochannels." J. Coll. Interf. Sci. 330, no. 1 (2009): 194-200.
  7. 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
  8. 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
  9. Fong, W., E. Darve, and A. Lew. "Stability of asynchronous variational integrators." J. Comp. Phys. 227, no. 18 (2008): 8367-8394.
  10. 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.
  11. Kia, A., D. Kim, and E. Darve. "Fast electrostatic force calculation on parallel computer clusters." J. Comp. Phys. 227, no. 19 (2007): 8551-8567.
  12. Li, S., S. Ahmed, and E. Darve. "Fast inverse using nested dissection for NEGF." J. Comput. Electron. 6 (2007): 187-190.
  13. Kim, D. and E. Darve. "Molecular dynamics simulation of electroosmotic flows in rough wall nanochannels." Phys. Rev. E 73 (2006): 051203.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. Rodríguez-Gómez, D., E. Darve, and A. Pohorille. "Assessing the efficiency of free energy calculation methods." J. Chem. Phys. 120 (2004): 3563–3578.
  22. Darve, E., and P. Havé. "Efficient fast multipole method for low-frequency scattering." J. Comp. Phys. 197 (2003): 341-363.
  23. Darve, E., M. Wilson, and A. Pohorille. "Calculating free energies using scaled force molecular dynamics algorithm." Mol. Sim. 28 (2002): 113–144.
  24. Darve, E., and A. Pohorille. "Calculating free energies using average force." J. Chem. Phys. 115 (2001): 9169-9183.
  25. Darve, E. "The fast multipole method: numerical implementation." J. Comp. Phys. 160 (2000): 195-240.
  26. Darve, E. "The fast multipole method (I): error analysis and asymptotic complexity." SIAM Num. Anal. 38 (2000): 98-128.
  27. 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.