@Misc{QB,
   url = {http://www.hpc.lsu.edu/systems/system.php?system=QueenBee},
}

@Misc{Ranger,
   url = {http://www.tacc.utexas.edu/resources/hpc},
}


=== hybrid research articles ===

=== 0. Ours
@inproceedings{ECCOMAS10,
author={S.-H. Ko and N. Kim and D. E. Nikitopoulos and D. Moldovan and S. Jha},
title={Parametric Study of a Multiscale Fluidic System using a Hybrid CFD-MD Approach},
year = {2010},
booktitle = {The 5th European Conference on Computational Fluid Dynamics (ECCOMAS CFD 2010)},
volume={},
number={},
pages={},
keywords={},
doi={},
ISSN={}
}

#@inproceedings{AJK2011,
#author={S.-H. Ko and N. Kim and S. Jha and D. E. Nikitopoulos and D. Moldovan},
#title={Numerical Experiments of Solving Moderate Velocity Flow Field using a Hybrid CFD-MD Approach},
#year = {2011},
#booktitle = {ASME-JSME-KSME 2011 Joint Fluids Engineering Conference: Volume 1, Symposia - Parts A, B, C, and D},
#volume={},
#number={},
#pages={1129-1137},
#keywords={},
#doi={10.1115/AJK2011-01021},
#ISBN={978-0-7918-4440-3}
#}

@article{AJK2011,
author = {Soon-Heum Ko and Nayong Kim and Shantenu Jha and Dimitris E. Nikitopoulos and Dorel Moldovan},
collaboration = {},
title = {Numerical Experiments of Solving Moderate-Velocity Flow Field Using a Hybrid CFD-MD Approach},
publisher = {ASME},
year = {2011},
journal = {ASME Conference Proceedings},
volume = {2011},
number = {44403},
pages = {1129-1137},
url = {http://link.aip.org/link/abstract/ASMECP/v2011/i44403/p1129/s1},
doi = {10.1115/AJK2011-01021}
}


@Article{JoCS2012,
title={Accurate and Efficient Multi-scale Flow Simulation using a Hybrid CFD-MD Approach},
author={S.-H. Ko and N. Kim and D. E. Nikitopoulos and D. Moldovan and S. Jha},
journal={Journal of Computational Science},
year={Submitted},
volume={},
pages={}
}


=== 1. CCLD (crude constrained Lagrangian Dynamics)

@Article{Thompson,
title={Molecular Dynamics Continuum Hybrid Computations: a Tool for Studying Complex Fuid Flows},
author={S. T. O'Connell and P. A. Thompson},
journal={Phys. Rev. E},
year={1995},
volume={52},
pages={R5792-R5795}
}

@Article{Nie,
title={A Continuum and Molecular Dynamics Hybrid Method for Micro- and Nano-Fluid Flow},
author={X. B. Nie and S. Y. Chen and W. N. E and M. O. Robbins},
journal={J. Fluid Mech.},
year={2004},
volume={500},
pages={55-64}
}

@Article{Nie_cavity,
title={Hybrid Continuum-Atomistic Simulation of Singular Corner Flow},
author={X. Nie and S. Chen and M. O. Robbins},
journal={Phys. Fluids},
year={2004},
volume={16},
number={10},
pages={3579-3591}
}

@Article{Cui,
title={A Constrained Particle Dynamics for Continuum-Particle Hybrid Method in Micro- and Nano-fluidics},
author={J. Cui and G. W. He and D. Qi},
journal={Acta. Mech. Sin.},
year={2006},
volume={22},
pages={503-508}
}

@Article{Wang,
title={A Dynamic Coupling Model for Hybrid Atomistic-Continuum Computations},
author={Y. C. Wang and G. He},
journal={J. Comput. Phys.},
year={2007},
volume={62},
number={},
pages={3574-3579},
keywords={},
doi={},
ISSN={}
}

@Article{Yen,
title={Hybrid Molecular Dynamics-Continuum Simulation for Nano/Mesoscale Channel Flow},
author={T. H. Yen and C. Y. Soong and P. Y. Tzeng},
journal={Microfluid Nanofluid},
year={2007},
volume={3},
pages={665-675}
}

@Article{Liu,
title={A Continuum-Atomistic Multi-Timescale Algorithm for Micro/Nano Flows},
author={J. Liu and S. Chen and X. Nie and M. O. Robbins},
journal={Commun. Comp. Phys.},
year={2008},
volume={4},
number={5},
pages={1279-1291}
}


=== 2. Flux based

@Article{Flekkoy,
title={Hybrid Model for Combined Particle and Continuum Dynamics},
author={E. G. Flekk$\phi$y and G. Wagner and J. Feder},
journal={Europhys Lett.},
year={2000},
volume={52},
number={},
pages={271-276},
keywords={},
doi={},
ISSN={}
}

@Article{Wagner,
title={Coupling Molecular Dynamics and Continuum Dynamics},
author={G. Wagner and E. G. Flekk$\phi$y and J. Feder and T. Jossang},
journal={Comput. Phys. Commun.},
year={2002},
volume={147},
number={},
pages={670-673},
keywords={},
doi={},
ISSN={}
}

@Article{Delgado1,
title={Continuum-particle Hybrid Coupling for Mass, Momentum and Energy Transfers in Unsteady Flow},
author={R. Delgado-Buscalioni and P. V. Coveney},
journal={Phys. Rev. E},
year={2003},
volume={67},
number={046704},
pages={1-13},
keywords={},
doi={},
ISSN={},
}

@Article{USHER,
title={USHER: An algorithm for particle insertion in dense fluids},
author={R. Delgado-Buscalioni and P. V. Coveney},
journal={J. Chem. Phys.},
year={2003},
volume={119},
number={2},
pages={978-987},
keywords={},
doi={},
ISSN={},
}

@Article{Time_Mechanism,
title={Hybrid Molecular-Continuum Fluid Dynamics},
author={R. Delgado-Buscalioni and P. V. Coveney},
journal={Phil. Trans. R. Soc. Lond. A},
year={2004},
volume={362},
number={},
pages={1639-1654},
keywords={},
doi={},
ISSN={},
}

@Article{Giupponi,
title={A Hybrid Method Coupling Fluctuating Hydrodynamics and Molecular Dynamics for the Simulation of Macromolecules},
author={G. Giupponi and G. D. Fabritiis and P. V. Covney},
journal={J. Chem. Phys.},
year={2007},
volume={126},
number={},
pages={154903-1--154903-8},
keywords={},
doi={},
ISSN={},
}


=== 3. alternating Schwartz

@Article{Hadjicon1,
title={Heterogeneous Atomistic Continuum Representations for Dense Fluid Systems},
author={N. G. Hadjiconstantinou and A. T. Patera},
journal={International Journal of Modern Physics C},
year={1997},
volume={8},
number={},
pages={967-976},
keywords={},
doi={},
ISSN={}
}

@Article{Hadjicon2,
title={Hybrid Atomistic-Continuum Formulations and the Moving Contact-Line Problem},
author={N. G. Hadjiconstantinou},
journal={J. Comput. Phys.},
year={1999},
volume={154},
pages={245-265},
keywords={},
doi={},
ISSN={}
}

@Article{Hadjicon3,
title={Statistical Error in Particle Simulations of Hydrodynamic Phenomena},
author={N. G. Hadjiconstantinou and A. L. Garcia and M. Z. Bazant and G. He},
journal={J. Comput. Phys.},
year={2003},
volume={187},
number={},
pages={274-297},
keywords={},
doi={},
ISSN={}
}

@Article{Werder,
title={Hybrid Atomistic-Continuum Method for the Simulation of Dense Fluid Flows},
author={T. Werder, J. H. Walther, P. Koumoutsakos},
journal={J. Comput. Phys.},
year={2005},
volume={205},
pages={373-390},
keywords={},
doi={},
ISSN={}
}

@Article{Kotsalis,
title={Control Algorithm for Multiscale Flow Simulations of Water},
author={E. M. Kotsalis and J. H. Walter and E. Kaxiras and P. Koumoutsakos},
journal={Phys. Rev. E.},
year={2009},
volume={79},
pages={045701}
}

@Article{Garcia,
title={Generation of the Chapman-Enskog Distribution},
author={A. Garcia and B. Alder},
journal={J. Comput. Phys.},
year={1998},
volume={140},
pages={66-70}
}




=== 4. Other approaches

== DSMC

@Article{Garcia,
title={Adaptive Mesh and Algorithm Refinement Using Direct Simulation Monte Carlo},
author={A. Garcia and J. Bell and W. Crutchfield and B. Alder},
journal={J. Comput. Phys.},
year={1999},
volume={154},
pages={134-155}
}

@Article{Sun,
title={A Hybrid Continuum/Particle Approach for Modeling Subsonic, Rarefied Gas Flows},
author={Q. Sun and I. Boyd and G. Candler},
journal={J. Comput. Phys.},
year={2004},
volume={194},
pages={256-277}
}

== DPD

@Article{Fedosov1,
title={Velocity Limit in DPD Simulations of Wall-bounded Flows},
author={D. A. Fedosov and I. V. Pivkin and G. E. Karniadakis},
journal={J. Comput. Phys.},
year={2008},
volume={227},
pages={2540-2559}
}

@Article{Fedosov2,
title={Triple-decker: Interfacing Atomistic-Mesoscopic-Continuum Flow Regimes},
author={D. A. Fedosov and G. E. Karniadakis},
journal={J. Comput. Phys.},
year={2009},
volume={228},
pages={1157-1171}
}



=== 5. BC control and parallel

@Article{Ren,
title={Heterogeneous Multiscale Method for the Modeling of Complex Fluids and Micro-fluidics},
author={W. Ren and W. E},
journal={J. Comput. Phys.},
year={2005},
volume={204},
number={},
pages={1-26}
}


@Article{Steijl,
title={Coupled Navier-Stokes--Molecular Dynamics Simulations Using a Multi-physics Flow Simulation Framework},
author={R. Steijl and G. N. Barakos},
journal={Int. J. Numer. Meth. Fluids},
year={2001},
volume={62},
number={10},
pages={1081-1106}
}



=== 6. review articles

@Article{Koumoutsakos,
title={Multiscale Flow Simulations Using Particles},
author={P. Koumoutsakos},
journal={Annu. Rev. Fluid Mech.},
year={2005},
volume={37},
pages={457-487}
}


=== 7. MD simulation on those problems

@Article{Travis,
title={Poiseuille flow of Lennard-Jones fluids in narrow slit pores},
author={Travis, K.P and Gubbins, K.E},
journal={J. Chem. Phys.},
year={2000},
volume={112},
pages={1984-1994}
}



=== CFD article ===

@Article{Lee,
title={Design of Flapping Airfoil for Optimal Aerodynamic Performance in Low-Reynolds Number Flows},
author={Jung-Sang Lee and Chongam Kim and Kyu Hong Kim},
journal={AIAA Journal},
year={2006},
volume={44},
pages={1960-1972}
}

@Article{PseudoCompressibility,
title={An Upwind Differecing Scheme for the Time-Accurate Incompressible Navier-Stokes Equations},
author={S. E. Rosers and D. Kwak},
journal={AIAA J.},
year={1990},
volume={28},
number={},
pages={253-262},
keywords={},
doi={},
ISSN={}
}

@Article{LU-SGS,
title={Lower-Upper Symmetric-Gauss-Seidel Method for the Euler and Navier-Stokes Equations},
author={S. Yoon and A. Jameson},
journal={AIAA J.},
year={1988},
volume={26},
number={},
pages={1025-1026},
keywords={},
doi={},
ISSN={}
}

@Article{Osher,
title={An Implicit Form of the Osher Upwind Scheme},
author={M. M. Rai and S. R. Chakaravarthy},
journal={AIAA J.},
year={1986},
volume={24},
number={},
pages={735-743},
keywords={},
doi={},
ISSN={}
}

@Article{MUSCL,
title={Towards the Ultimate Conservative Difference Scheme. V. A Second Order Sequel to Godunov's Methods},
author={B. Van Leer},
journal={J. Comput. Phys.},
year={1979},
volume={32},
number={},
pages={101-136},
keywords={},
doi={},
ISSN={}
}

@Article{Chimera,
title={A Chimera Grid Scheme},
author={J. L. Steger and F. C. Dougherty and J. A. Benek},
journal={Advances in Grid Generation},
year={1983},
volume={FED Vol. 5},
number={},
pages={59-69},
keywords={},
doi={},
ISSN={},
publisher = {American Society of Mechanical Engineers},
address = {New York}
}


=== MD article ===

@book{Allen, author = {M. Allen and D. Tildesley},  title = {Computer Simulation of Liquids},  year = {1987},  isbn = {},  publisher = {Oxford Science Publications},  address = {}  }

@book{Haile, author = {J. M. Haile},  title = {Molecular Dynamics Simulation. Elementary Methods},  year = {1992},  isbn = {},  publisher = {Wiley, Chichester},  address = {}  }

@book{Rapaport, author = {D C. Rapaport},  title = {The Art of Motecutar Dynamics Simulation},  year = {1995},  isbn = {},  publisher = {Cambridge University Press},  address = {}  }

@book{,  author = {},  title = {The Art of Motecutar Dynamics Simulation},  year = {1995},  isbn = {},  publisher = {Cambridge University Press},  address = {}  }

@Link{LAMMPS_url,
      author = "LAMMPS",
      howpublished  = "\url{http://lammps.sandia.gov}",
}

@Article{REMD,
title={Replica-exchange Molecular Dynamics Method for Protein Folding},
author={Yuji Sugita and Yuko Okamoto},
journal={Chemical Physics Letters},
year={1999},
volume={314},
number={},
pages={141-151},
keywords={},
doi={},
ISSN={},
}


=== Framework related ===

=== 0. Ours

@inproceedings{CCGrid_Hybrid,
author={S.-H. Ko and N. Kim and J. Kim and A. Thota and S. Jha},
title={Efficient Runtime Environment for Coupled Multi-Physics Simulations: Dynamic Resource Allocation and Load-Balancing},
year = {2010},
booktitle = { The 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2010)},
volume={},
number={},
pages={},
keywords={},
doi={},
ISSN={}
}


=== 1. Load balancing

@Article{Ko,
title={Load Balancing for CFD Applications in Grid Computing Environment},
author={Soon-Heum Ko and Chongam Kim and Oh-Hyun Rho and Kum Won Cho},
journal={KSAS International Journal},
year={2004},
volume={5},
pages={77-87}
}


=== 2. Components for the framework design

--- Versioning
@misc{CVS,
        author = {{Concurrent Versioning System}},
        note  = {{http://www.cvshome.org/eng/}},
        url  = {{http://www.cvshome.org/eng/}}
}

@misc{SVN,
        author = {{Apache Subversion}},
        note  = {{http://subversion.apache.org/}},
        url  = {{http://subversion.apache.org/}}
}

@misc{GIT,
        author = {{The fast version control system}},
        note  = {{http://git-scm.com/}},
        url  = {{http://git-scm.com/}}
}

--- Data management
@misc{PetaShare,
        author = {{A Distributed Data Archival, Analysis and Visualization Cyberinfrastructure for Data-intensive Collaborative Research}},
        note  = {{http://www.petashare.org/}},
        url  = {{http://www.petashare.org/}}
}

--- Compilation
@misc{SimFactory,
        author = {{The Simulation Factory}},
        note  = {{http://simfactory.org/}},
        url  = {{http://simfactory.org/}}
}

--- Scheduling and runtime
@misc{Condor,
        author = {{Condor Project}},
        note  = {{http://www.cs.wisc.edu/condor/}}
}
     
@article{PilotFactory,
  author    = {Chiu, Po-Hsiang and
               Potekhin, Maxim},
  title     = {Pilot Factory ??a Condor-based system for scalable Pilot Job
               generation in the Panda WMS framework},
  journal   = {Journal fo Physics: Conference Series},
  volume = {219},
  issue = {},
  year      = {2010},
  pages = {062041:1-7}
}