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ibm.bib
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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for Lorena A Barba at 2019-03-24 09:47:43 -0400
%% Saved with string encoding Unicode (UTF-8)
@string{annu = {Annu.\ Rev.\ Fluid Mech.}}
@string{cnf = {Comput.\ Fluids}}
@string{jcp = {J. Comput.\ Phys.}}
@string{jeb = {J. Exp.\ Biol.}}
@string{jfm = {J. Fluid Mech.}}
@string{pnas = {P.\ Natl.\ Acad.\ Sci. USA}}
@string{pof = {Phys.\ Fluids}}
@string{rsb = {Philos.\ T.\ R. Soc.\ B}}
@article{ChuangBarba2017,
Author = {Chuang, Pi-Yueh and Lorena A. Barba},
Date-Added = {2019-03-24 09:12:37 -0400},
Date-Modified = {2019-03-24 09:12:48 -0400},
Doi = {10.21105/joss.00280},
Journal = {J. Open Source Software},
Month = {August},
Note = {\href{https://doi.org/10.21105/joss.00280}{10.21105/joss.00280}},
Number = {16},
Publisher = {The Open Journal},
Title = {{AmgXWrapper}: An interface between {PETSc} and the {NVIDIA} {AmgX} library},
Url = {https://doi.org/10.21105/joss.00280},
Volume = {2},
Year = {2017},
Bdsk-Url-1 = {https://doi.org/10.21105/joss.00280},
Bdsk-Url-2 = {http://dx.doi.org/10.21105/joss.00280}}
@article{ChuangETal2018,
Author = {Chuang, Pi-Yueh and Mesnard, Olivier and Krishnan Anush and Barba, Lorena A.},
Date-Added = {2019-03-24 09:10:56 -0400},
Date-Modified = {2019-03-24 09:11:13 -0400},
Journal = {J. Open Source Software},
Note = {\href{https://doi.org/10.21105/joss.00558}{doi:10.21105/joss.00558}},
Number = {25},
Pages = {558},
Title = {{PetIBM}: toolbox and applications of the immersed-boundary method on distributed-memory architectures},
Volume = {3},
Year = {2018}}
@article{KrishnanETal2017,
Author = {Krishnan, Anush and Mesnard, Olivier and Lorena A. Barba},
Date-Added = {2019-03-23 18:45:54 -0400},
Date-Modified = {2019-03-23 18:46:08 -0400},
Doi = {10.21105/joss.00301},
Journal = {J. Open Source Software},
Keywords = {cuIBM, JOSS},
Month = {July},
Note = {\href{http://dx.doi.org/10.21105/joss.00301}{10.21105/joss.00301}},
Number = {15},
Publisher = {The Open Journal},
Title = {{cuIBM}: a {GPU}-based immersed boundary method code},
Url = {https://doi.org/10.21105/joss.00301},
Volume = {2},
Year = {2017},
Bdsk-Url-1 = {https://doi.org/10.21105/joss.00301},
Bdsk-Url-2 = {http://dx.doi.org/10.21105/joss.00301}}
@misc{KrishnanBarba-share92789,
Author = {Krishnan, Anush and Barba, L.~A.},
Doi = {10.6084/m9.figshare.92789},
Howpublished = {Technical Report on \textbf{figshare}, CC-BY license, \href{http://dx.doi.org/10.6084/m9.figshare.92789}{doi:10.6084/m9.figshare.92789}},
Month = {6 July},
Title = {Validation of the \texttt{{cuIBM}} code for {Navier-Stokes} equations with immersed boundary methods},
Year = {2012},
Bdsk-Url-1 = {https://doi.org/10.6084/m9.figshare.92789}}
@article{FauciPeskin88,
Author = {Fauci, L. J. and Peskin, C. S.},
Journal = jcp,
Pages = {85},
Title = {A computational model of aquatic animal locomotion},
Volume = {77},
Year = 1988}
@article{PeskinMcqueen89,
Author = {Peskin, C. S. and McQueen, D.M.},
Journal = jcp,
Pages = {372},
Title = {A three-dimensional computational method for blood flow in the heart. {I}. {I}mmersed elastic fibers in a viscous incompressible fluid},
Volume = {81},
Year = 1989}
@article{PeskinMcqueen93,
Author = {Peskin, C. S. and McQueen, D. M.},
Date-Added = {2012-02-28 12:22:34 -0500},
Date-Modified = {2012-02-28 12:23:42 -0500},
Journal = {Contemp.\ Math.},
Pages = {161--186},
Title = {Computational biofluid dynamics},
Volume = {141},
Year = 1993}
@article{Peskin72,
Author = {Peskin, C. S.},
Date-Added = {2012-02-28 12:22:34 -0500},
Date-Modified = {2012-02-28 12:24:20 -0500},
Journal = jcp,
Pages = {252--271},
Title = {Flow patterns around heart valves: {A} numerical method},
Volume = {10},
Year = 1972}
@article{Peskin77,
Author = {Peskin, C. S.},
Date-Added = {2012-02-28 12:22:34 -0500},
Date-Modified = {2012-02-28 12:24:10 -0500},
Journal = jcp,
Pages = {220--252},
Title = {Numerical analysis of blood flow in the heart},
Volume = {25},
Year = 1977}
@article{Peskin82,
Author = {Peskin, C. S.},
Date-Added = {2012-02-28 12:22:34 -0500},
Date-Modified = {2012-02-28 12:23:59 -0500},
Journal = annu,
Pages = {235},
Title = {The fluid dynamics of heart valves: Experimental, theoretical and computational methods},
Volume = {14},
Year = 1982}
@article{ArthursETal98,
Author = {Arthurs, K. M. and Moore, L. C. and Peskin, C. S. and Pitman, E. B. and Layton, H. E.},
Date-Added = {2012-02-28 12:21:56 -0500},
Date-Modified = {2012-02-28 12:22:21 -0500},
Journal = jcp,
Pages = {402--440},
Title = {Modeling arteriolar flow and mass transport using the immersed boundary method},
Volume = {147},
Year = {1998}}
@unpublished{LaytonKrishnanBarba2012,
Author = {Layton, Simon K. and Krishnan, Anush and Barba, L.~A.},
Date-Added = {2012-02-27 15:27:09 -0500},
Date-Modified = {2014-01-08 20:40:40 +0000},
Note = {Unpublished preprint on \href{http://arxiv.org/abs/1109.3524}{arXiv:1109.3524}},
Title = {{cuIBM---A GPU} accelerated immersed boundary method},
Year = {2012}}
@article{Lewin2003,
Author = {G. C. Lewin and H. Haj-Hariri},
Date-Added = {2011-09-12 22:04:41 -0400},
Date-Modified = {2011-09-12 22:05:42 -0400},
Journal = jfm,
Pages = {339--362},
Title = {Modelling thrust generation of a two-dimensional heaving airfoil in a viscous flow},
Volume = {492},
Year = {2003}}
@article{Koumoutsakos1995,
Author = {P. Koumoutsakos and A. Leonard},
Date-Added = {2011-09-10 19:01:45 -0400},
Date-Modified = {2011-09-10 19:02:38 -0400},
Journal = jfm,
Pages = {1--38},
Title = {High-resolution simulations of the flow around an impulsively started cylinder using vortex methods},
Volume = {296},
Year = {1995}}
@article{WangZJ2004,
Author = {Z Jane Wang and James M Birch and Michael H Dickinson},
Date-Added = {2011-09-10 18:29:22 -0400},
Date-Modified = {2012-02-27 15:37:22 -0500},
Journal = jeb,
Pages = {449--460},
Title = {Unsteady forces and flows in low {R}eynolds number hovering flight: two-dimensional computations vs robotic wing experiments},
Volume = {207},
Year = {2004}}
@article{Angot1999,
Author = {Angot, Philippe and Bruneau, Charles-henri and Fabrie, Pierre},
Journal = {Numerische Mathematik},
Pages = {497--520},
Title = {{A penalization method to take into account obstacles in incompressible viscous flows}},
Url = {http://www.springerlink.com/index/98TK9N6DBT5VP51L.pdf},
Year = {1999},
Bdsk-Url-1 = {http://www.springerlink.com/index/98TK9N6DBT5VP51L.pdf}}
@phdthesis{Bandringa2010,
Author = {Bandringa, Henry},
Booktitle = {International Journal for Numerical Methods in Fluids},
Doi = {10.1002/fld.1077},
Number = {6},
School = {Institute of Mathematics and Computing},
Title = {{Immersed boundary methods}},
Type = {Master Thesis},
Volume = {191},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1002/fld.1077}}
@article{Bonfigli2010,
Author = {Bonfigli, Giuseppe},
Doi = {10.1016/j.compfluid.2010.10.014},
Issn = {0045-7930},
Journal = {Comput. Fluids},
Month = nov,
Publisher = {Elsevier},
Title = {{High-order finite-difference implementation of the immersed-boundary technique for incompressible flows}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0045793010002823},
Volume = {di},
Year = {2010},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0045793010002823},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.compfluid.2010.10.014}}
@article{Chiu2010,
Author = {Chiu, P.H. and Lin, R.K. and Sheu, Tony W.H.},
Doi = {10.1016/j.jcp.2010.02.013},
Issn = {00219991},
Journal = jcp,
Keywords = {dispersion-relation-preserving},
Month = jun,
Number = {12},
Pages = {4476--4500},
Publisher = {Elsevier Inc.},
Title = {{A differentially interpolated direct forcing immersed boundary method for predicting incompressible Navier--Stokes equations in time-varying complex geometries}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999110000860},
Volume = {229},
Year = {2010},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999110000860},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2010.02.013}}
@article{Choi2007,
Author = {Choi, J and Oberoi, R and Edwards, J and Rosati, J},
Doi = {10.1016/j.jcp.2006.10.032},
Issn = {00219991},
Journal = jcp,
Keywords = {high reynolds number flows,immersed boundary method,incompressible navier,stokes equations},
Month = jun,
Number = {2},
Pages = {757--784},
Title = {{An immersed boundary method for complex incompressible flows}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999106005481},
Volume = {224},
Year = {2007},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999106005481},
Bdsk-Url-2 = {https://doi.org/10.1016/j.jcp.2006.10.032}}
@article{Colonius2008,
Author = {Colonius, T. and Taira, K.},
Date-Modified = {2011-03-26 21:32:22 -0400},
Doi = {10.1016/j.cma.2007.08.014},
Issn = {00457825},
Journal = {Computer Methods in Applied Mechanics and Engineering},
Keywords = {boundary conditions,far-field,fast poisson solver,finite volume method,fractional step method,immersed boundary method,incompressible viscous flow,multi-domain method,nullspace method,projection method,streamfunction formulation,vorticity},
Number = {25-28},
Pages = {2131--2146},
Title = {A fast immersed boundary method using a nullspace approach and multi-domain far-field boundary conditions},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0045782507003362},
Volume = {197},
Year = {2008},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0045782507003362},
Bdsk-Url-2 = {https://doi.org/10.1016/j.cma.2007.08.014}}
@article{Fadlun2000,
Author = {Fadlun, E. and Verzicco, R. and Orlandi, P. and Mohd-Yusof, J.},
Date-Modified = {2012-07-07 20:05:31 +0000},
Journal = jcp,
Keywords = {immersed boundaries},
Number = {1},
Pages = {35--60},
Title = {Combined Immersed-Boundary Finite-Difference Methods for Three-Dimensional Complex Flow Simulations},
Volume = {161},
Year = {2000}}
@article{Ge2007,
Author = {Ge, Liang and Sotiropoulos, Fotis},
Doi = {10.1016/j.jcp.2007.02.017},
Journal = jcp,
Keywords = {curvilinear coordinates,fractional step method,heart valves,immersed boundaries,incompressible flow,krylov solvers,navier,staggered grid,stokes},
Month = aug,
Number = {2},
Pages = {1782--1809},
Pmid = {19194533},
Title = {{A Numerical Method for Solving the 3D Unsteady Incompressible Navier-Stokes Equations in Curvilinear Domains with Complex Immersed Boundaries.}},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19194533},
Volume = {225},
Year = {2007},
Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/19194533},
Bdsk-Url-2 = {https://doi.org/10.1016/j.jcp.2007.02.017}}
@article{Ghias2004,
Author = {Ghias, Reza and Mittal, Rajat and Lund, T.S.},
Journal = {AIAA Paper},
Number = {January},
Pages = {2004},
Title = {{A non-body conformal grid method for simulation of compressible flows with complex immersed boundaries}},
Url = {http://project.seas.gwu.edu/\~{}fsagmae/papers/AIAA2004-0080.pdf},
Volume = {80},
Year = {2004},
Bdsk-Url-1 = {http://project.seas.gwu.edu/%5C~%7B%7Dfsagmae/papers/AIAA2004-0080.pdf}}
@article{Goddeke2008,
Author = {Goddeke, D and Strzodka, Robert and Mohd-Yusof, J and P},
Date-Modified = {2011-03-25 16:23:44 -0400},
Journal = {International Journal of Computational Science and Engineering},
Keywords = {domain decomposition,finite element calculations,gpus,mixed precision,multigrid solvers,oddeke et al,parallel scientific computing,point co-processors,reference to this paper,should be made as,using},
Number = {1991},
Title = {{Using GPUs to improve multigrid solver performance on a cluster}},
Url = {http://inderscience.metapress.com/index/92MM0GG171405064.pdf},
Year = {2008},
Bdsk-Url-1 = {http://inderscience.metapress.com/index/92MM0GG171405064.pdf}}
@article{Goldstein2006,
Author = {Goldstein, D. and Handler, R. and Sirovich, L.},
Doi = {10.1017/S0022112095004125},
Issn = {0022-1120},
Journal = jfm,
Month = apr,
Pages = {333},
Title = {{Direct numerical simulation of turbulent flow over a modeled riblet covered surface}},
Volume = {302},
Year = {2006},
Bdsk-Url-1 = {https://doi.org/10.1017/S0022112095004125}}
@article{Goldstein1993,
Author = {Goldstein, D and Handler, R and Sirovich, L},
Journal = jcp,
Title = {{Modeling a No-Slip Flow Boundary with an External Force Field}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999183710818},
Year = {1993},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999183710818}}
@unpublished{Griffith,
Author = {Griffith, B.E.},
Booktitle = {math.nyu.edu},
Date-Modified = {2011-03-25 21:03:23 -0400},
Keywords = {collocated,finite-difference method,fluid-structure interaction,immersed boundary method,staggered grid discretization,volume conservation},
Title = {{On the volume conservation of the immersed boundary method}},
Url = {http://www.math.nyu.edu/\~{}griffith/docs/griffith\_ib\_volume\_conservation\_sub.pdf},
Volume = {c},
Bdsk-Url-1 = {http://www.math.nyu.edu/%5C~%7B%7Dgriffith/docs/griffith%5C_ib%5C_volume%5C_conservation%5C_sub.pdf}}
@article{Griffith2007,
Author = {Griffith, B and Hornung, R and Mcqueen, D and Peskin, C},
Date-Modified = {2011-03-25 16:23:14 -0400},
Doi = {10.1016/j.jcp.2006.08.019},
Issn = {00219991},
Journal = jcp,
Keywords = {adaptive mesh refinement,immersed boundary method,projection method},
Month = {April},
Number = {1},
Pages = {10--49},
Title = {{An adaptive, formally second order accurate version of the immersed boundary method}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999106004207},
Volume = {223},
Year = {2007},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999106004207},
Bdsk-Url-2 = {https://doi.org/10.1016/j.jcp.2006.08.019}}
@article{Hieber2008,
Author = {Hieber, S and Koumoutsakos, P},
Doi = {10.1016/j.jcp.2008.06.017},
Issn = {00219991},
Journal = jcp,
Month = oct,
Number = {19},
Pages = {8636--8654},
Title = {{An immersed boundary method for smoothed particle hydrodynamics of self-propelled swimmers}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999108003343},
Volume = {227},
Year = {2008},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999108003343},
Bdsk-Url-2 = {https://doi.org/10.1016/j.jcp.2008.06.017}}
@article{Hou2008,
Author = {Hou, T and Shi, Z},
Doi = {10.1016/j.jcp.2008.07.005},
Issn = {00219991},
Journal = jcp,
Keywords = {immersed boundary method,implicit discretization,navier,stokes equations},
Month = oct,
Number = {20},
Pages = {8968--8991},
Title = {{An efficient semi-implicit immersed boundary method for the Navier--Stokes equations}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999108003732},
Volume = {227},
Year = {2008},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999108003732},
Bdsk-Url-2 = {https://doi.org/10.1016/j.jcp.2008.07.005}}
@article{Hou2008a,
Author = {Hou, T and Shi, Z},
Doi = {10.1016/j.jcp.2008.03.002},
Issn = {00219991},
Journal = jcp,
Keywords = {immersed boundary method,incompressible flow,removing the stiffness,stokes equations},
Month = nov,
Number = {21},
Pages = {9138--9169},
Title = {{Removing the stiffness of elastic force from the immersed boundary method for the 2D Stokes equations}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S002199910800137X},
Volume = {227},
Year = {2008},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S002199910800137X},
Bdsk-Url-2 = {https://doi.org/10.1016/j.jcp.2008.03.002}}
@article{Huang2009,
Author = {Huang, Wei-Xi and Sung, Hyung Jin},
Doi = {10.1016/j.cma.2009.03.008},
Issn = {00457825},
Journal = {Computer Methods in Applied Mechanics and Engineering},
Keywords = {fluid,structure interaction},
Month = jul,
Number = {33-36},
Pages = {2650--2661},
Publisher = {Elsevier B.V.},
Title = {{An immersed boundary method for fluid--flexible structure interaction}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0045782509001339},
Volume = {198},
Year = {2009},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0045782509001339},
Bdsk-Url-2 = {https://doi.org/10.1016/j.cma.2009.03.008}}
@article{Iaccarino2003,
Author = {Iaccarino, Gianluca and Verzicco, Roberto},
Doi = {10.1115/1.1563627},
Issn = {00036900},
Journal = {Appl.\ Mech.\ Rev.},
Number = {3},
Pages = {331},
Title = {{Immersed boundary technique for turbulent flow simulations}},
Url = {http://link.aip.org/link/AMREAD/v56/i3/p331/s1\&Agg=doi},
Volume = {56},
Year = {2003},
Bdsk-Url-1 = {http://link.aip.org/link/AMREAD/v56/i3/p331/s1%5C&Agg=doi},
Bdsk-Url-2 = {https://doi.org/10.1115/1.1563627}}
@article{Kalitzin2003,
Author = {Kalitzin, G. and Iaccarino, Gianluca},
Institution = {Center for Turbulence Research, Stanford University},
Journal = {Annual Research Briefs},
Title = {{Toward immersed boundary simulation of high Reynolds number flows}},
Year = {2003}}
@article{Kang2000,
Author = {Kang, Myungjoo and Fedkiw, RP and Liu, XD},
Journal = {Journal of Scientific Computing},
Title = {{A boundary condition capturing method for multiphase incompressible flow}},
Url = {http://www.springerlink.com/index/W123625121021441.pdf},
Year = {2000},
Bdsk-Url-1 = {http://www.springerlink.com/index/W123625121021441.pdf}}
@phdthesis{Kang2008,
Author = {Kang, Seongwon},
Number = {June},
School = {Stanford University},
Title = {{An improved immersed boundary method for computation of turbulent flows with heat transfer}},
Year = {2008}}
@article{Kevlahan2001,
Author = {Kevlahan, N},
Doi = {10.1016/S0997-7546(00)01121-3},
Issn = {09977546},
Journal = {European Journal of Mechanics - B/Fluids},
Month = jun,
Number = {3},
Pages = {333--350},
Title = {{Computation of turbulent flow past an array of cylinders using a spectral method with Brinkman penalization}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0997754600011213},
Volume = {20},
Year = {2001},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0997754600011213},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/S0997-7546(00)01121-3}}
@article{Khadra2000,
Author = {Khadra, Khodor and Angot, Philippe and Parneix, Sacha and Caltagirone, Jean-Paul},
Doi = {10.1002/1097-0363(20001230)34:8<651::AID-FLD61>3.0.CO;2-D},
Issn = {0271-2091},
Journal = {International Journal for Numerical Methods in Fluids},
Keywords = {backward-facing step flow,brinkman model,fictitious domain method,multi-grid local mesh refinement,multi-level zoom fic method,navier,obstacle,stokes,wake of a bluff},
Month = dec,
Number = {8},
Pages = {651--684},
Title = {{Fictitious domain approach for numerical modelling of Navier-Stokes equations}},
Url = {http://doi.wiley.com/10.1002/1097-0363\%2820001230\%2934\%3A8\%3C651\%3A\%3AAID-FLD61\%3E3.0.CO\%3B2-D},
Volume = {34},
Year = {2000},
Bdsk-Url-1 = {http://doi.wiley.com/10.1002/1097-0363%5C%2820001230%5C%2934%5C%3A8%5C%3C651%5C%3A%5C%3AAID-FLD61%5C%3E3.0.CO%5C%3B2-D},
Bdsk-Url-2 = {https://doi.org/10.1002/1097-0363(20001230)34:8%3C651::AID-FLD61%3E3.0.CO;2-D}}
@article{Kim2006,
Author = {Kim, D and Choi, H},
Doi = {10.1016/j.jcp.2005.07.010},
Journal = jcp,
Keywords = {arbitrarily moving body,entum forcing,fluid,immersed boundary method,mass source or sink,mom-,non-inertial reference frame,structure interaction},
Month = mar,
Number = {2},
Pages = {662--680},
Title = {{Immersed boundary method for flow around an arbitrarily moving body}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999105003505},
Volume = {212},
Year = {2006},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999105003505},
Bdsk-Url-2 = {https://doi.org/10.1016/j.jcp.2005.07.010}}
@article{Lai2000,
Author = {Lai, M.C. and Peskin, Charles S},
Date-Modified = {2011-03-25 21:23:28 -0400},
Journal = jcp,
Number = {2},
Pages = {705--719},
Publisher = {Elsevier},
Title = {An Immersed Boundary Method with Formal Second-Order Accuracy and Reduced Numerical Viscosity},
Volume = {160},
Year = {2000}}
@article{Li2001,
Author = {Li, Z},
Doi = {10.1006/jcph.2001.6813},
Issn = {00219991},
Journal = jcp,
Keywords = {discontinuous and nonsmooth so-,immersed boundary method,immersed interface method,interface,lution,navier,projection method,stokes equations},
Month = aug,
Number = {2},
Pages = {822--842},
Title = {{The Immersed Interface Method for the Navier--Stokes Equations with Singular Forces}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999101968135},
Volume = {171},
Year = {2001},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999101968135},
Bdsk-Url-2 = {https://doi.org/10.1006/jcph.2001.6813}}
@article{LimaESilva2003,
Author = {{Lima E Silva}, a},
Doi = {10.1016/S0021-9991(03)00214-6},
Issn = {00219991},
Journal = jcp,
Keywords = {drag coefficient,eulerian,finite-difference method,immersed-boundary method,lagrangian formulation},
Month = aug,
Number = {2},
Pages = {351--370},
Title = {{Numerical simulation of two-dimensional flows over a circular cylinder using the immersed boundary method}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999103002146},
Volume = {189},
Year = {2003},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999103002146},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/S0021-9991(03)00214-6}}
@article{Linnick2005,
Author = {Linnick, M and Fasel, H},
Date-Modified = {2011-03-25 16:26:55 -0400},
Doi = {10.1016/j.jcp.2004.09.017},
Issn = {00219991},
Journal = jcp,
Keywords = {immersed boundaries},
Month = mar,
Number = {1},
Pages = {157--192},
Title = {{A high-order immersed interface method for simulating unsteady incompressible flows on irregular domains}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999104004127},
Volume = {204},
Year = {2005},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999104004127},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2004.09.017}}
@article{Marella2005,
Author = {Marella, S and Krishnan, S and Liu, H and Udaykumar, H},
Doi = {10.1016/j.jcp.2005.03.031},
Issn = {00219991},
Journal = jcp,
Keywords = {cartesian grid,level-sets,moving boundaries,sharp interface method},
Month = nov,
Number = {1},
Pages = {1--31},
Title = {{Sharp interface Cartesian grid method I: An easily implemented technique for 3D moving boundary computations}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999105001956},
Volume = {210},
Year = {2005},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999105001956},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2005.03.031}}
@article{Miller2004,
Abstract = {We have used computational fluid dynamics to study changes in lift generation and vortex dynamics for Reynolds numbers (Re) between 8 and 128. The immersed boundary method was used to model a two-dimensional wing through one stroke cycle. We calculated lift and drag coefficients as a function of time and related changes in lift to the shedding or attachment of the leading and trailing edge vortices. We find that the fluid dynamics around the wing fall into two distinct patterns. For Re> or =64, leading and trailing edge vortices are alternately shed behind the wing, forming the von Karman vortex street. For Re< or =32, the leading and trailing edge vortices remain attached to the wing during each 'half stroke'. In three-dimensional studies, large lift forces are produced by 'vortical asymmetry' when the leading edge vortex remains attached to the wing for the duration of each half stroke and the trailing edge vortex is shed. Our two-dimensional study suggests that this asymmetry is lost for Re below some critical value (between 32 and 64), resulting in lower lift forces. We suggest that this transition in fluid dynamics is significant for lift generation in tiny insects.},
Author = {Miller, Laura A and Peskin, Charles S},
Date-Modified = {2011-03-25 16:24:52 -0400},
Doi = {10.1242/jeb.01138},
Issn = {0022-0949},
Journal = {The Journal of Experimental Biology},
Keywords = {insect flight},
Month = aug,
Number = {Pt 17},
Pages = {3073--88},
Pmid = {15277562},
Title = {{When vortices stick: an aerodynamic transition in tiny insect flight.}},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/15277562},
Volume = {207},
Year = {2004},
Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/15277562},
Bdsk-Url-2 = {http://dx.doi.org/10.1242/jeb.01138}}
@article{Mittal2002,
Author = {Mittal, R and Utturkar, Y and Udaykumar, HS},
Journal = {AIAA Paper},
Pages = {2002},
Title = {{Computational modeling and analysis of biomimetic flight mechanisms}},
Url = {http://www.me.jhu.edu/fsag/Publications/Papers/AIAA02\_bio.pdf},
Volume = {865},
Year = {2002},
Bdsk-Url-1 = {http://www.me.jhu.edu/fsag/Publications/Papers/AIAA02%5C_bio.pdf}}
@article{Mittal2005,
Author = {Mittal, R. and Iaccarino, G.},
Date-Modified = {2011-03-26 21:28:59 -0400},
Doi = {10.1146/annurev.fluid.37.061903.175743},
Journal = {Ann.\ Rev.\ Fluid Mech.},
Number = {1},
Pages = {239--261},
Title = {Immersed Boundary Methods},
Url = {http://arjournals.annualreviews.org/doi/abs/10.1146\%2Fannurev.fluid.37.061903.175743},
Volume = {37},
Year = {2005},
Bdsk-Url-1 = {http://arjournals.annualreviews.org/doi/abs/10.1146%5C/annurev.fluid.37.061903.175743},
Bdsk-Url-2 = {http://dx.doi.org/10.1146/annurev.fluid.37.061903.175743}}
@article{Mittal2004,
Author = {Mittal, Rajat and Seshadri, Veeraraghavan and Udaykumar, Holavanahalli S.},
Doi = {10.1007/s00162-003-0101-5},
Journal = {Theoretical and Computational Fluid Dynamics},
Month = apr,
Number = {3},
Pages = {165--170},
Title = {{Flutter, Tumble and Vortex Induced Autorotation}},
Url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s00162-003-0101-5},
Volume = {17},
Year = {2004},
Bdsk-Url-1 = {http://www.springerlink.com/openurl.asp?genre=article%5C&id=doi:10.1007/s00162-003-0101-5},
Bdsk-Url-2 = {http://dx.doi.org/10.1007/s00162-003-0101-5}}
@article{Mohd-Yusof1998,
Author = {Mohd-Yusof, J.},
Journal = {Annual Research Briefs},
Pages = {325--336},
Title = {{Development of immersed boundary methods for complex geometries}},
Url = {http://ctr-sgi1.stanford.edu/CTR/ResBriefs98/myusof.pdf},
Year = {1998},
Bdsk-Url-1 = {http://ctr-sgi1.stanford.edu/CTR/ResBriefs98/myusof.pdf}}
@article{Newren2007,
Author = {Newren, E and Fogelson, a and Guy, R and Kirby, R},
Doi = {10.1016/j.jcp.2006.08.004},
Issn = {00219991},
Journal = jcp,
Keywords = {fluid,immersed boundary method,immersed interface method,navier,projection methods,stability,structure interaction},
Month = mar,
Number = {2},
Pages = {702--719},
Title = {{Unconditionally stable discretizations of the immersed boundary equations}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999106003743},
Volume = {222},
Year = {2007},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999106003743},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2006.08.004}}
@article{Newren2008,
Author = {Newren, E and Fogelson, a and Guy, R and Kirby, R},
Date-Modified = {2011-03-25 16:25:15 -0400},
Doi = {10.1016/j.cma.2007.11.030},
Issn = {00457825},
Journal = {Computer Methods in Applied Mechanics and Engineering},
Keywords = {immersed boundary method,immersed interface method,implicit solvers,krylov methods,navier,projection methods,stokes,structure interaction},
Month = apr,
Number = {25-28},
Pages = {2290--2304},
Title = {{A comparison of implicit solvers for the immersed boundary equations}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0045782507004781},
Volume = {197},
Year = {2008},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0045782507004781},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.cma.2007.11.030}}
@phdthesis{Newren2007a,
Author = {Newren, Elijah Paul},
Number = {May},
School = {The University of Utah},
Title = {{Enhancing the Immersed Boundary Method : Stability, Volume Conservation, and Implicit Solvers}},
Volume = {C},
Year = {2007}}
@article{Peskin1977,
Author = {Peskin, Charles S},
Year = {1977}}
@article{Peskin2002,
Author = {Peskin, Charles S},
Title = {{The immersed boundary method}},
Url = {http://journals.cambridge.org/abstract\_S0962492902000077},
Year = {2002},
Bdsk-Url-1 = {http://journals.cambridge.org/abstract%5C_S0962492902000077}}
@article{Peskin2003,
Author = {Peskin, Charles S.},
Date-Modified = {2011-03-25 16:22:15 -0400},
Doi = {10.1017/S0962492902000077},
Journal = {Acta Numerica},
Keywords = {immersed boundary method},
Month = {July},
Number = {1},
Pages = {19--45},
Title = {The immersed boundary method},
Url = {http://www.journals.cambridge.org/abstract\_S0962492902000077},
Volume = {11},
Year = {2003},
Bdsk-Url-1 = {http://www.journals.cambridge.org/abstract%5C_S0962492902000077},
Bdsk-Url-2 = {http://dx.doi.org/10.1017/S0962492902000077}}
@article{Pinelli2010,
Author = {Pinelli, a. and Naqavi, I.Z. and Piomelli, U. and Favier, J.},
Doi = {10.1016/j.jcp.2010.08.021},
Issn = {00219991},
Journal = jcp,
Month = dec,
Number = {24},
Pages = {9073--9091},
Publisher = {Elsevier Inc.},
Title = {{Immersed-boundary methods for general finite-difference and finite-volume Navier--Stokes solvers}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999110004687},
Volume = {229},
Year = {2010},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999110004687},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2010.08.021}}
@article{Roma1999,
Author = {Roma, A. M. and Peskin, C. S. and Berger, M. J.},
Date-Modified = {2012-07-07 20:30:04 +0000},
Journal = jcp,
Number = {2},
Pages = {509--534},
Publisher = {Elsevier},
Title = {An adaptive version of the immersed boundary method},
Volume = {153},
Year = {1999}}
@article{Saiki1996,
Author = {Saiki, E M and Biringen, S},
Doi = {10.1006/jcph.1996.0036},
Issn = {00219991},
Journal = jcp,
Month = feb,
Number = {2},
Pages = {450--465},
Title = {{Numerical Simulation of a Cylinder in Uniform Flow: Application of a Virtual Boundary Method}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999196900364},
Volume = {123},
Year = {1996},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999196900364},
Bdsk-Url-2 = {http://dx.doi.org/10.1006/jcph.1996.0036}}
@article{Taira2007,
Author = {Taira, K. and Colonius, T.},
Date-Modified = {2011-03-26 21:33:44 -0400},
Doi = {10.1016/j.jcp.2007.03.005},
Journal = jcp,
Keywords = {finite-volume method,fractional step method,immersed boundary method,incom-,pressible viscous flow,projection method,staggered grid},
Number = {2},
Pages = {2118--2137},
Title = {The immersed boundary method: A projection approach},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999107001234},
Volume = {225},
Year = {2007},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999107001234},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2007.03.005}}
@article{Tryggvason2001,
Author = {Tryggvason, G},
Doi = {10.1006/jcph.2001.6726},
Journal = jcp,
Month = may,
Number = {2},
Pages = {708--759},
Title = {{A Front-Tracking Method for the Computations of Multiphase Flow}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999101967269},
Volume = {169},
Year = {2001},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999101967269},
Bdsk-Url-2 = {http://dx.doi.org/10.1006/jcph.2001.6726}}
@article{Tseng2003,
Author = {Tseng, Y},
Doi = {10.1016/j.jcp.2003.07.024},
Journal = jcp,
Month = dec,
Number = {2},
Pages = {593--623},
Title = {{A ghost-cell immersed boundary method for flow in complex geometry}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999103004108},
Volume = {192},
Year = {2003},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999103004108},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2003.07.024}}
@article{Udaykumar1999,
Author = {Udaykumar, H},
Doi = {10.1006/jcph.1999.6294},
Issn = {00219991},
Journal = jcp,
Month = aug,
Number = {2},
Pages = {535--574},
Title = {{Computation of Solid--Liquid Phase Fronts in the Sharp Interface Limit on Fixed Grids}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999199962940},
Volume = {153},
Year = {1999},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999199962940},
Bdsk-Url-2 = {http://dx.doi.org/10.1006/jcph.1999.6294}}
@article{Udaykumar1997,
Author = {Udaykumar, H},
Doi = {10.1006/jcph.1997.5805},
Journal = jcp,
Month = nov,
Number = {2},
Pages = {366--405},
Title = {{Multiphase Dynamics in Arbitrary Geometries on Fixed Cartesian Grids}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999197958058},
Volume = {137},
Year = {1997},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999197958058},
Bdsk-Url-2 = {http://dx.doi.org/10.1006/jcph.1997.5805}}
@article{Udaykumar2001,
Author = {Udaykumar, H},
Doi = {10.1006/jcph.2001.6916},
Issn = {00219991},
Journal = jcp,
Month = nov,
Number = {1},
Pages = {345--380},
Title = {{A Sharp Interface Cartesian Grid Method for Simulating Flows with Complex Moving Boundaries}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999101969165},
Volume = {174},
Year = {2001},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999101969165},
Bdsk-Url-2 = {http://dx.doi.org/10.1006/jcph.2001.6916}}
@article{Uhlmann2005,
Author = {Uhlmann, M},
Doi = {10.1016/j.jcp.2005.03.017},
Issn = {00219991},
Journal = jcp,
Keywords = {direct interaction force,finite-difference method,immersed-boundary method,navier,particulate flow,stokes equations},
Month = nov,
Number = {2},
Pages = {448--476},
Title = {{An immersed boundary method with direct forcing for the simulation of particulate flows}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999105001385},
Volume = {209},
Year = {2005},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999105001385},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2005.03.017}}
@article{Verzicco1996,
Author = {Verzicco, R},
Doi = {10.1006/jcph.1996.0033},
Issn = {00219991},
Journal = jcp,
Month = feb,
Number = {2},
Pages = {402--414},
Title = {{A Finite-Difference Scheme for Three-Dimensional Incompressible Flows in Cylindrical Coordinates}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999196900339},
Volume = {123},
Year = {1996},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999196900339},
Bdsk-Url-2 = {http://dx.doi.org/10.1006/jcph.1996.0033}}
@article{Wei,
Abstract = {We present an approach for simulating the natural dynamics that emerge from the interaction between a flow field and immersed objects. We model the flow field using the Lattice Boltzmann Model (LBM) with boundary conditions appropriate for moving objects and accelerate the computation on commodity graphics hardware (GPU) to achieve real-time performance. The boundary conditions mediate the exchange of momentum between the flow field and the moving objects resulting in forces exerted by the flow on the objects as well as the back-coupling on the flow. We demonstrate our approach using soap bubbles and a feather. The soap bubbles illustrate Fresnel reflection, reveal the dynamics of the unseen flow field in which they travel, and display spherical harmonics in their undulations. Our simulation allows the user to directly interact with the flow field to influence the dynamics in real time. The free feather flutters and gyrates in response to lift and drag forces created by its motion relative to the flow. Vortices are created as the free feather falls in an otherwise quiescent flow.},
Author = {Wei, Xiaoming and Zhao, Ye and Fan, Zhe and Li, Wei and Qiu, Feng and Yoakum-Stover, Suzanne and Kaufman, Arie E},
Doi = {10.1109/TVCG.2004.48},
Issn = {1077-2626},
Journal = {IEEE T. Vis.\ Comput.\ Gr.},
Number = {6},
Pages = {719--29},
Pmid = {15527053},
Title = {{Lattice-based flow field modeling.}},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/15527053},
Volume = {10},
Bdsk-Url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/15527053},
Bdsk-Url-2 = {http://dx.doi.org/10.1109/TVCG.2004.48}}
@article{Xu2008,
Author = {Xu, S},
Doi = {10.1016/j.jcp.2008.01.053},
Issn = {00219991},
Journal = jcp,
Keywords = {complex moving geometries,flow around multiple objects,jump conditions,poisson solvers,singular forces,the immersed boundary method,the immersed interface method},
Month = may,
Number = {10},
Pages = {5045--5071},
Title = {{The immersed interface method for simulating prescribed motion of rigid objects in an incompressible viscous flow}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999108000582},
Volume = {227},
Year = {2008},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999108000582},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2008.01.053}}
@article{Xu2006,
Author = {Xu, S and Wang, Z},
Doi = {10.1016/j.jcp.2005.12.016},
Issn = {00219991},
Journal = jcp,
Keywords = {cartesian grid method,complex,flow around multiple objects,geometries,immersed boundary method,immersed interface method,moving deformable boundaries,singular force},
Month = aug,
Number = {2},
Pages = {454--493},
Title = {{An immersed interface method for simulating the interaction of a fluid with moving boundaries}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999105005607},
Volume = {216},
Year = {2006},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999105005607},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2005.12.016}}
@article{Yang2009,
Author = {Yang, Xiaolei and Zhang, Xing and Li, Zhilin and He, Guo-Wei},
Doi = {10.1016/j.jcp.2009.07.023},
Issn = {00219991},
Journal = jcp,
Keywords = {immersed boundary method},
Month = nov,
Number = {20},
Pages = {7821--7836},
Publisher = {Elsevier Inc.},
Title = {{A smoothing technique for discrete delta functions with application to immersed boundary method in moving boundary simulations}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999109004136},
Volume = {228},
Year = {2009},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999109004136},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2009.07.023}}
@article{Ye1999,
Author = {Ye, T},
Doi = {10.1006/jcph.1999.6356},
Issn = {00219991},
Journal = jcp,
Keywords = {cartesian grid,finite volume method,immersed boundaries,method,viscous incompressible flow},
Month = dec,
Number = {2},
Pages = {209--240},
Title = {{An Accurate Cartesian Grid Method for Viscous Incompressible Flows with Complex Immersed Boundaries}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999199963568},
Volume = {156},
Year = {1999},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999199963568},
Bdsk-Url-2 = {http://dx.doi.org/10.1006/jcph.1999.6356}}
@article{Zhang2007,
Author = {Zhang, N and Zheng, Z},
Date-Modified = {2011-03-25 16:25:45 -0400},
Doi = {10.1016/j.jcp.2006.06.012},
Issn = {00219991},
Journal = jcp,
Keywords = {flow over a cylinder,flow over a sphere,immersed-boundary method},
Month = jan,
Number = {1},
Pages = {250--268},
Title = {{An improved direct-forcing immersed-boundary method for finite difference applications}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999106002877},
Volume = {221},
Year = {2007},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0021999106002877},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2006.06.012}}
@misc{Zhu2002,
Author = {Zhu, L and Peskin, CS},
Booktitle = jcp,
Title = {{Simulation of a flapping flexible filament in a flowing soap film by the immersed boundary method}},
Url = {http://linkinghub.elsevier.com/retrieve/pii/S002199910297066X},
Year = {2002},
Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S002199910297066X}}
@article{Brown2001,
Author = {Brown, David L},
Title = {{Accuracy of Projection Methods for the Incompressible Navier- Stokes Equations}},
Year = {2001}}
@article{Chang2002,
Author = {Chang, Wang and Giraldo, Francis and Perot, Blair},
Doi = {10.1006/jcph.2002.7087},
Journal = jcp,
Keywords = {fractional step method,incompressible,navier,numerical,projection method,stokes,unstructured},
Month = jul,
Number = {1},