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%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.io/
%% Created for Lorena Barba at 2022-05-17 20:56:59 -0400
%% Saved with string encoding Unicode (UTF-8)
@misc{Barba2022,
author = {Lorena A. Barba},
date-added = {2022-04-27 20:59:45 -0400},
date-modified = {2022-05-17 20:56:59 -0400},
howpublished = {Preprint \href{https://arxiv.org/abs/2204.12564}{arXiv:2204.12564} [cs.CY]. Accepted in IEEE Computer.},
title = {Defining the role of open source software in research reproducibility},
year = {2022}}
@article{MesnardBarba2021,
author = {Mesnard$\,\star$, Olivier and Barba, L.~A.},
date-added = {2021-09-27 14:54:26 -0400},
date-modified = {2021-09-27 15:31:11 -0400},
journal = {ReScience C},
month = {August},
note = {\href{http://rescience.github.io/bibliography/Mesnard_2021.html}{http://rescience.github.io/bibliography/Mesnard\_2021.html}},
number = {1},
pages = {7},
title = {{[Re] Three-dimensional} wake topology and propulsive performance of low-aspect-ratio pitching-rolling plates},
volume = {7},
year = {2021}}
@article{BarbaETal2021,
author = {Barba, L.~A. and Kloeckner, Andreas and Ramachandran, Prabhu and Thomas, Rollin},
date-added = {2022-02-11 16:37:52 -0500},
date-modified = {2022-02-11 16:41:57 -0500},
journal = {Comput.\ Science \& Eng.},
note = {\href{https://doi.org/hgk4}{doi:10/hgk4}},
number = {4},
pages = {5--7},
title = {Scientific Computing With {Python} on High-Performance Heterogeneous Systems},
volume = {23},
year = {2021}}
@techreport{NISO-2021,
author = {{Jan Aalbersberg},I. and Baillieul, J. and Barba, L. and Beisel, A. and Boisvert, R. and Chirigati, F. and {Chue Hong}, N. and Coward, C. and Goldfarb, R. and Graves, W. and Grenier, G. and Hahnel, M. and Heroux, M. and McKerahan, T. and Mellor, D. and Parashar, M. and Pastrana, E. and Smit, E. and Stodden, V.},
date-added = {2021-04-22 12:55:34 +0100},
date-modified = {2021-04-22 13:14:02 +0100},
institution = {National Information Standards Organization},
month = {January},
note = {\href{https://doi.org/10.3789/niso-rp-31-2021 }{doi:10.3789/niso-rp-31-2021 }},
number = {NISO RP-31-2021},
title = {Reproducibility Badging and Definitions, {NISO} Recommended Practice},
year = {2021}}
@article{Barba2021b,
author = {Barba, L.~A.},
date-added = {2021-04-22 12:46:56 +0100},
date-modified = {2022-02-11 16:35:52 -0500},
journal = {Comput.\ Science \& Eng.},
month = {June},
note = {\href{https://doi.org/gxhf}{doi:10/gxhf}. Preprint on Authorea \href{https://doi.org/f7zv}{doi:10/f7zv}},
number = {3},
pages = {5--9},
title = {The {Python/Jupyter} ecosystem: today's problem-solving environment for computational science},
volume = {23},
year = {2021}}
@article{ChuangETal2021,
author = {Chuang$\,\star$, Pi-Yueh and Thorleifson, Tracy and Barba, L.~A.},
date-added = {2021-04-22 12:35:00 +0100},
date-modified = {2022-02-11 16:04:13 -0500},
doi = {10.21105/joss.03114},
journal = {J. Open Source Software},
month = {June},
note = {\href{https://doi.org/10.21105/joss.03114}{doi:10.21105/joss.03114}},
number = {62},
pages = {3114},
title = {Geoclaw-landspill: an oil land-spill and overland flow simulator for pipeline rupture events},
volume = {6},
year = {2021},
bdsk-url-1 = {https://doi.org/10.21105/joss.03114}}
@article{WangETal2021b,
author = {Wang$\,\star$, Tingyu and Yokota, Rio and Barba, L.~A.},
date-added = {2021-04-22 12:20:13 +0100},
date-modified = {2022-02-11 15:57:44 -0500},
doi = {10.21105/joss.03145},
journal = {J. Open Source Software},
month = {May},
note = {\href{https://doi.org/10.21105/joss.03145}{doi:10.21105/joss.03145}},
number = {61},
pages = {3145},
title = {{ExaFMM}: a high-performance fast multipole method library with {C++ and Python} interfaces},
volume = {6},
year = {2021},
bdsk-url-1 = {https://doi.org/10.21105/joss.03145}}
@article{Barba2020b,
author = {Barba, L.~A.},
date-added = {2021-04-22 10:19:30 +0100},
date-modified = {2021-04-22 13:11:29 +0100},
journal = {Comput.\ Science \& Eng.},
month = {Nov./Dec.},
note = {\href{https://doi.org/f7x2}{doi:10/f7x2}. Preprint on Authorea \href{https://doi.org/f7zz}{doi:10/f7zz}},
number = {6},
pages = {5--7},
title = {Computational science and engineering in 2020},
volume = {25},
year = {2020}}
@article{Barba2021a,
author = {Barba, L.~A.},
date-added = {2021-04-21 20:20:46 +0100},
date-modified = {2021-04-21 20:22:26 +0100},
journal = {Comput.\ Science \& Eng.},
note = {\href{https://doi.org/f7v5}{doi:10/f7v5}.},
number = {1},
pages = {58--64},
title = {Trustworthy computational evidence through transparency and reproducibility},
volume = {23},
year = {2021}}
@unpublished{WangETal2021,
author = {Wang$\,\star$, Tingyu and Cooper, Christopher D. and Betcke, Timo and Barba, L.~A.},
date-added = {2021-04-21 20:18:05 +0100},
date-modified = {2021-04-22 12:28:23 +0100},
note = {Preprint \href{http://arxiv.org/abs/2103.01048}{arXiv:2103.01048}. Under review},
title = {High-productivity, high-performance workflow for virus-scale electrostatic simulations with {Bempp-Exafmm}},
year = {2021}}
@article{Barba2020,
author = {Barba, L.~A.},
date-added = {2021-04-21 20:09:20 +0100},
date-modified = {2021-04-21 20:11:22 +0100},
journal = {Comput.\ Science \& Eng.},
note = {\href{https://doi.org/d2js}{doi:10/d2js}. Preprint \href{http://arxiv.org/abs/2001.00228}{arXiv:2001.00228}.},
number = {4},
pages = {26--35},
title = {Engineers Code: reusable open learning modules for engineering computations},
volume = {22},
year = {2020}}
@article{ClementiBarba2021,
author = {Clementi$\,\star$, Natalia C. and Barba, L.~A.},
date-added = {2021-04-21 20:04:19 +0100},
date-modified = {2021-04-21 20:08:34 +0100},
journal = {Phil.\ Trans.\ R. Soc.\ A.},
month = {March},
note = {\href{https://doi.org/f4cp}{doi:10/f4cp}. Preprint \href{http://arxiv.org/abs/2008.05414}{arXiv:2008.05414}},
pages = {20200068},
title = {Reproducible validation and replication studies in nanoscale physics},
volume = {379},
year = {2021}}
@article{MesnardBarba2019-jose,
author = {Barba, Lorena A. and Mesnard$\,\star$, Olivier},
date-added = {2019-06-16 16:33:01 +0100},
date-modified = {2019-07-24 09:13:42 +0100},
doi = {10.21105/jose.00045},
journal = {J. Open Source Education},
note = {\href{https://doi.org/10.21105/jose.00045}{doi:10.21105/jose.00045}},
number = {15},
pages = {45},
title = {{Aero Python}: classical aerodynamics of potential flow using {Python}},
volume = {2},
year = {2019},
bdsk-url-1 = {https://doi.org/10.21105/jose.00045}}
@book{NASEM2019,
address = {Washington, D.C.},
author = {{National Academies of Sciences, Engineering, and Medicine}},
date-added = {2019-06-16 15:28:05 +0100},
date-modified = {2019-06-16 15:40:19 +0100},
month = {May},
note = {(As committee member, Barba is uncredited co-author.) \href{http://doi.org/c5jp}{doi:c5jp}},
publisher = {The National Academies Press},
title = {Reproducibility and Replicability in Science},
url = {https://doi.org/10.17226/25303},
year = {2019},
bdsk-url-1 = {https://doi.org/10.17226/25303}}
@article{MesnardBarba2019,
author = {Mesnard$\,\star$, Olivier and Barba, Lorena A.},
date-added = {2019-06-16 14:47:09 +0100},
date-modified = {2021-04-21 20:02:39 +0100},
doi = {10/d2hr},
journal = {Comput.\ Science \& Eng.},
note = {\href{http://doi.org/d2hr}{doi:10/d2hr}. Preprint on \href{https://arxiv.org/abs/1904.07981}{arxiv:1904.07981}},
number = {1},
pages = {102--116},
title = {Reproducible Workflow on a Public Cloud for Computational Fluid Dynamics},
volume = {22},
year = {2020},
bdsk-url-1 = {https://doi.org/10/d2hr}}
@article{BarbaForsyth2018,
author = {Barba, L.~A. and Forsyth$\,\star$, Gilbert},
date-added = {2019-01-27 18:13:28 -0500},
date-modified = {2019-01-27 18:15:14 -0500},
journal = {J. Open Source Education},
note = {\href{https://doi.org/10.21105/jose.00021}{doi:10.21105/jose.00021}},
number = {19},
pages = {21},
title = {{CFD Python: the 12 steps to Navier-Stokes equations}},
volume = {1},
year = {2018}}
@conference{Barba-scipy2018,
address = {Austin, TX},
author = {Barba, Lorena A.},
booktitle = {Scientific Python Conference (SciPy)},
date-added = {2019-01-10 18:00:54 -0300},
date-modified = {2019-01-10 18:02:02 -0300},
month = {July 9--15},
title = {{Engineers Code}: re-usable, open educational modules for engineering undergraduates},
year = {2018}}
@conference{Barba2018-openedx,
address = {Montreal, Canada},
author = {Barba, Lorena A. and Amigot, Miguel},
booktitle = {Open edX Conference},
date-added = {2019-01-10 17:58:34 -0300},
date-modified = {2019-01-10 17:59:44 -0300},
month = {May 29--31},
title = {Jupyter-based courses in {Open edX}: authoring and grading with notebooks},
year = {2018}}
@conference{MesnardBarba-parcfd18,
address = {Indianapolis, IN},
author = {Mesnard$\,\star$, Olivier and Barba, Lorena A.},
booktitle = {International Conference in Parallel CFD (ParCFD)},
date-added = {2019-01-10 17:53:43 -0300},
date-modified = {2019-01-10 17:58:17 -0300},
month = {May 14--17},
title = {Three-dimensional flow simulations of the flying snake using {Microsoft Azure}},
year = {2018}}
@conference{Barba2018-delft,
address = {Delft},
author = {Barba, Lorena A.},
booktitle = {Open Education Global Conference},
date-added = {2019-01-10 17:50:18 -0300},
date-modified = {2019-01-10 17:51:40 -0300},
month = {Apr. 24--26},
title = {A Qualitative Study of Open Educational Practice using {Jupyter} Notebooks},
year = {2018}}
@article{KatzETal2018,
author = {Katz, Daniel S. and Allen, Gabrielle and Barba, Lorena A. and Berg, Devin R. and Bik, Holly and Boettiger, Carl and Borgman, Christine L. and Brown et al., C. Titus},
date-added = {2019-01-10 17:25:17 -0300},
date-modified = {2019-07-24 08:11:45 +0100},
journal = {F1000 Research},
month = {December},
note = {\href{https://doi.org/10.12688/f1000research.17425.1}{doi:10.12688/f1000research.17425.1}},
pages = {1926},
title = {The principles of tomorrow's university [version 1; referees: 2 approved]},
volume = {7},
year = {2018}}
@article{ChuangETal2018,
author = {Chuang$\,\star$, Pi-Yueh and Mesnard$\,\star$, Olivier and Krishnan$\,\star$, Anush and Barba, Lorena A.},
date-added = {2019-01-10 17:17:36 -0300},
date-modified = {2019-01-27 18:21:45 -0500},
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}}
@book{NASEM2018,
address = {Washington, D.C.},
author = {{National Academies of Sciences, Engineering, and Medicine}},
date-added = {2019-01-10 16:45:41 -0300},
date-modified = {2019-06-16 15:36:29 +0100},
month = {October},
note = {(As committee member, Barba is uncredited co-author.) \href{http://doi.org/c7bz}{doi:10/c7bz}},
publisher = {The National Academies Press},
title = {Open Source Software Policy Options for NASA Earth and Space Sciences},
url = {https://doi.org/10.17226/25217},
year = {2018},
bdsk-url-1 = {https://doi.org/10.17226/25217}}
@misc{Barba2018,
author = {Lorena A. Barba},
date-added = {2019-01-10 16:25:17 -0300},
date-modified = {2021-04-22 10:23:46 +0100},
howpublished = {Preprint \href{https://arxiv.org/abs/1802.03311}{arxiv:1802.03311}},
month = {February},
title = {Terminologies for reproducible research},
year = {2018}}
@article{ClementiETal2019,
author = {Clementi$\,\star$, Natalia C. and Cooper, Christopher D. and Barba, L.~A.},
date-added = {2019-01-10 16:10:34 -0300},
date-modified = {2021-04-21 20:00:14 +0100},
journal = {Phys.\ Rev.\ E},
month = {December},
note = {\href{https://doi.org/f4cv}{doi:10/f4cv} Preprint on \href{http://arxiv.org/abs/1812.10722}{arxiv:1812.10722}},
pages = {063305},
title = {Computational nanoplasmonics in the quasistatic limit for biosensing applications},
volume = {100},
year = {2019}}
@article{Barba2018-praxis,
author = {Barba, L.~A.},
date-added = {2019-01-10 13:46:44 -0300},
date-modified = {2021-04-21 20:24:05 +0100},
doi = {10.1109/MCSE.2018.2881905},
journal = {Comput.\ Science \& Eng.},
month = {Jan.--Feb.},
note = {\href{http://doi.org/c7bv}{doi:10/c7bv}. Preprint on Authorea \href{http://doi.org/cztp}{doi:10/cztp}},
number = {1},
pages = {73--78},
publisher = {IEEE},
title = {Praxis of Reproducible Computational Science},
volume = {21},
year = {2019},
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author = {Mesnard$\,\star$, Olivier and Barba, L.~A.},
booktitle = {International Conference in Parallel CFD},
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month = {May},
title = {{PetIBM} - A {PETSc}-based Immersed Boundary Method code},
year = {2015}}
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publisher = {The Open Journal},
title = {{AmgXWrapper}: An interface between {PETSc} and the {NVIDIA} {AmgX} library},
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keywords = {cuIBM, JOSS},
month = {July},
note = {\href{http://dx.doi.org/10.21105/joss.00301}{doi: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},
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publisher = {American Association for the Advancement of Science ({AAAS})},
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author = {Lorena A. Barba and Rio Yokota},
date-added = {2016-09-04 23:44:47 +0000},
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howpublished = {Poster on \textbf{Figshare}, under CC-BY license, \href{https://dx.doi.org/10.6084/m9.figshare.92166.v1}{https://dx.doi.org/10.6084/m9.figshare.92166.v1}},
keywords = {figshare},
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url = {10.6084/m9.figshare.92166.v1},
year = {2012},
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author = {Cooper$\,\star$, Christopher D. and Clementi$\,\star$, Natalia C. and Forsyth$\,\star$, Gilbert and Lorena A. Barba},
date-added = {2016-08-24 17:26:42 +0000},
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journal = {J. Open Source Software},
keywords = {PyGBe, JOSS},
month = {August},
note = {\href{http://dx.doi.org/10.21105/joss.00043}{doi:10.21105/joss.00043}},
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publisher = {The Open Journal},
title = {{PyGBe}: Python, {GPUs} and Boundary elements for biomolecular electrostatics},
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@inproceedings{MesnardBarba-parcfd17,
address = {Glasgow, Scotland},
author = {Mesnard$\,\star$, Olivier and Barba, L.~A.},
booktitle = {International Conference in Parallel CFD},
date-added = {2016-07-02 20:45:12 +0000},
date-modified = {2017-09-10 22:55:40 +0000},
month = {15--17 May},
title = {Using {AmgX} to accelerate a {PETSc}-based Immersed Boundary Method code},
year = {2017}}
@inproceedings{ChuangBarba-gtc16,
address = {San Jose, CA},
author = {Chuang$\,\star$, Pi-Yueh and Barba, L.~A.},
booktitle = {GPU Technology Conference},
date-added = {2016-07-02 20:38:54 +0000},
date-modified = {2016-07-02 20:41:51 +0000},
month = {April},
title = {Using {AmgX} to Accelerate {PETSc}-Based {CFD} Codes},
year = {2016}}
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journal = {Comput.\ Science \& Eng.},
month = {August},
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publisher = {IEEE},
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volume = {19},
year = {2017}}
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author = {Wang$\,\star$, Tingyu and Layton$\,\star$, Simon K. and Barba, L.~A.},
date-added = {2016-07-02 20:07:26 +0000},
date-modified = {2022-05-10 10:32:20 -0400},
doi = {10.1007/s10444-022-09932-8},
journal = {Advances in Computational Mathematics},
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title = {Inexact {GMRES} iterations and relaxation strategies with fast-multipole boundary element method},
volume = {48},
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@incollection{MesnardBarba2016bids,
author = {Mesnard$\,\star$, Olivier and Barba, L.~A.},
booktitle = {The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences},
date-added = {2016-07-02 20:05:13 +0000},
date-modified = {2022-02-14 16:39:27 -0500},
editor = {Justin Kitzes, Daniel Turek, Fatma Deniz},
note = {\href{http://www.practicereproducibleresearch.org}{http://www.practicereproducibleresearch.org}},
pages = {191--199},
publisher = {University of California Press},
title = {Full replication of computational fluid dynamics results},
year = {2017}}
@article{CooperBarba2016,
author = {Cooper$\,\star$, Christopher D. and Barba, L.~A.},
date-added = {2016-07-02 20:01:50 +0000},
date-modified = {2021-04-21 20:14:35 +0100},
doi = {10.1016/j.cpc.2015.12.019},
journal = {Comput. Phys. Comm.},
note = {\href{http://doi.org/f8g7ft}{doi:10/f8g7ft}. Preprint \href{http://arxiv.org/abs/1506.03745}{arXiv:1506.03745}},
pages = {23--32},
title = {Poisson-{Boltzmann} model for protein-surface electrostatic interactions and grid-convergence study using the {PyGBe} code},
volume = {202},
year = {2016},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.cpc.2015.12.019}}
@inproceedings{Barba-siamcse15b,
address = {Salt Lake City, UT},
author = {Barba, L.~A.},
booktitle = {SIAM Conference on Computational Science and Engineering},
date-added = {2015-04-26 19:40:15 +0000},
date-modified = {2015-04-26 19:47:19 +0000},
month = {March},
organization = {Society of Industrial and Applied Mathematics},
title = {Teaching Computational Thinking and Practice ({MS78}): Teaching Computing to Engineers},
year = {2015}}
@inproceedings{Barba-siamcse15a,
address = {Salt Lake City, UT},
author = {Barba, L.~A.},
booktitle = {SIAM Conference on Computational Science and Engineering},
date-added = {2015-04-26 19:35:47 +0000},
date-modified = {2015-04-26 19:47:10 +0000},
month = {March},
organization = {Society of Industrial and Applied Mathematics},
title = {Fast Multipole Methods Maturing at 30 Years ({MS27}): Overview of the Field and the Community of Fast Multipole Methods},
year = {2015}}
@conference{Barba-OpenEdX2014,
address = {Cambridge, MA},
author = {Barba, L.~A.},
booktitle = {Open edX Technology Conference},
date-added = {2014-12-04 23:15:10 +0000},
date-modified = {2014-12-04 23:33:06 +0000},
month = {Nov. 18--19},
title = {Teaching numerical computing in {STEM}},
year = {2014}}
@conference{Barba-GTC2013,
address = {San Jose, CA},
author = {Barba, L.~A. and Ujald{\'o}n, Manuel},
booktitle = {GPU Technology Conference},
date-added = {2014-12-04 23:10:26 +0000},
date-modified = {2014-12-04 23:13:21 +0000},
month = {Mar. 24--27},
title = {Raising the roofline on {GPU} applications with stacked memory},
year = {2013}}
@article{CooperClementiBarba2015,
author = {Cooper$\,\star$, Christopher D. and Clementi$\,\star$, Natalia C. and Barba, L.~A.},
date-added = {2014-12-04 22:53:15 +0000},
date-modified = {2019-01-20 21:18:30 -0500},
doi = {10.1063/1.4931113},
journal = {J. Chem. Phys.},
note = {\href{http://doi.org/cztm}{doi:10/cztm}; preprint on \href{http://arxiv.org/abs/1503.08150}{arXiv: 1503.08150}},
pages = {124709},
title = {Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design},
volume = {143},
year = {2015},
bdsk-url-1 = {http://dx.doi.org/10.1063/1.4931113}}
@article{Barba-SHPE2014,
author = {Lorena A. Barba},
date-added = {2014-05-10 23:35:20 +0000},
date-modified = {2022-05-10 10:17:00 -0400},
journal = {SHPE Magazine},
month = {January},
number = {1},
organization = {Society of Hispanic Professional Engineers},
pages = {28--30},
title = {The Gathering Storm: Flipping the Classroom},
volume = {16},
year = {2014}}
@article{BarbaYokota2013,
author = {Barba, L.~A. and Yokota$\,\star$, Rio},
date-added = {2014-01-03 23:15:40 +0000},
date-modified = {2014-01-03 23:40:49 +0000},
journal = {SIAM News},
month = {July},
number = {6},
pages = {1},
title = {How will the fast multipole method fare in the exascale era?},
volume = {46},
year = {2013}}
@conference{KrishnanBarba-APS2013,
address = {Pittsburgh, PA},
author = {Krishnan$\,\star$, Anush and Barba, L.~A.},
booktitle = {APS \href{http://www.apsdfd2013.pitt.edu}{Division of Fluid Dynamics 66th Annual Meeting}},
date-added = {2014-01-02 22:31:19 +0000},
date-modified = {2014-01-02 22:35:39 +0000},
month = {24--26 November},
note = {\href{http://meetings.aps.org/Meeting/DFD13/Session/E17.1}{Session E17.1}},
organization = {American Physical Society},
title = {Lift enhancement in flying snakes},
year = {2013}}
@conference{KrishnanBarba-Euromech2013,
address = {Leiden, The Netherlands},
author = {Krishnan$\,\star$, Anush and Barba, L.~A.},
booktitle = {EUROMECH /ERCOFTAC \href{http://dutw1479.wbmt.tudelft.nl/~wim/euromech549/}{Colloquium 549 on Immersed Boundary Methods}},
date-added = {2014-01-02 22:21:52 +0000},
date-modified = {2014-01-02 22:29:30 +0000},
month = {17--19 June},
title = {Analysis of the direct-forcing method},
year = {2013}}
@conference{CooperBarbaGTC2013,
address = {San Jose, CA},
author = {Cooper$\,\star$, Christopher D. and Barba, L.~A.},
booktitle = {GPU Technology Conference},
date-added = {2014-01-02 22:13:26 +0000},
date-modified = {2014-01-02 22:30:06 +0000},
month = {18--21 March},
note = {Poster, \href{http://on-demand.gputechconf.com/gtc/2013/poster/pdf/P0231_Barba.pdf}{PDF online} at GTC On-Demand.},
organization = {Nvidia},
title = {{PyGBe: Python} on the surface, {GPUs} at the heart. {BEM} solver for Electrostatics of Biomolecules},
year = {2013}}
@conference{BarbaGTC2013,
address = {San Jose, CA},
author = {Barba, L.~A.},
booktitle = {GPU Technology Conference},
date-added = {2014-01-02 19:09:48 +0000},
date-modified = {2014-01-02 22:29:52 +0000},
month = {18--21 March},
note = {\href{http://on-demand.gputechconf.com/gtc/2013/video/S3394-CUDA-Treecode-Python-App-Biomolecular-Electrostatics.mp4}{Streaming video} via GTC On-Demand.},
organization = {Nvidia},
title = {{CUDA} Treecode in a {Python} Application for Biomolecular Electrostatics},
year = {2013}}
@conference{ParhamBarba2014,
address = {National Harbor, MD},
author = {Parham$\,\star$, J.~Brent and Barba, L.~A.},
booktitle = {AIAA Science and Technology Forum and Exposition (SciTech2014)},
date-added = {2014-01-02 17:36:13 +0000},
date-modified = {2014-01-02 17:42:37 +0000},
month = {January 13--17},
note = {Preprint on \href{http://arxiv.org/abs/1312.3691}{arXiv:1312.3691}},
organization = {American Institute of Aeronautics and Astronautics},
title = {Finding the Force---Consistent Particle Seeding for Satellite Aerodynamics},
year = {2014}}
@article{CooperBardhanBarba2013,
author = {Cooper$\,\star$, Christopher D. and Bardhan, Jaydeep P. and Barba, L.~A.},
date-added = {2014-01-02 17:21:20 +0000},
date-modified = {2019-01-20 21:15:14 -0500},
doi = {10.1016/j.cpc.2013.10.028},
journal = {Comp.\ Phys.\ Comm.},
month = {March},
note = {Published online Nov. 2013, \href{http://doi.org/cztk}{doi:10/cztk}; preprint on \href{http://arxiv.org/abs/1309.4018}{arXiv:1309.4018}},
number = {3},
pages = {720--729},
title = {A biomolecular electrostatics solver using {Python, GPUs} and boundary elements that can handle solvent-filled cavities and {Stern} layers},
volume = {185},
year = {2014},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.cpc.2013.10.028}}
@inproceedings{Yokota-SIAM2013,
author = {Yokota$\,\star$, Rio and Layton$\,\star$, Simon K. and Barba, L.~A.},
booktitle = {SIAM Computational Science and Engineering Conference, PP1: Poster Session},
date-added = {2013-05-28 09:28:16 +0000},
date-modified = {2013-05-28 09:40:53 +0000},
organization = {Society of Industrial and Applied Mathematics},
title = {Hardware-Aware Optimizations for Using {exaFMM} As a Preconditioner},
year = {2013},
bdsk-url-1 = {http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=15801},
bdsk-url-2 = {http://meetings.siam.org/sess/dsp_talk.cfm?p=54299}}
@inproceedings{CooperBarba-siamcse13,
address = {Boston, MA},
author = {Cooper$\,\star$, Christopher D. and Bardhan, Jaydeep P. and Barba, L.~A.},
booktitle = {SIAM Computational Science and Engineering Conference, CP3: Numerical Methods and Their Applications II},
date-added = {2013-03-12 22:30:11 +0000},
date-modified = {2013-05-28 09:40:00 +0000},
keywords = {BEM},
month = {February},
organization = {Society of Industrial and Applied Mathematics},
title = {Efficient Boundary Element Methods for Molecular Electrostatics Using {Python} and {GPUs}},
year = {2013},
bdsk-url-1 = {http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=15943}}
@inproceedings{BarbaKrishnan-siamcse13,
address = {Boston, MA},
author = {Barba, L.~A. and Krishnan$\,\star$, Anush},
booktitle = {SIAM Computational Science and Engineering Conference, MS38: Recent Advances in Immersed Boundary Methods - Part II of II},
date-added = {2013-03-12 22:27:16 +0000},
date-modified = {2013-05-28 09:37:05 +0000},
keywords = {IBM},
month = {February},
organization = {Society of Industrial and Applied Mathematics},
title = {Comparative Review of Fractional-step Approaches to the Immersed Boundary Method},
year = {2013}}
@misc{CooperBarba-share154331,
author = {Cooper$\,\star$, Christopher D. and Barba, L.~A.},
date-added = {2013-01-25 23:50:34 +0000},
date-modified = {2013-01-26 00:05:50 +0000},
doi = {10.6084/m9.figshare.154331},
howpublished = {Technical Report on \textbf{figshare}, CC-BY license, \href{http://dx.doi.org/10.6084/m9.figshare.154331}{doi:10.6084/m9.figshare.154331}},
month = {January 25},
title = {Validation of the \texttt{{PyGBe}} code for {P}oisson-{B}oltzmann equation with boundary element methods},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.6084/m9.figshare.154331}}
@misc{KrishnanBarba-share92789,
author = {Krishnan$\,\star$, Anush and Barba, L.~A.},
date-added = {2013-01-24 01:56:55 +0000},
date-modified = {2013-01-26 00:05:02 +0000},
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}},
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title = {Validation of the \texttt{{cuIBM}} code for {Navier-Stokes} equations with immersed boundary methods},
year = {2012},
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author = {Krishnan$\,\star$, Anush and Socha, J.~J. and Vlachos, P.~P. and Barba, L.~A.},
date-added = {2013-01-24 01:43:41 +0000},
date-modified = {2019-01-20 21:17:01 -0500},
journal = {Phys.\ Fluids},
note = {\href{http://doi.org/gbf3hf}{doi:10/gbf3hf}; preprint on \href{http://arxiv.org/abs/1309.2969}{arXiv:1309.2969}},
pages = {031901},
title = {Lift and wakes of flying snakes},
volume = {26},
year = {2014}}
@inproceedings{CooperIABM2013,
address = {Santiago, Chile},
author = {Cooper$\,\star$, Christopher D. and Barba, L.~A.},
booktitle = {Symposium of the International Association for Boundary Element Methods, IABEM 2013},
date-added = {2013-01-18 01:39:33 +0000},
date-modified = {2013-01-18 01:43:51 +0000},
month = {9--11 January},
note = {\href{http://iabem2013.mat.puc.cl}{http://iabem2013.mat.puc.cl}},
organization = {Pontificia Universidad Catolica de Chile},
title = {Fast tree methods and {GPUs} for protein electrostatics},
year = {2013}}
@inproceedings{CooperBarba-wccm12,
address = {Sao Paulo, Brazil},
author = {Cooper$\,\star$, Christopher D. and Barba, L.~A.},
booktitle = {World Congress on Computational Mechanics (WCCM)},
date-added = {2012-08-28 17:46:39 +0000},
date-modified = {2013-03-12 21:08:25 +0000},
month = {July 8--13},
title = {Efficient boundary element method on {Python} using {GPUs}},
year = {2012}}
@inproceedings{KrishnanBarba-wccm12,
address = {Sao Paulo, Brazil},
author = {Krishnan$\,\star$, Anush and Barba, L.~A.},
booktitle = {World Congress on Computational Mechanics (WCCM)},
date-added = {2012-08-28 17:16:42 +0000},
date-modified = {2014-01-02 17:59:54 +0000},
month = {July 8--13},
title = {Projection-based immersed boundary method in {CUDA}},
year = {2012}}
@misc{YokotaBarba-share91439,
author = {Yokota, R. and Barba, L.~A.},
date-added = {2012-08-05 00:05:52 +0000},
date-modified = {2013-01-24 01:56:36 +0000},
doi = {10.6084/m9.figshare.91439},
howpublished = {Figure on \textbf{figshare}, under CC-BY license, \href{http://dx.doi.org/10.6084/m9.figshare.91439}{http://dx.doi.org/10.6084/m9.figshare.91439}},
keywords = {figshare,FMM},
month = {March 17},
title = {Fast multipole method upward and downward sweeps},
urldate = {00:06, Aug 05, 2012 (GMT)},
year = {2012},
bdsk-url-1 = {http://dx.doi.org/10.6084/m9.figshare.92425}}
@misc{YokotaBarba-share92425,
author = {Yokota, R. and Barba, L.~A.},
date-added = {2012-08-04 23:51:27 +0000},
date-modified = {2013-01-24 01:56:26 +0000},
doi = {10.6084/m9.figshare.92425},
howpublished = {Figure on \textbf{figshare}, under CC-BY license, \href{http://dx.doi.org/10.6084/m9.figshare.92425}{http://dx.doi.org/10.6084/m9.figshare.92425}},
keywords = {figshare},
month = {July 18},
title = {Weak scaling of parallel {FMM vs. FFT} up to 4096 processes},
urldate = {23:46, Aug 04, 2012 (GMT)},
year = {2012},
bdsk-url-1 = {http://dx.doi.org/10.6084/m9.figshare.92425}}
@conference{KrishnanBarba2012a,
address = {Atlanta, GA},
author = {Krishnan$\,\star$, Anush and Barba, L.~A.},
booktitle = {24th International Conference on Parallel Computational Fluid Dynamics},
date-added = {2012-06-06 20:36:05 -0400},
date-modified = {2012-06-06 20:48:25 -0400},
month = {May 21--25},
title = {Aerodynamics of flying snakes using an immersed boundary method},
year = {2012}}
@conference{Barba2012b,
author = {Barba, L.~A.},
booktitle = {2012 New England Numerical Analysis Day},
date-added = {2012-06-06 20:16:38 -0400},
date-modified = {2012-06-06 20:19:00 -0400},
editor = {Hans Johnston},
organization = {University of Massachusetts Amherst},
title = {The Success of Multipole Methods: Are We There Yet?},
year = {2012}}
@conference{Barba2012a,
author = {Barba, L. A.},
booktitle = {Boston University Center for Excellence \& Innovation in Teaching, CEIT, 4th Annual Instructional Innovation Conference},
date-added = {2012-06-06 20:09:49 -0400},
date-modified = {2013-05-28 17:49:53 +0000},
note = {On \href{http://figshare.com/authors/Lorena%20A.%20Barba/97553}{\textbf{figshare}}, \href{http://doi.org/mns}{doi:10/mns} and screencast on \url{http://youtu.be/Zit1fgu_i1s}},
title = {Digital Pedagogy in Three Parts: Screencasting, Course Blog, Remote Guests},
year = {2012}}
@article{YokotaBarba2012b,
author = {Yokota$\,\star$, Rio and Barba, L.~A.},
date-added = {2011-12-09 11:55:32 -0500},
date-modified = {2013-05-28 17:46:00 +0000},
journal = {Computers \& Fluids},
note = {\href{http://doi.org/mnq}{doi:10/mnq}; preprint on \href{http://arxiv.org/abs/1110.2921}{arXiv:1110.2921}},
pages = {17--27},
title = {{FMM}-based vortex method for simulation of isotropic turbulence on {GPUs}, compared with a spectral method},
volume = {80},
year = {2013},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S0045793012003003}}
@unpublished{LaytonKrishnanBarba2012,
author = {Layton$\,\star$, Simon K. and Krishnan$\,\star$, Anush and Barba, L.~A.},
date-added = {2011-12-09 11:53:38 -0500},
date-modified = {2019-06-16 14:46:06 +0100},
note = {Preprint on \href{http://arxiv.org/abs/1109.3524}{arXiv:1109.3524}},
title = {{cuIBM---A GPU} accelerated immersed boundary method},
year = {2012}}
@article{YokotaBarba2012a,
author = {Yokota$\,\star$, Rio and Barba, L.~A.},
date-added = {2011-12-09 11:50:27 -0500},
date-modified = {2014-05-11 00:50:14 +0000},
doi = {10.1109/MCSE.2012.1},
journal = {Computing in Science and Engineering},
month = {May/June},
note = {\href{http://doi.org/fzmgzq}{doi:10/fzmgzq}; preprint on \href{http://arxiv.org/abs/1108.5815}{arXiv:1108.5815}},
number = {3},
pages = {30--39},
title = {Hierarchical {$N$}-body simulations with auto-tuning for heterogeneous systems},
volume = {14},
year = {2012},
bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2012.1}}
@misc{SCAT-3,
author = {Barba, L.~A.},
date-added = {2011-07-21 15:22:15 -0400},
date-modified = {2011-07-21 15:25:31 -0400},
howpublished = {\url{http://www.scat-alfa.eu/news/articles_and_archive3/nov09_report.html}},
month = {November},
title = {Final report---{ALFA} project on Scientific Computing Advanced Training, {SCAT}},
year = {2009}}
@inproceedings{parCFD11b,
address = {Barcelona, Spain},
author = {Layton$\,\star$, Simon K. and Krishnan$\,\star$, Anush and Barba, L.~A.},
booktitle = {23rd International Conference on Parallel CFD},
date-added = {2011-07-20 17:59:36 -0400},
date-modified = {2011-07-20 18:01:27 -0400},
month = {16--20 May},
title = {{cuIBM---A GPU} accelerated immersed boundary method},
year = {2011}}
@inproceedings{parCFD08,
address = {Lyon, France},
author = {Cruz$\,\star$, Felipe A. and Barba, L.~A. and Knepley, Matthew G.},
booktitle = {20th International Conference on Parallel CFD},
date-added = {2011-07-20 16:39:51 -0400},
date-modified = {2011-07-20 16:40:31 -0400},
month = {19--22 May},
title = {Fast multipole method for particle interactions: an open source parallel library component.},
year = {2008}}
@inproceedings{caches2011,
address = {Tucson, Arizona},
author = {Yokota$\,\star$, Rio and Barba, L.~A.},
booktitle = {CACHES'11: Characterizing Applications for Heterogeneous Exascale Systems, at the 25th International Conference on Supercomputing},
date-added = {2011-07-20 16:37:11 -0400},
date-modified = {2011-07-20 17:52:49 -0400},
month = {31 May--4 June},
organization = {ACM/SIGARCH},
title = {Parameter tuning of a hybrid treecode-{FMM on GPUs}},
year = {2011}}
@article{YokotaETal2011b,
author = {Yokota$\,\star$, Rio and Barba, L.~A. and Narumi, Tetsu and Yasuoka, Kenji},
date-added = {2011-07-20 16:05:20 -0400},
date-modified = {2013-05-28 17:47:05 +0000},
doi = {10.1016/j.cpc.2012.09.011},
journal = {Comp.\ Phys.\ Comm.},
note = {\href{http://doi.org/mnr}{doi:10/mnr}; preprint on \href{http://arxiv.org/abs/1106.5273}{ arXiv:1106.5273}},
number = {3},
pages = {445--455},
title = {Petascale turbulence simulation using a highly parallel fast multipole method},
volume = {184},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.cpc.2012.09.011}}
@article{YokotaBarba2011a,
author = {Yokota$\,\star$, Rio and Barba, L.~A.},
date-added = {2011-05-05 21:14:29 -0400},
date-modified = {2014-05-11 00:46:50 +0000},
doi = {10/fzgqgm},
journal = {Int.\ J. High-perf.\ Comput.\ Appl.},
note = {\href{http://doi.org/10/fzgqgm}{doi:10/fzgqgm}; preprint on \href{http://arxiv.org/abs/1106.5273}{arXiv:1106.2176}},
number = {4},
pages = {337--346},
title = {A tuned and scalable fast multipole method as a preeminent algorithm for exascale systems},
volume = {26},
year = {2012},
bdsk-url-1 = {http://dx.doi.org/10/fzgqgm}}
@conference{Barba-gpuatbu09,
address = {Boston University Center for Computational Science},
author = {Barba, L.~A.},
booktitle = {GPU at BU: Exploiting a disruptive technology for scientific computing},
date-added = {2011-01-24 21:00:28 -0500},
date-modified = {2011-01-24 21:02:07 -0500},
month = {12---13 November},
title = {Toward {GPU}-accelerated meshfree flow simulation},
year = {2009}}
@conference{Barba-scat10,
address = {Valparaiso, Chile},
author = {Barba, L.~A.},
booktitle = {5th Latin American SCAT Workshop and Satellite School ``High-performance computing trends for 2010 and beyond''},
date-added = {2011-01-23 17:10:18 -0500},
date-modified = {2011-01-23 17:12:03 -0500},
month = {20--24 July},
title = {Parallel and meshfree: new frontiers of {CFD}},
year = {2009}}
@conference{Barba-scat7,
address = {Instituto de Matematica Pura e Aplicada, IMPA, Rio de Janeiro},
author = {Barba, L.~A.},
booktitle = {3rd Latin American SCAT Workshop ``Computational and Mathematical challenges in Wells, Waves \& Weather''},
date-added = {2011-01-23 16:43:10 -0500},
date-modified = {2011-01-23 16:47:20 -0500},