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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for Lorena Barba at 2021-09-27 18:27:37 -0400
%% Saved with string encoding Unicode (UTF-8)
@article{ClementiBarba2021,
author = {Clementi, Natalia C. and Barba, L.~A.},
date-added = {2021-09-27 18:20:50 -0400},
date-modified = {2021-09-27 18:27:36 -0400},
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{ClementiETal2019,
author = {Clementi, Natalia C. and Cooper, Christopher D. and Barba, Lorena A.},
date-added = {2019-03-24 13:55:34 -0400},
date-modified = {2021-09-27 18:13:57 -0400},
journal = {Phys.\ Rev.\ E},
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 for biosensing applications using {PyGBe-LSPR}},
volume = {100},
year = {2019}}
@misc{ClementiETal2018f,
author = {Clementi, Natalia C. and Cooper, Christopher D. and Barba, Lorena A.},
date-added = {2018-12-25 13:53:35 -0300},
date-modified = {2018-12-25 14:19:21 -0300},
doi = {10.6084/m9.figshare.7506167.v1},
howpublished = {figshare. Fileset.},
month = {December},
title = {{LSPR} response of a silver nanosphere to bovine serum albumin ({BSA}), using {PyGBE}},
year = {2018},
bdsk-url-1 = {https://doi.org/10.6084/m9.figshare.7506167.v1}}
@misc{ClementiETal2018e,
author = {Clementi, Natalia C. and Cooper, Christopher D. and Barba, Lorena A.},
date-added = {2018-12-23 20:08:49 -0300},
date-modified = {2018-12-23 22:12:44 -0300},
doi = {10.6084/m9.figshare.7504484.v1},
howpublished = {figshare. Fileset.},
month = {December},
title = {Mesh visualizations for {PyGBE} calculations of {LSPR} response to bovine serum albumin ({BSA})},
year = {2018},
bdsk-url-1 = {https://doi.org/10.6084/m9.figshare.7504484.v1}}
@misc{ClementiETal2018d,
author = {Clementi, Natalia C. and Cooper, Christopher D. and Barba, Lorena A.},
date-added = {2018-12-23 10:50:05 -0300},
date-modified = {2018-12-23 10:51:11 -0300},
doi = {10.6084/m9.figshare.7504307.v1},
howpublished = {figshare. Fileset.},
month = {December},
title = {Verification of {PyGBE-LSPR} on the extinction cross-section of a single nanosphere},
year = {2018},
bdsk-url-1 = {https://doi.org/10.6084/m9.figshare.7504307.v1}}
@misc{ClementiETal2018c,
author = {Clementi, Natalia C. and Cooper, Christopher D. and Barba, Lorena A.},
date-added = {2018-12-23 10:14:15 -0300},
date-modified = {2018-12-23 10:16:18 -0300},
doi = {10.6084/m9.figshare.7504271.v1},
howpublished = {figshare. Fileset.},
month = {December},
title = {Grid convergence of {PyGBE-LSPR} with a silver nano sphere and with {BSA} sensor system},
year = {2018},
bdsk-url-1 = {https://doi.org/10.6084/m9.figshare.7504271.v1}}
@misc{ClementiETal2018a,
author = {Clementi, Natalia C. and Cooper, Christopher D. and Barba, Lorena A.},
date-added = {2018-12-22 19:32:10 -0300},
date-modified = {2018-12-22 19:32:10 -0300},
doi = {10.5281/zenodo.2511600},
howpublished = {[Data set]. Zenodo},
month = {December},
title = {{PyGBe-LSPR}---Computational nanoplasmonics for biosensing applications (problem datasets)},
year = {2018},
bdsk-url-1 = {https://doi.org/10.5281/zenodo.2511600}}
@misc{ClementiETal2018b,
author = {Clementi, Natalia C. and Cooper, Christopher D. and Barba, Lorena A.},
date-added = {2018-12-22 18:00:31 -0300},
date-modified = {2018-12-22 19:34:08 -0300},
doi = {10.5281/zenodo.2513715},
howpublished = {Zenodo},
month = {December},
title = {{PyGBe-LSPR}---Computational nanoplasmonics for biosensing applications (execution files)},
year = {2018},
bdsk-url-1 = {https://doi.org/10.5281/zenodo.2513715}}
@article{Dolinsky04,
author = {T. J. Dolinsky and J. E. Nielsen and J. A. {McCammon} and N. A. Baker},
date-added = {2018-12-21 15:25:43 -0300},
date-modified = {2018-12-21 15:25:43 -0300},
journal = {Nucleic Acids Research},
pages = {W665-W667},
title = {{PDB2PQR}: an automated pipeline for the setup of {Poisson}--{Boltzmann} electrostatics calculations},
volume = 32,
year = 2004}
@book{Jackson,
author = {J. D. Jackson},
city = {New York},
date-added = {2018-12-21 15:25:22 -0300},
date-modified = {2018-12-21 15:25:22 -0300},
edition = {3$^{rd}$},
publisher = {Wiley},
title = {Classical Electrodynamics},
year = {1998}}
@article{IoriCorni2008,
author = {Iori, Federico and Corni, Stefano},
journal = {Journal of computational chemistry},
number = {10},
pages = {1656--1666},
publisher = {Wiley Online Library},
title = {Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces},
volume = {29},
year = {2008}}
@article{FogolariETal2015,
author = {Fogolari, Federico and Corazza, Alessandra and Esposito, Gennaro},
journal = {Journal of computational chemistry},
number = {9},
pages = {585--596},
publisher = {Wiley Online Library},
title = {Accuracy assessment of the linear Poisson--Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid--protein complexes},
volume = {36},
year = {2015}}
@article{BuVakninTravesset2006,
author = {Bu, Wei and Vaknin, David and Travesset, Alex},
journal = {Langmuir},
number = {13},
pages = {5673--5681},
publisher = {ACS Publications},
title = {How accurate is Poisson-Boltzmann theory for monovalent ions near highly charged interfaces?},
volume = {22},
year = {2006}}
@article{LiuLiu2006-rheology,
author = {Liu, Yaling and Liu, Wing Kam},
date-added = {2015-06-01 16:52:08 +0000},
date-modified = {2015-06-01 16:55:04 +0000},
journal = {J. Comp.\ Phys.},
keywords = {blood, red blood cells},
number = {1},
pages = {139--154},
publisher = {Elsevier},
title = {Rheology of red blood cell aggregation by computer simulation},
volume = {220},
year = {2006}}
@article{EvansFung1972,
author = {Evans, Evan and Fung, Yuan-Cheng},
date-added = {2015-06-01 11:30:46 +0000},
date-modified = {2015-06-01 16:55:27 +0000},
journal = {Microvascular research},
keywords = {blood, red blood cells},
number = {4},
pages = {335--347},
publisher = {Elsevier},
title = {Improved measurements of the erythrocyte geometry},
volume = {4},
year = {1972}}
@book{Kruger2012,
author = {Kr{\"u}ger, Timm},
date-added = {2015-06-01 09:32:38 +0000},
date-modified = {2015-06-01 11:30:46 +0000},
doi = {10.1007/978-3-8348-2376-2},
note = {PhD Thesis, Bochum University},
publisher = {Springer},
title = {Computer Simulation Study of Collective Phenomena in Dense Suspensions of Red Blood Cells under Shear},
year = {2012},
bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-8348-2376-2}}
@article{FedosovETal2011,
abstract = {The pathogenicity of Plasmodium falciparum (Pf) malaria results from the stiffening of red blood cells (RBCs) and its ability to adhere to endothelial cells (cytoadherence). The dynamics of Pf-parasitized RBCs is studied by three-dimensional mesoscopic simulations of flow in cylindrical capillaries in order to predict the flow resistance enhancement at different parasitemia levels. In addition, the adhesive dynamics of Pf-RBCs is explored for various parameters revealing several types of cell dynamics such as firm adhesion, very slow slipping along the wall, and intermittent flipping. The parasite inside the RBC is modeled explicitly in order to capture phenomena such as ``hindered tumbling'' motion of the RBC and the sudden transition from firm RBC cytoadherence to flipping on the endothelial surface. These predictions are in quantitative agreement with recent experimental observations, and thus the three-dimensional modeling method presented here provides new capabilities for guiding and interpreting future in vitro and in vivo studies of malaria.},
author = {Fedosov, D. A. and Caswell, B. and Suresh, S. and Karniadakis, G. E.},
date-added = {2015-06-01 09:02:24 +0000},
date-modified = {2015-06-01 09:03:34 +0000},
doi = {10.1073/pnas.1009492108},
eprint = {http://www.pnas.org/content/108/1/35.full.pdf},
journal = {Proc. Natl. Acad. Sci.},
number = {1},
pages = {35--39},
title = {Quantifying the biophysical characteristics of {Plasmodium}-falciparum-parasitized red blood cells in microcirculation},
url = {http://www.pnas.org/content/108/1/35.abstract},
volume = {108},
year = {2011},
bdsk-url-1 = {http://www.pnas.org/content/108/1/35.abstract},
bdsk-url-2 = {http://dx.doi.org/10.1073/pnas.1009492108}}
@article{Freund2014,
author = {Freund, Jonathan B},
date-added = {2015-06-01 08:15:39 +0000},
date-modified = {2015-06-01 08:16:40 +0000},
journal = {Ann.\ Rev.\ Fluid Mech.},
pages = {67--95},
publisher = {Annual Reviews},
title = {Numerical simulation of flowing blood cells},
volume = {46},
year = {2014},
bdsk-url-1 = {http://jbfreund.mechse.illinois.edu/Papers/freund-annreview-2014.pdf}}
@article{BuijsETal1997,
author = {Buijs, Jos and White, David D and Norde, Willem},
date-added = {2015-05-11 00:01:21 +0000},
date-modified = {2015-06-07 18:11:02 +0000},
journal = {Colloids and Surfaces B: Biointerfaces},
number = {4},
pages = {239--249},
publisher = {Elsevier},
title = {The effect of adsorption on the antigen binding by {IgG} and its {F}(ab′) 2 fragments},
volume = {8},
year = {1997}}
@article{CooperClementiBarba2015,
author = {Cooper, Christopher D and Clementi, Natalia C and Barba, Lorena A},
journal = {J. Chem. Phys.},
note = {Preprint on \href{arxiv:1503.08150}{arxiv:1503.08150}},
number = {12},
pages = {124709},
publisher = {AIP Publishing},
title = {Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design},
volume = {143},
year = {2015}}
@article{CooperBarba2016,
author = {Cooper, Christopher D. and Barba, L.~A.},
date-added = {2015-05-07 00:52:27 +0000},
date-modified = {2018-12-25 14:53:40 -0300},
doi = {10.1016/j.cpc.2015.12.019},
journal = {Comput. Phys. Comm.},
keywords = {pygbe},
month = {May},
note = {Preprint on \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 = {https://doi.org/10.1016/j.cpc.2015.12.019}}
@article{XieZhowJiang2010,
author = {Xie, Yun and Zhou, Jian and Jiang, Shaoyi},
date-added = {2015-05-04 00:26:26 +0000},
date-modified = {2015-05-04 00:27:34 +0000},
doi = {http://dx.doi.org/10.1063/1.3305244},
eid = 065101,
journal = {J. Chem.\ Phys.},
number = {6},
pages = {065101},
title = {Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces},
url = {http://scitation.aip.org/content/aip/journal/jcp/132/6/10.1063/1.3305244},
volume = {132},
year = {2010},
bdsk-url-1 = {http://scitation.aip.org/content/aip/journal/jcp/132/6/10.1063/1.3305244},
bdsk-url-2 = {http://dx.doi.org/10.1063/1.3305244}}
@article{MijajlovicETal2013,
author = {Mijajlovic, Milan and Penna, Matthew J. and Biggs, Mark J.},
date-added = {2015-05-03 23:04:46 +0000},
date-modified = {2015-05-03 23:05:21 +0000},
doi = {10.1021/la3047966},
eprint = {http://dx.doi.org/10.1021/la3047966},
journal = {Langmuir},
note = {PMID: 23394469},
number = {9},
pages = {2919--2926},
title = {Free Energy of Adsorption for a Peptide at a Liquid/Solid Interface via Nonequilibrium Molecular Dynamics},
url = {http://dx.doi.org/10.1021/la3047966},
volume = {29},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.1021/la3047966}}
@article{LotanHead-Gordon2006,
author = {Lotan, Itay and Head-Gordon, Teresa},
date-added = {2015-04-30 22:10:21 +0000},
date-modified = {2015-04-30 22:10:21 +0000},
journal = {J. Chem.\ Theory Comput.},
number = {3},
pages = {541--555},
publisher = {ACS Publications},
title = {An analytical electrostatic model for salt screened interactions between multiple proteins},
volume = {2},
year = {2006}}
@article{JufferArgosDevlieg1996,
author = {Juffer, Andr{\'e} H and Argos, P and De Vlieg, J},
date-modified = {2015-06-07 18:05:35 +0000},
doi = {0.1002/(SICI)1096-987X(199612)17:16<1783::AID-JCC1>3.0.CO;2-J},
journal = {J. Comp.\ Chem.},
number = {16},
pages = {1783--1803},
publisher = {Wiley Online Library},
title = {Adsorption of proteins onto charged surfaces: a {Monte Carlo} approach with explicit ions},
volume = {17},
year = {1996},
bdsk-url-1 = {http://dx.doi.org/0.1002/(SICI)1096-987X(199612)17:16%3C1783::AID-JCC1%3E3.0.CO;2-J}}
@misc{CooperBarba2015-share1348801,
author = {Cooper, Christopher D. and Barba, L.~A.},
date-added = {2015-03-24 14:08:40 +0000},
date-modified = {2015-05-04 00:20:26 +0000},
howpublished = {Data, figures and plottings script on \textbf{figshare}, CC-BY license, \href{http://dx.doi.org/10.6084/m9.figshare.1348801}{http://dx.doi.org/10.6084/m9.figshare. 1348801}},
keywords = {pygbe},
month = {March},
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