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%% Previous PyGBe work
@article{CooperBardhanBarba2013,
Author = {Cooper, Christopher D. and Bardhan, Jaydeep P. and Barba, L.~A.},
Date-Added = {2013-12-04 20:15:44 +0000},
Date-Modified = {2015-05-03 23:44:12 +0000},
Doi = {10.1016/j.cpc.2013.10.028},
Journal = {Comput. Phys. Commun.},
Keywords = {pygbe, Poisson-Boltzmann, BEM, barbagroup},
Month = {March},
Note = {Preprint on \href{http://arxiv.org/abs/1309.4018}{arXiv:/1309.4018}},
Number = {3},
Pages = {720--729},
Title = {A biomolecular electrostatics solver using {Python}, {GPU}s and boundary elements that can handle solvent-filled cavities and {S}tern layers.},
Volume = {185},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cpc.2013.10.028}}
@misc{CooperBarba-share154331,
Author = {Cooper, Christopher D. and Barba, L.~A.},
Date-Added = {2013-09-15 03:25:32 +0000},
Date-Modified = {2015-06-08 15:08:02 +0000},
Doi = {10.6084/m9.figshare.154331},
Howpublished = {Technical Report on \textbf{figshare}, CC-BY license},
Keywords = {pygbe},
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}}
@article{CooperClementiBarba2015,
title={Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design},
author={Cooper, Christopher D and Clementi, Natalia C and Barba, Lorena A},
journal={J. Chem. Phys.},
volume={143},
number={12},
pages={124709},
year={2015},
note = {Preprint on \href{https://arxiv.org/abs/1503.08150}{arxiv:1503.08150}},
publisher={AIP Publishing}}
@article{CooperETal2016,
Author = {Cooper, Christopher D. and Clementi, Natalia C. and Forsyth, Gilbert and Lorena A. Barba},
Date-Added = {2020-07-23 18:46:36 +0100},
Date-Modified = {2020-07-23 18:46:52 +0100},
Doi = {10.21105/joss.00043},
Journal = {J. Open Source Software},
Keywords = {PyGBe, JOSS},
Month = {August},
Note = {\href{http://dx.doi.org/10.21105/joss.00043}{10.21105/joss.00043}},
Number = {4},
Publisher = {The Open Journal},
Title = {{PyGBe}: Python, {GPUs} and Boundary elements for biomolecular electrostatics},
Url = {http://dx.doi.org/10.21105/joss.00043},
Volume = {1},
Year = {2016},
Bdsk-Url-1 = {http://dx.doi.org/10.21105/joss.00043}}
@article{ClementiETal2017,
Author = {Clementi, Natalia C. and Forsyth, Gilbert and Cooper, Christopher D. and Barba, Lorena A.},
Date-Added = {2020-07-23 18:45:39 +0100},
Date-Modified = {2020-07-23 18:45:55 +0100},
Doi = {10.21105/joss.00306},
Journal = {J. Open Source Software},
Note = {\href{https://doi.org/10.21105/joss.00306}{10.21105/joss.00306}},
Number = {19},
Pages = {306},
Title = {{PyGBe-LSPR}: Python and {GPU} Boundary-integral solver for electrostatics},
Volume = {2},
Year = {2017},
Bdsk-Url-1 = {http://dx.doi.org/10.21105/joss.00306}}
@article{ClementiETal2019,
Author = {Clementi, Natalia C. and Cooper, Christopher D. and Barba, L.~A.},
Date-Added = {2020-07-23 18:50:02 +0100},
Date-Modified = {2020-07-23 18:50:17 +0100},
Journal = {Phys.\ Rev.\ E},
Month = {December},
Note = {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{ClementiBarba2020,
title={Reproducible Validation and Replication Studies in Nanoscale Physics},
author={Clementi, Natalia C and Barba, Lorena A},
journal={arXiv preprint arXiv:2008.05414},
year={2020}}
%%BEM theory
@misc{Green1828,
Author = {G. Green},
Date-Added = {2014-04-07 21:34:50 +0000},
Date-Modified = {2014-04-07 21:53:01 +0000},
Howpublished = {Nottingham.},
Title = {An Essay on the Application of Mathematical Analysis to the Theories of Electricity and Magnetism},
Year = {1828}}
@article{Fredholm1903,
Author = {I. Fredholm},
Date-Added = {2014-04-07 21:32:25 +0000},
Date-Modified = {2014-04-07 21:34:07 +0000},
Journal = {Acta Mathematica},
Number = {1},
Pages = {365-390},
Title = {Sur une Classe d'\'{e}quations functionnelles},
Volume = {27},
Year = {1903}}
@article{Somigliana1885,
Author = {C. Somigliana},
Date-Added = {2014-04-07 21:29:07 +0000},
Date-Modified = {2014-04-07 21:31:58 +0000},
Journal = {Il Nuovo Cimento},
Pages = {17-20},
Title = {Sopra l' Equilibrio di' un Corpo Elastico Isotropo},
Volume = {3},
Year = {1885}}
@article{Betti1872,
Author = {E. Betti},
Date-Added = {2014-04-07 21:26:31 +0000},
Date-Modified = {2014-04-07 21:29:00 +0000},
Journal = {Il Nuovo Cimento},
Number = {1},
Pages = {69-97},
Title = {Theoria dell' Elasticita},
Volume = {7-8},
Year = {1872}}
@article{Symm1963,
Author = {G. T. Symm},
Date-Added = {2014-04-07 21:41:33 +0000},
Date-Modified = {2014-04-07 21:42:04 +0000},
Journal = {Proc. R. Soc. A},
Number = {33-46},
Title = {Integral Equation Methods in Potential Theory {II}},
Volume = {275},
Year = {1963}}
@article{Jawson1963,
Author = {M. A. Jawson},
Date-Added = {2014-04-07 21:39:29 +0000},
Date-Modified = {2014-04-07 21:41:26 +0000},
Journal = {Proc. R. Soc. A},
Pages = {23-32},
Title = {Integral Equation Methods in Potential Theory {I}},
Volume = {275},
Year = {1963}}
@article{Cruse1969,
Author = {T. Cruse},
Date-Added = {2014-04-07 21:44:03 +0000},
Date-Modified = {2014-04-07 21:46:11 +0000},
Journal = {Int.\ J. \ Solids Struct.},
Pages = {1259-1274},
Title = {Numerical Solutions in Three Dimensional Elastostatics},
Volume = {5},
Year = {1969}}
@article{Rizzo1967,
Author = {F. J. Rizzo},
Date-Added = {2014-04-07 21:42:08 +0000},
Date-Modified = {2014-04-07 21:43:56 +0000},
Journal = {Quarterly of Applied Mathematics},
Pages = {83-95},
Title = {An Integral Equation Approach to Baundary Value Problems of Classical Elastostatics},
Volume = {25},
Year = {1967}}
@book{Atkinson1997,
Author = {K. E. Atkinson},
Date-Added = {2011-12-19 18:16:39 -0500},
Date-Modified = {2011-12-19 18:38:12 -0500},
Keywords = {bie},
Publisher = {Cambridge Monographs on Applied and Computational Mechanics},
Title = {The Numerical Solution of Integral Equations of the Second Kind},
Year = {1997}}
@book{Steinbach2008,
Author = {O. Steinbach},
Date-Added = {2014-04-07 21:24:33 +0000},
Date-Modified = {2014-04-07 21:25:36 +0000},
Publisher = {Springer},
Title = {Numerical Approximation Methods for Elliptic Boundary Value Problems. Finite and Boundary Elements.},
Year = {2008}}
@book{McLean2000,
Author = {William Mc{L}ean},
Date-Added = {2014-04-07 21:22:55 +0000},
Date-Modified = {2014-04-07 21:23:56 +0000},
Publisher = {Cambridge University Press},
Title = {Strongly Elliptic Systems and Boundary Integral Equations},
Year = {2000}}
@book{Katsikadelis2002,
Author = {J. T. Katsikadelis},
Date-Added = {2011-12-19 17:54:05 -0500},
Date-Modified = {2011-12-19 18:19:40 -0500},
Keywords = {bem},
Publisher = {Elsevier Science},
Title = {Boundary Elements Theory and Applications},
Year = {2002}}
%%Nanoplamsonics modelling
@article{SolisTaboadaObelleiroLiz-MaarzanGarciadeabajo2014,
Author = {Solis, Diego M. and Taboada, Jos\'{e} M. and Obelleiro, Fernando and Liz-Marz\'{a}n, Luis M. and Garc\'{i}a de Abajo, F. Javier},
Date-Added = {2014-10-16 15:47:00 +0000},
Date-Modified = {2014-10-16 15:50:15 +0000},
Journal = {ACS Nano},
Number = {8},
Pages = {7559-7570},
Title = {Toward Ultimate Nanoplasmonics Modeling},
Volume = {8},
Year = {2014}}
%%%Metallic nanoparticles
@article{JungPedersenSondergaardPedersenLarsenNielsen2010,
Author = {Jesper Jung and Thomas G. Pedersen and Thomas Sondergaard and Kield Pedersen and Arne N. Larsen and Brian B. Nielsen},
Date-Added = {2013-12-04 19:57:36 +0000},
Date-Modified = {2013-12-04 19:59:54 +0000},
Journal = {Phys.\ Rev.\ B},
Number = {12},
Title = {Electrostatic plasmon resonances of metal nanospheres in layered geometries},
Volume = {81},
Year = {2010}}
@article{VideenSun2003,
Author = {Videen, Gorden and Sun, Wenbo},
Journal = {Applied optics},
Number = {33},
Pages = {6724--6727},
Publisher = {Optical Society of America},
Title = {Yet another look at light scattering from particles in absorbing media},
Volume = {42},
Year = {2003}}
@article{MayergoyzFredkinZhang2005,
Author = {Isaak D.~ Mayergoyz and Donald R.~ Fredkin and Zhenyu Zhang},
Date-Added = {2013-07-10 19:52:05 +0000},
Date-Modified = {2019-12-03 16:58:45 -0500},
Doi = {10.1103/PhysRevB.72.155412},
Journal = {Phys.\ Rev.\ B},
Number = {15},
Pages = {155412},
Title = {Electrostatic (plasmon) resonances in nanoparticles},
Volume = {72},
Year = {2005}}
@article{GarciadeabajoAizpurua1997,
Author = {Garc\'{i}a de Abajo, F. Javier and Aizpurua, Javier},
Date-Added = {2014-10-16 15:35:17 +0000},
Date-Modified = {2014-10-16 15:39:06 +0000},
Journal = {Phys.\ Rev.\ B},
Number = {24},
Pages = {15873(12)},
Title = {Numerical simulation of electron energy loss near inhomogeneous dielectrics},
Volume = {56},
Year = {1997}}
@article{GarciadeabajoHowie2002,
Author = {F. Javier Garcia de Abajo and Archibald Howie},
Date-Added = {2013-12-04 20:03:38 +0000},
Date-Modified = {2014-12-10 17:19:22 +0000},
Journal = {Phys.\ Rev.\ B},
Number = {11},
Pages = {115418},
Title = {Retarded field calculation of electron energy loss in inhommogeneous dielectrics},
Volume = {65},
Year = {2002}}
%% Small particles theory
@article{MayergoyzZhang2007,
Author = {Mayergoyz, Isaak D. and Zhang, Zhenyu},
Date-Added = {2014-10-16 15:10:23 +0000},
Date-Modified = {2014-10-16 15:13:01 +0000},
Journal = {IEEE Trans.\ Magn.},
Number = {4},
Pages = {1681-1684},
Title = {The Computation of Extinction Cross Sections of Resonant Metallic Nanoparticles Subject to Optical Radiation},
Volume = {43},
Year = {2007}}
@article{Mishchenko2007,
Author = {Mishchenko, Michael I.},
Journal = {Opt. Express},
Number = {15},
Pages = {13188-13202},
Title = {Electromagnetic scattering by a fixed finite object embedded in an absorbing medium},
Volume = {20},
Year = {2007}}
@article{Mie1908,
Author = {Mie, Gustav},
Journal = {Annalen der Physik},
Number = {3},
Pages = {377-445},
Title = {Beitr\"{a}ge zur Optik tr\"{u}ber Medien, speziell kolloidaler Metall\"{o}sungen},
Volume = {330},
Year = {1908}}
%% Optical properties of materials
@article{JohnsonChristy1972,
Author = {Johnson, P. B. and Christy, R. W.},
Journal = {Phys. Rev. B},
Number = {6},
Pages = {4370-4379},
Title = {Optical Constants of Noble Metals},
Volume = {12},
Year = {1972}}
@article{HaleQuerry1972,
Author = {Hale, George M. and Querry, Marvin R.},
Journal = {Appl. Opt.},
Number = {3},
Pages = {555-563},
Title = {Optical Constants of Water in the 200-nm to 200-$\mu$m Wavelength Region},
Volume = {12},
Year = {1972}}
%% Semi-analytical integration - integral formulation
@article{HessSmith1967,
Author = {Hess, John L and Smith, AMO},
Date-Added = {2015-06-04 17:36:26 +0000},
Date-Modified = {2015-06-04 17:37:50 +0000},
Journal = {Progress in Aerospace Sciences},
Keywords = {panel method},
Pages = {1--138},
Publisher = {Elsevier},
Title = {Calculation of potential flow about arbitrary bodies},
Volume = {8},
Year = {1967},
Bdsk-Url-1 = {http://www.dtic.mil/dtic/tr/fulltext/u2/755480.pdf}}
@inproceedings{ZhuHuangSongWhite2001,
Author = {Zhu, Z. and Huang, J. and Song, B. and White, J.},
Booktitle = {Proceedings of the 2001 IEEE/ACM Int.\ Conf.\ on Computer-Aided Design},
Date-Added = {2012-05-23 19:05:32 +0000},
Date-Modified = {2013-01-25 01:23:20 +0000},
Pages = {592--597},
Title = {Improving the Robustness of a Surface Integral Formulation for Wideband Impedance Extraction of {3D} Structures},
Year = {2001}}
%% Treecode
@article{BarnesHut1986,
Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
Adsurl = {http://adsabs.harvard.edu/abs/1986Natur.324..446B},
Author = {Barnes, J. and Hut, P.},
Date-Added = {2008-02-27 11:17:49 +0000},
Date-Modified = {2011-04-28 18:29:12 -0400},
Doi = {10.1038/324446a0},
Journal = {Nature},
Keywords = {treecodes},
Month = {December},
Pages = {446--449},
Title = {A Hierarchical {$O(N \log N)$} Force-Calculation Algorithm},
Volume = {324},
Year = {1986},
Bdsk-Url-1 = {http://dx.doi.org/10.1038/324446a0}}
@article{DuanKrasny2001,
Author = {Z.-H. Duan and R. Krasny},
Date-Added = {2012-05-23 19:15:45 +0000},
Date-Modified = {2013-01-25 01:42:27 +0000},
Journal = {J. Comp.\ Chem.},
Number = {2},
Pages = {184--195},
Title = {An Adaptive Treecode for Computing Nonbonded Potential Energy in Classical Molecular Systems},
Volume = {22},
Year = {2001}}
%% Protein mesher and pdb2pqr
@article{Nanoshaper,
title={A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale},
author={Decherchi, Sergio and Rocchia, Walter},
journal={PloS one},
volume={8},
number={4},
pages={e59744},
year={2013},
publisher={Public Library of Science}
}
@article{Dolinsky04,
Author = {T. J. Dolinsky and J. E. Nielsen and J. A. {McCammon} and N. A. Baker},
Journal = {Nucleic Acids Research},
Pages = {W665-W667},
Title = {{PDB2PQR}: an automated pipeline for the setup of {Poisson}--{Boltzmann} electrostatics calculations},
Volume = 32,
Year = 2004}
%% Biosensors Reviews
@article{Turner2000,
title={Biosensors--sense and sensitivity},
author={Turner, Anthony PF},
journal={Science},
volume={290},
number={5495},
pages={1315--1317},
year={2000},
publisher={American Association for the Advancement of Science}
}
@article{Mohanty2006,
title={Biosensors: a tutorial review},
author={Mohanty, Saraju P and Kougianos, Elias},
journal={Ieee Potentials},
volume={25},
number={2},
pages={35--40},
year={2006},
publisher={IEEE}
}
@article{Mehrotra2016,
title={Biosensors and their applications--A review},
author={Mehrotra, Parikha},
journal={Journal of oral biology and craniofacial research},
volume={6},
number={2},
pages={153--159},
year={2016},
publisher={Elsevier}
}
%%LSPR Biosensors reviews
%% Biosensors
@article{HaesVanduyne2002,
Author = {Haes, Amanda J. and Van Duyne, Richard P.},
Journal = {J. Am. Chem. Soc.},
Number = {35},
Pages = {10596-10604},
Title = {A Nanoscale Optical Biosensor: Sensitivity and Selectivity of an Approach Based on the Localized Surface Plasmon Resonance Spectroscopy of Triangular Silver Nanoparticles},
Volume = {124},
Year = {2002}}
@article{PetryayevaKrull2011,
Author = {Petryayeva, Eleonora and Krull, Ulrich J.},
Date-Added = {2014-10-16 14:14:06 +0000},
Date-Modified = {2014-10-16 14:20:19 +0000},
Journal = {Anal. Chim. Acta},
Pages = {8-24},
Title = {Localized surface plasmon resonance: Nanostructures, bioassays and biosensing --- A review},
Volume = {706},
Year = {2011}}
@article{OlsonETal2015,
title={Optical characterization of single plasmonic nanoparticles},
author={Olson, Jana and Dominguez-Medina, Sergio and Hoggard, Anneli and Wang, Lin-Yung and Chang, Wei-Shun and Link, Stephan},
journal={Chemical Society Reviews},
volume={44},
number={1},
pages={40--57},
year={2015},
publisher={Royal Society of Chemistry}
}
@article{WilletsVandyune2007,
Author = {Willets, Katherine A. and Van Dyune, Richard P.},
Date-Added = {2014-10-16 14:11:00 +0000},
Date-Modified = {2014-10-16 14:12:58 +0000},
Journal = {Annu. Rev. Phys. Chem.},
Pages = {267-297},
Title = {Localized Surface Plasmon Resonance Spectroscopy and Sensing},
Volume = {58},
Year = {2007}}
@article{PhanETal2013,
Author = {Phan,Anh D. and Hoang,Trinh X. and Nghiem,Thi H. L. and Woods,Lilia M. },
Journal = {Applied Physics Letters},
Number = {16},
Pages = {163702},
Title = {Surface plasmon resonances of protein-conjugated gold nanoparticles on graphitic substrates},
Volume = {103},
Year = {2013}}
@article{TangETal2010,
Author = {Tang, Bin and Xu, Shuping and Tao, Jinlong and Wu, Yuqing and Xu, Weiqing and Ozaki, Yukihiro},
Journal = {The Journal of Physical Chemistry C},
Number = {49},
Pages = {20990-20996},
Title = {Two-Dimensional Correlation Localized Surface Plasmon Resonance Spectroscopy for Analysis of
the Interaction between Metal Nanoparticles and Bovine Serum Albumin},
Volume = {114},
Year = {2010}}
@article{TeichroebETal2008,
title={Size-dependent denaturing kinetics of bovine serum albumin adsorbed onto gold nanospheres},
author={Teichroeb, JH and Forrest, JA and Jones, LW},
journal={The European Physical Journal E},
volume={26},
number={4},
pages={411--415},
year={2008},
publisher={Springer}
}
@article{PuETal2018,
title={Biomolecule-templated photochemical synthesis of silver nanoparticles: Multiple readouts of localized surface plasmon resonance for pattern recognition},
author={Pu, Fang and Ran, Xiang and Guan, Meng and Huang, Yanyan and Ren, Jinsong and Qu, Xiaogang},
journal={Nano Research},
volume={11},
number={6},
pages={3213--3221},
year={2018},
publisher={Springer}
}
@article{Sepulveda2009,
title={LSPR-based nanobiosensors},
author={Sep{\'u}lveda, Borja and Angelom{\'e}, Paula C and Lechuga, Laura M and Liz-Marz{\'a}n, Luis M},
journal={nano today},
volume={4},
number={3},
pages={244--251},
year={2009},
publisher={Elsevier}
}
@article{Homola2008,
title={Surface plasmon resonance sensors for detection of chemical and biological species},
author={Homola, Ji{\v{r}}{\'\i}},
journal={Chemical reviews},
volume={108},
number={2},
pages={462--493},
year={2008},
publisher={ACS Publications}
}
@article{RaphaelETal2013,
Author = {Raphael, Marc P. and Christodoulides, Joseph A. and Delehanty, James B. and Long, James P. and Pehrsson, Pehr E. and Byers, Jeff M.},
Date-Added = {2014-10-16 15:06:53 +0000},
Date-Modified = {2014-12-10 17:23:40 +0000},
Journal = {Biophys.\ J.},
Pages = {30-36},
Title = {Quantitative {LSPR} Imaging for Biosensing with Single Nanostructure Resolution},
Volume = {104},
Year = {2013}}
@article{HaesETal2004,
Author = {Haes, Amanda J. and Zou, Shengli and Schantz, George C. and Van Duyne, Richard P.},
Journal = {J. Phys. Chem B},
Pages = {109-116},
Title = {A Nanoscale Optical Biosensor: The Long Range Distance Dependence of the Localized Surface Plasmon Resonance of Noble Metal Nanoparticles},
Volume = {108},
Year = {2004}}
@article{ZhangZhangETal2013,
title={Chemical mapping of a single molecule by plasmon-enhanced Raman scattering},
author={Zhang, Renhe and Zhang, Y and Dong, ZC and Jiang, S and Zhang, C and Chen, LG and Zhang, L and Liao, Y and Aizpurua, J and Luo, Y ea and others},
journal={Nature},
volume={498},
number={7452},
pages={82},
year={2013},
publisher={Nature Publishing Group}
}
@article{Wang2010,
title={Gold nanorod-based localized surface plasmon resonance biosensor for sensitive detection of hepatitis B virus in buffer, blood serum and plasma},
author={Wang, Xiaohui and Li, Yuan and Wang, Huafen and Fu, Qiuxia and Peng, Jianchun and Wang, Yingli and Du, Juan and Zhou, Yong and Zhan, Linsheng},
journal={Biosensors and Bioelectronics},
volume={26},
number={2},
pages={404--410},
year={2010},
publisher={Elsevier}
}
@article{Liu2014,
title={Effects of nanoparticle size and cell type on high sensitivity cell detection using a localized surface plasmon resonance biosensor},
author={Liu, Fei and Wong, Matthew Man-Kin and Chiu, Sung-Kay and Lin, Hao and Ho, Johnny C and Pang, Stella W},
journal={Biosensors and Bioelectronics},
volume={55},
pages={141--148},
year={2014},
publisher={Elsevier}
}
@article{Zhu2016,
title={High sensitivity plasmonic biosensor based on nanoimprinted quasi 3D nanosquares for cell detection},
author={Zhu, Shuyan and Li, Hualin and Yang, Mengsu and Pang, Stella W},
journal={Nanotechnology},
volume={27},
number={29},
pages={295101},
year={2016},
publisher={IOP Publishing}
}
@article{BeuwervanHoofZijlstra2018,
title={Spatially resolved sensitivity of single-particle plasmon sensors},
author={Beuwer, Michael A and Van Hoof, Bas and Zijlstra, Peter},
journal={The Journal of Physical Chemistry C},
volume={122},
number={8},
pages={4615--4621},
year={2018},
publisher={ACS Publications}
}
@article{HenkelETal2018,
title={Narrowing the Plasmonic Sensitivity Distribution by Considering the Individual Size of Gold Nanorods},
author={Henkel, Andreas and Ye, Weixiang and Khalavka, Yuriy and Neiser, Andreas and Lambertz, Christina and Schmachtel, Sebastian and Ahijado-Guzm{\'a}n, Rub{\'e}n and S{\"o}nnichsen, Carsten},
journal={The Journal of Physical Chemistry C},
volume={122},
number={18},
pages={10133--10137},
year={2018},
publisher={ACS Publications}
}
@article{HallETal2011,
title={A conformation-and ion-sensitive plasmonic biosensor},
author={Hall, W Paige and Modica, Justin and Anker, Jeffrey and Lin, Yao and Mrksich, Milan and Van Duyne, Richard P},
journal={Nano letters},
volume={11},
number={3},
pages={1098--1105},
year={2011},
publisher={ACS Publications}
}
%% Refs to show that classical approach is ok at d=0.5
@article{SavageETal2012,
title={Revealing the quantum regime in tunnelling plasmonics},
author={Savage, Kevin J and Hawkeye, Matthew M and Esteban, Rub{\'e}n and Borisov, Andrei G and Aizpurua, Javier and Baumberg, Jeremy J},
journal={Nature},
volume={491},
number={7425},
pages={574},
year={2012},
publisher={Nature Publishing Group}
}
@article{EstebanETal2012,
title={Bridging quantum and classical plasmonics with a quantum-corrected model},
author={Esteban, Ruben and Borisov, Andrei G and Nordlander, Peter and Aizpurua, Javier},
journal={Nature communications},
volume={3},
pages={825},
year={2012},
publisher={Nature Publishing Group}
}
%% Other BEM softwares
@article{SmigajETal2015,
title={Solving boundary integral problems with {BEM++}},
author={{\'S}migaj, Wojciech and Betcke, Timo and Arridge, Simon and Phillips, Joel and Schweiger, Martin},
journal={ACM Transactions on Mathematical Software (TOMS)},
volume={41},
number={2},
pages={6},
year={2015},
publisher={ACM}
}
@article{HohenesterTrugler2012,
Author = {Ulrich Hohenester and Andreas Trugler},
Date-Added = {2013-12-04 20:00:47 +0000},
Date-Modified = {2015-05-11 02:31:33 +0000},
Journal = {Comput. Phys. Commun.},
Pages = {370--381},
Title = {{MNPBEM} --- {A} {M}atlab toolbox for the simulation of plasmonic nanoparticles},
Volume = {183},
Year = {2012}}
@article{Hohenester2018,
title={Making simulations with the {MNPBEM} toolbox big: Hierarchical matrices and iterative solvers},
author={Hohenester, Ulrich},
journal={Computer Physics Communications},
volume={222},
pages={209--228},
year={2018},
publisher={Elsevier}
}
%% Books
@book{Jackson,
Author = {J. D. Jackson},
City = {New York},
Edition = {3$^{rd}$},
Publisher = {Wiley},
Title = {Classical Electrodynamics},
Year = {1998}}
@book{BrebbiaDominguez1992,
Author = {Brebbia, C and Dominguez, I},
Date-Added = {2011-12-19 18:12:58 -0500},
Date-Modified = {2013-03-18 19:09:18 +0000},
Edition = {2nd},
Keywords = {bem},
Publisher = {WIT Press},
Title = {Boundary Elements An Introductory Course},
Year = {1992}}
@book{BohrenHuffman1983,
Author = {Craig F. Bohren and Donald R. Huffman},
Date-Added = {2013-12-04 19:43:05 +0000},
Date-Modified = {2013-12-04 22:21:48 +0000},
Publisher = {{J}ohn {W}iley \& Sons},
Title = {Absorption and scattering of light by small particles},
Year = {1983}}
@book{Roache1998,
Author = {Roache, Patrick J.},
Date-Added = {2020-07-25 16:58:49 +0100},
Date-Modified = {2020-07-25 17:03:13 +0100},
Publisher = {Hermosa Albuquerque, NM},
Title = {Verification and validation in computational science and engineering},
Volume = {895},
Year = {1998}}
%% Repropacks
@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{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{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}}
@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{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{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{ClementiBarba2020-Zen_b,
Author = {Clementi, Natalia C. and Barba, Lorena A.},
Date-Added = {2020-07-27 20:54:40 +0100},
Date-Modified = {2020-07-27 21:01:02 +0100},
Howpublished = {Zenodo archive, \href{https://doi.org/10.5281/zenodo.3962576}{doi:10.5281/zenodo.3962576}},
Month = {July},
Title = {Reproducible Validation and Replication Studies in Nanoscale Physics (execution files)},
Year = {2020}}
@misc{ClementiBarba2020-Zen_a,
Author = {Clementi, Natalia C. and Barba, Lorena A.},
Date-Added = {2020-07-27 20:50:08 +0100},
Date-Modified = {2020-07-27 21:00:56 +0100},
Howpublished = {Zenodo archive, \href{https://doi.org/10.5281/zenodo.3962534}{doi:10.5281/zenodo.3962534}},
Month = {July},
Title = {Reproducible Validation and Replication Studies in Nanoscale Physics (problem datasets for Rockstuhl et al. 2005 replication)},
Year = {2020}}
@misc{ClementiBarba2020-Zen_c,
Author = {Clementi, Natalia C. and Barba, Lorena A.},
Date-Added = {2020-07-27 21:03:54 +0100},
Date-Modified = {2020-07-27 21:03:54 +0100},
Howpublished = {Zenodo archive, \href{https://doi.org/10.5281/zenodo.3962584}{doi:10.5281/zenodo.3962584}},
Month = {July},
Title = {Reproducible Validation and Replication Studies in Nanoscale Physics (problem datasets for Validation and Ellis et al.2005 replication)},
Year = {2020}}
@misc{ClementiBarba2020-Zen_d,
Author = {Clementi, Natalia C. and Barba, Lorena A.},
Date-Added = {2020-07-27 21:08:47 +0100},
Date-Modified = {2020-07-27 21:11:19 +0100},
Howpublished = {Zenodo archive, \href{https://doi.org/10.5281/zenodo.3962791}{doi:10.5281/zenodo.3962791}},
Month = {July},
Title = {Validation and Replication Studies in Nanoscale Physics (repro results plots - Rockstuhl et al., 2005)},
Year = {2020}}
@misc{ClementiBarba2020-Zen_e,
Author = {Clementi, Natalia C. and Barba, Lorena A.},
Date-Added = {2020-07-27 20:39:42 +0100},
Date-Modified = {2020-07-27 21:19:44 +0100},
Howpublished = {Zenodo archive, \href{https://doi.org/3962797/zenodo.3962797}{doi:10.5281/zenodo.3962797}},
Month = {July},
Title = {Reproducible Validation and Replication Studies in Nanoscale Physics (repro results plots - Ellis et al., 2016)},
Year = {2020}}
%ROM repropacks
@misc{Clementi2021-Zen_IF,
Author = {Clementi, Natalia C.},
Howpublished = {Zenodo archive, \href{https://doi.org/10.5281/zenodo.4558105}{10.5281/zenodo.4558105}},
title = {Reduced Order Models Chapter - N.C. Clementi PhD Thesis (problem data set)},
month = {Feb},
year = {2021},
doi = {10.5281/zenodo.4558105},
url = {https://doi.org/10.5281/zenodo.4558105}
}
@misc{Clementi2021-Zen_EF,
Author = {Clementi, Natalia C.},
Howpublished = {Zenodo archive, \href{https://doi.org/10.5281/zenodo.4558114}{10.5281/zenodo.4558114}},
title = {Reduced Order Models Chapter - N.C. Clementi PhD Thesis (execution files)},
month = {Feb},
year = {2021},
doi = {10.5281/zenodo.4558114},
url = {https://doi.org/10.5281/zenodo.4558114}
}
@misc{Clementi2021-Zen_RP,
Author = {Clementi, Natalia C.},
Howpublished = {Zenodo archive, \href{https://doi.org/10.5281/zenodo.4558118}{10.5281/zenodo.4558118}},
title = {Reduced Order Models Chapter - N.C. Clementi PhD Thesis (repro results plots)},
month = {Feb},
year = {2021},
doi = {10.5281/zenodo.4558118},
url = {https://doi.org/10.5281/zenodo.4558118}
}
%% Reduced Order model for protein representation
@article{NghiemETal2012,
title={Capping and in vivo toxicity studies of gold nanoparticles},
author={Nghiem, Thi Ha Lien and Nguyen, Thi Tuyen and Fort, Emmanuel and Nguyen, Thanh Phuong and Hoang, Thi My Nhung and Nguyen, Thi Quy and Tran, Hong Nhung},
journal={Advances in Natural Sciences: Nanoscience and Nanotechnology},
volume={3},
number={1},
pages={015002},
year={2012},
publisher={IOP Publishing},
Bdsk-Url-1={https://doi.org/10.1088/2043-6262/3/1/015002}
}
@article{DanHu2014,
title={Plasmon resonance based analysis of a single protein conjugated Au nanoshell},
author={Dan, Berco and Hu, Chin-Kun},
journal={Biointerphases},
volume={9},
number={3},
pages={031017},
year={2014},
publisher={American Vacuum Society},
Bdsk-Url-1={https://doi.org/10.1116/1.4895964}
}
@article{SantiagoCordobaETal2011,
title={Nanoparticle-based protein detection by optical shift of a resonant microcavity},
author={Santiago-Cordoba, Miguel A and Boriskina, Svetlana V and Vollmer, Frank and Demirel, Melik C},
journal={Applied Physics Letters},
volume={99},
number={7},
pages={073701},
year={2011},
publisher={American Institute of Physics},
Bdsk-Url-1={https://doi.org/10.1063/1.3599706}
}
@article{UngerETal2009,
title={Sensitivity of crescent-shaped metal nanoparticles to attachment of dielectric colloids},
author={Unger, Andreas and Rietzler, Uwe and Berger, R{\"u}diger and Kreiter, Maximilian},
journal={Nano Letters},
volume={9},
number={6},
pages={2311--2315},
year={2009},
publisher={ACS Publications},
Bdsk-Url-1={https://doi.org/10.1021/nl900505a}
}
@article{ShenETal2013,
title={Shape effect on a single-nanoparticle-based plasmonic nanosensor},
author={Shen, Hongming and Lu, Guowei and Zhang, Tianyue and Liu, Jie and Gu, Ying and Perriat, Pascal and Martini, Matteo and Tillement, Olivier and Gong, Qihuang},
journal={Nanotechnology},
volume={24},
number={28},
pages={285502},
year={2013},
publisher={IOP Publishing},
Bdsk-Url-1={https://iopscience.iop.org/article/10.1088/0957-4484/24/28/285502}
}
@article{MoserETal1966,
title={Electric Polarization in Proteins—Dielectric Dispersion and Kerr Effect Studies of Isoionic Bovine Serum Albumin1},
author={Moser, P and Squire, PG and O'Konski, CT},
journal={The Journal of Physical Chemistry},
volume={70},
number={3},
pages={744--756},
year={1966},
publisher={ACS Publications},
Bdsk-Url-1={https://pubs.acs.org/doi/pdf/10.1021/j100875a023}
}
@article{SquireETal1968,
title={Hydrodynamic properties of bovine serum albumin monomer and dimer},
author={Squire, Phil G and Moser, Peter and O'Konski, Chester T},
journal={Biochemistry},
volume={7},
number={12},
pages={4261--4272},
year={1968},
publisher={ACS Publications},
Bdsk-Url-1={https://pubs.acs.org/doi/pdf/10.1021/bi00852a018}
}
@article{WrightETal1975,
title={Hydrodynamic structure of bovine serum albumin determined by transient electric birefringence.},
author={Wright, A Kent and Thompson, MR},
journal={Biophysical journal},
volume={15},
number={2 Pt 1},
pages={137},
year={1975},
publisher={The Biophysical Society},
Bdsk-Url-1={https://doi.org/10.1016/s0006-3495(75)85797-3}}
@article{DavisGomezVernon2010,
Author = {Tim J. Davis and D. E. Gomez and K. C. Vernon},
Date-Added = {2013-12-04 20:13:30 +0000},
Date-Modified = {2013-12-04 20:14:26 +0000},
Journal = {Phys.\ Rev.\ B},
Number = {4},
Title = {Interaction of molecules with localized surface plasmons in metallic nanoparticles},
Volume = {81},
Year = {2010}}
@article{AntosiewiczApellClaudioKall2011,
Author = {Antosiewicz, Tomasz J. and Apell, S. Peter and Claudio, Virginia and K\"{a}ll, Mikael},
Date-Added = {2014-10-16 15:44:16 +0000},
Date-Modified = {2014-10-16 15:46:45 +0000},
Journal = {Opt. Express},
Number = {1},
Pages = {524-533},
Title = {A simple model for the resonance shift of localized plasmons due to dielectric particle adhesion},
Volume = {20},
Year = {2011}}
@article{JungCampbellChinowskyMarYee1998,
Author = {Jung, Linda S. and Campbell, Charles T. and Chinowsky, Timothy M. and Mar, Mimi N. and Yee, Sinclair S.},
Journal = {Langmuir},
Pages = {5636-5648},
Title = {Quantitative INterpretation of the Response of Surface Plasmon Resonance Sensors to Adsorbed Fields},
Volume = {14},
Year = {1998}}
%% Replication and Validation refs and SPhP
@article{rockstuhl2005,
Author = {Rockstuhl, Carsten and Salt, Martin G and Herzig, Hans P},
Date-Modified = {2020-07-27 14:36:42 +0100},