-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathpygbe_rep_val.bib
363 lines (329 loc) · 14.5 KB
/
pygbe_rep_val.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for Lorena A Barba at 2020-09-05 18:28:18 +0100
%% Saved with string encoding Unicode (UTF-8)
@article{wiley-etal-2006,
Author = {Wiley, Benjamin J. and Im, Sang Hyuk and Li, Zhi-Yuan and McLellan, Joeseph and Siekkinen, Andrew and Xia, Younan},
Date-Added = {2020-09-05 18:21:08 +0100},
Date-Modified = {2020-09-05 18:28:18 +0100},
Doi = {10.1021/jp0608628},
Journal = {J. Phys. Chem. B},
Note = {https://doi.org/10.1021/jp0608628},
Number = {32},
Pages = {15666---15675},
Publisher = {ACS Publications},
Title = {Maneuvering the surface plasmon resonance of silver nanostructures through shape-controlled synthesis},
Volume = {110},
Year = {2006}}
@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 = {alidation and Replication Studies in Nanoscale Physics (repro results plots - Rockstuhl et al., 2005)},
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_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_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}}
@article{BarbaThiruvathukal2017,
Author = {L. A. Barba and G. K. Thiruvathukal},
Date-Added = {2020-07-27 11:13:56 +0100},
Date-Modified = {2020-07-27 11:13:56 +0100},
Doi = {10.1109/MCSE.2017.3971172},
Issn = {1521-9615},
Journal = {Computing in Science \& Engineering},
Keywords = {reproducible research;peer review;open access;scientific computing},
Month = {November/December},
Note = {\href{http://doi.org/c7bw}{doi:10/c7bw}},
Number = {6},
Pages = {85--87},
Publisher = {IEEE},
Title = {Reproducible Research for Computing in Science and Engineering},
Volume = {19},
Year = {2017},
Bdsk-Url-1 = {https://doi.org/10.1109/MCSE.2017.3971172}}
@misc{barba2012manifesto,
Author = {Barba, Lorena A.},
Date-Added = {2020-07-27 10:42:49 +0100},
Date-Modified = {2020-07-27 10:44:19 +0100},
Howpublished = {Figshare \href{https://doi.org/10.6084/m9.figshare.104539.v1}{doi:10.6084/m9.figshare.104539.v1}},
Title = {Reproducibility {PI} manifesto},
Year = {2012}}
@article{mesnard-barba2019,
Author = {Mesnard, Olivier and Barba, Lorena A.},
Date-Added = {2020-07-25 19:59:02 +0100},
Date-Modified = {2020-07-25 19:59:02 +0100},
Doi = {10/d2hr},
Journal = {Computing in Science \& Engineering},
Month = {September},
Note = {\href{http://doi.org/d2hr}{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 = {2019},
Bdsk-Url-1 = {https://doi.org/10/d2hr}}
@article{barba2019praxis,
Author = {Barba, Lorena A},
Date-Added = {2020-07-25 19:58:33 +0100},
Date-Modified = {2020-07-25 19:58:44 +0100},
Doi = {10.1109/MCSE.2018.2881905},
Journal = {Computing in Science \& Engineering},
Note = {doi:10.1109/MCSE.2018.2881905},
Number = {1},
Pages = {73--78},
Publisher = {IEEE},
Title = {Praxis of reproducible computational science},
Volume = {21},
Year = {2019},
Bdsk-Url-1 = {https://doi.org/10.1109/MCSE.2018.2881905}}
@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}}
@incollection{otte-etal-2012,
Author = {Otte, Marinus A and Sepulveda, Borja},
Booktitle = {Nanoplasmonic Sensors. Integrated Analytical Systems.},
Date-Added = {2020-07-25 13:15:32 +0100},
Date-Modified = {2020-07-25 13:34:23 +0100},
Doi = {10.1007/978-1-4614-3933-2_13},
Note = {doi:10.1007/978-1-4614-3933-2\_13},
Pages = {317--331},
Publisher = {Springer},
Title = {Figures of merit for refractometric {LSPR} biosensing},
Year = {2012},
Bdsk-Url-1 = {https://doi.org/10.1007/978-1-4614-3933-2_13}}
@article{klockner2012pycuda,
Author = {Kl{\"o}ckner, Andreas and Pinto, Nicolas and Lee, Yunsup and Catanzaro, Bryan and Ivanov, Paul and Fasih, Ahmed},
Date-Added = {2020-07-24 16:05:08 +0100},
Date-Modified = {2020-07-24 16:07:07 +0100},
Doi = {10.1016/j.parco.2011.09.001},
Journal = {Parallel Computing},
Note = {doi:10.1016/j.parco.2011.09.001},
Number = {3},
Pages = {157--174},
Publisher = {Elsevier},
Title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code generation},
Volume = {38},
Year = {2012},
Bdsk-Url-1 = {https://doi.org/10.1016/j.parco.2011.09.001}}
@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 = {2020-07-24 16:02:43 +0100},
Date-Modified = {2020-07-24 16:02:43 +0100},
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{stodden-etal-2018,
Author = {Stodden, Victoria and Seiler, Jennifer and Ma, Zhaokun},
Date-Added = {2020-07-24 15:16:27 +0100},
Date-Modified = {2020-07-24 15:16:27 +0100},
Doi = {10.1073/pnas.1708290115},
Journal = {Proceedings of the National Academy of Sciences},
Note = {\href{https://doi.org/10.1073/pnas.1708290115}{doi:10.1073/pnas.1708290115}},
Number = {11},
Pages = {2584--2589},
Publisher = {National Academies Press},
Title = {An empirical analysis of journal policy effectiveness for computational reproducibility},
Volume = {115},
Year = {2018},
Bdsk-Url-1 = {https://doi.org/10.1073/pnas.1708290115}}
@article{chang-li2018,
Author = {Chang, Andrew C. and Li, Phillip and others},
Date-Added = {2020-07-24 15:16:12 +0100},
Date-Modified = {2020-07-24 15:16:12 +0100},
Journal = {Critical Finance Review},
Note = {\href{https://doi.org/10.1561/104.00000053}{doi:10.1561/104.00000053}. Available as preprint SSRN 2669564},
Publisher = {Now Publishers, Inc.},
Title = {Is Economics Research Replicable? {S}ixty Published Papers From Thirteen Journals Say ``Often Not''},
Volume = {7},
Year = {2018}}
@article{iqbal-etal-2016,
Author = {Iqbal, Shareen A. and Wallach, Joshua D. and Khoury, Muin J. and Schully, Sheri D. and Ioannidis, John P.A.},
Date-Added = {2020-07-24 15:15:49 +0100},
Date-Modified = {2020-07-24 15:15:49 +0100},
Doi = {10.1371/journal.pbio.1002333},
Journal = {{PLoS Biology}},
Note = {\href{https://doi.org/10.1371/journal.pbio.1002333}{doi:10.1371/journal.pbio.1002333}},
Number = {1},
Pages = {e1002333},
Publisher = {Public Library of Science San Francisco, CA USA},
Title = {Reproducible research practices and transparency across the biomedical literature},
Volume = {14},
Year = {2016},
Bdsk-Url-1 = {https://doi.org/10.1371/journal.pbio.1002333}}
@techreport{moraila-etal-2014,
Author = {Moraila, Gina and Shankaran, Akash and Shi, Zuoming and Warren, Alex M.},
Date-Added = {2020-07-24 15:15:30 +0100},
Date-Modified = {2020-07-24 15:15:30 +0100},
Institution = {Department of Computer Science, University of Arizona},
Note = {Available online at \url{http://reproducibility.cs.arizona.edu/v1/tr.pdf}},
Number = {37},
Title = {Measuring reproducibility in computer systems research},
Url = {http://reproducibility.cs.arizona.edu/v1/tr.pdf},
Year = {2014},
Bdsk-Url-1 = {http://reproducibility.cs.arizona.edu/v1/tr.pdf}}
@book{winsberg-2010,
Author = {Winsberg, Eric},
Date-Added = {2020-07-24 12:15:58 +0100},
Date-Modified = {2020-07-24 12:15:58 +0100},
Note = {ISBN-10: 0226902048},
Publisher = {University of Chicago Press},
Title = {Science in the age of computer simulation},
Year = {2010}}
@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{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}}
@book{NASEM2019,
Address = {Washington, D.C.},
Author = {{National Academies of Sciences, Engineering, and Medicine}},
Date-Added = {2020-07-23 18:30:49 +0100},
Date-Modified = {2020-07-23 18:31:08 +0100},
Month = {May},
Note = {\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}}
@misc{barba2018,
Author = {Lorena A. Barba},
Date-Added = {2020-07-23 18:28:05 +0100},
Date-Modified = {2020-07-23 18:28:42 +0100},
Howpublished = {Preprint on \href{https://arxiv.org/abs/1802.03311}{arxiv:1802.03311}},
Month = {February},
Title = {Terminologies for reproducible research},
Year = {2018}}
@article{rockstuhl2005,
Author = {Rockstuhl, Carsten and Salt, Martin G and Herzig, Hans P},
Date-Modified = {2020-07-27 14:36:42 +0100},
Doi = {10/dsxw9d},
Journal = {J. Optical Society of America B},
Note = {doi:10/dsxw9d},
Number = {2},
Pages = {481--487},
Publisher = {Optical Society of America},
Title = {Analysis of the phonon-polariton response of silicon carbide microparticles and nanoparticles by use of the boundary element method},
Volume = {22},
Year = {2005},
Bdsk-Url-1 = {https://doi.org/10.1364/JOSAB.22.000481}}
@article{ellis2016,
Author = {Ellis, Chase T and Tischler, Joseph G and Glembocki, Orest J and Bezares, Francisco J and Giles, Alexander J and Kasica, Richard and Shirey, Loretta and Owrutsky, Jeffrey C and Chigrin, Dmitry N and Caldwell, Joshua D},
Date-Modified = {2020-07-27 14:45:36 +0100},
Doi = {10/f83zcb},
Journal = {Scientific Reports},
Note = {doi:10/f83zcb},
Pages = {32959},
Publisher = {Nature Publishing Group},
Title = {Aspect-ratio driven evolution of high-order resonant modes and near-field distributions in localized surface phonon polariton nanostructures},
Volume = {6},
Year = {2016},
Bdsk-Url-1 = {https://doi.org/10.1038/srep32959}}
@article{rockstuhl2003,
Author = {Carsten Rockstuhl and Martin Guy Salt and Hans Peter Herzig},
Doi = {10.1364/JOSAA.20.001969},
Journal = {J. Opt. Soc. Am. A},
Keywords = {Diffraction theory; Surface plasmons; Electric fields; Resonance; Scattering; Surface enhanced Raman spectroscopy; Surface plasmons; Visible light},
Month = {Oct},
Number = {10},
Pages = {1969--1973},
Publisher = {OSA},
Title = {Application of the boundary-element method to the interaction of light with single and coupled metallic nanoparticles},
Url = {http://josaa.osa.org/abstract.cfm?URI=josaa-20-10-1969},
Volume = {20},
Year = {2003},
Bdsk-Url-1 = {http://josaa.osa.org/abstract.cfm?URI=josaa-20-10-1969},
Bdsk-Url-2 = {https://doi.org/10.1364/JOSAA.20.001969}}
@article{caldwell2015,
Address = {Berlin, Boston},
Author = {Joshua D. Caldwell and Lucas Lindsay and Vincenzo Giannini and Igor Vurgaftman and Thomas L. Reinecke and Stefan A. Maier and Orest J. Glembocki},
Doi = {https://doi.org/10.1515/nanoph-2014-0003},
Journal = {Nanophotonics},
Number = {1},
Pages = {44 - 68},
Publisher = {De Gruyter},
Title = {Low-loss, infrared and terahertz nanophotonics using surface phonon polaritons},
Url = {https://www.degruyter.com/view/journals/nanoph/4/1/article-p44.xml},
Volume = {4},
Year = {2015},
Bdsk-Url-1 = {https://www.degruyter.com/view/journals/nanoph/4/1/article-p44.xml},
Bdsk-Url-2 = {https://doi.org/10.1515/nanoph-2014-0003}}