Computational nanoplasmonics in the quasistatic limit for biosensing applications

Natalia C. Clementi, Christopher D, Cooper, Lorena A. Barba

Manuscript source files and reproducibility packages for all the computational results presented in the paper.

Published in: Phys. Rev. E 100, 063305 (2019), https://doi.org/10.1103/PhysRevE.100.063305 Preprint: https://arxiv.org/abs/1812.10722

Reproducibility package archives

Clementi, Natalia C.; D. Cooper, Christopher; Barba, Lorena A. (2019): PyGBe-LS PR—Computational nanoplasmonics for biosensing applications (reproducibility packages). figshare. Collection. https://doi.org/10.6084/m9.figshare.c.4346156

Clementi, Natalia C.; D. Cooper, Christopher; Barba, Lorena A. (2018): PyGBe-LSPR—Computational nanoplasmonics for biosensing applications (execution files). Zenodo. https://doi.org/10.5281/zenodo.2513715

Clementi, Natalia C.; D. Cooper, Christopher; Barba, Lorena A. (2018): PyGBe-LSPR—Computational nanoplasmonics for biosensing applications (problem datasets). Zenodo. https://doi.org/10.5281/zenodo.2511600

Article history

• ArXiv preprint v1 appeared on 12/31/2018.
• Submitted to Comput. Phys. Comm. on 12/31/2018. Desk rejection on 01/14/2019. Editor: "I feel such a (numerical case study is now better placed in a journal of biophysics."
• Second submission to J. Comput. Phys. on 01/20/2019. Desk rejection on 02/02/2019. Editor: "I feel your manuscript is not appropriate for the journal's readership." Editor offered journal transfer service to ... Comput. Phys. Comm. (!) Asked EiC to have a second look, giving links to a few papers already published in JCP on the same subject. EiC replied that he sent the paper to 3 other executive editors and they all agreed with his original assessment.
• ArXiv preprint v2 appeared on 03/12/2019. Edited for a submission to an APS journal.
• Third submission to Phys. Rev. E on 03/20/2019.
• First round of referee reports received on 05/23/2019. See Issues for full referee reports, and our working responses.
• Revision submitted to PRE on 07/9/2019.
• ArXiv preprint v3 appeared on 07/10/2019.
• Second round of referee reports received on 08/20/2019. See Issues for full referee reports, and our working responses.
• Revision submitted to PRE on 10/1/2019.
• Acceptance decision received on 11/1/2019. Journal flags issues with figures: remove grid, add sub-plot letters.
• On 11/4/2019, requested clarification on Copyright Transfer Agreement, due to posting of repro-packs on Figshare. Reply received 11/15/2019.
• Replaced figures flagged by production (background grid, etc.) on 11/18/2019.
• Journal requests title change on 11/22/2019L "provide a title that may be understood by the general reader." Supplied.
• Electronic proof received 12/3/2019. Corrections/replies submitted 12/4/2019.

LICENSE

Not all content in this repository is open source. The Python code for creating the figures is shared under a BSD3 License. The written content in any Jupyter Notebooks is shared under a Creative Commons Attribution (CC-BY) license. But please note that the manuscript text is not open source; we reserve rights to the article content, which will be submitted for publication in a journal. Only fair use applies in this case.