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
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
- 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.
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.