-
Notifications
You must be signed in to change notification settings - Fork 21
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #6258 from openjournals/joss.07244
Merging automatically
- Loading branch information
Showing
3 changed files
with
794 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,266 @@ | ||
<?xml version="1.0" encoding="UTF-8"?> | ||
<doi_batch xmlns="http://www.crossref.org/schema/5.3.1" | ||
xmlns:ai="http://www.crossref.org/AccessIndicators.xsd" | ||
xmlns:rel="http://www.crossref.org/relations.xsd" | ||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
version="5.3.1" | ||
xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd"> | ||
<head> | ||
<doi_batch_id>20241217083246-dee07d7649bec92603cda195631ac3575ef9e248</doi_batch_id> | ||
<timestamp>20241217083246</timestamp> | ||
<depositor> | ||
<depositor_name>JOSS Admin</depositor_name> | ||
<email_address>[email protected]</email_address> | ||
</depositor> | ||
<registrant>The Open Journal</registrant> | ||
</head> | ||
<body> | ||
<journal> | ||
<journal_metadata> | ||
<full_title>Journal of Open Source Software</full_title> | ||
<abbrev_title>JOSS</abbrev_title> | ||
<issn media_type="electronic">2475-9066</issn> | ||
<doi_data> | ||
<doi>10.21105/joss</doi> | ||
<resource>https://joss.theoj.org</resource> | ||
</doi_data> | ||
</journal_metadata> | ||
<journal_issue> | ||
<publication_date media_type="online"> | ||
<month>12</month> | ||
<year>2024</year> | ||
</publication_date> | ||
<journal_volume> | ||
<volume>9</volume> | ||
</journal_volume> | ||
<issue>104</issue> | ||
</journal_issue> | ||
<journal_article publication_type="full_text"> | ||
<titles> | ||
<title>RNMC: kinetic Monte Carlo implementations for complex reaction networks</title> | ||
</titles> | ||
<contributors> | ||
<person_name sequence="first" contributor_role="author"> | ||
<given_name>Laura</given_name> | ||
<surname>Zichi</surname> | ||
<affiliations> | ||
<institution><institution_name>Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720</institution_name></institution> | ||
<institution><institution_name>Department of Physics, University of Michigan - Ann Arbor, Ann Arbor, MI, United States of America 48109</institution_name></institution> | ||
</affiliations> | ||
<ORCID>https://orcid.org/0000-0003-3897-3097</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Daniel</given_name> | ||
<surname>Barter</surname> | ||
<affiliations> | ||
<institution><institution_name>Energy Storage and Distributed Resources, Lawrence Berkeley National Laboratory, Berkeley, CA United States of America 94720</institution_name></institution> | ||
</affiliations> | ||
<ORCID>https://orcid.org/0000-0002-6408-1255</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Eric</given_name> | ||
<surname>Sivonxay</surname> | ||
<affiliations> | ||
<institution><institution_name>Energy Storage and Distributed Resources, Lawrence Berkeley National Laboratory, Berkeley, CA United States of America 94720</institution_name></institution> | ||
</affiliations> | ||
<ORCID>https://orcid.org/0000-0002-6408-1255</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Evan Walter Clark</given_name> | ||
<surname>Spotte-Smith</surname> | ||
<affiliations> | ||
<institution><institution_name>Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720</institution_name></institution> | ||
<institution><institution_name>Department of Materials Science and Engineering, University of California - Berkeley, CA, United States of America 94720</institution_name></institution> | ||
</affiliations> | ||
<ORCID>https://orcid.org/0000-0003-1554-197X</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Rohith Srinivaas</given_name> | ||
<surname>Mohanakrishnan</surname> | ||
<affiliations> | ||
<institution><institution_name>Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720</institution_name></institution> | ||
<institution><institution_name>Department of Materials Science and Engineering, University of California - Berkeley, CA, United States of America 94720</institution_name></institution> | ||
</affiliations> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Emory M.</given_name> | ||
<surname>Chan</surname> | ||
<affiliations> | ||
<institution><institution_name>Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720</institution_name></institution> | ||
</affiliations> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Kristin Aslaug</given_name> | ||
<surname>Persson</surname> | ||
<affiliations> | ||
<institution><institution_name>Department of Materials Science and Engineering, University of California - Berkeley, CA, United States of America 94720</institution_name></institution> | ||
<institution><institution_name>Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America 94720</institution_name></institution> | ||
</affiliations> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Samuel M.</given_name> | ||
<surname>Blau</surname> | ||
<affiliations> | ||
<institution><institution_name>Energy Storage and Distributed Resources, Lawrence Berkeley National Laboratory, Berkeley, CA United States of America 94720</institution_name></institution> | ||
</affiliations> | ||
</person_name> | ||
</contributors> | ||
<publication_date> | ||
<month>12</month> | ||
<day>17</day> | ||
<year>2024</year> | ||
</publication_date> | ||
<pages> | ||
<first_page>7244</first_page> | ||
</pages> | ||
<publisher_item> | ||
<identifier id_type="doi">10.21105/joss.07244</identifier> | ||
</publisher_item> | ||
<ai:program name="AccessIndicators"> | ||
<ai:license_ref applies_to="vor">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
<ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
<ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
</ai:program> | ||
<rel:program> | ||
<rel:related_item> | ||
<rel:description>Software archive</rel:description> | ||
<rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.14360064</rel:inter_work_relation> | ||
</rel:related_item> | ||
<rel:related_item> | ||
<rel:description>GitHub review issue</rel:description> | ||
<rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/7244</rel:inter_work_relation> | ||
</rel:related_item> | ||
</rel:program> | ||
<doi_data> | ||
<doi>10.21105/joss.07244</doi> | ||
<resource>https://joss.theoj.org/papers/10.21105/joss.07244</resource> | ||
<collection property="text-mining"> | ||
<item> | ||
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.07244.pdf</resource> | ||
</item> | ||
</collection> | ||
</doi_data> | ||
<citation_list> | ||
<citation key="marcus1965theory"> | ||
<article_title>On the theory of electron-transfer reactions. VI. Unified treatment for homogeneous and electrode reactions</article_title> | ||
<author>Marcus</author> | ||
<journal_title>The Journal of Chemical Physics</journal_title> | ||
<issue>2</issue> | ||
<volume>43</volume> | ||
<doi>10.1063/1.1696792</doi> | ||
<cYear>1965</cYear> | ||
<unstructured_citation>Marcus, R. A. (1965). On the theory of electron-transfer reactions. VI. Unified treatment for homogeneous and electrode reactions. The Journal of Chemical Physics, 43(2), 679–701. https://doi.org/10.1063/1.1696792</unstructured_citation> | ||
</citation> | ||
<citation key="gillespie1977exact"> | ||
<article_title>Exact stochastic simulation of coupled chemical reactions</article_title> | ||
<author>Gillespie</author> | ||
<journal_title>The Journal of Physical Chemistry</journal_title> | ||
<issue>25</issue> | ||
<volume>81</volume> | ||
<cYear>1977</cYear> | ||
<unstructured_citation>Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry, 81(25), 2340–2361.</unstructured_citation> | ||
</citation> | ||
<citation key="garcia2009crossing"> | ||
<article_title>Crossing the mesoscale no-mans land via parallel kinetic monte carlo</article_title> | ||
<author>Garcia Cardona</author> | ||
<cYear>2009</cYear> | ||
<unstructured_citation>Garcia Cardona, C., Wagner, G. J., Tikare, V., Holm, E. A., Plimpton, S. J., Thompson, A. P., Slepoy, A., Zhou, X. W., Battaile, C. C., & Chandross, M. E. (2009). Crossing the mesoscale no-mans land via parallel kinetic monte carlo. Sandia National Laboratories (SNL), Albuquerque, NM,; Livermore, CA.</unstructured_citation> | ||
</citation> | ||
<citation key="hoffmann2014kmos"> | ||
<article_title>Kmos: A lattice kinetic monte carlo framework</article_title> | ||
<author>Hoffmann</author> | ||
<journal_title>Computer Physics Communications</journal_title> | ||
<issue>7</issue> | ||
<volume>185</volume> | ||
<doi>10.1016/j.cpc.2014.04.003</doi> | ||
<cYear>2014</cYear> | ||
<unstructured_citation>Hoffmann, M. J., Matera, S., & Reuter, K. (2014). Kmos: A lattice kinetic monte carlo framework. Computer Physics Communications, 185(7), 2138–2150. https://doi.org/10.1016/j.cpc.2014.04.003</unstructured_citation> | ||
</citation> | ||
<citation key="newman2021electrochemical"> | ||
<volume_title>Electrochemical systems</volume_title> | ||
<author>Newman</author> | ||
<cYear>2021</cYear> | ||
<unstructured_citation>Newman, J., & Balsara, N. P. (2021). Electrochemical systems. John Wiley & Sons.</unstructured_citation> | ||
</citation> | ||
<citation key="spotte2022toward"> | ||
<article_title>Toward a mechanistic model of solid–electrolyte interphase formation and evolution in lithium-ion batteries</article_title> | ||
<author>Spotte-Smith</author> | ||
<journal_title>ACS Energy Letters</journal_title> | ||
<issue>4</issue> | ||
<volume>7</volume> | ||
<doi>10.1021/acsenergylett.2c00517</doi> | ||
<cYear>2022</cYear> | ||
<unstructured_citation>Spotte-Smith, E. W. C., Kam, R. L., Barter, D., Xie, X., Hou, T., Dwaraknath, S., Blau, S. M., & Persson, K. A. (2022). Toward a mechanistic model of solid–electrolyte interphase formation and evolution in lithium-ion batteries. ACS Energy Letters, 7(4), 1446–1453. https://doi.org/10.1021/acsenergylett.2c00517</unstructured_citation> | ||
</citation> | ||
<citation key="barter2023predictive"> | ||
<article_title>Predictive stochastic analysis of massive filter-based electrochemical reaction networks</article_title> | ||
<author>Barter</author> | ||
<journal_title>Digital Discovery</journal_title> | ||
<issue>1</issue> | ||
<volume>2</volume> | ||
<doi>10.1039/D2DD00117A</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Barter, D., Spotte-Smith, E. W. C., Redkar, N. S., Khanwale, A., Dwaraknath, S., Persson, K. A., & Blau, S. M. (2023). Predictive stochastic analysis of massive filter-based electrochemical reaction networks. Digital Discovery, 2(1), 123–137. https://doi.org/10.1039/D2DD00117A</unstructured_citation> | ||
</citation> | ||
<citation key="spotte2023chemical"> | ||
<article_title>Chemical reaction networks explain gas evolution mechanisms in Mg-ion batteries</article_title> | ||
<author>Spotte-Smith</author> | ||
<journal_title>Journal of the American Chemical Society</journal_title> | ||
<issue>22</issue> | ||
<volume>145</volume> | ||
<doi>10.1021/jacs.3c02222</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Spotte-Smith, E. W. C., Blau, S. M., Barter, D., Leon, N. J., Hahn, N. T., Redkar, N. S., Zavadil, K. R., Liao, C., & Persson, K. A. (2023). Chemical reaction networks explain gas evolution mechanisms in Mg-ion batteries. Journal of the American Chemical Society, 145(22), 12181–12192. https://doi.org/10.1021/jacs.3c02222</unstructured_citation> | ||
</citation> | ||
<citation key="xia2023accelerating"> | ||
<article_title>Accelerating the design of multishell upconverting nanoparticles through bayesian optimization</article_title> | ||
<author>Xia</author> | ||
<journal_title>Nano Letters</journal_title> | ||
<issue>23</issue> | ||
<volume>23</volume> | ||
<doi>10.1021/acs.nanolett.3c03568</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Xia, X., Sivonxay, E., Helms, B. A., Blau, S. M., & Chan, E. M. (2023). Accelerating the design of multishell upconverting nanoparticles through bayesian optimization. Nano Letters, 23(23), 11129–11136. https://doi.org/10.1021/acs.nanolett.3c03568</unstructured_citation> | ||
</citation> | ||
<citation key="chan2015combinatorial"> | ||
<article_title>Combinatorial approaches for developing upconverting nanomaterials: High-throughput screening, modeling, and applications</article_title> | ||
<author>Chan</author> | ||
<journal_title>Chemical Society Reviews</journal_title> | ||
<issue>6</issue> | ||
<volume>44</volume> | ||
<doi>10.1039/C4CS00205A</doi> | ||
<cYear>2015</cYear> | ||
<unstructured_citation>Chan, E. M. (2015). Combinatorial approaches for developing upconverting nanomaterials: High-throughput screening, modeling, and applications. Chemical Society Reviews, 44(6), 1653–1679. https://doi.org/10.1039/C4CS00205A</unstructured_citation> | ||
</citation> | ||
<citation key="skripka2023NL"> | ||
<article_title>A generalized approach to photon avalanche upconversion in luminescent nanocrystals</article_title> | ||
<author>Skripka</author> | ||
<journal_title>Nano Letters</journal_title> | ||
<issue>15</issue> | ||
<volume>23</volume> | ||
<doi>10.1021/acs.nanolett.3c01955</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Skripka, A., Lee, M., Qi, X., Pan, J.-A., Yang, H., Lee, C., Schuck, P. J., Cohen, B. E., Jaque, D., & Chan, E. M. (2023). A generalized approach to photon avalanche upconversion in luminescent nanocrystals. Nano Letters, 23(15), 7100–7106. https://doi.org/10.1021/acs.nanolett.3c01955</unstructured_citation> | ||
</citation> | ||
<citation key="teitelboim2019energy"> | ||
<article_title>Energy transfer networks within upconverting nanoparticles are complex systems with collective, robust, and history-dependent dynamics</article_title> | ||
<author>Teitelboim</author> | ||
<journal_title>The Journal of Physical Chemistry C</journal_title> | ||
<issue>4</issue> | ||
<volume>123</volume> | ||
<doi>10.1021/acs.jpcc.9b00161</doi> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Teitelboim, A., Tian, B., Garfield, D. J., Fernandez-Bravo, A., Gotlin, A. C., Schuck, P. J., Cohen, B. E., & Chan, E. M. (2019). Energy transfer networks within upconverting nanoparticles are complex systems with collective, robust, and history-dependent dynamics. The Journal of Physical Chemistry C, 123(4), 2678–2689. https://doi.org/10.1021/acs.jpcc.9b00161</unstructured_citation> | ||
</citation> | ||
</citation_list> | ||
</journal_article> | ||
</journal> | ||
</body> | ||
</doi_batch> |
Binary file not shown.
Oops, something went wrong.