Merge pull request #69 from cmelab/joss

Joss paper md files

.github/workflows/draft-pdf.yml

@@ -0,0 +1,36 @@
+on:
+  push:
+    # Action will run when any changes to these paths are pushed or pr'ed to master
+    branches: [ joss ]
+    paths:
+      - paper/**
+      - .github/workflows/draft-pdf.yml
+  pull_request:
+    branches: [ joss ]
+    paths:
+      - paper/**
+      - .github/workflows/draft-pdf.yml
+  # Allows workflow to be manually triggered
+  workflow_dispatch:
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

paper/paper.bib

@@ -0,0 +1,259 @@
+
+@article{radonpy_2022,
+	title = {{RadonPy}: automated physical property calculation using all-atom classical molecular dynamics simulations for polymer informatics},
+	volume = {8},
+	issn = {2057-3960},
+	url = {https://www.nature.com/articles/s41524-022-00906-4},
+	doi = {10.1038/s41524-022-00906-4},
+	shorttitle = {{RadonPy}},
+	pages = {222},
+	number = {1},
+	journaltitle = {npj Computational Materials},
+	shortjournal = {npj Comput Mater},
+	author = {Hayashi, Yoshihiro and Shiomi, Junichiro and Morikawa, Junko and Yoshida, Ryo},
+	urldate = {2023-09-26},
+	date = {2022-11-08},
+	langid = {english},
+}
+
+@article{TRUE_2020,
+	title = {Towards molecular simulations that are transparent, reproducible, usable by others, and extensible ({TRUE})},
+	volume = {118},
+	issn = {0026-8976, 1362-3028},
+	url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2020.1742938},
+	doi = {10.1080/00268976.2020.1742938},
+	pages = {e1742938},
+	number = {9},
+	journaltitle = {Molecular Physics},
+	shortjournal = {Molecular Physics},
+	author = {Thompson, Matthew W. and Gilmer, Justin B. and Matsumoto, Ray A. and Quach, Co D. and Shamaprasad, Parashara and Yang, Alexander H. and Iacovella, Christopher R. and {McCabe}, Clare and Cummings, Peter T.},
+	urldate = {2023-09-27},
+	date = {2020-06-01},
+	langid = {english},
+}
+
+@article{biosimspace_2019,
+	title = {{BioSimSpace}: An interoperable Python framework for biomolecular simulation},
+	volume = {4},
+	issn = {2475-9066},
+	url = {https://joss.theoj.org/papers/10.21105/joss.01831},
+	doi = {10.21105/joss.01831},
+	shorttitle = {{BioSimSpace}},
+	pages = {1831},
+	number = {43},
+	journaltitle = {Journal of Open Source Software},
+	shortjournal = {{JOSS}},
+	author = {Hedges, Lester and Mey, Antonia and Laughton, Charles and Gervasio, Francesco and Mulholland, Adrian and Woods, Christopher and Michel, Julien},
+	urldate = {2023-09-27},
+	date = {2019-11-22},
+	langid = {english},
+}
+
+@article{shirts_statistically_2008,
+	title = {Statistically optimal analysis of samples from multiple equilibrium states},
+	volume = {129},
+	issn = {0021-9606, 1089-7690},
+	url = {https://pubs.aip.org/jcp/article/129/12/124105/957527/Statistically-optimal-analysis-of-samples-from},
+	doi = {10.1063/1.2978177},
+	pages = {124105},
+	number = {12},
+	journaltitle = {The Journal of Chemical Physics},
+	author = {Shirts, Michael R. and Chodera, John D.},
+	urldate = {2023-10-02},
+	date = {2008-09-28},
+	langid = {english},
+}
+
+@article{chodera_2007,
+	title = {Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations},
+	volume = {3},
+	issn = {1549-9618, 1549-9626},
+	url = {https://pubs.acs.org/doi/10.1021/ct0502864},
+	doi = {10.1021/ct0502864},
+	pages = {26--41},
+	number = {1},
+	journaltitle = {Journal of Chemical Theory and Computation},
+	shortjournal = {J. Chem. Theory Comput.},
+	author = {Chodera, John D. and Swope, William C. and Pitera, Jed W. and Seok, Chaok and Dill, Ken A.},
+	urldate = {2023-10-02},
+	date = {2007-01-01},
+	langid = {english},
+}
+
+@misc{hoomd_2019,
+	title = {{HOOMD}-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations},
+	url = {http://arxiv.org/abs/1308.5587},
+	shorttitle = {{HOOMD}-blue},
+	number = {{arXiv}:1308.5587},
+	publisher = {{arXiv}},
+	author = {Anderson, Joshua A. and Glaser, Jens and Glotzer, Sharon C.},
+	urldate = {2023-10-03},
+	date = {2019-10-18},
+	langid = {english},
+	eprinttype = {arxiv},
+	eprint = {1308.5587 [physics]},
+	keywords = {Physics - Computational Physics},
+}
+
+@article{polyply_2022,
+	title = {Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials},
+	volume = {13},
+	issn = {2041-1723},
+	url = {https://www.nature.com/articles/s41467-021-27627-4},
+	doi = {10.1038/s41467-021-27627-4},
+	pages = {68},
+	number = {1},
+	journaltitle = {Nature Communications},
+	shortjournal = {Nat Commun},
+	author = {Grünewald, Fabian and Alessandri, Riccardo and Kroon, Peter C. and Monticelli, Luca and Souza, Paulo C. T. and Marrink, Siewert J.},
+	urldate = {2023-10-03},
+	date = {2022-01-10},
+	langid = {english},
+}
+@article{eastman2017openmm,
+  title={OpenMM 7: Rapid development of high performance algorithms for molecular dynamics},
+  author={Eastman, Peter and Swails, Jason and Chodera, John D and McGibbon, Robert T and Zhao, Yutong and Beauchamp, Kyle A and Wang, Lee-Ping and Simmonett, Andrew C and Harrigan, Matthew P and Stern, Chaya D and others},
+  journal={PLoS computational biology},
+  volume={13},
+  number={7},
+  pages={e1005659},
+  year={2017},
+  publisher={Public Library of Science San Francisco, CA USA}
+}
+
+@article{Santana-Bonilla_2023,
+	title = {Modular Software for Generating and Modeling Diverse Polymer Databases},
+	volume = {63},
+	issn = {1549-9596, 1549-960X},
+	url = {https://pubs.acs.org/doi/10.1021/acs.jcim.3c00081},
+	doi = {10.1021/acs.jcim.3c00081},
+	pages = {3761--3771},
+	number = {12},
+	journaltitle = {Journal of Chemical Information and Modeling},
+	shortjournal = {J. Chem. Inf. Model.},
+	author = {Santana-Bonilla, Alejandro and López-Ríos De Castro, Raquel and Sun, Peike and Ziolek, Robert M. and Lorenz, Christian D.},
+	urldate = {2023-10-03},
+	date = {2023-06-26},
+	langid = {english},
+}
+@article{martin2018pyprism,
+  title={pyPRISM: a computational tool for liquid-state theory calculations of macromolecular materials},
+  author={Martin, Tyler B and Gartner III, Thomas E and Jones, Ronald L and Snyder, Chad R and Jayaraman, Arthi},
+  journal={Macromolecules},
+  volume={51},
+  number={8},
+  pages={2906--2922},
+  year={2018},
+  publisher={ACS Publications}
+}
+
+@Inbook{Klein2016mBuild,
+    author      = "Klein, Christoph and Sallai, János and Jones, Trevor J. and Iacovella, Christopher R. and McCabe, Clare and Cummings, Peter T.",
+    editor      = "Snurr, Randall Q and Adjiman, Claire S. and Kofke, David A.",
+    title       = "A Hierarchical, Component Based Approach to Screening Properties of Soft Matter",
+    bookTitle   = "Foundations of Molecular Modeling and Simulation: Select Papers from FOMMS 2015",
+    year        = "2016",
+    publisher   = "Springer Singapore",
+    address     = "Singapore",
+    pages       = "79--92",
+    isbn        = "978-981-10-1128-3",
+    doi         = "10.1007/978-981-10-1128-3_5",
+    url         = "https://doi.org/10.1007/978-981-10-1128-3_5"
+}
+
+@article{lammps_2022,
+	title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
+	volume = {271},
+	issn = {00104655},
+	url = {https://linkinghub.elsevier.com/retrieve/pii/S0010465521002836},
+	doi = {10.1016/j.cpc.2021.108171},
+	pages = {108171},
+	journaltitle = {Computer Physics Communications},
+	shortjournal = {Computer Physics Communications},
+	author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and In 'T Veld, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
+	urldate = {2023-10-05},
+	date = {2022-02},
+	langid = {english},
+}
+
+@software{gmso,
+    author = {mosdef-hub, Vanderbilt University},
+	title = {{GMSO: General Molecular Simulation Object}},
+	url = {https://gmso.mosdef.org/en/stable/},
+	version = {0.11.2},
+	year = {2023},
+    publisher = {GitHub},
+}
+
+@software{parmed,
+  author = {Swails, Jason and Hernandez, Carlos and Mobley, David L. and Nguyen, Hai and Wang, Lee-Ping and Janowski, Pawel},
+  title = {{ParmED: Cross-program parameter and topology file editor and molecular mechanical simulator engine}},
+  url = {https://github.com/ParmEd/ParmEd},
+  version = {4.1.0},
+  year = {2014},
+  publisher = {GitHub},
+}
+@article{aggarwal_molecular_2020,
+	title = {Molecular dynamics studies on the strength and ductility of symmetric thermally welded joints},
+	issn = {0965-0393, 1361-651X},
+	url = {https://iopscience.iop.org/article/10.1088/1361-651X/ab6a44},
+	doi = {10.1088/1361-651X/ab6a44},
+	journaltitle = {Modelling and Simulation in Materials Science and Engineering},
+	shortjournal = {Modelling Simul. Mater. Sci. Eng.},
+	author = {Aggarwal, Ishu and Paul, Saptarshi and Sinha, Nishant K and Basu, Sumit},
+	urldate = {2023-08-09},
+	date = {2020-01-10},
+	langid = {english},
+}
+
+@article{bukowski_load-bearing_2021,
+	title = {Load-bearing entanglements in polymer glasses},
+	volume = {7},
+	issn = {2375-2548},
+	url = {https://www.science.org/doi/10.1126/sciadv.abg9763},
+	doi = {10.1126/sciadv.abg9763},
+	pages = {eabg9763},
+	number = {38},
+	journaltitle = {Science Advances},
+	shortjournal = {Sci. Adv.},
+	author = {Bukowski, Cynthia and Zhang, Tianren and Riggleman, Robert A. and Crosby, Alfred J.},
+	urldate = {2023-10-06},
+	date = {2021-09-17},
+	langid = {english},
+}
+
+@article{fan_wetting_1995,
+	title = {Wetting of crystalline polymer surfaces: A molecular dynamics simulation},
+	volume = {103},
+	issn = {0021-9606, 1089-7690},
+	url = {https://pubs.aip.org/jcp/article/103/20/9053/179676/Wetting-of-crystalline-polymer-surfaces-A},
+	doi = {10.1063/1.470016},
+	shorttitle = {Wetting of crystalline polymer surfaces},
+	abstract = {Molecular dynamics has been used to study the wetting of model polymer surfaces, the crystal surfaces of polyethylene ({PE}), poly(tetrafluoroethylene) ({PTFE}), and poly(ethylene terephthalate) ({PET}) by water and methylene iodide. In the simulation a liquid droplet is placed on a model surface and constant temperature, rigid body molecular dynamics is carried out while the model surface is kept fixed. A generally defined microscopic contact angle between a liquid droplet and a solid surface is quantitatively calculated from the volume of the droplet and the interfacial area between the droplet and the surface. The simulation results agree with the trend in experimental data for both water and methylene iodide. The shape of the droplets on the surface is analyzed and no obvious anisotropy of the droplets is seen in the surface plane, even though the crystal surfaces are highly oriented. The surface free energies of the model polymer surfaces are estimated from their contact angles with the two different liquid droplets.},
+	pages = {9053--9061},
+	number = {20},
+	journaltitle = {The Journal of Chemical Physics},
+	author = {Fan, Cun Feng and Caǧin, Tahir},
+	urldate = {2023-10-06},
+	date = {1995-11-22},
+	langid = {english},
+	file = {Accepted Version:/home/marjan/Zotero/storage/X8LJLYKB/Fan and Caǧin - 1995 - Wetting of crystalline polymer surfaces A molecul.pdf:application/pdf},
+}
+
+@article{bamane_wetting_2021,
+	title = {Wetting Simulations of High-Performance Polymer Resins on Carbon Surfaces as a Function of Temperature Using Molecular Dynamics},
+	volume = {13},
+	issn = {2073-4360},
+	url = {https://www.mdpi.com/2073-4360/13/13/2162},
+	doi = {10.3390/polym13132162},
+	abstract = {Resin/reinforcement wetting is a key parameter in the manufacturing of carbon nanotube ({CNT})-based composite materials. Determining the contact angle between combinations of liquid resin and reinforcement surfaces is a common method for quantifying wettability. As experimental measurement of contact angle can be difficult when screening multiple high-performance resins with {CNT} materials such as {CNT} bundles or yarns, computational approaches are necessary to facilitate {CNT} composite material design. A molecular dynamics simulation method is developed to predict the contact angle of high-performance polymer resins on {CNT} surfaces dominated by aromatic carbon, aliphatic carbon, or a mixture thereof (amorphous carbon). Several resin systems are simulated and compared. The results indicate that the monomer chain length, chemical groups on the monomer, and simulation temperature have a significant impact on the predicted contact angle values on the {CNT} surface. Difunctional epoxy and cyanate ester resins show the overall highest levels of wettability, regardless of the aromatic/aliphatic nature of the {CNT} material surface. Tetrafunctional epoxy demonstrates excellent wettability on aliphatic-dominated surfaces at elevated temperatures. Bismaleimide and benzoxazine resins show intermediate levels of wetting, while typical molecular weights of polyether ether ketone demonstrate poor wetting on the {CNT} surfaces.},
+	pages = {2162},
+	number = {13},
+	journaltitle = {Polymers},
+	shortjournal = {Polymers},
+	author = {Bamane, Swapnil S. and Gaikwad, Prashik S. and Radue, Matthew S. and Gowtham, S. and Odegard, Gregory M.},
+	urldate = {2023-10-06},
+	date = {2021-06-30},
+	langid = {english},
+	file = {Bamane et al. - 2021 - Wetting Simulations of High-Performance Polymer Re.pdf:/home/marjan/Zotero/storage/JPFTYNU9/Bamane et al. - 2021 - Wetting Simulations of High-Performance Polymer Re.pdf:application/pdf},
+}