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Trends in atomistic simulation software usage [article]

Leopold Talirz, Luca M. Ghiringhelli, Berend Smit
<span title="2021-08-27">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Driven by the unprecedented computational power available to scientific research, the use of computers in solid-state physics, chemistry and materials science has been on a continuous rise. This review focuses on the software used for the simulation of matter at the atomic scale. We provide a comprehensive overview of major codes in the field, and analyze how citations to these codes in the academic literature have evolved since 2010. An interactive version of the underlying data set is available at https://atomistic.software .
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2108.12350v1">arXiv:2108.12350v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o3s43p3cybcirmyws33azzndxa">fatcat:o3s43p3cybcirmyws33azzndxa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210901085145/https://arxiv.org/pdf/2108.12350v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6a/06/6a06686b2f97770f48b2260982a409e799a276fe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2108.12350v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

On-Surface Synthesis of Atomically Precise Graphene Nanoribbons

Leopold Talirz, Pascal Ruffieux, Roman Fasel
<span title="2016-02-12">2016</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eiwzqueihbaftmngl7dgw6sb7e" style="color: black;">Advanced Materials</a> </i> &nbsp;
Talirz, P. Ruffieux, R.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/adma.201505738">doi:10.1002/adma.201505738</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26867990">pmid:26867990</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gtgpj472pfcflooe2i3pvltpfi">fatcat:gtgpj472pfcflooe2i3pvltpfi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201106163643/https://www.dora.lib4ri.ch/empa/islandora/object/empa%3A7732/datastream/PDF2/Talirz-2016-On-surface_synthesis_of_atomically_precise-%28accepted_version%29.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/20/e8/20e8b7873bd127bcd6ef5c7084a4c642d68c566c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/adma.201505738"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Capturing chemical intuition in synthesis of metal-organic frameworks

Seyed Mohamad Moosavi, Arunraj Chidambaram, Leopold Talirz, Maciej Haranczyk, Kyriakos C. Stylianou, Berend Smit
<span title="2019-02-01">2019</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
We report a methodology using machine learning to capture chemical intuition from a set of (partially) failed attempts to synthesize a metal-organic framework. We define chemical intuition as the collection of unwritten guidelines used by synthetic chemists to find the right synthesis conditions. As (partially) failed experiments usually remain unreported, we have reconstructed a typical track of failed experiments in a successful search for finding the optimal synthesis conditions that yields
more &raquo; ... KUST-1 with the highest surface area reported to date. We illustrate the importance of quantifying this chemical intuition for the synthesis of novel materials.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-08483-9">doi:10.1038/s41467-019-08483-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30710082">pmid:30710082</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6358622/">pmcid:PMC6358622</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/v6k7hzrkybdzddlav3njubydqq">fatcat:v6k7hzrkybdzddlav3njubydqq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200313022919/https://escholarship.org/content/qt83j5q9dm/qt83j5q9dm.pdf?t=pwl7f7" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c6/95/c695e04cac2a924aba93034bba7f7b1db2b373d8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-08483-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358622" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Building a Consistent and Reproducible Database for Adsorption Evaluation in Covalent–Organic Frameworks

Daniele Ongari, Aliaksandr V. Yakutovich, Leopold Talirz, Berend Smit
<span title="2019-09-26">2019</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3qlufbxyhnaqljdbzr3sgsf2yq" style="color: black;">ACS Central Science</a> </i> &nbsp;
We present a workflow that traces the path from the bulk structure of a crystalline material to assessing its performance in carbon capture from coal's postcombustion flue gases. This workflow is applied to a database of 324 covalent-organic frameworks (COFs) reported in the literature, to characterize their CO2 adsorption properties using the following steps: (1) optimization of the crystal structure (atomic positions and unit cell) using density functional theory, (2) fitting atomic point
more &raquo; ... ges based on the electron density, (3) characterizing the pore geometry of the structures before and after optimization, (4) computing carbon dioxide and nitrogen isotherms using grand canonical Monte Carlo simulations with an empirical interaction potential, and finally, (5) assessing the CO2 parasitic energy via process modeling. The full workflow has been encoded in the Automated Interactive Infrastructure and Database for Computational Science (AiiDA). Both the workflow and the automatically generated provenance graph of our calculations are made available on the Materials Cloud, allowing peers to inspect every input parameter and result along the workflow, download structures and files at intermediate stages, and start their research right from where this work has left off. In particular, our set of CURATED (Clean, Uniform, and Refined with Automatic Tracking from Experimental Database) COFs, having optimized geometry and high-quality DFT-derived point charges, are available for further investigations of gas adsorption properties. We plan to update the database as new COFs are being reported.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acscentsci.9b00619">doi:10.1021/acscentsci.9b00619</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31681834">pmid:31681834</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6822289/">pmcid:PMC6822289</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qadz5gwtfbh3jiforgeblnh7wq">fatcat:qadz5gwtfbh3jiforgeblnh7wq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717115049/https://escholarship.org/content/qt7gm9r34b/qt7gm9r34b.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/7f/257fb5e52e7b7631e2e191400492f9d8bc0a976c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acscentsci.9b00619"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822289" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Too Many Materials and Too Many Applications: An Experimental Problem Waiting for a Computational Solution

Daniele Ongari, Leopold Talirz, Berend Smit
<span title="2020-10-02">2020</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3qlufbxyhnaqljdbzr3sgsf2yq" style="color: black;">ACS Central Science</a> </i> &nbsp;
Talirz − Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingeńierie Chimiques, Ećole Polytechnique Fedeŕale de Lausanne (EPFL), Sion CH-1951, Valais, Switzerland; Theory and Simulation  ...  Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingeńierie Chimiques, Ećole Polytechnique Fedeŕale de Lausanne (EPFL), Sion CH-1951, Valais, Switzerland; orcid.org/0000-0001-6197-2901 Leopold  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acscentsci.0c00988">doi:10.1021/acscentsci.0c00988</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33274268">pmid:33274268</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7706098/">pmcid:PMC7706098</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ha4vzwnr55fwpardwv5dsk6ysi">fatcat:ha4vzwnr55fwpardwv5dsk6ysi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428115354/https://escholarship.org/content/qt7522j5c5/qt7522j5c5.pdf?t=qlp3d3" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/83/7083fad94f22e6f15f6071729da4341a0dbca2b4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acscentsci.0c00988"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706098" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

AiiDAlab – an ecosystem for developing, executing, and sharing scientific workflows [article]

Aliaksandr V. Yakutovich, Kristjan Eimre, Ole Schütt, Leopold Talirz, Carl S. Adorf, Casper W. Andersen, Edward Ditler, Dou Du, Daniele Passerone, Berend Smit, Nicola Marzari, Giovanni Pizzi (+1 others)
<span title="2020-09-29">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Yakutovich *,a,b,c, * * , Kristjan Eimre a,d, * * , Ole Schütt a,d, * * , Leopold Talirz a,b,c , Carl S. Adorf b , Casper W.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2010.02731v1">arXiv:2010.02731v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/big7wvp6dnb7hg33hthi76gbli">fatcat:big7wvp6dnb7hg33hthi76gbli</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201008002556/https://arxiv.org/pdf/2010.02731v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2010.02731v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Giant edge state splitting at atomically precise graphene zigzag edges

Shiyong Wang, Leopold Talirz, Carlo A. Pignedoli, Xinliang Feng, Klaus Müllen, Roman Fasel, Pascal Ruffieux
<span title="2016-05-16">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Zigzag edges of graphene nanostructures host localized electronic states that are predicted to be spin-polarized. However, these edge states are highly susceptible to edge roughness and interaction with a supporting substrate, complicating the study of their intrinsic electronic and magnetic structure. Here, we focus on atomically precise graphene nanoribbons whose two short zigzag edges host exactly one localized electron each. Using the tip of a scanning tunneling microscope, the graphene
more &raquo; ... ribbons are transferred from the metallic growth substrate onto insulating islands of NaCl in order to decouple their electronic structure from the metal. The absence of charge transfer and hybridization with the substrate is confirmed by scanning tunneling spectroscopy (STS), which reveals a pair of occupied / unoccupied edge states. Their large energy splitting of 1.9 eV is in accordance with ab initio many-body perturbation theory calculations and reflects the dominant role of electron-electron interactions in these localized states.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms11507">doi:10.1038/ncomms11507</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27181701">pmid:27181701</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4873614/">pmcid:PMC4873614</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/62ma7ys5trcrhhn25gob54wboe">fatcat:62ma7ys5trcrhhn25gob54wboe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190414141222/https://core.ac.uk/download/pdf/79440539.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c5/6d/c56d79227f500a82662c8e82bb211d18443d5628.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms11507"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873614" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Band Gap of Atomically Precise Graphene Nanoribbons as a Function of Ribbon Length and Termination [article]

Leopold Talirz, Hajo Söde, Shigeki Kawai, Pascal Ruffieux, Ernst Meyer, Xinliang Feng, Klaus Müllen, Roman Fasel, Carlo A. Pignedoli, Daniele Passerone
<span title="2019-10-03">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We study the band gap of finite N_A=7 armchair graphene nanoribbons (7-AGNRs) on Au(111) through scanning tunneling microscopy/spectroscopy combined with density functional theory calculations. The band gap of 7-AGNRs with lengths of 6 nm and more is converged to within 0.1 eV of its bulk value of 2.3 eV, while the band gap opens by several hundred meV in very short 7-AGNRs. The termination has a significant effect on the band gap, doubly hydrogenated termini yielding a lower band gap than singly hydrogenated ones.
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1910.01385v1">arXiv:1910.01385v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uvi4nx3zn5h5tgrliofj2o23xi">fatcat:uvi4nx3zn5h5tgrliofj2o23xi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200929185708/https://arxiv.org/pdf/1910.01385v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/39/4b/394b4fe3cb940a832a047075e54a947b31796c23.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1910.01385v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Materials Cloud, a platform for open computational science [article]

Leopold Talirz, Snehal Kumbhar, Elsa Passaro, Aliaksandr V. Yakutovich, Valeria Granata, Fernando Gargiulo, Marco Borelli, Martin Uhrin, Sebastiaan P. Huber, Spyros Zoupanos, Carl S. Adorf, Casper W. Andersen, Ole Schütt (+7 others)
<span title="2020-03-27">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Materials Cloud is a platform designed to enable open and seamless sharing of resources for computational science, driven by applications in materials modelling. It hosts 1) archival and dissemination services for raw and curated data, together with their provenance graph, 2) modelling services and virtual machines, 3) tools for data analytics, and pre-/post-processing, and 4) educational materials. Data is citable and archived persistently, providing a comprehensive embodiment of the FAIR
more &raquo; ... iples that extends to computational workflows. Materials Cloud leverages the AiiDA framework to record the provenance of entire simulation pipelines (calculations performed, codes used, data generated) in the form of graphs that allow to retrace and reproduce any computed result. When an AiiDA database is shared on Materials Cloud, peers can browse the interconnected record of simulations, download individual files or the full database, and start their research from the results of the original authors. The infrastructure is agnostic to the specific simulation codes used and can support diverse applications in computational science that transcend its initial materials domain.
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2003.12510v1">arXiv:2003.12510v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w5fgpmixyrctdhkhidh6pvfj4i">fatcat:w5fgpmixyrctdhkhidh6pvfj4i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200331001257/https://arxiv.org/pdf/2003.12510v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2003.12510v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

AiiDAlab – an ecosystem for developing, executing, and sharing scientific workflows

Aliaksandr V. Yakutovich, Kristjan Eimre, Ole Schütt, Leopold Talirz, Carl S. Adorf, Casper W. Andersen, Edward Ditler, Dou Du, Daniele Passerone, Berend Smit, Nicola Marzari, Giovanni Pizzi (+1 others)
<span title="">2021</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mrzxdmgkxfepljvmf6cqk55iyu" style="color: black;">Computational materials science</a> </i> &nbsp;
Leopold Talirz: Conceptualization, Software, Investigation, Project administration, Writing -review & editing. Carl S.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.commatsci.2020.110165">doi:10.1016/j.commatsci.2020.110165</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yj5fdrpjtbc3vholgf2t6eoiqu">fatcat:yj5fdrpjtbc3vholgf2t6eoiqu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717032430/https://os.zhdk.cloud.switch.ch/tind-tmp-epfl/d0d40413-8c2f-41a7-acd7-d3a80157d40e?response-content-disposition=attachment%3B%20filename%2A%3DUTF-8%27%271-s2.0-S092702562030656X-main.pdf&amp;response-content-type=application%2Fpdf&amp;AWSAccessKeyId=ded3589a13b4450889b2f728d54861a6&amp;Expires=1626519547&amp;Signature=Gpwi8DzQYYQ53rJnV3esOeSv3Go%3D" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/65/4c/654c04ec4ec2cef057efc16fa30a648bf352bb89.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.commatsci.2020.110165"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

Electronic band dispersion of graphene nanoribbons via Fourier-transformed scanning tunneling spectroscopy

Hajo Söde, Leopold Talirz, Oliver Gröning, Carlo Antonio Pignedoli, Reinhard Berger, Xinliang Feng, Klaus Müllen, Roman Fasel, Pascal Ruffieux
<span title="2015-01-23">2015</span> <i title="American Physical Society (APS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lqjgbsoa65gghi2p2esulcqqqm" style="color: black;">Physical Review B</a> </i> &nbsp;
Atomically precise armchair graphene nanoribbons of width N=7 (7-AGNRs) are investigated by scanning tunneling spectroscopy (STS) on Au(111). The analysis of energy-dependent standing wave patterns of finite length ribbons allows, by Fourier transformation, the direct extraction of the dispersion relation of frontier electronic states. Aided by density functional theory calculations, we assign the states to the valence band, the conduction band and the next empty band of 7-AGNRs, determine
more &raquo; ... tive masses of 0.42± 0.08 m_e, 0.40± 0.18 m_e and 0.20± 0.03 m_e, respectively, and a band gap of 2.37± 0.06 eV.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physrevb.91.045429">doi:10.1103/physrevb.91.045429</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s2j7heimavhafh46asu7psveri">fatcat:s2j7heimavhafh46asu7psveri</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726010950/https://link.aps.org/accepted/10.1103/PhysRevB.91.045429" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/64/aa/64aade0860e679b4b99cad3965b1c973eb7e98e0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physrevb.91.045429"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> aps.org </button> </a>

On-surface synthesis of graphene nanoribbons with zigzag edge topology

Pascal Ruffieux, Shiyong Wang, Bo Yang, Carlos Sánchez-Sánchez, Jia Liu, Thomas Dienel, Leopold Talirz, Prashant Shinde, Carlo A. Pignedoli, Daniele Passerone, Tim Dumslaff, Xinliang Feng (+2 others)
<span title="">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
Graphene-based nanostructures exhibit a vast range of exciting electronic properties that are absent in extended graphene. For example, quantum confinement in carbon nanotubes and armchair graphene nanoribbons (AGNRs) leads to the opening of substantial electronic band gaps that are directly linked to their structural boundary conditions. Even more intriguing are nanostructures with zigzag edges, which are expected to host spin-polarized electronic edge states and can thus serve as key elements
more &raquo; ... for graphene-based spintronics. The most prominent example is zigzag graphene nanoribbons (ZGNRs) for which the edge states are predicted to couple ferromagnetically along the edge and antiferromagnetically between them. So far, a direct observation of the spin-polarized edge states for specifically designed and controlled zigzag edge topologies has not been achieved. This is mainly due to the limited precision of current top-down approaches, which results in poorly defined edge structures. Bottom-up fabrication approaches, on the other hand, were so far only successfully applied to the growth of AGNRs and related structures. Here, we describe the successful bottom-up synthesis of ZGNRs, which are fabricated by the surface-assisted colligation and cyclodehydrogenation of specifically designed precursor monomers including carbon groups that yield atomically precise zigzag edges. Using scanning tunnelling spectroscopy we prove the existence of edge-localized states with large energy splittings. We expect that the availability of ZGNRs will finally allow the characterization of their predicted spin-related properties such as spin confinement and filtering, and ultimately add the spin degree of freedom to graphene-based circuitry.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature17151">doi:10.1038/nature17151</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27008967">pmid:27008967</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qiwwmvhkuzdt7bny646vgp6dyu">fatcat:qiwwmvhkuzdt7bny646vgp6dyu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170921215403/http://pubman.mpdl.mpg.de/pubman/item/escidoc:2262428/component/escidoc:2262427/On-surface_synthesis(104).pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/29/86/2986f682864972053f3fa569d15c80de3f3e9b1c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature17151"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

Materials Cloud, a platform for open computational science

Leopold Talirz, Snehal Kumbhar, Elsa Passaro, Aliaksandr V Yakutovich, Valeria Granata, Fernando Gargiulo, Marco Borelli, Martin Uhrin, Sebastiaan P Huber, Spyros Zoupanos, Carl S Adorf, Casper Welzel Andersen (+8 others)
<span title="2020-09-08">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a577b42d4nfhddl7kurxnuyzem" style="color: black;">Scientific Data</a> </i> &nbsp;
Materials Cloud is a platform designed to enable open and seamless sharing of resources for computational science, driven by applications in materials modelling. It hosts (1) archival and dissemination services for raw and curated data, together with their provenance graph, (2) modelling services and virtual machines, (3) tools for data analytics, and pre-/post-processing, and (4) educational materials. Data is citable and archived persistently, providing a comprehensive embodiment of entire
more &raquo; ... ulation pipelines (calculations performed, codes used, data generated) in the form of graphs that allow retracing and reproducing any computed result. When an AiiDA database is shared on Materials Cloud, peers can browse the interconnected record of simulations, download individual files or the full database, and start their research from the results of the original authors. The infrastructure is agnostic to the specific simulation codes used and can support diverse applications in computational science that transcend its initial materials domain.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41597-020-00637-5">doi:10.1038/s41597-020-00637-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32901046">pmid:32901046</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7479138/">pmcid:PMC7479138</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wggd4mdjv5dj5kvbh4cguvayoi">fatcat:wggd4mdjv5dj5kvbh4cguvayoi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428112816/https://escholarship.org/content/qt6151499x/qt6151499x.pdf?t=qlp3du" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c1/7c/c17c24677aa94fc69dcd406724301306e29a9d7c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41597-020-00637-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7479138" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance [article]

Sebastiaan. P. Huber, Spyros Zoupanos, Martin Uhrin, Leopold Talirz, Leonid Kahle, Rico Häuselmann, Dominik Gresch, Tiziano Müller, Aliaksandr V. Yakutovich, Casper W. Andersen, Francisco F. Ramirez, Carl S. Adorf, Fernando Gargiulo, Snehal Kumbhar (+7 others)
<span title="2020-03-24">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (http://www.aiida.net), a robust open-source
more &raquo; ... oughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with any simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible.
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2003.12476v1">arXiv:2003.12476v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ig6kkzbvjrbjrlqvusrkgjzsg4">fatcat:ig6kkzbvjrbjrlqvusrkgjzsg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200331001223/https://arxiv.org/pdf/2003.12476v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2003.12476v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Aiida And The Materials Cloud: Workflow Engine With Automated Provenance And Dissemination Platform For Open Science

Sebastiaan P. Huber, Spyros Zoupanos, Leonid Kahle, Martin Uhrin, Nicolas Mounet, Rico Andreas Häuselmann, Snehal Kumbhar, Leopold Talirz, Aliaksandr Yakutovich, Elsa Passaro, Marco Borelli, Fernando Gargiulo (+9 others)
<span title="2018-07-14">2018</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Modern advances in computational technology have facilitated great strides in a wide variety of scientific disciplines and have led to the production of a wealth of valuable research data. However, the extraordinarily quick growth of computational capabilities has left the scientific world wanting for a simple yet effective way of managing these new workflows and the vast amount of data that they produce. We present AiiDA[1], a highly-automated and robust workflow engine written in Python,
more &raquo; ... ned for high-throughput computational science. AiiDA automatically tracks data provenance (and stores it in the form of a directed graph) while managing and automating simulations running either locally or on supercomputers. All data and calculations are stored in a database and can be efficiently queried thanks to a simple but powerful query language. AiiDA enables computational science that is fully reproducible and facilitates sharing of research results. Its symbiotic counterpart, the Materials Cloud [2], is an interactive online platform powered by AiiDA. It is designed to enable seamless sharing and dissemination of resources, of raw data with their provenance as well as of curated open research data in computational science, and to provide cloud resources for simulations. The combination of AiiDA and Materials Cloud (whose architecture is shown in the figure) provides an Open Science Framework fully compliant with the FAIR (findable, accessible, interoperable and reusable) data principles [3]. The diligent and dedicated data management of AiiDA, combined with the user-friendly and ergonomic Materials Cloud, form an invaluable tool to any computational scientist. [1] G. Pizzi et al., Comp. Mat. Sci. 111, 218 (2016) - www.aiida.net [2] http://www.materialscloud.org [3] M. D. Wilkinson et al, Sci. Data 3, 160018 (2016)
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1311933">doi:10.5281/zenodo.1311933</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ggiclcwl5vbbdlz4sseeqfza4i">fatcat:ggiclcwl5vbbdlz4sseeqfza4i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201226162009/https://zenodo.org/record/1311933/files/abstract_AiiDA_MaterialsCloud.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/74/2574998d6315d4bbde34155aba76234d751c63f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1311933"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>
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