{"data":{"id":"10.6084/m9.figshare.799692.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.799692.v1","prefix":"10.6084","suffix":"m9.figshare.799692.v1","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Cooper, Christopher D.","nameType":"Personal","givenName":"Christopher D.","familyName":"Cooper","affiliation":[],"nameIdentifiers":[]},{"name":"Jaydeep Bardhan","affiliation":[],"nameIdentifiers":[]},{"name":"Barba, Lorena A.","nameType":"Personal","givenName":"Lorena A.","familyName":"Barba","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Convergence of PyGBE with Kirkwood sphere"}],"publisher":"figshare","container":{},"publicationYear":2013,"subjects":[{"subject":"Molecular Physics"},{"subject":"Computational Biology"},{"subject":"Computational Physics"},{"subject":"Mechanical Engineering"},{"subject":"FOS: Mechanical engineering","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Mechanical engineering","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Biophysics"}],"contributors":[],"dates":[{"date":"2013-09-15","dateType":"Created"},{"date":"2016-01-18","dateType":"Updated"},{"date":"2013","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsIdenticalTo","relatedIdentifier":"10.6084/m9.figshare.799692","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["3299381 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"This file bundle includes data, figures and plotting scripts of convergence results for PyGBe and APBS using a spherical molecule of radius 4 Armstrong with a centered charge of –1e. The errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —\"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers\", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. \u003cem\u003eComput. Phys. Comm.\u003c/em\u003e, \u003cstrong\u003e185\u003c/strong\u003e(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA and is open-source under MIT license. More information about the PyGBe code in: —\u003cem\u003eValidation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods.\u003c/em\u003e Christopher Cooper, Lorena A. Barba. figshare.\u003cbr\u003ehttp://dx.doi.org/10.6084/m9.figshare.154331 \u003cstrong\u003eAcknowledgement:\u003c/strong\u003e\u003cbr\u003eThis research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://figshare.com/articles/dataset/Convergence_of_PyGBE_with_Kirkwood_sphere/799692/1","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":15,"viewsOverTime":[{"yearMonth":"2025-03","total":1},{"yearMonth":"2025-03","total":1},{"yearMonth":"2025-04","total":1},{"yearMonth":"2025-04","total":1},{"yearMonth":"2025-06","total":1},{"yearMonth":"2025-10","total":9},{"yearMonth":"2026-01","total":1}],"downloadCount":0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