{"data":{"id":"10.6084/m9.figshare.154331.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.154331.v1","prefix":"10.6084","suffix":"m9.figshare.154331.v1","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Cooper, Christopher","nameType":"Personal","givenName":"Christopher","familyName":"Cooper","affiliation":[],"nameIdentifiers":[]},{"name":"Barba, Lorena A.","nameType":"Personal","givenName":"Lorena A.","familyName":"Barba","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods"}],"publisher":"figshare","container":{},"publicationYear":2013,"subjects":[{"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":"Molecular Physics"},{"subject":"Computational Physics"},{"subject":"Applied Computer Science"},{"subject":"Molecular Biology"},{"subject":"Biophysics"}],"contributors":[],"dates":[{"date":"2013-01-25","dateType":"Created"},{"date":"2016-01-11","dateType":"Updated"},{"date":"2013","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsPreviousVersionOf","relatedIdentifier":"10.6084/m9.figshare.154331","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["0 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":"The PyGBe code solves the linearized Poisson-Boltzmann equation using a boundary-integral formulation. We use a boundary element method with a collocation approach, and solve it via a Krylov-subspace method. To do this efficiently, the matrix-vector multiplications in the Krylov iterations are accelerated with a treecode, achieving O(N log N) complexity. The code presents a Python environment for the user, while being efficient and fast. The core computational kernels are implemented in Cuda and interface with the user-visible code with PyCuda, for maximum ease-of-use combined with high performance on \\GPU hardware. This document provides background on the model and formulation of the numerical method, evidence of a validation exercise with well-known benchmarks---a spherical shell with a centered charge and one with an off-center charge--- and a demonstration with a realistic biological geometry (lysozyme molecule)","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz4KPHJlc291cmNlIHhtbG5zPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCIgeG1sbnM6eHNpPSJodHRwOi8vd3d3LnczLm9yZy8yMDAxL1hNTFNjaGVtYS1pbnN0YW5jZSIgeHNpOnNjaGVtYUxvY2F0aW9uPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCBodHRwOi8vc2NoZW1hLmRhdGFjaXRlLm9yZy9tZXRhL2tlcm5lbC00LjEvbWV0YWRhdGEueHNkIj4KICA8aWRlbnRpZmllciBpZGVudGlmaWVyVHlwZT0iRE9JIj4xMC42MDg0L005LkZJR1NIQVJFLjE1NDMzMS5WMTwvaWRlbnRpZmllcj4KICA8Y3JlYXRvcnM+CiAgICA8Y3JlYXRvcj4KICAgICAgPGNyZWF0b3JOYW1lPkNocmlzdG9waGVyIENvb3BlcjwvY3JlYXRvck5hbWU+CiAgICA8L2NyZWF0b3I+CiAgICA8Y3JlYXRvcj4KICAgICAgPGNyZWF0b3JOYW1lPkxvcmVuYSBBLiBCYXJiYTwvY3JlYXRvck5hbWU+CiAgICA8L2NyZWF0b3I+CiAgPC9jcmVhdG9ycz4KICA8dGl0bGVzPgogICAgPHRpdGxlPlZhbGlkYXRpb24gb2YgdGhlIFB5R0JlIGNvZGUgZm9yIFBvaXNzb24tQm9sdHptYW5uIGVxdWF0aW9uIHdpdGggYm91bmRhcnkgZWxlbWVudCBtZXRob2RzPC90aXRsZT4KICA8L3RpdGxlcz4KICA8ZGVzY3JpcHRpb25zPgogICAgPGRlc2NyaXB0aW9uIGRlc2NyaXB0aW9uVHlwZT0iQWJzdHJhY3QiPiZsdDtwJmd0O1RoZSBQeUdCZcKgY29kZSBzb2x2ZXMgdGhlIGxpbmVhcml6ZWQgUG9pc3Nvbi1Cb2x0em1hbm4gZXF1YXRpb24gdXNpbmcgYSBib3VuZGFyeS1pbnRlZ3JhbCBmb3JtdWxhdGlvbi4gV2UgdXNlIGEgYm91bmRhcnkgZWxlbWVudCBtZXRob2Qgd2l0aCBhIGNvbGxvY2F0aW9uIGFwcHJvYWNoLCBhbmQgc29sdmUgaXQgdmlhIGEgS3J5bG92LXN1YnNwYWNlIG1ldGhvZC4gVG8gZG8gdGhpcyBlZmZpY2llbnRseSwgdGhlIG1hdHJpeC12ZWN0b3IgbXVsdGlwbGljYXRpb25zIGluIHRoZSBLcnlsb3YgaXRlcmF0aW9ucyBhcmUgYWNjZWxlcmF0ZWQgd2l0aCBhIHRyZWVjb2RlLCBhY2hpZXZpbmcgTyhOIGxvZyBOKSBjb21wbGV4aXR5LiBUaGUgY29kZSBwcmVzZW50cyBhIFB5dGhvbiBlbnZpcm9ubWVudCBmb3IgdGhlIHVzZXIsIHdoaWxlIGJlaW5nIGVmZmljaWVudCBhbmQgZmFzdC4gVGhlIGNvcmUgY29tcHV0YXRpb25hbCBrZXJuZWxzIGFyZSBpbXBsZW1lbnRlZCBpbiBDdWRhIGFuZCBpbnRlcmZhY2Ugd2l0aCB0aGUgdXNlci12aXNpYmxlIGNvZGUgd2l0aCBQeUN1ZGEsIGZvciBtYXhpbXVtIGVhc2Utb2YtdXNlIGNvbWJpbmVkIHdpdGggaGlnaCBwZXJmb3JtYW5jZSBvbiBcR1BVIGhhcmR3YXJlLiBUaGlzIGRvY3VtZW50IHByb3ZpZGVzIGJhY2tncm91bmQgb24gdGhlIG1vZGVsIGFuZCBmb3JtdWxhdGlvbiBvZiB0aGUgbnVtZXJpY2FsIG1ldGhvZCwgZXZpZGVuY2Ugb2YgYSB2YWxpZGF0aW9uIGV4ZXJjaXNlIHdpdGggd2VsbC1rbm93biBiZW5jaG1hcmtzLS0tYSBzcGhlcmljYWwgc2hlbGwgd2l0aCBhIGNlbnRlcmVkIGNoYXJnZSBhbmQgb25lIHdpdGggYW4gb2ZmLWNlbnRlciBjaGFyZ2UtLS0gYW5kIGEgZGVtb25zdHJhdGlvbiB3aXRoIGEgcmVhbGlzdGljIGJpb2xvZ2ljYWwgZ2VvbWV0cnkgKGx5c296eW1lIG1vbGVjdWxlKSZsdDsvcCZndDs8L2Rlc2NyaXB0aW9uPgogIDwvZGVzY3JpcHRpb25zPgogIDxzdWJqZWN0cz4KICAgIDxzdWJqZWN0Pk1lY2hhbmljYWwgRW5naW5lZXJpbmc8L3N1YmplY3Q+CiAgICA8c3ViamVjdD5Nb2xlY3VsYXIgUGh5c2ljczwvc3ViamVjdD4KICAgIDxzdWJqZWN0PkNvbXB1dGF0aW9uYWwgUGh5c2ljczwvc3ViamVjdD4KICAgIDxzdWJqZWN0PkFwcGxpZWQgQ29tcHV0ZXIgU2NpZW5jZTwvc3ViamVjdD4KICAgIDxzdWJqZWN0Pk1vbGVjdWxhciBCaW9sb2d5PC9zdWJqZWN0PgogICAgPHN1YmplY3Q+QmlvcGh5c2ljczwvc3ViamVjdD4KICA8L3N1YmplY3RzPgogIDxwdWJsaXNoZXI+Zmlnc2hhcmU8L3B1Ymxpc2hlcj4KICA8cHVibGljYXRpb25ZZWFyPjIwMTM8L3B1YmxpY2F0aW9uWWVhcj4KICA8ZGF0ZXM+CiAgICA8ZGF0ZSBkYXRlVHlwZT0iQ3JlYXRlZCI+MjAxMy0wMS0yNTwvZGF0ZT4KICAgIDxkYXRlIGRhdGVUeXBlPSJVcGRhdGVkIj4yMDE2LTAxLTExPC9kYXRlPgogIDwvZGF0ZXM+CiAgPHJlc291cmNlVHlwZSByZXNvdXJjZVR5cGVHZW5lcmFsPSJEYXRhc2V0Ij5EYXRhc2V0PC9yZXNvdXJjZVR5cGU+CiAgPHNpemVzPgogICAgPHNpemU+MCBCeXRlczwvc2l6ZT4KICA8L3NpemVzPgogIDxyZWxhdGVkSWRlbnRpZmllcnM+CiAgICA8cmVsYXRlZElkZW50aWZpZXIgcmVsYXRlZElkZW50aWZpZXJUeXBlPSJET0kiIHJlbGF0aW9uVHlwZT0iSXNQcmV2aW91c1ZlcnNpb25PZiI+MTAuNjA4NC9tOS5maWdzaGFyZS4xNTQzMzE8L3JlbGF0ZWRJZGVudGlmaWVyPgogIDwvcmVsYXRlZElkZW50aWZpZXJzPgogIDxyaWdodHNMaXN0PgogICAgPHJpZ2h0cyByaWdodHNVUkk9Imh0dHBzOi8vY3JlYXRpdmVjb21tb25zLm9yZy9saWNlbnNlcy9ieS80LjAvIj5DQyBCWSA0LjA8L3JpZ2h0cz4KICA8L3JpZ2h0c0xpc3Q+CjwvcmVzb3VyY2U+","url":"https://figshare.com/articles/dataset/Validation_of_the_PyGBe_code_for_Poisson_Boltzmann_equation_with_boundary_element_methods/154331/1","contentUrl":null,"metadataVersion":4,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":1,"viewsOverTime":[{"yearMonth":"2026-05","total":1}],"downloadCount":0,"downloadsOverTime":[{"yearMonth":"2026-05","total":0}],"referenceCount":0,"citationCount":0,"citationsOverTime":[],"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2016-01-11T15:49:37.000Z","registered":"2016-01-11T15:49:38.000Z","published":"2013","updated":"2020-09-05T02:53:59.000Z"},"relationships":{"client":{"data":{"id":"figshare.ars","type":"clients"}},"provider":{"data":{"id":"otjm","type":"providers"}},"media":{"data":{"id":"10.6084/m9.figshare.154331.v1","type":"media"}},"references":{"data":[]},"citations":{"data":[]},"parts":{"data":[]},"partOf":{"data":[]},"versions":{"data":[]},"versionOf":{"data":[]}}}}