{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T03:57:32Z","timestamp":1768276652965,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: In this work, we present a CUDA-based GPU implementation of a Poisson\u2013Boltzmann equation solver, in both the linear and non-linear versions, using double precision. A finite difference scheme is adopted and made suitable for the GPU architecture. The resulting code was interfaced with the electrostatics software for biomolecules DelPhi, which is widely used in the computational biology community. The algorithm has been implemented using CUDA and tested over a few representative cases of biological interest. Details of the implementation and performance test results are illustrated. A speedup of \u223c10 times was achieved both in the linear and non-linear cases.<\/jats:p>\n               <jats:p>Availability and implementation: The module is open-source and available at http:\/\/www.electrostaticszone.eu\/index.php\/downloads.<\/jats:p>\n               <jats:p>Contact: \u00a0walter.rocchia@iit.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt699","type":"journal-article","created":{"date-parts":[[2013,12,1]],"date-time":"2013-12-01T01:09:43Z","timestamp":1385860183000},"page":"569-570","source":"Crossref","is-referenced-by-count":12,"title":["GPU linear and non-linear Poisson\u2013Boltzmann solver module for DelPhi"],"prefix":"10.1093","volume":"30","author":[{"given":"Jos\u00e9","family":"Colmenares","sequence":"first","affiliation":[{"name":"1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jes\u00fas","family":"Ortiz","sequence":"additional","affiliation":[{"name":"1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Walter","family":"Rocchia","sequence":"additional","affiliation":[{"name":"1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,11,30]]},"reference":[{"key":"2023012710422964000_btt699-B1","first-page":"420","article-title":"Solving the linearized Poisson-Boltzmann equation on GPUs using CUDA","volume-title":"21st Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)","author":"Colmenares","year":"2013"},{"key":"2023012710422964000_btt699-B2","first-page":"185","article-title":"Zur theorie der elektrolyte","volume":"24","author":"Debye","year":"1923","journal-title":"Physik. 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