{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T04:50:48Z","timestamp":1747198248916,"version":"3.40.5"},"reference-count":12,"publisher":"Walter de Gruyter GmbH","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>It has been shown that when using a Monte Carlo algorithm to estimate the electrostatic free energy of a biomolecule in a solution, individual random walks can become entrapped in the geometry. We examine a proposed solution, using a sharp restart during the Walk-on-Subdomains step, in more detail. We show that the point at which this solution introduces significant bias is related to properties intrinsic to the molecule being examined. We also examine two potential methods of generating a sharp restart point and show that they both cause no significant bias in the examined molecules and increase the stability of the run times of the individual walks.<\/jats:p>","DOI":"10.1515\/mcma-2020-2069","type":"journal-article","created":{"date-parts":[[2020,8,18]],"date-time":"2020-08-18T07:41:52Z","timestamp":1597736512000},"page":"223-244","source":"Crossref","is-referenced-by-count":3,"title":["Examining sharp restart in a Monte Carlo method for the linearized Poisson\u2013Boltzmann equation"],"prefix":"10.1515","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5487-5545","authenticated-orcid":false,"given":"W. John","family":"Thrasher","sequence":"first","affiliation":[{"name":"Department of Computer Science , Florida State University , Tallahassee , FL 32306-4530 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3058-4580","authenticated-orcid":false,"given":"Michael","family":"Mascagni","sequence":"additional","affiliation":[{"name":"Department of Computer Science , Florida State University , Tallahassee , FL 32306-4530 ; and National Institute of Standards & Technology, ITL, Gaithersburg, MD 20899-8910 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"374","published-online":{"date-parts":[[2020,8,11]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"M. E.  Davis and J. A.  McCammon,\nElectrostatics in biomolecular structure and dynamics,\nChem. Rev. 90 (1990), no. 3, 509\u2013521.","key":"2023040102133932804_j_mcma-2020-2069_ref_001_w2aab3b7d813b1b6b1ab2ab1Aa","DOI":"10.1021\/cr00101a005"},{"doi-asserted-by":"crossref","unstructured":"M. O.  Fenley, M.  Mascagni, J.  McClain, A. R. J.  Silalahi and N. A.  Simonov,\nUsing correlated Monte Carlo sampling for efficiently solving the linearized Poisson\u2013Boltzmann equation over a broad range of salt concentration,\nJ. Chem. Theory Comput. 6 (2009), no. 1, 300\u2013314.","key":"2023040102133932804_j_mcma-2020-2069_ref_002_w2aab3b7d813b1b6b1ab2ab2Aa","DOI":"10.1021\/ct9003806"},{"doi-asserted-by":"crossref","unstructured":"C.  Fleming, M.  Mascagni and N.  Simonov,\nAn efficient Monte Carlo approach for solving linear problems in biomolecular electrostatics,\nComputational Science\u2013ICCS 2005,\nSpringer, Berlin (2005), 760\u2013765.","key":"2023040102133932804_j_mcma-2020-2069_ref_003_w2aab3b7d813b1b6b1ab2ab3Aa","DOI":"10.1007\/11428862_103"},{"doi-asserted-by":"crossref","unstructured":"F.  Fogolari, P.  Zuccato, G.  Esposito and P.  Viglino,\nBiomolecular electrostatics with the linearized Poisson\u2013Boltzmann equation,\nBiophys. J. 76 (1999), no. 1, 1\u201316.","key":"2023040102133932804_j_mcma-2020-2069_ref_004_w2aab3b7d813b1b6b1ab2ab4Aa","DOI":"10.1016\/S0006-3495(99)77173-0"},{"doi-asserted-by":"crossref","unstructured":"P.  Hamlin, W. J.  Thrasher, W.  Keyrouz and M.  Mascagni,\nGeometry entrapment in walk-on-subdomains,\nMonte Carlo Methods Appl. 25 (2019), no. 4, 329\u2013340.","key":"2023040102133932804_j_mcma-2020-2069_ref_005_w2aab3b7d813b1b6b1ab2ab5Aa","DOI":"10.1515\/mcma-2019-2052"},{"unstructured":"C.-O.  Hwang, M.  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Phys. 13 (2013), no. 1, 195\u2013206.","key":"2023040102133932804_j_mcma-2020-2069_ref_008_w2aab3b7d813b1b6b1ab2ab8Aa","DOI":"10.4208\/cicp.220711.041011s"},{"doi-asserted-by":"crossref","unstructured":"M.  Mascagni and N. A.  Simonov,\nMonte Carlo method for calculating the electrostatic energy of a molecule,\nComputational Science\u2014ICCS 2003. Part I,\nLecture Notes in Comput. Sci. 2657,\nSpringer, Berlin (2003), 63\u201372.","key":"2023040102133932804_j_mcma-2020-2069_ref_009_w2aab3b7d813b1b6b1ab2ab9Aa","DOI":"10.1007\/3-540-44860-8_7"},{"doi-asserted-by":"crossref","unstructured":"M.  Mascagni and N. A.  Simonov,\nMonte Carlo methods for calculating some physical properties of large molecules,\nSIAM J. Sci. Comput. 26 (2004), no. 1, 339\u2013357.","key":"2023040102133932804_j_mcma-2020-2069_ref_010_w2aab3b7d813b1b6b1ab2ac10Aa","DOI":"10.1137\/S1064827503422221"},{"doi-asserted-by":"crossref","unstructured":"A.  Pal and S.  Reuveni,\nFirst passage under restart,\nPhys. Rev. Lett. 118 (2017), no. 3, Article ID 030603.","key":"2023040102133932804_j_mcma-2020-2069_ref_011_w2aab3b7d813b1b6b1ab2ac11Aa","DOI":"10.1103\/PhysRevLett.118.030603"},{"unstructured":"E. W.  Weisstein,\nSphere\u2013sphere intersection. From MathWorld\u2014A Wolfram Web Resource,\nhttp:\/\/mathworld.wolfram.com\/Sphere-SphereIntersection.html, Last visited on 9\/8\/2019.","key":"2023040102133932804_j_mcma-2020-2069_ref_012_w2aab3b7d813b1b6b1ab2ac12Aa"}],"container-title":["Monte Carlo Methods and Applications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyter.com\/view\/journals\/mcma\/26\/3\/article-p223.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/mcma-2020-2069\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/mcma-2020-2069\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,2]],"date-time":"2023-04-02T00:46:35Z","timestamp":1680396395000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/mcma-2020-2069\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8,11]]},"references-count":12,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,9,1]]},"published-print":{"date-parts":[[2020,9,1]]}},"alternative-id":["10.1515\/mcma-2020-2069"],"URL":"https:\/\/doi.org\/10.1515\/mcma-2020-2069","relation":{},"ISSN":["1569-3961","0929-9629"],"issn-type":[{"type":"electronic","value":"1569-3961"},{"type":"print","value":"0929-9629"}],"subject":[],"published":{"date-parts":[[2020,8,11]]}}}