{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T04:37:14Z","timestamp":1750307834016,"version":"3.41.0"},"reference-count":92,"publisher":"Association for Computing Machinery (ACM)","issue":"2","license":[{"start":{"date-parts":[[2008,4,1]],"date-time":"2008-04-01T00:00:00Z","timestamp":1207008000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":["J. Emerg. Technol. Comput. Syst."],"published-print":{"date-parts":[[2008,4]]},"abstract":"<jats:p>\n            The need to determine electrostatic fields in domains bounded by molecular surfaces arises in a number of nanotechnology applications including: biomolecule design, carbon nanotube simulation, and molecular electron transport analysis. Molecular surfaces are typically smooth, without the corners common in electrical interconnect problems, but are often so geometrically complicated that numerical evaluation of the associated electrostatic fields is extremely time-consuming. In this paper we describe and demonstrate a meshless spectrally-accurate integral equation method that\n            <jats:italic>only<\/jats:italic>\n            requires a description of the molecular surface in the form of a collection of surface points. Our meshless method is a synthesis of techniques, suitably adapted, including: spherical harmonic surface interpolation, spectral-element-like integral equation discretization, integral desingularization via variable transformation, and matrix-implicit iterative matrix solution. The spectral accuracy of this combined method is verified using analytically solvable sphere and ellipsoid problems, and then its accuracy and efficiency is demonstrated numerically by solving capacitance and coupled Poisson\/linearized Poisson-Boltzmann problems associated with a commonly used model of a molecule in solution. The results demonstrate that for a tolerance of 10\n            <jats:sup>\u22123<\/jats:sup>\n            this new approach reduces the number of unknowns by as much as two orders of magnitude over the more commonly used flat panel methods.\n          <\/jats:p>","DOI":"10.1145\/1350763.1350766","type":"journal-article","created":{"date-parts":[[2008,4,29]],"date-time":"2008-04-29T13:01:12Z","timestamp":1209474072000},"page":"1-30","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["A meshless, spectrally accurate, integral equation solver for molecular surface electrostatics"],"prefix":"10.1145","volume":"4","author":[{"given":"Shih-Hsien","family":"Kuo","sequence":"first","affiliation":[{"name":"Massachusetts Institute of Technology, Cambridge, MA"}]},{"given":"Bruce","family":"Tidor","sequence":"additional","affiliation":[{"name":"Massachusetts Institute of Technology, Cambridge, MA"}]},{"given":"Jacob","family":"White","sequence":"additional","affiliation":[{"name":"Massachusetts Institute of Technology, Cambridge, MA"}]}],"member":"320","published-online":{"date-parts":[[2008,4,23]]},"reference":[{"key":"e_1_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2005.855946"},{"key":"e_1_2_1_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/nme.124"},{"key":"e_1_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.2743423"},{"key":"e_1_2_1_4_1","unstructured":"Baxansky A. and Kiryati N. 2005. Calculating geometric properties of three-dimensional objects from the spherical harmonic representation. Tech. rep. VIA-2005-6-1 Tel Aviv University.  Baxansky A. and Kiryati N. 2005. Calculating geometric properties of three-dimensional objects from the spherical harmonic representation. Tech. rep. VIA-2005-6-1 Tel Aviv University."},{"key":"e_1_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"e_1_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1137\/S0036144502417715"},{"key":"e_1_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/cpa.3160440202"},{"key":"e_1_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540160707"},{"key":"e_1_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp013607q"},{"key":"e_1_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.1006\/cviu.1995.1013"},{"key":"e_1_2_1_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/9780470141205"},{"key":"e_1_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1006\/jcph.2001.6714"},{"key":"e_1_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0363(20000515)33:1<125::AID-FLD5>3.0.CO;2-Q"},{"key":"e_1_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889883010985"},{"key":"e_1_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1021\/cr00101a005"},{"key":"e_1_2_1_16_1","unstructured":"de Queiroz A. C. M. Capacitance calculations. http:\/\/www.coe.ufrj.br\/~acmq\/tesla\/capcalc.pdf.  de Queiroz A. C. M. Capacitance calculations. http:\/\/www.coe.ufrj.br\/~acmq\/tesla\/capcalc.pdf."},{"key":"e_1_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360330204"},{"key":"e_1_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00466-005-0694-1"},{"key":"e_1_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0008-8846(02)00836-0"},{"key":"e_1_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1109\/TAP.2003.816305"},{"key":"e_1_2_1_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(85)90297-9"},{"key":"e_1_2_1_22_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540090407"},{"key":"e_1_2_1_23_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.1032"},{"key":"e_1_2_1_24_1","doi-asserted-by":"crossref","unstructured":"Greengard L. 1988. The Rapid Evaluation of Potential Fields in Particle Systems. MIT Press.  Greengard L. 1988. The Rapid Evaluation of Potential Fields in Particle Systems. MIT Press.","DOI":"10.7551\/mitpress\/5750.001.0001"},{"key":"e_1_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.5555\/2718233.2718596"},{"key":"e_1_2_1_26_1","unstructured":"Harrington R. F. 1968. Field Computation by Moment Methods. MacMillan.   Harrington R. F. 1968. Field Computation by Moment Methods. MacMillan."},{"key":"e_1_2_1_27_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10825-006-0139-x"},{"key":"e_1_2_1_28_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja0032273"},{"key":"e_1_2_1_29_1","unstructured":"Hess J. L. 1979. A higher order panel method for three-dimensional potential flow. Tech. rep. McDonald Douglas.  Hess J. L. 1979. A higher order panel method for three-dimensional potential flow. Tech. rep. McDonald Douglas."},{"key":"e_1_2_1_30_1","doi-asserted-by":"crossref","first-page":"22","DOI":"10.5957\/jsr.1964.8.4.22","article-title":"Calculation of nonlifting potential flow about arbitrary three-dimensional bodies","volume":"8","author":"Hess J. L.","year":"1964","journal-title":"J. Ship Res."},{"key":"e_1_2_1_31_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.7761829"},{"key":"e_1_2_1_32_1","doi-asserted-by":"publisher","DOI":"10.1109\/36.673667"},{"key":"e_1_2_1_33_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja00004a079"},{"key":"e_1_2_1_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(91)90043-K"},{"key":"e_1_2_1_35_1","doi-asserted-by":"publisher","DOI":"10.1109\/22.310584"},{"key":"e_1_2_1_36_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.481522"},{"key":"e_1_2_1_37_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp003449n"},{"key":"e_1_2_1_38_1","doi-asserted-by":"publisher","DOI":"10.1145\/288548.288604"},{"volume-title":"Proceedings of the IEEE\/ACM International Conference on Computer-Aided Design","author":"Kapur S.","key":"e_1_2_1_39_1"},{"key":"e_1_2_1_40_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340010109"},{"key":"e_1_2_1_41_1","doi-asserted-by":"crossref","unstructured":"Kong J. Franklin N. R. Zhou C. Chapline M. G. Peng S. Cho K. and Dai H. 2000. Nanotube molecular wires as chemical sensors. Science 287 5453 622--625.  Kong J. Franklin N. R. Zhou C. Chapline M. G. Peng S. Cho K. and Dai H. 2000. Nanotube molecular wires as chemical sensors. Science 287 5453 622--625.","DOI":"10.1126\/science.287.5453.622"},{"key":"e_1_2_1_42_1","doi-asserted-by":"crossref","unstructured":"Kress R. 1999. Linear Integral Equations 2nd Ed. Springer Verlag.  Kress R. 1999. Linear Integral Equations 2nd Ed. Springer Verlag.","DOI":"10.1007\/978-1-4612-0559-3"},{"key":"e_1_2_1_43_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01385694"},{"key":"e_1_2_1_44_1","doi-asserted-by":"publisher","DOI":"10.1145\/774572.774640"},{"key":"e_1_2_1_45_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja00117a038"},{"key":"e_1_2_1_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(71)90324-X"},{"key":"e_1_2_1_47_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0901-789"},{"key":"e_1_2_1_48_1","doi-asserted-by":"publisher","DOI":"10.1110\/ps.40001"},{"key":"e_1_2_1_49_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01169216"},{"key":"e_1_2_1_50_1","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(88)85008-2"},{"key":"e_1_2_1_51_1","doi-asserted-by":"publisher","DOI":"10.1145\/337292.337767"},{"key":"e_1_2_1_52_1","doi-asserted-by":"publisher","DOI":"10.1021\/j100197a004"},{"key":"e_1_2_1_53_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0605166103"},{"key":"e_1_2_1_54_1","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(95)00043-F"},{"key":"e_1_2_1_55_1","unstructured":"Manier H. D. 1995. A three dimensional higher order panel method based on B-splines. Ph.D. thesis Massachusetts Institute of Technology Cambridge MA.  Manier H. D. 1995. A three dimensional higher order panel method based on B-splines. Ph.D. thesis Massachusetts Institute of Technology Cambridge MA."},{"key":"e_1_2_1_56_1","doi-asserted-by":"publisher","DOI":"10.1109\/38.7748"},{"key":"e_1_2_1_57_1","doi-asserted-by":"crossref","unstructured":"McCammon J. A. and Harvey S. C. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press Cambridge UK.  McCammon J. A. and Harvey S. C. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press Cambridge UK.","DOI":"10.1017\/CBO9781139167864"},{"key":"e_1_2_1_58_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti337"},{"key":"e_1_2_1_59_1","first-page":"107","article-title":"Statistical analysis of the molecular surface electrostatic potential: an approach to describing noncovalent interactions in condensed phases. J. Molec. Struc.: THEOCHEM, Issues 1--2","volume":"425","author":"Murray J. S.","year":"1998","journal-title":"Proceedings of the Fifth Annual Conference on Current Trends in Computational Chemistry"},{"key":"e_1_2_1_60_1","doi-asserted-by":"publisher","DOI":"10.1137\/0915046"},{"key":"e_1_2_1_61_1","doi-asserted-by":"publisher","DOI":"10.1109\/43.97624"},{"key":"e_1_2_1_62_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00042771"},{"key":"e_1_2_1_63_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540120405"},{"key":"e_1_2_1_64_1","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(84)90128-1"},{"key":"e_1_2_1_65_1","doi-asserted-by":"publisher","DOI":"10.1109\/43.662670"},{"key":"e_1_2_1_66_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp961992r"},{"key":"e_1_2_1_67_1","first-page":"77","article-title":"Fast algorithms for 3-D simulation","volume":"1","author":"Ramaswamy D.","year":"1999","journal-title":"J. Model. Simul. Microsyst."},{"key":"e_1_2_1_68_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.bb.06.060177.001055"},{"key":"e_1_2_1_69_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja00088a034"},{"key":"e_1_2_1_70_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp010454y"},{"key":"e_1_2_1_71_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.1161"},{"key":"e_1_2_1_72_1","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(85)90002-6"},{"key":"e_1_2_1_73_1","doi-asserted-by":"publisher","DOI":"10.1137\/0907058"},{"key":"e_1_2_1_74_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y"},{"key":"e_1_2_1_75_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.bb.19.060190.001505"},{"key":"e_1_2_1_76_1","first-page":"1488","article-title":"Multilevel fast multipole algorithm for electromagnetic scattering by large complex objects","volume":"45","author":"Song J.","year":"1997","journal-title":"Int. J. Numer. Meth. Engin."},{"key":"e_1_2_1_77_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja00172a038"},{"key":"e_1_2_1_78_1","doi-asserted-by":"publisher","DOI":"10.1137\/0916058"},{"key":"e_1_2_1_79_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp047126t"},{"key":"e_1_2_1_80_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja01577a001"},{"volume-title":"Integral Methods in Science and Engineering","author":"Tausch J.","key":"e_1_2_1_81_1"},{"key":"e_1_2_1_82_1","doi-asserted-by":"publisher","DOI":"10.1145\/309847.309994"},{"key":"e_1_2_1_83_1","doi-asserted-by":"publisher","DOI":"10.2514\/6.1997-168"},{"key":"e_1_2_1_84_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(97)78105-0"},{"key":"e_1_2_1_85_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCAD.2005.855938"},{"volume-title":"Proceedings of the International Conference on Modeling and Simulation of Microsystems","author":"Wang X.","key":"e_1_2_1_86_1"},{"key":"e_1_2_1_87_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(82)90505-8"},{"key":"e_1_2_1_88_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540110911"},{"key":"e_1_2_1_89_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540090209"},{"key":"e_1_2_1_90_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540110509"},{"key":"e_1_2_1_91_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199605)17:7<864::AID-JCC10>3.0.CO;2-B"},{"key":"e_1_2_1_92_1","doi-asserted-by":"publisher","DOI":"10.1145\/775832.776015"}],"container-title":["ACM Journal on Emerging Technologies in Computing Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/1350763.1350766","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/1350763.1350766","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T13:57:59Z","timestamp":1750255079000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/1350763.1350766"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,4]]},"references-count":92,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2008,4]]}},"alternative-id":["10.1145\/1350763.1350766"],"URL":"https:\/\/doi.org\/10.1145\/1350763.1350766","relation":{},"ISSN":["1550-4832","1550-4840"],"issn-type":[{"type":"print","value":"1550-4832"},{"type":"electronic","value":"1550-4840"}],"subject":[],"published":{"date-parts":[[2008,4]]},"assertion":[{"value":"2008-01-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2008-01-01","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2008-04-23","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}