{"id":"https://openalex.org/W2059628341","doi":"https://doi.org/10.1145/2335755.2335812","title":"Membrane protein simulations under asymmetric ionic concentrations","display_name":"Membrane protein simulations under asymmetric ionic concentrations","publication_year":2012,"publication_date":"2012-07-16","ids":{"openalex":"https://openalex.org/W2059628341","doi":"https://doi.org/10.1145/2335755.2335812","mag":"2059628341"},"language":"en","primary_location":{"id":"doi:10.1145/2335755.2335812","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2335755.2335812","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond","raw_type":"proceedings-article"},"type":"conference-abstract","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003390039","display_name":"Fatemeh Khalili\u2010Araghi","orcid":"https://orcid.org/0000-0002-0756-5560"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fatemeh Khalili-Araghi","raw_affiliation_strings":["The University of Chicago, Chicago, IL","The University of Chicago, Chicago IL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Chicago, Chicago, IL","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"The University of Chicago, Chicago IL","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074967375","display_name":"Brigitte Ziervogel","orcid":null},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brigitte Ziervogel","raw_affiliation_strings":["The University of Chicago, Chicago, IL","The University of Chicago, Chicago IL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Chicago, Chicago, IL","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"The University of Chicago, Chicago IL","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102778212","display_name":"Beno\u0131\u0302t Roux","orcid":"https://orcid.org/0000-0002-5254-2712"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Beno\u00eet Roux","raw_affiliation_strings":["The University of Chicago, Chicago, IL","The University of Chicago, Chicago IL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Chicago, Chicago, IL","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"The University of Chicago, Chicago IL","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080510232","display_name":"James C. Gumbart","orcid":"https://orcid.org/0000-0002-1510-7842"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Gumbart","raw_affiliation_strings":["Argonne National Laboratory, S. Cass Avenue, Argonne, IL","Argonne National Laboratory, S. Cass Avenue, Argonne, IL#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, S. Cass Avenue, Argonne, IL","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Argonne National Laboratory, S. Cass Avenue, Argonne, IL#TAB#","institution_ids":["https://openalex.org/I1282105669"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9940000176429749,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9940000176429749,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9884999990463257,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9739000201225281,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6873412728309631},{"id":"https://openalex.org/keywords/lipid-bilayer","display_name":"Lipid bilayer","score":0.6693557500839233},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.6664024591445923},{"id":"https://openalex.org/keywords/ionic-bonding","display_name":"Ionic bonding","score":0.6491888761520386},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.6237607598304749},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.592780351638794},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.5815312266349792},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.5038334727287292},{"id":"https://openalex.org/keywords/membrane-protein","display_name":"Membrane protein","score":0.4789360463619232},{"id":"https://openalex.org/keywords/periodic-boundary-conditions","display_name":"Periodic boundary conditions","score":0.4759264290332794},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4698452353477478},{"id":"https://openalex.org/keywords/cell-membrane","display_name":"Cell membrane","score":0.46879085898399353},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.37633323669433594},{"id":"https://openalex.org/keywords/boundary-value-problem","display_name":"Boundary value problem","score":0.3614811897277832},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3498636782169342},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2058517336845398},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.19722890853881836},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10722264647483826},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10272973775863647},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.09820690751075745}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6873412728309631},{"id":"https://openalex.org/C39944091","wikidata":"https://www.wikidata.org/wiki/Q423279","display_name":"Lipid bilayer","level":3,"score":0.6693557500839233},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.6664024591445923},{"id":"https://openalex.org/C2182769","wikidata":"https://www.wikidata.org/wiki/Q62500","display_name":"Ionic bonding","level":3,"score":0.6491888761520386},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.6237607598304749},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.592780351638794},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.5815312266349792},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.5038334727287292},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.4789360463619232},{"id":"https://openalex.org/C112675119","wikidata":"https://www.wikidata.org/wiki/Q2992284","display_name":"Periodic boundary conditions","level":3,"score":0.4759264290332794},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4698452353477478},{"id":"https://openalex.org/C2778106830","wikidata":"https://www.wikidata.org/wiki/Q29548","display_name":"Cell membrane","level":3,"score":0.46879085898399353},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.37633323669433594},{"id":"https://openalex.org/C182310444","wikidata":"https://www.wikidata.org/wiki/Q1332643","display_name":"Boundary value problem","level":2,"score":0.3614811897277832},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3498636782169342},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2058517336845398},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19722890853881836},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10722264647483826},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10272973775863647},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.09820690751075745},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2335755.2335812","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2335755.2335812","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1977121829","https://openalex.org/W2097747021","https://openalex.org/W2075741622","https://openalex.org/W1974240269","https://openalex.org/W1550113321","https://openalex.org/W2151889417","https://openalex.org/W1235738081","https://openalex.org/W2062258289","https://openalex.org/W2044159875","https://openalex.org/W2003037477"],"abstract_inverted_index":{"Important":[0],"cellular":[1,26,69],"processes,":[2],"such":[3,42],"as":[4,22,43],"cell-cell":[5],"recognition,":[6],"signal":[7],"transduction,":[8],"and":[9,76,165,189],"transport":[10],"of":[11,24,31,52,58,100,118,136,173,180,186,201,206,230],"electrical":[12],"signals":[13,41],"are":[14],"controlled":[15],"by":[16,28,71,112],"membrane":[17,59,107,120,137],"proteins.":[18],"Membrane":[19],"proteins":[20,37,138],"act":[21],"gatekeepers":[23],"the":[25,68,73,77,97,101,106,119,145,160,167,174,177,181,187,199,202,204,207,214,227,231],"environment":[27,70],"allowing":[29],"passage":[30],"ions,":[32],"small":[33],"molecules,":[34],"or":[35,50],"nascent":[36],"under":[38,139],"specific":[39],"environmental":[40],"transmembrane":[44],"voltage,":[45],"changes":[46],"in":[47,62,79,89,226],"ionic":[48,113,147,169,196,216],"concentration,":[49],"binding":[51],"a":[53,63,130],"ligand.":[54],"Molecular":[55],"dynamics":[56,233],"simulations":[57,84,135],"proteins,":[60],"performed":[61],"lipid":[64],"bilayer":[65],"environment,":[66],"mimic":[67],"representing":[72],"solvent,":[74],"lipids,":[75],"protein":[78,108],"full":[80],"atomistic":[81],"detail.":[82],"These":[83],"employ":[85],"periodic":[86,140],"boundary":[87,141],"conditions":[88],"three":[90],"dimensions":[91],"to":[92,212],"avoid":[93],"artifacts":[94],"associated":[95],"with":[96],"finite":[98],"size":[99],"system.":[102],"Under":[103],"these":[104],"conditions,":[105],"system":[109],"is":[110,157,209],"surrounded":[111],"solutions":[114,148],"on":[115,183,218],"either":[116],"side":[117,185],"whose":[121],"properties":[122,149],"cannot":[123],"be":[124],"changed":[125],"independently.":[126,150],"We":[127],"have":[128],"developed":[129],"computational":[131],"method":[132,222],"that":[133],"allows":[134,191],"condition":[142],"while":[143],"controlling":[144],"two":[146,161,168],"In":[151],"this":[152],"method,":[153],"an":[154],"energy":[155],"barrier":[156,175,208],"introduced":[158],"between":[159],"adjacent":[162],"unit":[163],"cells":[164],"separates":[166],"solutions.":[170],"The":[171],"height":[172,205],"affects":[176],"chemical":[178],"potential":[179],"ions":[182],"each":[184,219],"barrier,":[188],"thus":[190],"for":[192],"individual":[193],"control":[194],"over":[195],"properties.":[197],"During":[198],"course":[200],"simulation,":[203],"adjusted":[210],"dynamically":[211],"reach":[213],"proper":[215],"concentration":[217],"side.":[220],"This":[221],"has":[223],"been":[224],"implemented":[225],"Tcl":[228],"interface":[229],"molecular":[232],"program":[234],"NAMD.":[235]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
