{"id":"https://openalex.org/W2521766584","doi":"https://doi.org/10.1021/acs.jcim.6b00356","title":"Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures","display_name":"Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures","publication_year":2016,"publication_date":"2016-09-21","ids":{"openalex":"https://openalex.org/W2521766584","doi":"https://doi.org/10.1021/acs.jcim.6b00356","mag":"2521766584","pmid":"https://pubmed.ncbi.nlm.nih.gov/27653992"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00356","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00356","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5066012318","display_name":"Stavros Chatzieleftheriou","orcid":"https://orcid.org/0000-0002-1836-4916"},"institutions":[{"id":"https://openalex.org/I174458059","display_name":"National Technical University of Athens","ror":"https://ror.org/03cx6bg69","country_code":"GR","type":"education","lineage":["https://openalex.org/I174458059"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Stavros Chatzieleftheriou","raw_affiliation_strings":["Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece","institution_ids":["https://openalex.org/I174458059"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017989946","display_name":"Matthew Adendorff","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew R. Adendorff","raw_affiliation_strings":["Laboratory of Computational Biology & Biophysics, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Biology & Biophysics, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010593826","display_name":"Nikos D. Lagaros","orcid":"https://orcid.org/0000-0001-6114-9632"},"institutions":[{"id":"https://openalex.org/I174458059","display_name":"National Technical University of Athens","ror":"https://ror.org/03cx6bg69","country_code":"GR","type":"education","lineage":["https://openalex.org/I174458059"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Nikos D. Lagaros","raw_affiliation_strings":["Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece","institution_ids":["https://openalex.org/I174458059"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010593826"],"corresponding_institution_ids":["https://openalex.org/I174458059"],"apc_list":null,"apc_paid":null,"fwci":0.6965,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.74743531,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"56","issue":"10","first_page":"1963","last_page":"1978"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9995999932289124,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9994000196456909,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hessian-matrix","display_name":"Hessian matrix","score":0.8891468048095703},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.58958899974823},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.5780776739120483},{"id":"https://openalex.org/keywords/potential-energy","display_name":"Potential energy","score":0.5673900842666626},{"id":"https://openalex.org/keywords/finite-element-method","display_name":"Finite element method","score":0.5346642732620239},{"id":"https://openalex.org/keywords/tangent-stiffness-matrix","display_name":"Tangent stiffness matrix","score":0.45547983050346375},{"id":"https://openalex.org/keywords/atomic-units","display_name":"Atomic units","score":0.4418407082557678},{"id":"https://openalex.org/keywords/classical-mechanics","display_name":"Classical mechanics","score":0.42530032992362976},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.41953927278518677},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4017419219017029},{"id":"https://openalex.org/keywords/stiffness-matrix","display_name":"Stiffness matrix","score":0.3778928518295288},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.36446094512939453},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.31323057413101196},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.26419612765312195},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25259339809417725},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2509608268737793},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.20641544461250305},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.11959719657897949},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.11123725771903992}],"concepts":[{"id":"https://openalex.org/C203616005","wikidata":"https://www.wikidata.org/wiki/Q620495","display_name":"Hessian matrix","level":2,"score":0.8891468048095703},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.58958899974823},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.5780776739120483},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.5673900842666626},{"id":"https://openalex.org/C135628077","wikidata":"https://www.wikidata.org/wiki/Q220184","display_name":"Finite element method","level":2,"score":0.5346642732620239},{"id":"https://openalex.org/C178295079","wikidata":"https://www.wikidata.org/wiki/Q919765","display_name":"Tangent stiffness matrix","level":4,"score":0.45547983050346375},{"id":"https://openalex.org/C66823137","wikidata":"https://www.wikidata.org/wiki/Q757568","display_name":"Atomic units","level":2,"score":0.4418407082557678},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.42530032992362976},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.41953927278518677},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4017419219017029},{"id":"https://openalex.org/C14198674","wikidata":"https://www.wikidata.org/wiki/Q3851930","display_name":"Stiffness matrix","level":3,"score":0.3778928518295288},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.36446094512939453},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.31323057413101196},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.26419612765312195},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25259339809417725},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2509608268737793},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.20641544461250305},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.11959719657897949},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.11123725771903992}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020342","descriptor_name":"Finite Element Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049329","descriptor_name":"Nanostructures","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D049329","descriptor_name":"Nanostructures","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D049329","descriptor_name":"Nanostructures","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6b00356","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00356","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:27653992","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27653992","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8899999856948853,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W15000766","https://openalex.org/W1506428013","https://openalex.org/W1573186872","https://openalex.org/W1967737979","https://openalex.org/W1975353473","https://openalex.org/W1975679096","https://openalex.org/W1982244038","https://openalex.org/W1993267444","https://openalex.org/W1996816533","https://openalex.org/W2002416684","https://openalex.org/W2003946565","https://openalex.org/W2013284377","https://openalex.org/W2018205479","https://openalex.org/W2019579526","https://openalex.org/W2020932060","https://openalex.org/W2026389134","https://openalex.org/W2028293394","https://openalex.org/W2035238557","https://openalex.org/W2036956509","https://openalex.org/W2037341542","https://openalex.org/W2043057618","https://openalex.org/W2051562530","https://openalex.org/W2052994616","https://openalex.org/W2072895616","https://openalex.org/W2075184363","https://openalex.org/W2076135827","https://openalex.org/W2081383153","https://openalex.org/W2082511916","https://openalex.org/W2082741569","https://openalex.org/W2099181260","https://openalex.org/W2099737063","https://openalex.org/W2106267572","https://openalex.org/W2110589863","https://openalex.org/W2119842211","https://openalex.org/W2126961173","https://openalex.org/W2130906772","https://openalex.org/W2134421334","https://openalex.org/W2135144854","https://openalex.org/W2138825634","https://openalex.org/W2140720401","https://openalex.org/W2145610814","https://openalex.org/W2146237780","https://openalex.org/W2156844537","https://openalex.org/W2190137557","https://openalex.org/W2202554670","https://openalex.org/W2205438255","https://openalex.org/W2329672018"],"related_works":["https://openalex.org/W2329096481","https://openalex.org/W2020937688","https://openalex.org/W2387895212","https://openalex.org/W1595647571","https://openalex.org/W2183512085","https://openalex.org/W2357685414","https://openalex.org/W2158552176","https://openalex.org/W2032960009","https://openalex.org/W4225567942","https://openalex.org/W2808017351"],"abstract_inverted_index":{"The":[0,69,158],"potential":[1,83,156,212],"energy":[2,21,70,84,213],"of":[3,62,75,141,154,160,168,177,185,195,201,214],"molecules":[4],"and":[5,18,43,72,146,171,232,237],"nanostructures":[6,64],"is":[7,55,88,136,147,194,263],"commonly":[8],"calculated":[9],"in":[10,111,118,166,220],"the":[11,41,59,66,107,123,128,142,151,155,161,175,183,186,191,196,202,211,230,252],"molecular":[12,124,215,227],"mechanics":[13],"formalism":[14],"by":[15,189],"superimposing":[16],"bonded":[17],"nonbonded":[19,38],"atomic":[20,67],"terms,":[22],"i.e.":[23],"bonds":[24],"between":[25],"two":[26,93],"atoms,":[27,32,37],"bond":[28],"angles":[29,34],"involving":[30,35],"three":[31],"dihedral":[33],"four":[36],"terms":[39,167],"expressing":[40],"Coulomb":[42],"Lennard-Jones":[44],"interactions,":[45],"etc.":[46],"In":[47,98,174,249],"this":[48,250],"work":[49],"a":[50,82,112],"new,":[51],"generalized":[52,100,143],"numerical":[53],"simulation":[54],"presented":[56],"for":[57,133,226,257],"studying":[58],"mechanical":[60],"behavior":[61],"three-dimensional":[63],"at":[65],"scale.":[68],"gradient":[71],"Hessian":[73,152,187],"matrix":[74,132,153,188],"such":[76,243],"assemblies":[77],"are":[78,95,103,164,235],"usually":[79],"computed":[80],"numerically;":[81],"finite":[85,101,144],"element":[86],"model":[87,163],"proposed":[89,162,192],"herein":[90],"where":[91,229],"these":[92],"components":[94],"expressed":[96],"analytically.":[97],"particular,":[99],"elements":[102,145],"developed":[104],"that":[105,116,200],"express":[106],"interactions":[108],"among":[109],"atoms":[110],"manner":[113],"equivalent":[114,149],"to":[115,150,209,222],"invoked":[117],"simulations":[119],"performed":[120],"based":[121],"on":[122],"dynamics":[125],"method.":[126],"Thus,":[127],"global":[129],"tangent":[130],"stiffness":[131],"any":[134],"nanostructure":[135],"formed":[137],"as":[138,199,241,244],"an":[139],"assembly":[140],"directly":[148],"energy.":[157],"advantages":[159],"identified":[165],"both":[169],"accuracy":[170],"computational":[172],"efficiency.":[173],"case":[176],"popular":[178],"force":[179],"fields":[180],"(e.g.,":[181],"CHARMM),":[182],"computation":[184],"implementing":[190],"method":[193],"same":[197],"order":[198,221],"gradient.":[203],"This":[204],"analysis":[205],"can":[206,238],"be":[207,239],"used":[208],"minimize":[210],"systems":[216,228],"under":[217],"nodal":[218],"loads":[219],"derive":[223],"constitutive":[224],"laws":[225],"entropy":[231],"solvent":[233],"effects":[234],"neglected":[236],"approximated":[240],"solids,":[242],"double":[245],"stranded":[246],"DNA":[247],"nanostructures.":[248],"context,":[251],"sequence":[253],"dependent":[254],"stretch":[255],"modulus":[256],"some":[258],"typical":[259],"base":[260],"pairs":[261],"step":[262],"calculated.":[264]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-17T08:01:34.144755","created_date":"2025-10-10T00:00:00"}