{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T20:14:49Z","timestamp":1775074489116,"version":"3.50.1"},"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2014,12,4]],"date-time":"2014-12-04T00:00:00Z","timestamp":1417651200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003917","type":"journal-article","created":{"date-parts":[[2014,12,4]],"date-time":"2014-12-04T19:25:43Z","timestamp":1417721143000},"page":"e1003917","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":67,"title":["Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion"],"prefix":"10.1371","volume":"10","author":[{"given":"Paraskevi","family":"Gkeka","sequence":"first","affiliation":[]},{"given":"Panagiotis","family":"Angelikopoulos","sequence":"additional","affiliation":[]},{"given":"Lev","family":"Sarkisov","sequence":"additional","affiliation":[]},{"given":"Zoe","family":"Cournia","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,12,4]]},"reference":[{"key":"ref1","first-page":"467","article-title":"Targeted therapy using nanotechnology: focus on cancer","volume":"9","author":"V Sanna","year":"2014","journal-title":"Int J Nanomedicine"},{"key":"ref2","article-title":"In silico design and enzymatic synthesis of functional RNA nanoparticles","author":"KA Afonin","year":"2014","journal-title":"Acc Chem Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.peptides.2009.10.002","article-title":"Recent developments in liposomes, microparticles and nanoparticles for protein and peptide drug delivery","volume":"31","author":"ML Tan","year":"2010","journal-title":"Peptides"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1146\/annurev-chembioeng-073009-100847","article-title":"Polymers for drug delivery systems","volume":"1","author":"WB Liechty","year":"2010","journal-title":"Annu Rev Chem Biomol Eng"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1021\/ar200011r","article-title":"Nanomedicine for cancer: lipid-based nanostructures for drug delivery and monitoring","volume":"44","author":"Y Namiki","year":"2011","journal-title":"Acc Chem Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"20120939","DOI":"10.1098\/rsif.2012.0939","article-title":"New views on cellular uptake and trafficking of manufactured nanoparticles","volume":"10","author":"L Treuel","year":"2013","journal-title":"J R Soc Interface"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"5421","DOI":"10.1021\/nn1010792","article-title":"Penetration of lipid membranes by gold nanoparticles: insights into cellular uptake, cytotoxicity, and their relationship","volume":"4","author":"JQ Lin","year":"2010","journal-title":"ACS Nano"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"12151","DOI":"10.1021\/jp105355y","article-title":"Molecular dynamics simulations of surfactant functionalized nanoparticles in the vicinity of an oil\/water interface","volume":"114","author":"RJK Udayana Ranatunga","year":"2010","journal-title":"J Phys Chem C"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1166\/jctn.2010.1358","article-title":"Nanoparticle's size effect on its translocation across a lipid bilayer: A molecular dynamics simulation","volume":"7","author":"XB Lin","year":"2010","journal-title":"J Comput Theor Nanosci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"3723","DOI":"10.1021\/la200236d","article-title":"Structure and phase transformations of DPPC lipid bilayers in the presence of nanoparticles: Insights from coarse-grained molecular dynamics simulations","volume":"27","author":"JPP Ramalho","year":"2011","journal-title":"Langmuir"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"690","DOI":"10.2174\/157341311797483754","article-title":"The role of patterned hydrophilic domains in nanoparticle-membrane interactions","volume":"7","author":"P Gkeka","year":"2011","journal-title":"Curr Nanosci"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1039\/C0SM00963F","article-title":"Nanoscale carbon particles and the stability of lipid bilayers","volume":"7","author":"A Jusufi","year":"2011","journal-title":"Soft Matter"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"10555","DOI":"10.1021\/nn3028858","article-title":"Nanoparticle-induced permeability of lipid membranes","volume":"6","author":"S Pogodin","year":"2012","journal-title":"ACS Nano"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1021\/nn2038862","article-title":"Designing nanoparticle translocation through membranes by computer simulations","volume":"6","author":"HM Ding","year":"2012","journal-title":"ACS Nano"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1021\/jz400679z","article-title":"Homogeneous hydrophobic-hydrophilic surface patterns enhance permeation of nanoparticles through lipid membranes","volume":"4","author":"P Gkeka","year":"2013","journal-title":"J Phys Chem Lett"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1038\/nmat1116","article-title":"Spontaneous assembly of subnanometre-ordered domains in the ligand shell of monolayer-protected nanoparticles","volume":"3","author":"AM Jackson","year":"2004","journal-title":"Nat Mater"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1038\/nmat2202","article-title":"Surface-structure-regulated cell-membrane penetration by monolayer-protected nanoparticles","volume":"7","author":"A Verma","year":"2008","journal-title":"Nat Mater"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"3714","DOI":"10.1002\/smll.201001465","article-title":"Stripy nanoparticles revisited","volume":"8","author":"Y Cesbron","year":"2012","journal-title":"Small"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"7812","DOI":"10.1021\/jp071097f","article-title":"The MARTINI force field: coarse grained model for biomolecular simulations","volume":"111","author":"SJ Marrink","year":"2007","journal-title":"J Phys Chem B"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nnano.2008.130","article-title":"Computer simulation study of fullerene translocation through lipid membranes","volume":"3","author":"J Wong-Ekkabut","year":"2008","journal-title":"Nat Nanotechnol"},{"key":"ref21","article-title":"The interaction of C-60 and its derivatives with a lipid bilayer via molecular dynamics simulations","volume":"20","author":"RSG D'rozario","year":"2009","journal-title":"Nanotechnol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"068102","DOI":"10.1103\/PhysRevLett.112.068102","article-title":"Lipid membranes as solvents for carbon nanoparticles","volume":"112","author":"J Barnoud","year":"2014","journal-title":"Phys Rev Lett"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"11392","DOI":"10.1039\/c1sm06405c","article-title":"Penetration of lipid bilayers by nanoparticles with environmentally-responsive surfaces: simulations and theory","volume":"7","author":"RC Van Lehn","year":"2011","journal-title":"Soft Matter"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"4060","DOI":"10.1021\/nl401365n","article-title":"Effect of particle diameter and surface composition on the spontaneous fusion of monolayer-protected gold nanoparticles with lipid bilayers","volume":"13","author":"RC Van Lehn","year":"2013","journal-title":"Nano Lett"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S1462399402005392","article-title":"Lipid rafts: structure, function and role in HIV, Alzheimer's and prion diseases","volume":"4","author":"J Fantini","year":"2002","journal-title":"Expert Rev Mol Med"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"S57","DOI":"10.1007\/BF02562229","article-title":"Changes in membrane microdomains and caveolae constituents in multidrug-resistant cancer cells","volume":"34 Suppl","author":"Y Lavie","year":"1999","journal-title":"Lipids"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1002\/smll.200901158","article-title":"Effect of surface properties on nanoparticle-cell interactions","volume":"6","author":"A Verma","year":"2010","journal-title":"Small"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/nmat2442","article-title":"Understanding biophysicochemical interactions at the nano-bio interface","volume":"8","author":"AE Nel","year":"2009","journal-title":"Nat Mater"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e1000810 EP","DOI":"10.1371\/journal.pcbi.1000810","article-title":"Polarizable water model for the coarse-grained MARTINI force field","volume":"6","author":"SO Yesylevskyy","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/0005-2736(92)90413-G","article-title":"The permeability and the effect of acyl-chain length for phospholipid bilayers containing cholesterol: theory and experiment","volume":"1107","author":"E Corvera","year":"1992","journal-title":"Biochim Biophys Acta"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/S0163-7827(01)00009-1","article-title":"Do sterols reduce proton and sodium leaks through lipid bilayers","volume":"40","author":"TH Haines","year":"2001","journal-title":"Prog Lipid Res"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/0021-9797(89)90413-X","article-title":"Lateral density-fluctuations in the chain-melting phase-transition of lipid monolayers","volume":"129","author":"OG Mouritsen","year":"1989","journal-title":"J Colloid Interface Sci"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1021\/bi00454a021","article-title":"Phase-Equilibria of Cholesterol Dipalmitoylphosphatidylcholine Mixtures - H-2 Nuclear Magnetic-Resonance and Differential Scanning Calorimetry","volume":"29","author":"MR Vist","year":"1990","journal-title":"Biochemistry"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1786","DOI":"10.1021\/jp065172i","article-title":"Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study","volume":"111","author":"Z Cournia","year":"2007","journal-title":"J Phys Chem B"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1016\/j.bpj.2012.10.014","article-title":"Phase transitions in coarse-grained lipid bilayers containing cholesterol by molecular dynamics simulations","volume":"103","author":"Q Waheed","year":"2012","journal-title":"Biophys J"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"134906","DOI":"10.1063\/1.4823500","article-title":"One-dimensional potential of mean force underestimates activation barrier for transport across flexible lipid membranes","volume":"139","author":"DI Kopelevich","year":"2013","journal-title":"J Chem Phys"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","article-title":"GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit","volume":"29","author":"S Pronk","year":"2013","journal-title":"Bioinformatics"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1016\/S0955-0674(00)00239-8","article-title":"Implications of lipid microdomains for membrane curvature, budding and fission - Commentary","volume":"13","author":"WB Huttner","year":"2001","journal-title":"Curr Opin Cell Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S0304-4157(00)00016-2","article-title":"Structure of lipid bilayers","volume":"1469","author":"JF Nagle","year":"2000","journal-title":"Biochim Biophys Acta"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics","volume":"14","author":"W Humphrey","year":"1996","journal-title":"J Mol Graph"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular-dynamics with coupling to an external bath","volume":"81","author":"HJC Berendsen","year":"1984","journal-title":"J Chem Phys"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1002\/jcc.540130812","article-title":"The weighted histogram analysis method for free-energy calculations on biomolecules.1. The method","volume":"13","author":"S Kumar","year":"1992","journal-title":"J Comput Chem"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1004769","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2016,2,17]],"date-time":"2016-02-17T00:00:00Z","timestamp":1455667200000}}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003917","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T21:03:49Z","timestamp":1540328629000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003917"}},"subtitle":[],"editor":[{"given":"Helmut","family":"Grubm\u00fcller","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,12,4]]},"references-count":42,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2014,12,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003917","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1004769","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12,4]]}}}