Publications

List of articles from our group, or in collaboration with others, featuring the Martini force field

(for a complete list of publications from our group, check here)

In press

2017

  • V. Maingi, J.R. Burns, J.J. Uusitalo, S. Howorka, S.J. Marrink, M.S.P. Sansom. Stability and dynamics of membrane-spanning DNA nanopores. Nature Comm. 8:14784, 2017. open access
  • R. Alessandri, J.J. Uusitalo, A.H. De Vries, R.W.A. Havenith, S.J. Marrink. Bulk heterojunction morphologies with atomistic resolution from coarse-grain solvent evaporation simulations. JACS, 139:3697–3705, 2017. open access
  • M.N. Melo, C. Arnarez, H. Sikkema, N. Kumar, M. Walko, H.J.C. Berendsen, A. Kocer, S.J. Marrink, H.I. Ingólfsson. High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating. JACS, 139:2664–2671, 2017. open access
  • R.M. Venable, H.I. Ingólfsson, M.G. Lerner, B.S. Perrin, Jr., B.A. Camley, S.J. Marrink, F.L.H. Brown, R.W. Pastor. Lipid and peptide diffusion in bilayers: The Saffman-Delbrück model and periodic boundary conditions. JPCB, 121:3443–3457, 2017. abstract
  • F.J. van Eerden, T. van den Berg, P.W.J.M. Frederix, D.H. de Jong, X. Periole, S.J. Marrink. Molecular dynamics of photosystem II embedded in the thylakoid membrane. JPCB, 121:3237–3249, 2017. open access
  • R.X. Gu, H.I. Ingólfsson, A.H. de Vries, S.J. Marrink, D.P. Tieleman. Ganglioside-lipid and ganglioside-protein interactions revealed by coarse-grained and atomistic molecular dynamics simulations. JPCB, 121:3262–3275, 2017. open access

2016

  • J. Zavadlav, R. Podgornik, M.N. Melo, S.J. Marrink, M. Praprotnik. Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution. Eur. Phys. J. Special Topics 225:1595-1607, 2016. abstract
  • J. Zavadlav, S.J. Marrink, M. Praprotnik. Adaptive resolution simulation of supramolecular water: The concurrent making, breaking, and remaking of water bundles. JCTC, 12:4138–4145, 2016. open access
  • C. Arnarez, S.J. Marrink, X. Periole. Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes. Chem. Sci., 7:4435-4443, 2016. open access
  • D.H. de Jong, S. Baoukina, H.I. Ingólfsson, S.J. Marrink. Martini straight: boosting performance using a shorter cutoff and GPUs. Comp. Phys. Comm., 199:1-7, 2016. abstract

2015

  • M.N. Melo, H.I. Ingólfsson, S.J. Marrink. Parameters for Martini sterols and hopanoids based on a virtual-site description. JCP, 143: 243152, 2015. abstract
  • Y. Qi, H.I. Ingólfsson, X. Cheng, J. Lee, S.J. Marrink, W. Im. CHARMM-GUI Martini Maker for coarse-grained simulations with the Martini force field. JCTC, 11:4486–4494, 2015. abstract
  • J.J. Uusitalo, H.I. Ingólfsson, P. Akhshi, D.P. Tieleman, S.J. Marrink.Martini coarse-grained force field: extension to DNA. JCTC 11:3932-3945, 2015. open access
  • J. Zavadlav, M.N. Melo, S.J. Marrink, M. Praprotnik. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models. J. Chem. Phys, 142:244118, 2015. abstract
  • D.H. de Jong, N. Liguori, T. van den Berg, C. Arnarez, X. Periole, S.J. Marrink. Atomistic and coarse grain topologies for the cofactors associated with the photosystem II core complex. JPCB, 119:7791–7803, 2015. abstract
  • T.A. Wassenaar, H.I. Ingólfsson, R.A. Böckmann, D.P. Tieleman, S.J. Marrink. Computational lipidomics with insane: a versatile tool for generating custom membranes for molecular simulations. JCTC, 11:2144–2155, 2015. abstract
  • T.A. Wassenaar, K. Pluhackova, A. Moussatova, D. Sengupta, S.J. Marrink, D.P. Tieleman, R.A. Böckmann. High-throughput simulations of dimer and trimer assembly of membrane proteins. The DAFT approach. JCTC, 11:2278–2291, 2015. abstract
  • N. Goga, M.N. Melo, A.J. Rzepiela, A.H. De Vries, A. Hadar, S.J. Marrink, H.J.C. Berendsen. Benchmark of schemes for multiscale molecular dynamics simulations. JCTC, 11:1389–1398, 2015.  open access
  • F.J. van Eerden, D.H. de Jong, A.H de Vries, T.A. Wassenaar, S.J. Marrink. Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. BBA Biomembranes, 1848:1319–1330, 2015. abstract
  • C. Arnarez, J.J. Uusitalo, M.F. Masman, H.I. Ingólfsson, D.H. de Jong, M.N. Melo, X. Periole, A.H. De Vries, S.J. Marrink. Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent. JCTC, 11:260–275, 2015. abstract
  • C.A. López, G. Bellesia, A. Redondo, P. Langan, S.P.S. Chundawat, B.E. Dale, S.J. Marrink, S. Gnanakaran. MARTINI coarse-grained model for crystalline cellulose microfibers. JPCB, 119:465–473, 2015. abstract

2014

  • A. Konijnenberg, D. Yilmaz, H.I. Ingólfsson, A. Dimitrova, S.J. Marrink, Z. Li, C. Vénien-­‐Bryan, F. Sobott, A. Koçer. Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry. PNAS, 111:17170-17175, 2014. abstract
  • G. Moiset, C.A. López, R. Bartelds, L. Syga, E. Rijpkema, A. Cukkemane, M. Baldus, B. Poolman, S.J. Marrink. Disaccharides impact the lateral organization of lipid membranes. JACS, 136:16167-16175, 2014. open access
  • N. Mukherjee, M.D. Jose, J.P. Birkner, M. Walko, H.I. Ingólfsson, A. Dimitrova, C. Arnarez, S.J. Marrink, A. Koçer. The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension-induced gating. FASEB J., 28:4292-4302, 2014
  • H.I. Ingólfsson, M.N. Melo, F.J. van Eerden, C. Arnarez, C.A. López, T.A. Wassenaar, X. Periole, A.H. De Vries, D.P. Tieleman, S.J. Marrink. Lipid organization of the plasma membrane. JACS, 136:14554-14559, 2014. open access
  • J. Barnoud, G. Rossi, S.J. Marrink, L. Monticelli. Hydrophobic compounds reshape membrane domains. PLoS Comp. Biol., 10: e1003873, 2014. open access
  • H.I. Ingólfsson, P. Thakur, K.F. Herold, E.A. Hobart, N.B. Ramsey, X. Periole, D.H. de Jong, M. Zwama, D. Yilmaz, K. Hall, T. Maretzky, H.C. Hemmings, C. Blobel, S.J. Marrink, A. Kocer, J.T. Sack, O.S. Andersen. Phytochemicals perturb membranes and promiscuously alter protein function. ACS Chem. Biol., 9:1788–1798, 2014. abstract
  • J. Zavadlav, M.N. Melo, A.V. Cunha, A.H. De Vries, S.J. Marrink, M. Praprotnik. Adaptive resolution simulation of MARTINI solvents. JCTC, 10:2591–2598, 2014. open access
  • F. Campelo, C. Arnarez, S.J. Marrink, M.M. Kozlov. Helfrich model of membrane bending: from Gibbs theory of liquid interfaces to membranes as thick anisotropic elastic layers. Adv. Colloid Interf. Sci., 208:25-33, 2014. abstract
  • H.I. Ingólfsson, C.A. Lopez, J.J. Uusitalo, D.H. de Jong, S. Gopal, X. Periole, S.J. Marrink. The power of coarse-graining in biomolecular simulations. WIREs Comput. Mol. Sci., 4:225–248, 2014. open access
  • M. Pannuzzo, D.H. de Jong, A. Raudino, S.J. Marrink. Simulation of polyethylene glycol and calcium-mediated membrane fusion. J. Chem. Phys., 140:124905, 2014. abstract
  • T.A. Wassenaar, K. Pluhackova, R.A. Böckmann, S.J. Marrink, D.P. Tieleman. Going backward:A flexible geometric approach to reverse transformation from coarse grained to atomistic models. JCTC, 10:676-690, 2014. abstract
  • J. Zavadlav, M.N. Melo, S.J. Marrink, M. Praprotnik. Adaptive resolution simulation of an atomistic protein in MARTINI water. J. Chem. Phys., 140:054114, 2014. open access

2013

  • M. Baaden, S.J. Marrink. Coarse-grain modelling of protein–protein interactions. Curr. Opin. Struct. Biol., 23:878-886, 2013. open access
  • Y.G. Smirnova, S. Aeffner, H.J. Risselada, T. Salditt, S.J. Marrink, R. Lipowsky, M. Mueller, V. Knecht. Interbilayer repulsion forces between tension-free lipid bilayers from simulation. Soft Matter, 9:10705-10718, 2013 . abstract
  • M. Bulacu, N. Goga, W. Zhao, G. Rossi, L. Monticelli, X. Periole, D.P. Tieleman, S.J. Marrink. Improved angle potentials for coarse-grained molecular dynamics simulations. JCTC, 9:3282–3292, 2013. abstract
  • C. Gobbo, I. Beurroies, D. de Ridder, R. Eelkema, S.J. Marrink, S. De Feyter, J.H. van Esch, A.H. de Vries. MARTINI model for physisorption of organic molecules on graphite. J. Phys. Chem. C, 117:15623–15631, 2013. abstract
  • S.J. Marrink, D.P. Tieleman. Perspective on the Martini model. Chem. Soc. Rev., 42:6801-6822, 2013. open access
  • A. Raudino, S.J. Marrink, M. Pannuzzo. Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: A theoretical and computational study. J. Chem. Phys., 138:234901, 2013. abstract
  • C.A. Lopez, A.H. de Vries, S.J. Marrink. Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Sci. Rep., 3:2071, 2013. open access
  • T.A. Wassenaar, H.I. Ingólfsson, M. Prieß, S.J. Marrink, L.V. Schäfer. Mixing Martini: electrostatic coupling in hybrid atomistic – coarse-grained biomolecular simulations. J. Phys. Chem. B, 117:3516–3530, 2013. open access
  • C.A. Lopez, Z. Sovova, F.J. van Eerden, A.H. de Vries, S.J. Marrink. Martini force field parameters for glycolipids. JCTC, 9:1694–1708, 2013. abstract
  • C. Arnarez, J.P. Mazat, J. Elezgaray, S.J. Marrink, X. Periole. Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1. JACS, 135:3112–3120, 2013. open access
  • C. Arnarez, S.J. Marrink, X. Periole. Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Sci. Rep., 3:1263, 2013. open access
  • M. Hu, D.H. de Jong, S.J. Marrink, M. Deserno. Gaussian curvature elasticity determined from global shape transformations and local stress distributions: A comparative study using the MARTINI model. Farad. Discuss., 161:365-382, 2013. abstract
  • D.H. de Jong, C.A. Lopez, S.J. Marrink. Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Farad. Discuss., 161:347-363, 2013. abstract
  • D.H. de Jong, G. Singh, W.F.D. Bennett, C. Arnarez, T.A. Wassenaar, L.V. Schäfer, X. Periole, D.P. Tieleman, S.J. Marrink. Improved parameters for the Martini coarse-grained protein force field, JCTC, 9:687–697, 2013. open access
  • X. Periole, S.J. Marrink. The Martini coarse-grained force field. In "Methods in molecular biology", Vol 924,  L. Monticelli & E. Salonen Eds., Springer, 2013, pp 533-565. abstract, reprint

 

2012

  • E. Deplazes, M. Louhivuori, D. Jayatilaka, S.J. Marrink, B. Corry. Structural investigation of MscL gating using experimental data and coarse grained MD simulations. PLoS Comp. Biol. 8:e1002683, 2012. open access
  • X. Periole, A.M. Knepp, T.P. Sakmar, S.J. Marrink, T. Huber. Structural determinants of the supra-molecular organization of G protein-coupled receptors in bilayers. JACS, 134:10959–10965, 2012. abstract
  • H.J. Risselada, G. Marelli, M. Fuhrmans, Y.G. Smirnova, H. Grubmüller, S.J. Marrink, M. Muller. Line-tension controlled mechanism for influenza fusion. PLoS ONE 7:e38302, 2012. open access
  • S. Baoukina, S.J. Marrink, D.P. Tieleman. Molecular structure of membrane tethers. Biophys. J., 102:1866-1871, 2012. open access
  • D.H. de Jong, X. Periole, S.J. Marrink. Dimerization of amino acid side chains: lessons from the comparison of different force fields. JCTC, 8:1003–1014, 2012. abstract
  • M. Fuhrmans, S.J. Marrink. Molecular view of the role of fusion peptides in promoting positive membrane curvature. JACS, 134:1543–1552, 2012. abstract
  • J. Domanski, S.J. Marrink, L.V. Schaefer. Transmembrane helices can induce domain formation in crowded model biomembranes. BBA Biomembr., 1818:984-994, 2012. abstract
  • M. Bulacu, X. Periole, S.J. Marrink. In-silico design of robust bolalipid membranes, Biomacromol., 13:196–205, 2012. abstract

 

2011

  • M. Velinova, D. Sengupta, A. Tadjer, S.J. Marrink. Sphere-to-rod transitions of nonionic surfactant micelles in aqueous solution modeled by molecular dynamics simulations, Langmuir, 27:14071–14077, 2011. abstract
  • J. Sørensen, X. Periole, K.K. Skeby, S.J. Marrink, B. Schiøtt. Protofibrillar assembly toward the formation of amyloid fibrils, J. Phys. Chem. Lett., 2:2385–2390, 2011. abstract
  • A.J. Markvoort, S.J. Marrink. Lipid acrobatics in the membrane fusion arena, Curr. Top. Membr., 68:259−294, 2011. abstract, reprint
  • T. Murtola, T.A. Vuorela, M.T. Hyvonen, S.J. Marrink, M. Karttunen, I. Vattulainen. Low density lipoprotein: Structure, dynamics, and interactions of ApoB-100 with lipids. Soft Matter, 7:8135-8141, 2011. abstract
  • M. Klacsová,  M. Bulacu, N. Kučerka, D. Uhríková, J. Teixeirad, S.J. Marrink, P. Balgavý. The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles – a small-angle neutron scattering and molecular dynamics study. BBA Biomembr., 808:2136-2146, 2011. abstract
  • A.J. Rzepiela, M. Louhivuori, C. Peter, S.J. Marrink. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Phys. Chem. Chem. Phys., 13:10437-10448, 2011. abstract
  • H.J. Risselada, S.J. Marrink, M. Muller. Curvature-dependent elastic properties of liquid-ordered domains result in inverted domain sorting on uniaxially compressed vesicles. Phys. Rev. Lett., 106:148102, 2011. abstract
  • O.H.S. Ollila, M. Louhivuori, S.J. Marrink, I. Vattulainen. Protein shape change has a major effect on the gating energy of a mechanosensitive channel. Biophys. J., 100:1651-1659, 2011. abstract
  • L.V. Schafer, D.H. de Jong, A. Holt, A.J. Rzepiela, A.H. de Vries, B. Poolman, J.A. Killian, S.J. Marrink. Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model biomembranes. PNAS, 108:1343-1348, 2011. open access

 

2010

  • M. Louhivuori, H.J. Risselada, E. van der Giessen, S.J. Marrink. Release of content through mechano-sensitive gates in pressurized liposomes. PNAS, 107:19856-19860, 2010.  open access
  • A.A. Polyansky, R. Ramaswarny, P.E. Volynsky, I.F. Sbalzarini, S.J. Marrink, R.G. Efremov. Antimicrobial peptides induce growth of phosphatidylglycerol domains in a model bacterial membrane. J. Phys. Chem. Letters, 1:3108–3111, 2010. abstract
  • L.V. Schäfer, S.J. Marrink. Partitioning of lipids at domain boundaries in model membranes. Biophys. J., 99:L91-L93, 2010. open access
  • T.A. Vuorela, A. Catte, P.S. Niemela, A. Hall, M.T. Hyvonen, S.J. Marrink, M. Karttunen, I. Vattulainen. Role of lipids in spheroidal high density lipoproteins. PLoS Comp. Biol., 6:e1000964, 2010. open access
  • D. Sengupta, S.J. Marrink. Lipid mediated Interactions tune the association of Glycophorin A helix and its disruptive mutants in membranes. Phys. Chem. Chem. Phys., 12:12987-12996, 2010. abstract
  • N. Kucerka, D. Marquardt, T.A. Harroun, M.P. Nieh, S.R. Wassall, D.H. de Jong, L.V. Schäfer, S.J. Marrink, J. Katsaras. Cholesterol in bilayers with PUFA chains: Doping with DMPC or POPC results in sterol reorientation and membrane-domain formation. Biochemistry, 49:7485-7493, 2010.abstract
  • S. Ramadurai, A. Holt, L.V. Schäfer, V.V. Krasnikov, D.T.S. Rijkers, S.J. Marrink, J.A. Killian, B. Poolman. Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides. Biophys. J.,99:1447-1454, 2010. abstract
  • J.A. Lycklama a Nijeholt, M. Bulacu, S.J. Marrink, A.J.M. Driessen. Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation. J. Biol. Chem., 285:23747-23754, 2010. abstract
  • Y.G. Smirnova, S.J. Marrink, R. Lipowsky, V. Knecht. Solvent-exposed tails as prestalk transition states for membrane fusion at low hydration. JACS, 132:6710-6718, 2010. abstract
  • S.O. Yesylevskyy, L.V. Schäfer, D. Sengupta, S.J. Marrink. Polarizable water model for the coarse-grained Martini force field. PLoS Comp. Biol, 6:e1000810, 2010. open access
  • A.J. Rzepiela, L.V. Schäfer, N. Goga, H.J. Risselada, A.H. de Vries, S.J. Marrink. Reconstruction of atomistic details from coarse grained structures. J. Comp. Chem., 31:1333-1343, 2010. abstract
  • S.J. Marrink, X. Periole, D.P. Tieleman, A.H. de Vries. Comment on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. Phys. Chem. Chem. Phys., 12:2254-2256, 2010. abstract
  • M. Fuhrmans, B.P. Sanders, S.J. Marrink, A.H. de Vries. Effects of bundling on the properties of the SPC water model. Theor. Chem. Accounts, 125:335-344, 2010. open access
  • S. Baoukina, S.J. Marrink, D.P. Tieleman. Lateral pressure profiles in lipid monolayers. Farad. Discuss., 144:393-409, 2010. abstract
  • T. Apajalahti, P. Niemela, P.N. Govindan, M. Miettinen, E. Salonen, S.J. Marrink, I. Vattulainen. Concerted diffusion of lipids in raft-like membranes. Farad. Discuss., 144:411-430, 2010. abstract
  • A. Rzepiela, D. Sengupta, N. Goga, S.J. Marrink. Membrane poration by antimicrobial peptides combining atomistic and coarse grained descriptions. Farad. Discuss., 144:431-443, 2010. abstract

 

2009

  • M.J. Hinner, S.J. Marrink, A.H. de Vries. Location, tilt, and binding: a molecular dynamics study of voltage sensitve dyes in biomembranes. J. Phys. Chem. B, 113:15807-15819, 2009. abstract
  • C.A. Lopez, A. Rzepiela, A.H. de Vries, L. Dijkhuizen, P.H. Huenenberger, S.J. Marrink. The Martini coarse grained force field: extension to carbohydrates. J. Chem. Th. Comp., 5:3195-3210, 2009. abstract
  • D. Sengupta, A. Rampioni, S.J. Marrink. Simulations of the C-subunit of ATP-synthase reveal helix rearrangements. Mol. Membr. Biol., 26:422-434, 2009. abstract
  • H.J. Risselada, S.J. Marrink. The freezing process of small lipid vesicles at molecular resolution. Soft Matter, 5:4531-4541, 2009. abstract
  • H. Lee, A.H. de Vries, S.J. Marrink, R.W. Pastor. A coarse-grained model for polyethylene oxide: conformation and hydrodynamics. J. Phys. Chem. B, 113:13186-13194, 2009. abstract
  • X. Periole, M. Cavalli, S.J. Marrink, M. Ceruso. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics and intermolecular recognition. J. Chem. Th. Comp., 5:2531-2543, 2009. abstract
  • W.F.D. Bennett, J.L. MacCallum, M.J. Hinner, S.J. Marrink, D.P. Tieleman. A molecular view of cholesterol flip-flop and chemical potential in different membrane environments. JACS, 131:12714-12720, 2009. abstract
  • N. Kucerka, J. Gallova, D. Uhrikova, P. Balgavy, M. Bulacu, S.J. Marrink, J. Katsaras. Areas of monounsaturated diacylphosphatidylcholines. Biophys. J., 97:1926-1932, 2009. abstract
  • M. Fuhrmans, V. Knecht, S.J. Marrink. A single bicontinuous cubic phase induced by fusion peptides. JACS, 131:9166-9167, 2009. abstract
  • R.P.A. Berntsson, M.K. Doeven, F. Fusetti, R.H. Duurkens, D. Sengupta, S.J. Marrink, A.M.W.H. Thunnissen, B. Poolman, D.J. Slotboom. The structural basis for peptide selection by the transport receptor OppA. EMBO J., 28:1332-1340, 2009. open access
  • H.J. Risselada, S.J. Marrink. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations. Phys. Chem. Chem. Phys., 11:2056-2067, 2009. abstract
  • O.H.S. Ollila, H.J. Risselada, M. Louhivuori, E. Lindahl, I. Vattulainen, S.J. Marrink. 3D Pressure distribution in lipid membranes and membrane-protein complexes. Phys. Rev. Lett., 102:078101, 2009. abstract

 

2008

  • H.J. Risselada, S.J. Marrink.The molecular face of lipid rafts in model membranes. PNAS, 105:17367-17372, 2008.open access
  • S. Baoukina, L. Monticelli, H.J. Risselada, S.J. Marrink, D.P. Tieleman. The molecular mechanism of lipid monolayer collapse. PNAS, 105:10803-10808, 2008.open access
  • H.J. Risselada, A.E. Mark, S.J. Marrink. The application of mean field boundary potentials in simulations of lipid vesicles. JPC-B, 112:7438-7447, 2008. abstract
  • W. Treptow, S.J. Marrink, M. Tarek. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. JPC-B, 112:3277-3282, 2008. abstract
  • S.J. Marrink, A.H. de Vries, T.A. Harroun, J. Katsaras, S.R. Wassall. Cholesterol shows preference for the interior of polyunsaturated lipid membranes. JACS, 130:10-11, 2008. abstract
  • A. Catte, J.C. Patterson, D. Bashtovyy, M.K. Jones, F. Gu, L. Li, A. Rampioni, D. Sengupta, T. Vuorela, P. Niemela, M. Karttunen, S.J. Marrink, I. Vattulainen, J.P. Segrest. Structure of spheroidal HDL particles revealed by combined atomistic and coarse grained simulations. Biophys. J., 94:2306-2319, 2008. abstract
  • S.J. Marrink, M. Fuhrmans, H.J. Risselada, X. Periole. The MARTINI force field. In "Coarse graining of condensed phase and biomolecular systems", G. Voth ed., CRC press, Chapter 2, 2008.pdf reprint
  • L. Monticelli, S.K. Kandasamy, X. Periole, R.G. Larson, D.P. Tieleman, S.J. Marrink.The MARTINI coarse grained forcefield: extension to proteins. JCTC, 4:819-834, 2008. abstract
  • S. Yefimov, E. van der Giessen, P.R. Onck, S.J. Marrink. Mechanosensitive membrane channels in action. Biophys. J., 94:2994-3002, 2008. abstract

 

2007

  • S. Baoukina, L. Monticelli, S.J. Marrink, D.P. Tieleman. The pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir, 23:12617-12623, 2007. abstract
  • X. Periole, T. Huber, S.J. Marrink, T. P. Sakmar. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. JACS, 129:10126-10132, 2007. abstract
  • R. Baron, D. Trzesniak, A.H. de Vries, A. Elsener, S.J. Marrink, W.F. van Gunsteren. Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models. Chem. Phys. Chem., 8:452-461, 2007. abstract
  • S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. The MARTINI forcefield: coarse grained model for biomolecular simulations. JPC-B, 111:7812-7824, 2007. abstract

 

2006

  • R. Baron, A.H. de Vries, P.H. Huenenberger, W.F. van Gunsteren. Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. J. Phys. Chem. B 110:8464-8473, 2006. abstract

 

2005

  • S.J. Marrink, J. Risselada, A.E. Mark. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chem. Phys. Lip., 135:223-244, 2005. abstract

 

2004

  • S.J. Marrink, A.E. Mark. Molecular view of hexagonal phase formation in phospholipid membranes. Biophys. J., 87:3894-3900, 2004. abstract
  • S.J. Marrink. Molecular dynamics simulation of cholesterol nucleation in mixed micelles modelling human bile. Proceedings of Falk Symposium 139, G. Adler etal Eds, Kluwer Academic Publishers, Dordrecht, chapter 13, 98-105, 2004. pdf reprint
  • R. Faller, S.J. Marrink. Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir, 20:7686-7693, 2004. abstract
  • S.J. Marrink, A.H. de Vries, A.E. Mark. Coarse grained model for semi-quantitative lipid simulations. JPC-B, 108:750-760, 2004. abstract

 

2003

  • S.J. Marrink, A.E. Mark. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. JACS, 125:15233-15242, 2003. abstract
  • S.J. Marrink, A.E. Mark. The mechanism of vesicle fusion as revealed by molecular dynamics simulations. JACS, 125:11144-11145, 2003. abstract