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

For a list of the main papers describing Martini, check here

2023

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Last Updated: Wednesday, 30 August 2023 11:01
  • C. Thangaratnarajah, M. Nijland, L. Borges-Araújo, A. Jeucken, J. Rheinberger, S.J. Marrink, P.C.T. Souza, C. Paulino, D.J. Slotboom. Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nature Commun. 14, 4484, 2023. doi:10.1038/s41467-023-40266-1
  • A. Blanco-González, S.J. Marrink, Á. Piñeiro, R. García-Fandiño. Molecular insights into the effects of focused ultrasound mechanotherapy on lipid bilayers: unlocking the keys to design effective treatments. J. Colloid Interf. Sci. 650 (B), 1201-1210, 2023. doi:10.1016/j.jcis.2023.07.077
  • B.R. Gilbert, Z.R. Thornburg, T.A. Brier, J.A. Stevens, F. Grunewald, J.E. Stone, S.J. Marrink, Z.A. Luthey-Schulten. Dynamics of Chromosome Organization in a Minimal Bacterial Cell. Front. Cell Dev. Biol., 2023, online. doi:10.3389/fcell.2023.1214962
  • A. Melcrova, S. Maity, J. Melcr, N.A.W. de Kok, M. Gabler, J. van der Eyden, W. Stensen, J.S M. Svendsen, A.J.M. Driessen, S.J. Marrink, W.H. Roos. Lateral membrane organization as target of an antimicrobial peptidomimetic compound. Nature Commun. 4, 4038, 2023. doi:10.1038/s41467-023-39726-5
  • S. Sami, S.J. Marrink. Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. J. Chem. Theory Comput., 2023, online. doi:10.1021/acs.jctc.2c01186
  • M. Ren, L. Zhao, Z. Ma, H. An, S.J. Marrink, F. Sun. Molecular basis of PIP2-dependent conformational switching of phosphorylated CD44 in binding FERM. Biophys. J., 122 (13), 2675-2685, 2023. doi:10.1016/j.bpj.2023.05.021
  • C. Empereur-Mot, K.B. Pedersen, C. Caruso, M. Perrone, M. Crippa, P.C.T. Souza, S.J. Marrink, G.M. Pavan. On the Automatic Optimization of Lipid Models in the Martini Force Field using SwarmCG. J. Chem. Inf. Model. 63 (12), 3827–3838, 2023. doi:10.1021/acs.jcim.3c00530
  • W. Pezeshkian, F. Grünewald, O. Narykov, S. Lu, T.A. Wassenaar, S.J. Marrink, D. Korkin. Molecular architecture of SARS-CoV-2 envelope by integrative modeling. Structure 31 (4), 492-503, 2023. doi:10.1016/j.str.2023.02.006
  • S. Sami, F. Grünewald, P.C.T. Souza, S.J. Marrink, A Guide to Titratable Martini Simulations, in A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules [AIP Publishing (online), Melville, New York, 2023], available at: doi:10.1063/9780735425279_004.
  • R. Alessandri, S. Thallmair, C.G. Herrero, R. Mera- Adasme, S.J. Marrink, P.C.T. Souza, A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations, in A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules [AIP Publishing (online), Melville, New York, 2023]. doi:10.1063/9780735425279_001
  • C. Hilpert, L. Beranger, P.C.T. Souza, P.A. Vainikka, V. Nieto, S.J. Marrink, L. Monticelli, G. Launay. Facilitating CG Simulations with MAD: The MArtini Database Server. J. Chem. Inf. Model., 63 (3), 702–710, 2023. doi:10.1021/acs.jcim.2c01375
  • M.G. Chiariello, F. Grünewald, R. Zarmiento-Garcia, S.J. Marrink. pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. J. Phys. Chem. Lett. 14, 905-911, 2023. doi:10.1021/acs.jpclett.2c03760
  • J.A. Stevens, F. Grünewald, P.A.M. van Tilburg, M. König, B.R. Gilbert, T.A. Brier, Z.R. Thornburg, Z. Luthey-Schulten, S.J. Marrink. Molecular dynamics simulation of an entire cell. Frontiers in Chemistry 11, 2023. doi:10.3389/fchem.2023.1106495
  • P. Vainikka, S.J. Marrink. Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches. J. Chem. Theory Comput., 2023, online. doi:org/10.1021/acs.jctc.2c00796
  • B. Waclawiková, P.C.T. Souza, M. Schwalbe, C.G. Neochoritis, W. Hoornenborg, S.A. Nelemans, S.J. Marrink, S. El Aidy. Potential binding modes of the gut bacterial metabolite, 5-hydroxyindole, to the intestinal L-type calcium channels and its impact on the microbiota in rats. Gut Microbes 15 (1), 2154544, 2023. doi:10.1080/19490976.2022.2154544
  • S.J. Marrink, L. Monticelli, M.N. Melo, R. Alessandri, D.P. Tieleman, P.C.T. Souza. Two decades of Martini: Better beads, broader scope. Wires Computational Molecular Science, 13(1), e1620, 2023. https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1620
  •  N. De Franceschi, W. Pezeshkian, A. Fragasso, B.M.H. Bruininks, S. Tsai, S.J. Marrink, C. Dekker. Synthetic Membrane Shaper for Controlled Liposome Deformation. ACS Nano, online, 2023. doi:10.1021/acsnano.2c06125

2022

Details
Last Updated: Tuesday, 24 January 2023 07:43
  • V. Thallmair, L. Schultz, W. Zhao, S.J. Marrink, D. Oliver, S. Thallmair. Two cooperative binding sites sensitize PI(4,5)P2 recognition by the tubby domain. Science Advances 8 (36), eabp9471, 2022. DOI: 10.1126/sciadv.abp9471
  • F. Grünewald, M.H. Punt, E.E. Jefferys, P.A. Vainikka, M. König, V. Virtanen, T.A. Meyer, W. Pezeshkian, A.J. Gormley, M. Karonen, M.S.P. Sansom, P.C.T. Souza, S.J. Marrink. Martini 3 Coarse-Grained Force Field for Carbohydrates. Journal of Chemical Theory and Computation, 18 (12), 7555–7569, 2022. https://pubs.acs.org/doi/10.1021/acs.jctc.2c00757
  • I. Patmanidis, P.C.T. Souza, S. Sami, R.W.A. Havenith, A.H. de Vries, S.J. Marrink. Modelling structural properties of cyanine dye nanotubes at coarse-grained level. Nanoscale Advances 4, 3033 - 3042, 2022. https://pubs.rsc.org/en/content/articlelanding/2022/na/d2na00158f
  • J. Frallicciardi, J. Melcr, P. Siginou, S.J. Marrink, B. Poolman. Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. Nature Communications 13, 1605, 2022. https://www.nature.com/articles/s41467-022-29272-x
  • F. Azadi-Chegeni, S. Thallmair, M.E. Ward, G. Perin, S.J. Marrink, M. Baldus, T. Morosinotto, A. Pandit. Protein dynamics and lipid affinity of monomeric, zeaxanthin-binding LHCII in thylakoid membranes. Biophysical Journal 121 (3), 396-409, 2022. https://www.sciencedirect.com/science/article/abs/pii/S0006349521039631
  • F. Grünewald, R. Alessandri, P.C. Kroon, L. Monticelli, P.C.T. Souza, S.J. Marrink. Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials. Nature Communications 13, 68, 2022. https://www.nature.com/articles/s41467-021-27627-4
  • R. Alessandri, J. Barnoud, A.S. Gertsen, I. Patmanidis, A.H. de Vries, P.C.T. Souza, S.J. Marrink. Martini 3 Coarse-Grained Force Field: Small Molecules. Advanced Theory and Simulations 5, 2100391, 2022. https://onlinelibrary.wiley.com/doi/full/10.1002/adts.202100391
  • N. Machado, B.M.H. Bruininks, ..., S.J. Marrink, P.C.T. Souza, P.P. Favero. Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes. Nanoscale 14, 506 - 514, 2022. https://doi.org/10.1039/D1NR04610A

2021

Details
Last Updated: Sunday, 27 November 2022 15:17
  • P. Vainikka, S. Thallmair, P.C.T. Souza, S.J. Marrink. Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties. ACS Sustainable Chemistry & Engineering 9 (51), 17338–17350, 2021. https://pubs.acs.org/doi/full/10.1021/acssuschemeng.1c06521
  • S. Zhang, G. Huang, R.C.A. Versloot, B.M.H. Bruininks, P.C.T. de Souza, S.J. Marrink, G. Maglia. Bottom-up fabrication of a proteasome–nanopore that unravels and processes single proteins. Nature Chemistry, 1-8, 2021. https://www.nature.com/articles/s41557-021-00824-w
  • A.M. Liaci, ..., S.J.Marrink, R.A.Scheltema, F. Förster. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Mol. Cell. 81, 3934-3948, 2021. https://doi.org/10.1016/j.molcel.2021.07.031
  • B.M.H. Bruininks, A.S. Thie, P.C.T. Souza, T.A. Wassenaar, S. Faraji, S.J. Marrink. Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies. J. Chem. Theory Comput., 17:7873–7885, 2021. doi.org/10.1021/acs.jctc.1c00446
  • Y. Liu, A.H. de Vries, W. Pezeshkian, S.J. Marrink. Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. J. Chem. Theory Comput. 17:5876–5884, 2021. https://doi.org/10.1021/acs.jctc.1c00151
  • S. Thallmair, M. Javanainen, B. Fábián, H. Martinez-Seara, S.J. Marrink. Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations. J. Phys. Chem. B 125 (33), 9537–9546, 2021. https://doi.org/10.1021/acs.jpcb.1c03665
  • R. Alessandri, F. Grünewald, S.J. Marrink. The Martini Model in Materials Science, Adv. Materials 33:2008635, 2021. https://doi.org/10.1002/adma.202008635
  • M. Tsanai, P.W.J.M. Frederix, C.F.E. Schroer, P.C.T. Souza, S.J. Marrink. Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chem. Sci.12:8521-8530, 2021. https://doi.org/10.1039/D1SC00374G
  • M. Nemchinova, J. Melcr, T.A. Wassenaar, S.J. Marrink, A. Guskov. Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. J. Chem. Inf. Model. 61:2407–2417, 2021. doi.10.1021/acs.jcim.1c00261
  • P.C.T. Souza, R. Alessandri, J. Barnoud, S. Thallmair, I. Faustino, ... S.J. Marrink. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods 18:382–388, 2021. doi:org/10.1038/s41592-021-01098-3
  • P.C.T. Souza, V. Limongelli, S. Wu, S.J. Marrink, L. Monticelli. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front. Mol. Biosciences 8:657222, 2021. doi:10.3389/fmolb.2021.657222
  • W. Pezeshkian, S.J. Marrink. Simulating Realistic Membrane Shapes. Curr. Opin. Cell Biol. 71:103-111, 2021. doi:10.1016/j.ceb.2021.02.009
  • F. Grünewald, P.C. Kroon, P.C.T. Souza, S.J. Marrink. Protocol for Simulations of PEGylated Proteins with Martini 3. Structural Genomics: Methods in Molecular Biology 2199:315-335, 2021. reprint

2020

Details
Last Updated: Saturday, 28 November 2020 17:23
  • L.I. Vazquez-Salazar, M. Selle, A.H. de Vries, S.J. Marrink, P.C.T. Souza. Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid-liquid extraction. Green Chemistry, 22:7376-7386, 2020. doi:10.1039/D0GC01823F
  • R. Alessandri, S. Sami, J. Barnoud, A.H. de Vries, S.J. Marrink, R.W.A. Havenith. Resolving donor–acceptor interfaces and charge carrier energy levels of organic semiconductors with polar side chains. Advanced Funct. Materials, 2004799, 2020 .doi:10.1002/adfm.202004799
  • A. Buyan, C.D. Cox, J. Barnoud, J. Li, H.S.M. Chan, B. Martinac, S.J. Marrink, B. Corry. Piezo1 forms specific, functionally important interactions with phosphoinositides and cholesterol. Biophys. J. 119:1683-1697, 2020. doi.10.1016/j.bpj.2020.07.043
  • S. Maity, J. Ottelé, G.M. Santiago, P.W.J.M. Frederix, P. Kroon, O. Markovitch, M.C.A. Stuart, S.J. Marrink, S. Otto, W.H Roos. Caught in the act: mechanistic insight into supramolecular polymerization-driven self-replication from real-time visualization. J. Amer. Chem. Soci. 142:13709–13717, 2020. doi:org/10.1021/jacs.0c02635
  • P.C.T. Souza, S. Thallmair, P. Conflitti, C. Ramírez-Palacios, R. Alessandri, S. Raniolo, V. Limongelli,  S.J. Marrink. Protein–ligand binding with the coarse-grained Martini model. Nature Commun. 11:3714, 2020. doi:10.1038/s41467-020-17437-5
  • F. Grunewald, P.C.T. Souza, H. Abdizadeh, J. Barnoud, A.H. de Vries, S.J. Marrink. Titratable Martini model for constant pH simulations. J. Chem. Phys, 153:024118, 2020. doi:10.1063/5.0014258
  • Y. Liu, W. Pezeshkian, J. Barnoud, A.H. de Vries, S.J. Marrink. Coupling coarse-grained to fine-grained models via Hamiltonian replica exchange. JCTC, 2020. doi.org/10.1021/acs.jctc.0c00429
  • W. Pezeshkian, M. Konig, T.A. Wassenaar, S.J. Marrink. Backmapping triangulated surfaces to coarse-grained membrane models. Nature Commun. 11:2296, 2020. doi.org/10.1038/s41467-020-16094-y
  • Y. Liu, A.H. de Vries, J. Barnoud, W. Pezeshkian, J. Melcr, S.J. Marrink. Dual resolution membrane simulations using virtual sites. JPCB 124:3944, 2020. doi.org/10.1021/acs.jpcb.0c01842
  • J. Su, S.J. Marrink, M.N. Melo. Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains. Front. Cell Dev. Biol., 8:350, 2020. doi.org/10.3389/fcell.2020.00350
  • B.M.H. Bruininks, P.C.T. Souza, H. Ingolfsson, S.J. Marrink.  A molecular view on the escape of lipoplexed DNA from the endosome. eLife,  9:e52012, 2020. doi.org/10.7554/eLife.52012
  • F. Sun, C.F.E. Schroer, C.R. Palacios, L. Xu, S.Z. Luo, S.J. Marrink. Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2. PLoS Comput. Biol. 16:e1007777, 2020. doi.org/10.1371/journal.pcbi.1007777
  • I. Faustino, H. Abdizadeh, P.C.T. Souza, A. Jeucken, W.K. Stanek, A. Guskov, D.J. Slotboom, S.J. Marrink. Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nature Commun. 11:1763, 2020. doi.org/10.1038/s41467-020-15554-9
  • N. Liguori, R. Croce, S.J. Marrink, S. Thallmair. Molecular dynamics simulations in photosynthesis. Photosynth Res. 144:273–295, 2020. doi.org/10.1007/s11120-020-00741-y
  • C.F.E. Schroer, L. Baldauf, L. van Buren, T.A. Wassenaar, M.N. Melo, G. Koenderink, S.J. Marrink. Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers. PNAS, 117: 5861-5872, 2020. doi.org/10.1073/pnas.1914884117
  • H.M. Khan, P.C.T. Souza, S. Thallmair, J. Barnoud, A.H. De Vries, S.J. Marrink, N. Reuter. Capturing choline-aromatics cation-π interactions in the MARTINI force field. JCTC, 16:2550-2560, 2020. doi.org/10.1021/acs.jctc.9b01194

2019

Details
Last Updated: Wednesday, 18 March 2020 13:56
  • P.C.T. Souza, S. Thallmair, S.J. Marrink, R. Mera-Adasme. An Allosteric Pathway in SOD1 Unravels the Molecular Mechanism of the G93A ALS-Linked Mutation. J. Phys. Chem. Letters, 10:7740-7744, 2019. doi.org/10.1021/acs.jpclett.9b02868
  • Y. Liu, J. Barnoud, S.J. Marrink. Gangliosides Destabilize Lipid Phase Separation in Multicomponent Membranes. Biophys. J. 117: 1215-1223, 2019. doi.org/10.1016/j.bpj.2019.08.037
  • B.M.H. Bruininks, P.C.T. Souza, S.J. Marrink. A Practical View of the Martini Force Field. Biomolecular Simulations, 105-127, 2019. doi:10.1007/978-1-4939-9608-7_5 , pdf-reprint.
  • R. Alessandri, P.C.T. Souza, S. Thallmair, M.N. Melo, A.H. De Vries, S.J. Marrink, Pitfalls of the MARTINI model. JCTC, 15:5448-5460, 2019. doi.org/10.1021/acs.jctc.9b00473
  • A. Newe, K. Rzeniewicz, M. König, C.F.E. Schroer, J. Joachim, A. Rey-Gallardo, S.J Marrink, J. Deka, M. Parsons, A. Ivetic. Serine phosphorylation of the L-selectin tail regulates ERM binding, clustering, and monocyte protrusion in transendothelial migration. Front. Immunol. 10, 2227, 2019. doi:10.3389/fimmu.2019.02227
  • W. Pezeshkian, M. König, S.J. Marrink, J.H. Ipsen. A multi-scale approach to membrane remodeling processes. Front. Mol. Biosci. 6, 59, 2019. doi:10.3389/fmolb.2019.00059
  • S. Koch, `M. Exterkate, C.A. López, M. Patro, S.J. Marrink, A.J.M. Driessen Two distinct anionic phospholipid-dependent events involved in SecA-mediated protein translocation. BBA-Biomembr. 1861, 183035, 2019. doi.10.1016/j.bbamem.2019.183035
  • T.K. Piskorz, C. Gobbo, S.J. Marrink, S. De Feyter, A.H. De Vries, J.H. van Esch. Nucleation Mechanisms of Self-Assembled Physisorbed Monolayers on Graphite. J. Phys. Chem. C 123, 17510, 2019. doi:10.1021/acs.jpcc.9b01234
  • S. Dadsena, S. Bockelmann, J.G.M. Mina, D.G. Hassan, S. Korneev, G. Razzera, H. Jahn, P. Niekamp, D. Müller, M. Schneider, F.G. Tafesse, S.J. Marrink, M.N. Melo, J.C.M. Holthuis, Ceramides bind VDAC2 to trigger mitochondrial apoptosis. Nature Commun. 10:1832, 2019. doi:10.1038/s41467-019-09654
  • J. Zavadlav, S.J. Marrink M. Praprotnik, SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus 9:20180075, 2019. doi.org/10.1098/rsfs.2018.0075
  • S. Thallmair, P.A. Vainikka, S.J. Marrink. Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes. Biophys. J., 116:1446-1455, 2019. doi:10.1016/j.bpj.2019.03.009
  • S.J. Marrink, V. Corradi, P.C.T. Souza, H.I. Ingolfsson, D.P. Tieleman, M.S.P. Sansom. Computational Modeling of Realistic Cell Membranes. Chem. Review, 119:6184–6226, 2019. doi:10.1021/acs.chemrev.8b00460
  • V. Corradi, B.I. Sejdiu, H. Mesa-Galloso, H. Abdizadeh, S.Y. Noskov, S.J. Marrink, D.P. Tieleman. Emerging Diversity in Lipid–Protein Interactions, Chem. Review, 119:5775–5848, 2019. doi:10.1021/acs.chemrev.8b00451

2018

Details
Last Updated: Monday, 14 January 2019 12:21
  • S. Thallmair, H.I. Ingólfsson, S.J. Marrink. Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models. J. Phys. Chem. Lett. 9:5527–5533, 2018. doi:10.1021/acs.jpclett.8b01877
  • V. Corradi, E. Mendez-Villuendas, H.I. Ingólfsson, R.X. Gu, I. Siuda, M.N. Melo, A. Moussatova, L.J. DeGagné, B.I. Sejdiu, G. Singh, T.A. Wassenaar, K. Delgado Magnero, S.J. Marrink, D.P. Tieleman. Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins. ACS Central Science 4:709–717, 2018. doi:10.1021/acscentsci.8b00143
  • S. Baoukina, H.I. Ingólfsson, S.J. Marrink, D.P. Tieleman. Curvature‐Induced Sorting of Lipids in Plasma Membrane Tethers. Advanced Theory Simul., 1:1800034, 2018. doi:10.1002/adts.201800034
  • F. Grunewald, G. Rossi, A.H. De Vries, S.J. Marrink, L. Monticelli. A Transferable MARTINI Model of Polyethylene Oxide. JPCB, 122:7436–7449, 2018. doi:10.1021/acs.jpcb.8b04760
  • M. Xue, L. Cheng, I. Faustino, W. Guo, S.J. Marrink. Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers. Biophys. J., 115:494-502, 2018. doi:10.1016/j.bpj.2018.06.018.
  • F. Sun, C.F.E. Schroer, L. Xu, H. Yin, S.J. Marrink, S.Z. Luo. Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2. Biophys. J., 114:1858–1868, 2018. doi:10.1016/j.bpj.2018.02.034
  • P.W.J.M. Frederix, I. Patmanidis, S.J. Marrink. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem. Soc. Review, 47:3470 - 3489, 2018. doi:10.1039/C8CS00040A
  • J. Liu, L. Qiu, R. Alessandri, X. Qiu, G. Portale, J. Dong, W. Talsma, G. Ye, A.A. Sengrian, P.C.T. Souza, M.A. Loi, R.C. Chiechi, S.J. Marrink, J.C. Hummelen, L.J.A. Koster. Enhancing Molecular n-Type Doping of Donor–Acceptor Copolymers by Tailoring Side Chains. Advanced Materials, 30:1704630, 2018. doi:10.1002/adma.201704630
  • J. Su, A.S. Thomas, T. Grabietz, C. Landgraf, R. Volkmer, S.J. Marrink, C. Williams,  M.N. Melo. The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission. BBA Biomembr., 1860, 6:1292-1300, 2018. doi:10.1016/j.bbamem.2018.02.029
  • J.N. Pedersen, P.W.J.M. Frederix, J.S. Pedersen, S.J. Marrink, D. Otzen. Role of charge and hydrophobicity in liprotide formation: a molecular dynamics study with experimental constraints. ChemBioChem, 19:263–271, 2018. doi:10.1002/cbic.201700496
  • J. Zavadlav, S.J. Marrink, M. Praprotnik. Multiscale simulation of protein hydration using the SWINGER dynamical clustering algorithm. J. Chem. Theory Comput., 14:1754-1761, 2018. doi:10.1021/acs.jctc.7b01129

2017

Details
Last Updated: Tuesday, 19 December 2017 18:23
  • F.J. van Eerden, M.N. Melo, P.W.J.M. Frederix, S.J. Marrink. Prediction of thylakoid lipid binding sites on photosystem II. Biophys. J. 113:2669-2681, 2017. open access
  • H.I. Ingólfsson, T.S. Carpenter, H. Bhatia, P.T. Bremer, S.J. Marrink, F.C. Lightstone. Computational Lipidomics of the Neuronal Plasma Membrane. Biophys. J. 113:2271–2280, 2017. open access
  • T. Kondela, J. Gallová, T. Hauß, J. Barnoud, S.J. Marrink, N. Kučerka. Alcohol interactions with lipid bilayers. Molecules, 22:2078, 2017. abstract
  • L. Qiu, J. Liu, R. Alessandri, X. Qiu, M. Koopmans, R.W.A. Havenith, S.J. Marrink, R.C. Chiechi, L.J.A. Koster, J.C. Hummelen. Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics. Journal of Material Chemistry A, 5:21234-2124, 2017. abstract
  • P.C. Hsu, B.M.H. Bruininks, D. Jefferies, P.C. Telles de Souza, J. Lee, D.S. Patel, S.J .Marrink, Y. Qi, S. Khalid, W. Im. CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. J. Comput. Chem., 38:2354–2363, 2017. abstract
  • J.J. Uusitalo, H.I. Ingólfsson, S.J. Marrink, I. Faustino. Martini coarse-grained force field: extension to RNA. Biophys. J., 113:246-256, 2017. abstract
  • F.J. van Eerden, M.N. Melo, P.W.J.M. Frederix, X. Periole, S.J. Marrink. Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nature Commun. 8:15214, 2017. open access
  • B. Liu, C. Åberg, F.J. van Eerden, S.J. Marrink, B. Poolman, A.J. Boersma. Design and properties of genetically encoded probes for sensing macromolecular crowding. Biophys. J.  112:1929–1939, 2017. abstract
  • 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
  • I. Faustino, S.J. Marrink. cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. Bioinformatics, 33:3813-3815, 2017. abstract

2016

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Last Updated: Thursday, 02 March 2017 01:39
  • 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
  • H.I. Ingólfsson, C. Arnarez, X. Periole, S.J. Marrink. Computational 'microscopy' of cellular membranes. J. Cell Science, 129:257-268, 2016. abstract
  • 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

Details
Last Updated: Thursday, 02 March 2017 01:40
  • 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

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Last Updated: Saturday, 18 July 2015 21:55
  • 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. abstract
  • 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

Details
Last Updated: Friday, 10 January 2014 12:59
  • 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

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Last Updated: Friday, 18 October 2013 13:57
  • 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

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Last Updated: Thursday, 22 August 2013 12:21
  • 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

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Last Updated: Thursday, 22 August 2013 12:21
  • 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

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Last Updated: Thursday, 22 August 2013 12:21
  • 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

Details
Last Updated: Thursday, 22 August 2013 12:21
  • 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

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Last Updated: Monday, 26 August 2013 11:54
  • 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

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Last Updated: Thursday, 22 August 2013 12:21

  • 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

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Last Updated: Thursday, 22 August 2013 12:21
  • 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

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Last Updated: Thursday, 22 August 2013 12:21
  • 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

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Last Updated: Thursday, 22 August 2013 12:21
  • 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