Skip to ContentSkip to Navigation
ResearchMolecular Dynamics GroupPublications

Publications

2019

Liu, Y., Barnoud, J., & Marrink, S. J. (2019). Gangliosides Destabilize Lipid Phase Separation in Multicomponent Membranes. Biophysical Journal, 117(7), 1215-1223. https://doi.org/10.1016/j.bpj.2019.08.037
Gholamjani Moghaddam, K., de Vries, A., Marrink, S. J., & Faraji, S. (2019). Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking. Biophysical Chemistry, 253, [106220]. https://doi.org/10.1016/j.bpc.2019.106220
Newe, A., Rzeniewicz, K., Konig, M., Schroer, C. F. E., Joachim, J., Rey-Gallardo, A., ... Ivetic, A. (2019). Serine Phosphorylation of L-Selectin Regulates ERM Binding, Clustering, and Monocyte Protrusion in Transendothelial Migration. Frontiers in Immunology, 10, [2227]. https://doi.org/10.3389/fimmu.2019.02227
Koch, S., Exterkate, M., López, C. A., Patro, M., Marrink, S. J., & Driessen, A. J. M. (2019). Two distinct anionic phospholipid-dependent events involved in SecA-mediated protein translocation. Biochimica et Biophysica Acta - Biomembranes, 1861(11), [183035]. https://doi.org/10.1016/j.bbamem.2019.183035
Pezeshkian, W., König, M., Marrink, S. J., & Ipsen, J. H. (2019). A Multi-Scale Approach to Membrane Remodeling Processes. Frontiers in Molecular Biosciences, 6, [59]. https://doi.org/10.3389/fmolb.2019.00059
Alessandri, R., Souza, P. C. T., Thallmair, S., Melo, M. N., De Vries, A. H., & Marrink, S. J. (Accepted/In press). Pitfalls of the Martini Model. Journal of Chemical Theory and Computation, [acs.jctc.9b00473]. https://doi.org/10.26434/chemrxiv.8113172
Corradi, V., Sejdiu, B. I., Mesa-Galloso, H., Abdizadeh, H., Noskov, S. Y., Marrink, S. J., & Tieleman, D. P. (2019). Emerging Diversity in Lipid-Protein Interactions. Chemical reviews, 119(9), 5775-5848. https://doi.org/10.1021/acs.chemrev.8b00451
Dadsena, S., Bockelmann, S., Mina, J. G. M., Hassan, D. G., Korneev, S., Razzera, G., ... Holthuis, J. C. M. (2019). Ceramides bind VDAC2 to trigger mitochondrial apoptosis. Nature Communications, 10(1), [1832]. https://doi.org/10.1038/s41467-019-09654-4
Zavadlav, J., Marrink, S. J., & Praprotnik, M. (2019). SWINGER: A clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus, 9(3), [20180075]. https://doi.org/10.1098/rsfs.2018.0075
Thallmair, S., & Marrink, S. (2019). Chromophore arrangement in light-harvesting complex II influenced by the protein dynamics on the microsecond time scale. In XXI International Conference on Ultrafast Phenomena 2018 (UP 2018) (Vol. 205). [09039] (EPJ Web of Conferences). EPJ Web of Conferences. https://doi.org/10.1051/epjconf/201920509039
Thallmair, S., Vainikka, P. A., & Marrink, S. J. (2019). Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes. Biophysical Journal, 116(8), 1446-1455. [j.bpj.2019.03.009]. https://doi.org/10.1016/j.bpj.2019.03.009
Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., ... Kuipers, O. P. (2019). Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. BMC Evolutionary Biology, 19(1), [15]. https://doi.org/10.1186/s12862-018-1331-x
Marrink, S. J., Corradi, V., Souza, P. C. T., Ingólfsson, H. I., Tieleman, D. P., & Sansom, M. S. P. (2019). Computational Modeling of Realistic Cell Membranes. Chemical reviews, 119(9), 6184-6226. [doi:10.1021/acs.chemrev.8b00460]. https://doi.org/10.1021/acs.chemrev.8b00460
Bruininks, B. M. H., Souza, P. C. T., & Marrink, S. J. (2019). A Practical View of the Martini Force Field. Methods in Molecular Biology, 2022, 105-127. https://doi.org/10.1007/978-1-4939-9608-7_5
Verkhnyatskaya, S. A., de Vries, A. H., Douma-de Vries, E., Sneep, R. J. L., & Walvoort, M. T. C. (2019). Direct and Regioselective Di-alpha-fucosylation on the Secondary Rim of beta-Cyclodextrin: Cover Profile. Chemistry, 25(27), 6649-6649. https://doi.org/10.1002/chem.201901257
Verkhnyatskaya, S. A., de Vries, A. H., Douma-de Vries, E., Sneep, E. J. L., & Walvoort, M. T. C. (2019). Direct and Regioselective Di-alpha-fucosylation on the Secondary Rim of beta-Cyclodextrin. Chemistry, 25(27), 6722-6727. https://doi.org/10.1002/chem.201806090

2018

Friedman, R., Khalid, S., Aponte-Santamaría, C., Arutyunova, E., Becker, M., Boyd, K. J., ... Domene, C. (2018). Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. Journal of membrane biology, 251(5-6), 609-631. https://doi.org/10.1007/s00232-018-0050-y
Thallmair, S., Ingólfsson, H. I., & Marrink, S. J. (2018). Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models. The Journal of Physical Chemistry Letters, 9(18), 5527-5533. https://doi.org/10.1021/acs.jpclett.8b01877
Zhang, M., Peyear, T., Patmanidis, I., Greathouse, D. V., Marrink, S. J., Andersen, O. S., & Ingólfsson, H. I. (2018). Fluorinated Alcohols' Effects on Lipid Bilayer Properties. Biophysical Journal, 115(4), 679-689. https://doi.org/10.1016/j.bpj.2018.07.010
Xue, M., Cheng, L., Faustino, I., Guo, W., & Marrink, S. J. (2018). Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers. Biophysical Journal, 115(3), 494-502. https://doi.org/10.1016/j.bpj.2018.06.018
Baoukina, S., Ingolfsson, H. I., Marrink, S. J., & Tieleman, D. P. (2018). Curvature-Induced Sorting of Lipids in Plasma Membrane Tethers. Advanced theory and simulations, 1(8), [1800034]. https://doi.org/10.1002/adts.201800034
Grunewald, F., Rossi, G., De Vries, A. H., Marrink, S. J., & Monticelli, L. (2018). A Transferable MARTINI Model of Polyethylene Oxide. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 122(29), 7436-7449. https://doi.org/10.1021/acs.jpcb.8b04760
Corradi, V., Mendez-Villuendas, E., Ingólfsson, H. I., Gu, R-X., Siuda, I., Melo, M. N., ... Tieleman, D. P. (2018). Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins. ACS central science, 4(6), 709-717. https://doi.org/10.1021/acscentsci.8b00143
Su, J., Thomas, A. S., Grabietz, T., Landgraf, C., Volkmer, R., Marrink, S. J., ... Melo, M. N. (2018). The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission. Biochimica et biophysica acta, 1860(6), 1292-1300. https://doi.org/10.1016/j.bbamem.2018.02.029
Frederix, P. W. J. M., Patmanidis, I., & Marrink, S. J. (2018). Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chemical Society Reviews, 47(10), 3470-3489. https://doi.org/10.1039/c8cs00040a
Sun, F., Schroer, C. F. E., Xu, L., Yin, H., Marrink, S. J., & Luo, S-Z. (2018). Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2. Biophysical Journal, 114(8), 1858-1868. https://doi.org/10.1016/j.bpj.2018.02.034
Zavadlav, J., Marrink, S. J., & Praprotnik, M. (2018). Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm. Journal of Chemical Theory and Computation, 14(3), 1754-1761. https://doi.org/10.1021/acs.jctc.7b01129
Liu, J., Qiu, L., Alessandri, R., Qiu, X., Portale, G., Dong, J., ... Koster, L. J. A. (2018). Enhancing Molecular n-Type Doping of Donor-Acceptor Copolymers by Tailoring Side Chains. Advanced materials, 30(7), [1704630]. https://doi.org/10.1002/adma.201704630
Thallmair, S., Vainikka, P. A., & Marrink, S. (2018). Molecular Dynamcis of Light-Harvesting Complex II Embedded in the Thylakoid Membrane. Biophysical Journal, 114(3, Suppl. 1), 522a. https://doi.org/10.1016/j.bpj.2017.11.2853
Bruininks, B. M., Telles De Souza, P. C., & Marrink, S. J. (2018). Microscopic View on Non-viral Mediated Transfection. Biophysical Journal, 114(3, Suppl. 1), 602a. [2989]. https://doi.org/10.1016/j.bpj.2017.11.3292
Souza, P. C. T., Wassenaar, T. A., Skaf, M. S., & Marrink, S. J. (2018). TLR4 Recruitment into Lipid Rafts Studied by Coarse Grained MD Simulation. Biophysical Journal, 114(3), 72a. [370]. https://doi.org/10.1016/j.bpj.2017.11.440
Piskorz, T. K., de Vries, A. H., De Feyter, S., & van Esch, J. H. (2018). Mechanism of Ostwald Ripening in 2D Physisorbed Assemblies at Molecular Time and Length Scale by Molecular Dynamics Simulations. Journal of Physical Chemistry C, 122(42), 24380-24385. https://doi.org/10.1021/acs.jpcc.8b06432
Lubbe, A. S., Liu, Q., Smith, S. J., de Vries, J. W., Kistemaker, J. C. M., De Vries, A. H., ... Feringa, B. L. (2018). Photoswitching of DNA Hybridization Using a Molecular Motor. Journal of the American Chemical Society, 140(15), 5069-5076. [jacs.7b09476]. https://doi.org/10.1021/jacs.7b09476
Yildirim, A., Wassenaar, T. A., & van der Spoel, D. (2018). Statistical efficiency of methods for computing free energy of hydration. Journal of Chemical Physics, 149(14), [144111]. https://doi.org/10.1063/1.5041835
Jayaraman, K., Morley, A. N., Szollosi, D., Wassenaar, T. A., Sitte, H. H., & Stockner, T. (2018). Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain. PLoS Computational Biology, 14(6), [1006229]. https://doi.org/10.1371/journal.pcbi.1006229

2017

Groves, M. R., Schroer, C. F. E., Middleton, A. J., Lunev, S., Danda, N., Ali, A. M., ... Williams, C. (2018). Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex. Biochemical and Biophysical Research Communications, 496(2), 562-567. https://doi.org/10.1016/j.bbrc.2017.12.150
Periole, X., Huber, T., Bonito-Oliva, A., Aberg, K. C., van der Wel, P. C. A., Sakmar, T. P., & Marrink, S. J. (2018). Energetics Underlying Twist Polymorphisms in Amyloid Fibrils. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 122(3), 1081–1091. https://doi.org/10.1021/acs.jpcb.7b10233
Nedergaard Pedersen, J., Wilhelmus Johannes Maria Frederix, P., Skov Pedersen, J., Marrink, S. J., & Otzen, D. (2018). Role of charge and hydrophobicity in liprotide formation: A molecular dynamics study with experimental constraints. ChemBioChem, 19, 263–271. https://doi.org/10.1002/cbic.201700496
Van Eerden, F. J., Melo, M. N., Frederix, P. W. J. M., & Marrink, S. J. (2017). Prediction of Thylakoid Lipid Binding Sites on Photosystem II. Biophysical Journal, 113(12), 2669-2681. https://doi.org/10.1016/j.bpj.2017.09.039
Faustino, I., & Marrink, S. J. (2017). cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. Bioinformatics, 33(23), 3813-3815. [btx444]. https://doi.org/10.1093/bioinformatics/btx444
Kondela, T., Gallová, J., Hauß, T., Barnoud, J., Marrink, S-J., & Kučerka, N. (2017). Alcohol Interactions with Lipid Bilayers. Molecules, 22(12), [2078]. https://doi.org/10.3390/molecules22122078
Ingólfsson, H. I., Carpenter, T. S., Bhatia, H., Bremer, P-T., Marrink, S. J., & Lightstone, F. C. (2017). Computational Lipidomics of the Neuronal Plasma Membrane. Biophysical Journal, 113(10), 2271-2280. [j.bpj.2017.10.017]. https://doi.org/10.1016/j.bpj.2017.10.017
Qiu, L., Liu, J., Alessandri, R., Qiu, X., Koopmans, M., Havenith, R. W. A., ... Hummelen, J. C. (2017). Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics. Journal of Materials Chemistry A, 5(40), 21234-21241. https://doi.org/10.1039/c7ta06609k
Hsu, P-C., Bruininks, B. M. H., Jefferies, D., Cesar Telles de Souza, P., Lee, J., Patel, D. S., ... Im, W. (2017). CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. Journal of Computational Chemistry, 38(27), 2354-2363. https://doi.org/10.1002/jcc.24895
Bartelds, R., Barnoud, J., J. Boersma, A., J. Marrink, S., & Poolman, B. (2017). Lipid phase separation in the presence of hydrocarbons in giant unilamellar vesicles. AIMS Biophysics, 4(4), 528-542. https://doi.org/10.3934/biophy.2017.4.528
Uusitalo, J. J., Ingolfsson, H. I., Marrink, S. J., & Faustino, I. (2017). Martini Coarse-Grained Force Field: Extension to RNA. Biophysical Journal, 113(2), 246-256. https://doi.org/10.1016/j.bpj.2017.05.043
Frederix, P. W. J. M., Idé, J., Altay, Y., Schaeffer, G., Surin, M., Beljonne, D., ... Marrink, S. J. (2017). Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles. Acs Nano, 11(8), 7858-7868. https://doi.org/10.1021/acsnano.7b02211
Van Eerden, F. J., Melo, M. N., Frederix, P. W. J. M., Periole, X., & Marrink, S. J. (2017). Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nature Communications, 8, 1-8. [15214]. https://doi.org/10.1038/ncomms15214
Liu, B., Åberg, C., van Eerden, F. J., Marrink, S., Poolman, B., & Boersma, A. J. (2017). Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding. Biophysical Journal, 112(9), 1929-1939. https://doi.org/10.1016/j.bpj.2017.04.004
Gu, R-X., Ingólfsson, H. I., De Vries, A. H., Marrink, S. J., & Tieleman, D. P. (2017). Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations. Journal of Physical Chemistry B, 121(15), 3262–3275. [jpcb.6b07142]. https://doi.org/10.1021/acs.jpcb.6b07142
Venable, R. M., Ingólfsson, H. I., Lerner, M. G., Perrin, B. S., Camley, B. A., Marrink, S. J., ... Pastor, R. W. (2017). Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions. The Journal of Physical Chemistry B, 121(15), 3443–3457. [jpcb.6b09111]. https://doi.org/10.1021/acs.jpcb.6b09111
van Eerden, F. J., van den Berg, T., Frederix, P. W. J. M., de Jong, D. H., Periole, X., & Marrink, S. J. (2017). Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane. Journal of Physical Chemistry B., 121(15), 3237–3249. [jpcb.6b06865]. https://doi.org/10.1021/acs.jpcb.6b06865
Melo, M. N., Arnarez, C., Sikkema, H., Kumar, N., Walko, M., Berendsen, H. J. C., ... Ingólfsson, H. I. (2017). High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. Journal of the American Chemical Society, 139(7), 2664-2671. https://doi.org/10.1021/jacs.6b11091
Alessandri, R., Uusitalo, J. J., De Vries, A. H., Havenith, R. W. A., & Marrink, S. J. (2017). Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations. Journal of the American Chemical Society, 139 (10), 3697–3705. [jacs.6b11717]. https://doi.org/10.1021/jacs.6b11717
Arnarez, C., & Marrink, S. J. (2017). Chapter 1: Computational Microscopy of Mitochondrial Membranes. In K. Kholmurodov (Ed.), Computer Design for New Drugs and Materials: Molecular Dynamics of Nanoscale Phenomena (pp. 1). Nova Science Publishers.
Swier, L. J. Y. M., Monjas, L., Reeßing, F., Oudshoorn, R. C., Aisyah, A., Primke, T., ... Slotboom, D. J. (2017). Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations. MedChemCommun, 8(5), 1121-1130. https://doi.org/10.1039/C7MD00079K
Maingi, V., Burns, J. R., Uusitalo, J. J., Howorka, S., Marrink, S. J., & Sansom, M. S. P. (2017). Stability and dynamics of membrane-spanning DNA nanopores. Nature Communications, 8, 1-12. [14784]. https://doi.org/10.1038/ncomms14784
Kanduc, M., Schlaich, A., de Vries, A. H., Jouhet, J., Marechal, E., Deme, B., ... Schneck, E. (2017). Tight cohesion between glycolipid membranes results from balanced water-headgroup interactions. Nature Communications, 8, [14899]. https://doi.org/10.1038/ncomms14899

2016

Zavadlav, J., Podgornik, R., Melo, M. N., Marrink, S. J., & Praprotnik, M. (2016). Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution. European physical journal-Special topics, 225(8-9), 1595-1607. https://doi.org/10.1140/epjst/e2016-60117-8
Antillón, A., De Vries, A. H., Espinosa-caballero, M., Falcón-gonzález, J. M., Flores Romero, D., González–damián, J., ... Ortega-blake, I. (2016). An Amphotericin B Derivative Equally Potent to Amphotericin B and with Increased Safety. PLoS ONE, 11(9), [e0162171]. https://doi.org/10.1371/journal.pone.0162171
Zavadlav, J., Marrink, S. J., & Praprotnik, M. (2016). Adaptive resolution simulation of supramolecular water: The concurrent making, breaking, and remaking of water bundles. Journal of Chemical Theory and Computation, 12(8), 4138-4145. [6b00536]. https://doi.org/10.1021/acs.jctc.6b00536
Smeets, C. J. L. M., Zmorzynska, J., Melo, M. N., Stargardt, A., Dooley, C., Bakalkin, G., ... Verbeek, D. S. (2016). Altered secondary structure of Dynorphin A associates with loss of opioid signalling and NMDA-mediated excitotoxicity in SCA23. Human Molecular Genetics, 25(13), 2728-2737. https://doi.org/10.1093/hmg/ddw130
Arnarez, C., Marrink, S. J., & Periole, X. (2016). Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes. Chemical Science, 7, 4435-4443. [C5SC04664E]. https://doi.org/10.1039/C5SC04664E
Baoukina, S., Ingolfsson, H. I., Marrink, S. J., & Tieleman, D. P. (2016). Curvature-Induced Lipid Sorting in Plasma Membrane Tethers. Biophysical Journal, 110(3, Suppl. 1), 580A-580A. https://doi.org/10.1016/j.bpj.2015.11.3101
Maingi, V., Uusitalo, J. J., Lelimousin, M., Howorka, S., Marrink, S. J., & Sansom, M. S. P. (2016). DNA-Origami Nanotubes and their Interaction with Membranes: Insights through Multiscale Molecular Dynamics Simulations. Biophysical Journal, 110(3, Suppl. 1), 406A-406A. https://doi.org/10.1016/j.bpj.2015.11.2195
Faustino, I., & Marrink, S-J. (2016). Effects of H2A Histone Variants on DNA Sequence and Nucleosome Structure using Coarse Grain Simulations. Biophysical Journal, 110(3), 561A-561A. https://doi.org/10.1016/j.bpj.2015.11.3002
Gu, R-X., Ingolfsson, H. I., de Vries, A. H., Marrink, S. J., & Tieleman, D. P. (2016). Ganglioside and Protein-Ganglioside Interactions in Martini and Atomistic Molecular Dynamics Simulations. Biophysical Journal, 110(3), 254A-254A. https://doi.org/10.1016/j.bpj.2015.11.1395
Ingolfsson, H. I., Melo, M. N., Baoukina, S., Wassenaar, T. A., Periole, X., de Vries, A. H., ... Marrink, S. J. (2016). In Silico Modeling of Biologically Complex Membranes. Biophysical Journal, 110(3), 83A-83A. https://doi.org/10.1016/j.bpj.2015.11.505
De Jong, D. H., Baoukina, S., Ingólfsson, H., & Marrink, S. J. (2016). Martini straight: Boosting performance using a shorter cutoff and GPUs. Computer Physics Communications, 199, 1-7. https://doi.org/10.1016/j.cpc.2015.09.014
Ingólfsson, H. I., Arnarez, C., Periole, X., & Marrink, S. J. (2016). Computational 'microscopy' of cellular membranes. Journal of Cell Science, 129(2), 257-268. https://doi.org/10.1242/jcs.176040
Guskov, A., Jensen, S., Faustino, I., Marrink, S. J., & Slotboom, D. J. (2016). Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk. Nature Communications, 7, 1-6. [13420]. https://doi.org/10.1038/ncomms13420
Pluhackova, K., Gahbauer, S., Kranz, F., Wassenaar, T. A., & Boeckmann, R. A. (2016). Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4. PLoS Computational Biology, 12(11), [1005169]. https://doi.org/10.1371/journal.pcbi.1005169
Smolyanitsky, A., Yakobson, B. I., Wassenaar, T. A., Paulechka, E., & Kroenlein, K. (2016). A MoS2-Based Capacitive Displacement Sensor for DNA Sequencing. Acs Nano, 10(9), 9009-9016. https://doi.org/10.1021/acsnano.6b05274

2015

Melo, M. N., Ingolfsson, H. I., & Marrink, S. J. (2015). Parameters for Martini sterols and hopanoids based on a virtual-site description. The Journal of Chemical Physics, 143(24), 1-12. [243152]. https://doi.org/10.1063/1.4937783
Uytterhoeven, V., Lauwers, E., Maes, I., Miskiewicz, K., Melo, M. N., Swerts, J., ... Verstreken, P. (2015). Hsc70-4 Deforms Membranes to Promote Synaptic Protein Turnover by Endosomal Microautophagy. Neuron, 88(4), 735-748. https://doi.org/10.1016/j.neuron.2015.10.012
Liguori, N., Periole, X., Marrink, S. J., & Croce, R. (2015). From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII). Scientific Reports, 5, [15661]. https://doi.org/10.1038/srep15661
Qi, Y., Ingolfsson, H. I., Cheng, X., Lee, J., Marrink, S. J., & Im, W. (2015). CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field. Journal of Chemical Theory and Computation, 11(9), 4486-4494. https://doi.org/10.1021/acs.jctc.5b00513
Uusitalo, J. J., Ingolfsson, H. I., Akhshi, P., Tieleman, D. P., & Marrink, S. J. (2015). Martini Coarse-Grained Force Field: Extension to DNA. Journal of Chemical Theory and Computation, 11(8), 3932-3945. https://doi.org/10.1021/acs.jctc.5b00286
Zavadlav, J., Melo, M. N., Marrink, S. J., & Praprotnik, M. (2015). Adaptive resolution simulation of polarizable supramolecular coarse-grained water models. Journal of Chemical Physics, 142(24), [244118]. https://doi.org/10.1063/1.4923008
de Jong, D. H., Liguori, N., van den Berg, T., Arnarez, C., Periole, X., & Marrink, S. J. (2015). Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex. The Journal of Physical Chemistry B, 119(25), 7791-7803. https://doi.org/10.1021/acs.jpcb.5b00809
van Eerden, F. J., de Jong, D. H., de Vries, A. H., Wassenaar, T. A., & Marrink, S. J. (2015). Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. Biochimica et Biophysica Acta-Biomembranes, 1848(6), 1319-1330. https://doi.org/10.1016/j.bbamem.2015.02.025
Wassenaar, T. A., Ingolfsson, H. I., Boeckmann, R. A., Tieleman, D. P., & Marrink, S. J. (2015). Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations. Journal of Chemical Theory and Computation, 11(5), 2144-2155. https://doi.org/10.1021/acs.jctc.5b00209
Wassenaar, T. A., Pluhackova, K., Moussatova, A., Sengupta, D., Marrink, S. J., Tieleman, D. P., & Boeckrnann, R. A. (2015). High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. Journal of Chemical Theory and Computation, 11(5), 2278-2291. https://doi.org/10.1021/ct5010092
Goga, N., Melo, M. N., Rzepiela, A. J., de Vries, A., Hadar, A., Marrink, S. J., & Berendsen, H. (2015). Benchmark of Schemes for Multiscale Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 11(4), 1389-1398. https://doi.org/10.1021/ct501102b
Heberling, M. M., Masman, M. F., Bartsch, S., Wybenga, G. G., Dijkstra, B. W., Marrink, S. J., & Janssen, D. B. (2015). Ironing out Their Differences: Dissecting the Structural Determinants of a Phenylalanine Aminomutase and Ammonia Lyase. ACS chemical biology, 10(4), 989-997. https://doi.org/10.1021/cb500794h
Wijma, H. J., Floor, R. J., Bjelic, S., Marrink, S. J., Baker, D., & Janssen, D. B. (2015). Enantioselective Enzymes by Computational Design and In Silico Screening. Angewandte Chemie - International Edition, 54(12), 3726-3730. https://doi.org/10.1002/anie.201411415
Ingolfsson, H. I., Melo, M. N., Wassenaar, T. A., Periole, X., de Vries, A. H., Tieleman, D. P., & Marrink, S. J. (2015). Computational Lipidomics and the Lipid Organization of Cell Envelopes. Biophysical Journal, 108(2), 342A-342A.
Lopez, C. A., Bellesia, G., Redondo, A., Langan, P., Chundawat, S. P. S., Dale, B. E., ... Gnanakaran, S. (2015). MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers. The Journal of Physical Chemistry B, 119(2), 465-473. https://doi.org/10.1021/jp5105938
Arnarez, C., Uusitalo, J. J., Masman, M. F., Ingolfsson, H. I., de Jong, D. H., Melo, M. N., ... Marrink, S. J. (2015). Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simblations with Implicit Solvent. Journal of Chemical Theory and Computation, 11(1), 260-275. https://doi.org/10.1021/ct500477k
van der Velde, J. H. M., Uusitalo, J. J., Ugen, L-J., Warszawik, E. M., Herrmann, A., Marrink, S. J., & Cordes, T. (2015). Intramolecular photostabilization via triplet-state quenching: design principles to make organic fluorophores "self-healing". Faraday Discussions. https://doi.org/10.1039/c5fd00114e
Paulechka, E., Wassenaar, T., Kroenlein, K., Kazakov, A., & Smolyanitsky, A. (2016). Nucleobase-functionalized grapheme nanoribbons for accurate high-speed DNA sequencing. Nanoscale, 8, 1861-1867. https://doi.org/10.1039/C5NR07061A

2014

Konijnenberg, A., Yilmaz, D., Ingólfsson, H. I., Dimitrova, A., Marrink, S. J., Li, Z., ... Koçer, A. (2014). Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America, 111(48), 17170-17175. https://doi.org/10.1073/pnas.1413118111
van Hell, A., Verheij, M., Marrink, S. J., & Koning, G. (2014). Compounds and their use in therapy. (Patent No. WO2014184726).
Ingólfsson, H. I., Melo, M. N., van Eerden, F. J., Arnarez, C., Lopez, C. A., Wassenaar, T. A., ... Marrink, S. J. (2014). Lipid organization of the plasma membrane. Journal of the American Chemical Society, 136(41), 14554-9. https://doi.org/10.1021/ja507832e
Moiset, G., López, C. A., Bartelds, R., Syga, L., Rijpkema, E., Cukkemane, A., ... Marrink, S. J. (2014). Disaccharides Impact the Lateral Organization of Lipid Membranes. Journal of the American Chemical Society, 136(46), 16167-16175. https://doi.org/10.1021/ja505476c
Barnoud, J., Rossi, G., Marrink, S. J., & Monticelli, L. (2014). Hydrophobic compounds reshape membrane domains. PLoS Computational Biology, 10(10), [e1003873]. https://doi.org/10.1371/journal.pcbi.1003873
Mukherjee, N., Jose, M., Birkner, J. P., Walko, M., Ingolfsson, H. I., Dimitrova, A., ... Kocer, A. (2014). The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension-induced gating. The FASEB Journal, 28(10), 4292-4302. https://doi.org/10.1096/fj.14-251579
Ingólfsson, H. I., Thakur, P., Herold, K. F., Hobart, E. A., Ramsey, N. B., Periole, X., ... Andersen, O. S. (2014). Phytochemicals Perturb Membranes and Promiscuously Alter Protein Function. ACS chemical biology, 9(8), 1788-1798. https://doi.org/10.1021/cb500086e
Milicevic, Z., Marrink, S. J., Smith, A-S., & Smith, D. M. (2014). Establishing conditions for simulating hydrophobic solutes in electric fields by molecular dynamics Effects of the long-range van der Waals treatment on the apparent particle mobility. Journal of Molecular Modeling, 20(8), [2359]. https://doi.org/10.1007/s00894-014-2359-5
Floor, R. J., Wijma, H. J., Colpa, D. I., Ramos-Silva, A., Jekel, P. A., Szymanski, W., ... Janssen, D. B. (2014). Computational Library Design for Increasing Haloalkane Dehalogenase Stability. ChemBioChem, 15(11), 1659-1671. https://doi.org/10.1002/cbic.201402128
Wijma, H. J., Marrink, S. J., & Janssen, D. B. (2014). Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations. Journal of chemical information and modeling, 54(7), 2079-2092. https://doi.org/10.1021/ci500126x
Zavadlav, J., Melo, M. N., Cunha, A. V., de Vries, A. H., Marrink, S. J., & Praprotnik, M. (2014). Adaptive Resolution Simulation of MARTINI Solvents. Journal of Chemical Theory and Computation, 10(6), 2591-2598. https://doi.org/10.1021/ct5001523
Campelo, F., Arnarez, C., Marrink, S. J., & Kozlov, M. M. (2014). Helfrich model of membrane bending: from Gibbs theory of liquid interfaces to membranes as thick anisotropic elastic layers. Progress in Colloid and Interface Science, 208, 25-33. https://doi.org/10.1016/j.cis.2014.01.018
Ingolfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., & Marrink, S. J. (2014). The power of coarse graining in biomolecular simulations. Wiley Interdisciplinary Reviews. Computational Molecular Science, 4(3), 225-248. https://doi.org/10.1002/wcms.1169
Kozlov, M. M., Campelo, F., Liska, N., Chernomordik, L. V., Marrink, S. J., & McMahon, H. T. (2014). Mechanisms shaping cell membranes. Current Opinion in Cell Biology, 29C, 53-60. https://doi.org/10.1016/j.ceb.2014.03.006
Pannuzzo, M., De Jong, D. H., Raudino, A., & Marrink, S. J. (2014). Simulation of polyethylene glycol and calcium-mediated membrane fusion. Journal of Chemical Physics, 140(12), [124905]. https://doi.org/10.1063/1.4869176
Zavadlav, J., Melo, M. N., Marrink, S. J., & Praprotnik, M. (2014). Adaptive resolution simulation of an atomistic protein in MARTINI water. The Journal of Chemical Physics, 140(5), [054114]. https://doi.org/10.1063/1.4863329
Wijma, H. J., Floor, R. J., Jekel, P. A., Baker, D., Marrink, S. J., & Janssen, D. B. (2014). Computationally designed libraries for rapid enzyme stabilization. Protein Engineering, Design & Selection, 27(2), 49-58. https://doi.org/10.1093/protein/gzt061
Wassenaar, T. A., Pluhackova, K., Böckmann, R. A., Marrink, S. J., & Tieleman, D. P. (2014). Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. Journal of Chemical Theory and Computation, 10(2), 676-690. https://doi.org/10.1021/ct400617g
Negro, E., Latsuzbaia, R., de Vries, A. H., & Koper, G. J. M. (2014). Experimental and molecular dynamics characterization of dense micro emulsion systems morphology, conductivity and SAXS. Soft Matter, 10(43), 8685-8697. https://doi.org/10.1039/c4sm01763c
Haverkort, F., Stradomska, A., Vries, A. H. D., & Knoester, J. (2014). First-Principles Calculation of the Optical Properties of an Amphiphilic Cyanine Dye Aggregate. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 118(6), 1012-1023. https://doi.org/10.1021/jp4112487
Boscia, A. L., Treece, B. W., Mohammadyani, D., Klein-Seetharaman, J., Braun, A. R., Wassenaar, T., ... Tristram-Nagle, S. (2014). X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes. Chemistry and physics of lipids, 178, 1-10. https://doi.org/10.1016/j.chemphyslip.2013.12.010

2013

Baaden, M., & Marrink, S. J. (2013). Coarse-grain modelling of protein-protein interactions. Current Opinion in Structural Biology, 23(6), 878-886. https://doi.org/10.1016/j.sbi.2013.09.004
Gobbo, C., Beurroies, I., de Ridder, D., Eelkema, R., Marrink, S. J., De Feyter, S., ... de Vries, A. H. (2013). MARTINI Model for Physisorption of Organic Molecules on Graphite. Journal of Physical Chemistry C, 117(30), 15623-15631. https://doi.org/10.1021/jp402615p
Bulacu, M., Goga, N., Zhao, W., Rossi, G., Monticelli, L., Periole, X., ... Marrink, S. J. (2013). Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 9(8), 3282-3292. https://doi.org/10.1021/ct400219n
Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2013). Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Scientific Reports, 3, [2071]. https://doi.org/10.1038/srep02071
Raudino, A., Marrink, S. J., & Pannuzzo, M. (2013). Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: A theoretical and computational study. Journal of Chemical Physics, 138(23), 234901-1-234901-16. [234901]. https://doi.org/10.1063/1.4809993
van Hell, A. J., Melo, M. N., van Blitterswijk, W. J., Gueth, D. M., Braumuller, T. M., Pedrosa, L. R. C., ... Verheij, M. (2013). Defined lipid analogues induce transient channels to facilitate drug-membrane traversal and circumvent cancer therapy resistance. Scientific Reports, 3, 1-8. [1949]. https://doi.org/10.1038/srep01949
Gomulya, W., Costanzo, G. D., Figueiredo de Carvalho, E., Bisri, S. Z., Derenskyi, V., Fritsch, M., ... Loi, M. A. (2013). Semiconducting single-walled carbon nanotubes on demand by polymer wrapping. Advanced materials, 25(21), 2948-2956. https://doi.org/10.1002/adma.201300267
Moiset, G., Cirac, A. D., Stuart, M. C. A., Marrink, S-J., Sengupta, D., & Poolman, B. (2013). Dual action of BPC194: a membrane active peptide killing bacterial cells. PLoS ONE, 8(4), [e61541]. https://doi.org/10.1371/journal.pone.0061541
Wassenaar, T. A., Ingólfsson, H. I., Priess, M., Marrink, S. J., & Schaefer, L. V. (2013). Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained Biomolecular Simulations. Journal of Physical Chemistry B, 117(13), 3516-3530. https://doi.org/10.1021/jp311533p
Lopez, C. A., Sovova, Z., van Eerden, F. J., de Vries, A. H., & Marrink, S. J. (2013). Martini Force Field Parameters for Glycolipids. Journal of Chemical Theory and Computation, 9(3), 1694-1708. https://doi.org/10.1021/ct3009655
Arnarez, C., Mazat, J-P., Elezgaray, J., Marrink, S-J., & Periole, X. (2013). Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc(1). Journal of the American Chemical Society, 135(8), 3112-3120. https://doi.org/10.1021/ja310577u
Arnarez, C., Marrink, S. J., & Periole, X. (2013). Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Scientific Reports, 3(21), 1263-1-1263-8. [1263]. https://doi.org/10.1038/srep01263
Liang, C., Louhivuori, M., Marrink, S. J., Jansen, T. L. C., & Knoester, J. (2013). Vibrational Spectra of a Mechanosensitive Channel. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4(3), 448-452. https://doi.org/10.1021/jz3019258
de Jong, D. H., Singh, G., Bennett, W. F. D., Arnarez, C., Wassenaar, T. A., Schafer, L. V., ... Marrink, S. J. (2013). Improved Parameters for the Martini Coarse-Grained Protein Force Field. Journal of Chemical Theory and Computation, 9(1), 687-697. https://doi.org/10.1021/ct300646g
Hu, M., de Jong, D. H., Marrink, S. J., & Deserno, M. (2013). Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model. Faraday Discussions, 161, 365-382. https://doi.org/10.1039/c2fd20087b
Smirnova, Y. G., Aeffner, S., Risselada, H. J., Salditt, T., Marrink, S. J., Mueller, M., & Knecht, V. (2013). Interbilayer repulsion forces between tension-free lipid bilayers from simulation. Soft Matter, 9(45), 10705-10718. https://doi.org/10.1039/c3sm51771c
de Jong, D. H., Lopez, C. A., & Marrink, S. J. (2013). Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Faraday Discussions, 161, 347-363. https://doi.org/10.1039/c2fd20086d
Marrink, S. J., & Tieleman, D. P. (2013). Perspective on the Martini model. Chemical Society Reviews, 42(16), 6801-6822. https://doi.org/10.1039/c3cs60093a
Periole, X., & Marrink, S. J. (2013). The Martini Coarse-Grained Force Field. In L. Monticelli, & E. Salonen (Eds.), Biomolecular Simulations: Methods and Protocols (1 ed., Vol. 1, pp. 533-565). (Methods in Molecular Biology; Vol. 924). Springer International Publishing. https://doi.org/10.1007/978-1-62703-017-5
Haverkort, F., Stradomska, A., de Vries, A. H., & Knoester, J. (2013). Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations. Journal of Physical Chemistry B, 117(19), 5857-5867. https://doi.org/10.1021/jp4005696

2012

Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2012). Amylose folding under the influence of lipids. Carbohydrate Research, 364, 1-7. https://doi.org/10.1016/j.carres.2012.10.007
Goga, N., Rzepiela, A. J., de Vries, A. H., Marrink, S. J., & Berendsen, H. J. C. (2012). Efficient Algorithms for Langevin and DPD Dynamics. Journal of Chemical Theory and Computation, 8(10), 3637-3649. https://doi.org/10.1021/ct3000876
Vandersteen, A., Masman, M. F., Baets, G. D., Jonckheere, W., Werf, K. V. D., Marrink, S. J., ... Broersen, K. (2012). Molecular plasticity regulates oligomerization and cytotoxicity of the multipeptide-length amyloid-β peptide pool. The Journal of Biological Chemistry, 287(44), 36732-36743. https://doi.org/10.1074/jbc.M112.394635
Deplazes, E., Louhivuori, M., Jayatilaka, D., Marrink, S. J., & Corry, B. (2012). Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations. PLoS Computational Biology, 8(9), [e1002683]. https://doi.org/10.1371/journal.pcbi.1002683
Periole, X., Knepp, A. M., Sakmar, T. P., Marrink, S. J., & Huber, T. (2012). Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers. Journal of the American Chemical Society, 134(26), 10959-10965. https://doi.org/10.1021/ja303286e
Risselada, H. J., Marelli, G., Fuhrmans, M., Smirnova, Y. G., Grubmueller, H., Marrink, S. J., & Mueller, M. (2012). Line-Tension Controlled Mechanism for Influenza Fusion. PLoS ONE, 7(6), [e38302]. https://doi.org/10.1371/journal.pone.0038302
Baoukina, S., Marrink, S. J., & Tieleman, D. P. (2012). Molecular Structure of Membrane Tethers. Biophysical Journal, 102(8), 1866-1871. https://doi.org/10.1016/j.bpj.2012.03.048
Domanski, J., Marrink, S. J., & Schäfer, L. V. (2012). Transmembrane helices can induce domain formation in crowded model membranes. Biochimica et Biophysica Acta-Biomembranes, 1818(4), 984-994. https://doi.org/10.1016/j.bbamem.2011.08.021
Knepp, A. M., Periole, X., Marrink, S-J., Sakmar, T. P., & Huber, T. (2012). Rhodopsin Forms a Dimer with Cytoplasmic Helix 8 Contacts in Native Membranes. Biochemistry, 51(9), 1819-1821. https://doi.org/10.1021/bi3001598
de Jong, D. H., Periole, X., & Marrink, S. J. (2012). Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields. Journal of Chemical Theory and Computation, 8(3), 1003-1014. https://doi.org/10.1021/ct200599d
Huber, T., Periole, X., Knepp, A. M., Marrink, S-J., Mukhopadhyay, P., & Sakmar, T. P. (2012). Dynamic Assembly of the Receptor-G-Protein Signaling Complex. Biophysical Journal, 102(3), 516a-516a. [2930]. https://doi.org/10.1016/j.bpj.2011.11.2823
Wassenaar, T. A., Schafer, L. V., Ingolfsson, H., & Marrink, S-J. (2012). Mixing Martinis: Atomistic Simulations of MscL in a Coarse Grained Environment. Biophysical Journal, 102(3), 241a-241a. https://doi.org/10.1016/j.bpj.2011.11.1326
Periole, X., Knepp, A. M., Sakmar, T. P., Marrink, S-J., & Huber, T. (2012). Probing the Receptor Dimer Interfaces of G-Protein Coupled Receptor in Model Membranes. Biophysical Journal, 102(3), 515a-516a. https://doi.org/10.1016/j.bpj.2011.11.2822
Fuhrmans, M., & Marrink, S. J. (2012). Molecular View of the Role of Fusion Peptides in Promoting Positive Membrane Curvature. Journal of the American Chemical Society, 134(3), 1543-1552. https://doi.org/10.1021/ja207290b
Bulacu, M., Periole, X., Marrink, S. J., & Périole, X. (2012). In Silico Design of Robust Bolalipid Membranes. Biomacromolecules, 13(1), 196-205. https://doi.org/10.1021/bm201454J
Goga, N., Marrink, S., Cioromela, R., & Moldoveanu, F. (2012). GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations. In Proceedings of the 2012 IEEE 12th International Conference on Bioinformatics (pp. 251-254). IEEE (The Institute of Electrical and Electronics Engineers).
Goga, N., Rzepiela, A., de Sousa Pereira Simoes de Melo, M., de Vries, A., Hadar, A., Markvoort, A. J., ... Berendsen, H. (2012). Methods for multiscale modeling of membranes. In A. Iglic (Ed.), Advances in Planar Lipid Bilayers and Liposomes (Vol. 15, pp. 139-170). Academic Press. https://doi.org/10.1016/B978-0-12-396533-2.00003-3
van Dijk, M., Wassenaar, T. A., & Bonvin, A. M. J. J. (2012). A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 8(10), 3463-3472. https://doi.org/10.1021/ct300102d
Wassenaar, T. A., de Vries, S., Bonvin, A. M. J. J., & Bekker, H. (2012). SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions. Journal of Chemical Theory and Computation, 8(10), 3618-3627. https://doi.org/10.1021/ct3000662

2011

Velinova, M., Sengupta, D., Tadjer, A. V., & Marrink, S-J. (2011). Sphere-to-Rod Transitions of Nonionic Surfactant Micelles in Aqueous Solution Modeled by Molecular Dynamics Simulations. Langmuir, 27(23), 14071-14077. https://doi.org/10.1021/la203055t
Sørensen, J., Periole, X., Skeby, K. K., Marrink, S-J., & Schiøtt, B. (2011). Protofibrillar Assembly Toward the Formation of Amyloid Fibrils. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2(19), 2385-2390. https://doi.org/10.1021/jz2010094
Mika, J. T., Moiset, G., Cirac, A. D., Feliu, L., Bardaji, E., Planas, M., ... Poolman, B. (2011). Structural basis for the enhanced activity of cyclic antimicrobial peptides: The case of BPC194. Biochimica et Biophysica Acta-Biomembranes, 1808(9), 2197-2205. https://doi.org/10.1016/j.bbamem.2011.05.001
Klacsova, M., Bulacu, M., Kucerka, N., Uhrikova, D., Teixeira, J., Marrink, S. J., & Balgavy, P. (2011). The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles - A small-angle neutron scattering and molecular dynamics study. Biochimica et Biophysica Acta-Biomembranes, 1808(9), 2136-2146. https://doi.org/10.1016/j.bbamem.2011.04.010
De Jong, D. H., Schafer, L. V., De Vries, A. H., Marrink, S. J., Berendsen, H. J. C., & Grubmueller, H. (2011). Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations. Journal of Computational Chemistry, 32(9), 1919-1928. https://doi.org/10.1002/jcc.21776
Fuhrmans, M., & Marrink, S-J. (2011). A tool for the morphological analysis of mixtures of lipids and water in computer simulations. Journal of Molecular Modeling, 17(7), 1755-1766. https://doi.org/10.1007/s00894-010-0858-6
Cirac, A. D., Moiset, G., Mika, J. T., Kocer, A., Salvador, P., Poolman, B., ... Sengupta, D. (2011). The Molecular Basis for Antimicrobial Activity of Pore-Forming Cyclic Peptides. Biophysical Journal, 100(10), 2422-2431. https://doi.org/10.1016/j.bpj.2011.03.057
Westerbeek, A., Szymanski, W., Wijma, H. J., Marrink, S., Feringa, B. L., & Janssen, D. B. (2011). Kinetic resolution of α-bromoamides: Experimental and theoretical investigation of highly enantioselective reactions catalyzed by haloalkane dehalogenases. Advanced Synthesis & Catalysis, 353(6), 931-944. https://doi.org/10.1002/adsc.201000726
Ollila, O. H. S., Louhivuori, M., Marrink, S. J., & Vattulainen, I. (2011). Protein Shape Change Has a Major Effect on the Gating Energy of a Mechanosensitive Channel. Biophysical Journal, 100(7), 1651-1659. https://doi.org/10.1016/j.bpj.2011.02.027
Risselada, H. J., Marrink, S. J., & Mueller, M. (2011). Curvature-Dependent Elastic Properties of Liquid-Ordered Domains Result in Inverted Domain Sorting on Uniaxially Compressed Vesicles. Physical Review Letters, 106(14), 148102-1-148102-4. [148102]. https://doi.org/10.1103/PhysRevLett.106.148102
Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2011). Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction. PLoS Computational Biology, 7(3), [e1002020]. https://doi.org/10.1371/journal.pcbi.1002020
Schaefer, L. V., de Jong, D. H., Holt, A., Rzepiela, A. J., de Vries, A. H., Poolman, B., ... Marrink, S. J. (2011). Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proceedings of the National Academy of Sciences of the United States of America, 108(4), 1343-1348. https://doi.org/10.1073/pnas.1009362108
Rzepiela, A. J., Louhivuori, M., Peter, C., & Marrink, S. J. (2011). Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Physical Chemistry Chemical Physics, 13(22), 10437-10448. https://doi.org/10.1039/c0cp02981e
Markvoort, A. J., & Marrink, S. J. (2011). Lipid Acrobatics in the Membrane Fusion Arena. In L. V. Chernomordik, & M. M. Kozlov (Eds.), Membrane Fusion (68 ed., pp. 259-294). (Current Topics in Membranes; Vol. 68). SAN DIEGO: Academic Press. https://doi.org/10.1016/B978-0-12-385891-7.00011-8
Murtola, T., Vuorela, T. A., Hyvonen, M. T., Marrink, S-J., Karttunen, M., & Vattulainen, I. (2011). Low density lipoprotein: structure, dynamics, and interactions of apoB-100 with lipids. Soft Matter, 7(18), 8135-8141. https://doi.org/10.1039/c1sm05367a

2010

Schafer, L. V., & Marrink, S. J. (2010). Partitioning of Lipids at Domain Boundaries in Model Membranes. Biophysical Journal, 99(12), L91-L93. https://doi.org/10.1016/j.bpj.2010.08.072
Louhivuori, M., Risselada, H., Giessen, E. V. D., & Marrink, S. J. (2010). Release of content through mechano-sensitive gates in pressurized liposomes. Proceedings of the National Academy of Sciences of the United States of America, 107(46), 19856-19860. https://doi.org/10.1073/pnas.1001316107
Vuorela, T., Catte, A., Niemela, P. S., Hall, A., Hyvonen, M. T., Marrink, S-J., ... Vattulainen, I. (2010). Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Computational Biology, 6(10), [e1000964]. https://doi.org/10.1371/journal.pcbi.1000964
Polyansky, A. A., Ramaswamy, R., Volynsky, P. E., Sbalzarini, I. F., Marrink, S. J., & Efremov, R. G. (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1(20), 3108-3111. https://doi.org/10.1021/jz101163e
Ramadurai, S., Holt, A., Schafer, L. V., Krasnikov, V. V., Rijkers, D. T. S., Marrink, S. J., ... Poolman, B. (2010). Influence of Hydrophobic Mismatch and Amino Acid Composition on the Lateral Diffusion of Transmembrane Peptides. Biophysical Journal, 99(5), 1447-1454. https://doi.org/10.1016/j.bpj.2010.05.042
Kucerka, N., Marquardt, D., Harroun, T. A., Nieh, M. P., Wassall, S. R., de Jong , D. H., ... Katsaras, J. (2010). Cholesterol in Bilayers with PUFA Chains: Doping with DMPC or POPC Results in Sterol Reorientation and Membrane-Domain Formation. Biochemistry, 49(35), 7485-7493. https://doi.org/10.1021/bi100891z
Lycklama a Nijeholt, J. A., Bulacu, M., Marrink, S. J., & Driessen, A. J. M. (2010). Immobilization of the Plug Domain Inside the SecY Channel Allows Unrestricted Protein Translocation. The Journal of Biological Chemistry, 285(31), 23747 - 23754. https://doi.org/10.1074/jbc.M110.124636
Yesylevskyy, S. O., Schafer, L. V., Sengupta, D., & Marrink, S. J. (2010). Polarizable Water Model for the Coarse-Grained MARTINI Force Field. PLoS Computational Biology, 6(6), [e1000810]. https://doi.org/10.1371/journal.pcbi.1000810
Smirnova, Y. G., Marrink, S-J., Lipowsky, R., & Knecht, V. (2010). Solvent-Exposed Tails as Prestalk Transition States for Membrane Fusion at Low Hydration. Journal of the American Chemical Society, 132(19), 6710-6718. https://doi.org/10.1021/ja910050x
Rzepiela, A. J., Schafer, L. V., Goga, N., Risselada, H. J., De Vries, A. H., & Marrink, S. J. (2010). Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures. Journal of Computational Chemistry, 31(6), 1333-1343. https://doi.org/10.1002/jcc.21415
Fuhrmans, M., Sanders, B. P., Marrink, S-J., & de Vries, A. H. (2010). Effects of bundling on the properties of the SPC water model. Theoretical Chemistry Accounts, 125(3-6), 335-344. https://doi.org/10.1007/s00214-009-0590-4
Marrink, S. J., Periole, X., Tieleman, D. P., & de Vries, A. H. (2010). Comment on "On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models'' by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934. Physical Chemistry Chemical Physics, 12(9), 2254-2256. https://doi.org/10.1039/b915293h
Apajalahti, T., Niemela, P., Govindan, P. N., Miettinen, M. S., Salonen, E., Marrink, S-J., & Vattulainen, I. (2010). Concerted diffusion of lipids in raft-like membranes. Faraday Discussions, 144, 411-430. https://doi.org/10.1039/b901487j
Baoukina, S., Marrink, S. J., & Tieleman, D. P. (2010). Lateral pressure profiles in lipid monolayers. Faraday Discussions, 144(8), 393-409. https://doi.org/10.1039/b905647e
Sengupta, D., & Marrink, S. J. (2010). Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes. Physical Chemistry Chemical Physics, 12(40), 12987-12996. https://doi.org/10.1039/c0cp00101e
Rzepiela, A. J., Sengupta, D., Goga, N., & Marrink, S. J. (2010). Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions. Faraday Discussions, 144(12), 431-443. https://doi.org/10.1039/b901615e
Horta, B. A. C., de Vries, A. H., & Hunenberger, P. H. (2010). Simulating the Transition between Gel and Liquid-Crystal Phases of Lipid Bilayers: Dependence of the Transition Temperature on the Hydration Level. Journal of Chemical Theory and Computation, 6(8), 2488-2500. https://doi.org/10.1021/ct100200w

2009

Hinner, M. J., Marrink, S-J., & de Vries, A. H. (2009). Location, Tilt, and Binding: A Molecular Dynamics Study of Voltage-Sensitive Dyes in Biomembranes. Journal of Physical Chemistry B, 113(48), 15807-15819. https://doi.org/10.1021/jp907981y
Lopez, C. A., Rzepiela, A. J., de Vries, A. H., Dijkhuizen, L., Huenenberger, P. H., & Marrink, S. J. (2009). Martini Coarse-Grained Force Field: Extension to Carbohydrates. Journal of Chemical Theory and Computation, 5(12), 3195-3210. https://doi.org/10.1021/ct900313w
Sengupta, D., Rampioni, A., & Marrink, S-J. (2009). Simulations of the c-subunit of ATP-synthase reveal helix rearrangements. Molecular Membrane Biology, 26(8), 422-434. https://doi.org/10.3109/09687680903321073
Esteban-Martin, S., Risselada, H. J., Salgado, J., & Marrink, S. J. (2009). Stability of asymmetric lipid bilayers assessed by molecular dynamics simulations. Journal of the American Chemical Society, 131(42), 15194-15202. https://doi.org/10.1021/ja904450t
Lee, H., de Vries, A. H., Marrink, S-J., & Pastor, R. W. (2009). A Coarse-Grained Model for Polyethylene Oxide and Polyethylene Glycol: Conformation and Hydrodynamics. Journal of Physical Chemistry B, 113(40), 13186-13194. https://doi.org/10.1021/jp9058966
Kucerka, N., Gallova, J., Uhrikova, D., Balgavy, P., Bulacu, M. I., Marrink, S. J., & Katsaras, J. (2009). Areas of monounsaturated diacylphosphatidylcholines. Biophysical Journal, 97(7), 1926-1932. https://doi.org/10.1016/j.bpj.2009.06.050
Bennett, W. F. D., MacCallum, J. L., Hinner, M. J., Marrink, S. J., & Tieleman, D. P. (2009). Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments. Journal of the American Chemical Society, 131(35), 12714-12720. https://doi.org/10.1021/ja903529f
Periole, X., Cavalli, M., Marrink, S-J., & Ceruso, M. A. (2009). Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. Journal of Chemical Theory and Computation, 5(9), 2531-2543. https://doi.org/10.1021/ct9002114
Goga, N., Costache, S., & Marrink, S. (2009). New Gromacs Implementations for Multiscaling Space MD. Materiale Plastice, 46(3), 220-223.
Masman, M. F., Eisel, U. L. M., Csizmadia, I. G., Penke, B., Enriz, R. D., Marrink, S. J., & Luiten, P. G. M. (2009). In Silico Study of Full-Length Amyloid β 1-42 Tri- and Penta-Oligomers in Solution. Journal of Physical Chemistry B., 113(34), 11710-11719. https://doi.org/10.1021/jp901057w
Fuhrmans, M., Knecht, V., & Marrink, S. J. (2009). A Single Bicontinuous Cubic Phase Induced by Fusion Peptides. Journal of the American Chemical Society, 131(26), 9166-+. https://doi.org/10.1021/ja903224q
Yesylevskyy, S., Marrink, S-J., & Mark, A. E. (2009). Alternative Mechanisms for the Interaction of the Cell-Penetrating Peptides Penetratin and the TAT Peptide with Lipid Bilayers. Biophysical Journal, 97(1), 40-49. https://doi.org/10.1016/j.bpj.2009.03.059
Berntsson, R. P-A., Doeven, M. K., Fusetti, F., Duurkens, R. H., Sengupta, D., Marrink, S-J., ... Slotboom, D-J. (2009). The structural basis for peptide selection by the transport receptor OppA. EMBO Journal, 28(9), 1332-1340. https://doi.org/10.1038/emboj.2009.65
Siwko, M. E., de Vries, A. H., Mark, A. E., Kozubek, A., & Marrink, S. J. (2009). Disturb or Stabilize? A Molecular Dynamics Study of the Effects of Resorcinolic Lipids on Phospholipid Bilayers. Biophysical Journal, 96(8), 3140-3153. https://doi.org/10.1016/j.bpj.2009.01.040
Ollila, O. H. S., Risselada, H. J., Louhivuori, M., Lindahl, E., Vattulainen, I., & Marrink, S. J. (2009). 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes. Physical Review Letters, 102(7-20), [078101]. https://doi.org/10.1103/physrevlett.102.078101
Marrink, S. J., de Vries, A. H., & Tieleman, D. P. (2009). Lipids on the move: Simulations of membrane pores, domains, stalks and curves. Biochimica et Biophysica Acta-Biomembranes, 1788(1), 149-168. https://doi.org/10.1016/j.bbamem.2008.10.006
Goga, N., Costache, S., & Marrink, S. (2009). A Multiscalling Constant Lambda Molecular Dynamic Gromacs Implementation. Materiale Plastice, 46(1), 53-57.
Risselada, H. J., & Marrink, S. J. (2009). Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations. Physical Chemistry Chemical Physics, 11(12), 2056-2067. https://doi.org/10.1039/b818782g
Louhivuori, M., Risselada, J., Giessen, E. V. D., & Marrink, S-J. (2009). MscL Gating In Liposomes. 254a-254a.
Baoukina, S., Marrink, S. J., & Tieleman, D. P. (2009). Structure and dynamics of lipid monolayers: theory and applications. In R. Faller, M. Longo, S. Risbud, & T. Jue (Eds.), Biomembrane Frontiers (pp. 75 - 99). (HANDBOOK OF MODERN BIOPHYSICS Series). Humana Press. https://doi.org/10.1007/978-1-60761-314-5_3
Risselada, H. J., & Marrink, S. J. (2009). The freezing process of small lipid vesicles at molecular resolution. Soft Matter, 5(22), 4531-4541. https://doi.org/10.1039/b913210d
Winger, M., de Vries, A. H., & van Gunsteren, W. F. (2009). Force-field dependence of the conformational properties of ,-dimethoxypolyethylene glycol. Molecular Physics, 107(13), 1313-1321. [911054506]. https://doi.org/10.1080/00268970902794826
Wassenaar, T. A., Daura, X., Padros, E., & Mark, A. E. (2009). Calcium binding to the purple membrane: A molecular dynamics study. Proteins, 74(3), 669-681. https://doi.org/10.1002/prot.22182

2008

Risselada, H. J., & Marrink, S. J. (2008). The molecular face of lipid rafts in model membranes. Proceedings of the National Academy of Sciences of the United States of America, 105(45), 17367-17372. https://doi.org/10.1073/pnas.0807527105
Sengupta, D., Leontiadou, H., Mark, A. E., & Marrink, S-J. (2008). Toroidal pores formed by antimicrobial peptides show significant disorder. Biochimica et Biophysica Acta-Biomembranes, 1778(10), 2308-2317. https://doi.org/10.1016/j.bbamem.2008.06.007
Baoukina, S., Monticelli, L., Risselada, H. J., Marrink, S. J., & Tieleman, D. P. (2008). The molecular mechanism of lipid monolayer collapse. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10803-10808. https://doi.org/10.1073/pnas.0711563105
Risselada, H. J., Mark, A. E., & Marrink, S. J. (2008). Application of mean field boundary potentials in simulations of lipid vesicles. Journal of Physical Chemistry B, 112(25), 7438-7447. https://doi.org/10.1021/jp0758519
Monticelli, L., Kandasamy, S. K., Periole, X., Larson, R. G., Tieleman, D. P., & Marrink, S-J. (2008). The MARTINI coarse-grained force field: Extension to proteins. Journal of Chemical Theory and Computation, 4(5), 819-834. https://doi.org/10.1021/ct700324x
Yefimov, S., Giessen, E. V. D., Onck, P. R., & Marrink, S. J. (2008). Mechanosensitive membrane channels in action. Biophysical Journal, 94(8), 2994-3002. https://doi.org/10.1529/biophysj.107.119966
Treptow, W., Marrink, S. J., & Tarek, M. (2008). Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. Journal of Physical Chemistry B., 112(11), 3277-3282. https://doi.org/10.1021/jp709675e
Catte, A., Patterson, J. C., Bashtovyy, D., Jones, M. K., Gu, F., Li, L., ... Segrest, J. P. (2008). Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations. Biophysical Journal, 94(6), 2306-2319. https://doi.org/10.1529/biophysj.107.115857
Knecht, V., Risselada, H. J., Mark, A. E., & Marrink, S. J. (2008). Electrophoretic mobility does not always reflect the charge on an oil droplet. Journal of Colloid and Interface Science, 318(2), 477-486. https://doi.org/10.1016/j.jcis.2007.10.035
Marrink, S. J., de Vries, A. H., Harroun, T. A., Katsaras, J., & Wassall, S. R. (2008). Cholesterol shows preference for the interior of polyunsaturated lipid. Journal of the American Chemical Society, 130(1), 10 - 11. https://doi.org/10.1021/ja076641c
Marrink, S. J., Fuhrmans, M., Risselada, H. J., & Periole, X. (2008). The MARTINI force field. In G. Voth (Ed.), Coarse graining of condensed phase and biomolecular systems (pp. 2). CRC Press.
Wassenaar, T. A., Quax, W. J., & Mark, A. E. (2008). The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: A molecular dynamics study. Proteins-Structure Function and Bioinformatics, 70(2), 333-343. https://doi.org/10.1002/prot.21541

2007

Baoukina, S., Monticelli, L., Marrink, S. J., & Tieleman, D. P. (2007). Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir, 23(25), 12617-12623. https://doi.org/10.1021/la702286h
Periole, X., Huber, T., Marrink, S-J., & Sakmar, T. P. (2007). G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. Journal of the American Chemical Society, 129(33), 10126-10132. https://doi.org/10.1021/ja0706246
Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H. (2007). The MARTINI force field: Coarse grained model for biomolecular simulations. Journal of Physical Chemistry B, 111(27), 7812-7824. https://doi.org/10.1021/jp071097f
Leontiadou, H., Mark, A. E., & Marrink, S-J. (2007). Ion transport across transmembrane pores. Biophysical Journal, 92(12), 4209-4215. https://doi.org/10.1529/biophysj.106.101295
Knecht, V., & Marrink, S-J. (2007). Molecular dynamics simulations of lipid vesicle fusion in atomic detail. Biophysical Journal, 92(12), 4254-4261. https://doi.org/10.1529/biophysj.106.103572
Baron, R., Trzesniak, D., de Vries, A. H., Elsener, A., Marrink, S. J., & van Gunsteren, W. F. (2007). Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. Chemphyschem, 8(3), 452 - 461. https://doi.org/10.1002/cphc.200600658
van den Bogaart, G., Hermans, N., Krasnikov, V., de Vries, A. H., & Poolman, B. (2007). On the decrease in lateral mobility of phospholipids by sugars. Biophysical Journal, 92(5), 1598-1605. https://doi.org/10.1529/biophysj.106.096461
Villa, A., Fan, H., Wassenaar, T., & Mark, A. E. (2007). How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field? Journal of Physical Chemistry B, 111(21), 6015-6025. https://doi.org/10.1021/jp068580v

2006

Siwko, M. E., Marrink, S. J., de Vries, A. H., Arkadiusz, K., Schoot Uiterkamp, A. J. M., & Mark, A. E. (2007). Does isoprene protect plant membranes for thermal shock? A molecular dynamics study. Biochimica et Biophysica Acta-Biomembranes, 1768(2), 198-206. https://doi.org/10.1016/j.bbamem.2006.09.023
Tieleman, D. P., & Marrink, S-J. (2006). Lipids out of equilibrium: Energetics of desorption and pore mediated flip-flop. Journal of the American Chemical Society, 128(38), 12462-12467. https://doi.org/10.1021/ja0624321
Leontiadou, H., Mark, A. E., & Marrink, S. J. (2006). Antimicrobial peptides in action. Journal of the American Chemical Society, 128(37), 12156-12161. https://doi.org/10.1021/ja062927q
Knecht, V., Mark, A. E., & Marrink, S-J. (2006). Phase Behavior of a Phospholipid/Fatty Acid/Water Mixture Studied in Atomic Detail. Journal of the American Chemical Society, 128(6), 2030 - 2034. https://doi.org/10.1021/ja056619o
Hozoi, L., de Vries, A. H., Broer, R., de Graaf, C., & Bagus, P. S. (2006). Ni 3s-hole states in NiO by non-orthogonal configuration interaction. Chemical Physics, 331(1), 178-185. https://doi.org/10.1016/j.chemphys.2006.10.015
Baron, R., de Vries, A. H., Huenenberger, P. H., & van Gunsteren, W. F. (2006). Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. Journal of Physical Chemistry B, 110(31), 15602-15614. https://doi.org/10.1021/jp061627s
Baron, R., de Vries, AH., Hunenberger, PH., & van Gunsteren, WF. (2006). Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. Journal of Physical Chemistry B, 110(16), 8464-8473. https://doi.org/10.1021/jp055888y
Wassenaar, T. A. (2006). Molecular dynamics of sense and sensibility in processing and analysis of data. s.n.

2005

Marrink, SJ., Risselada, J., & Mark, AE. (2005). Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chemistry and physics of lipids, 135(2), 223-244. https://doi.org/10.1016/j.chemphyslip.2005.03.001
de Vries, AH., Yefimov, S., Mark, AE., & Marrink, SJ. (2005). Molecular structure of the lecithin ripple phase. Proceedings of the National Academy of Sciences of the United States of America, 102(15), 5392-5396. https://doi.org/10.1073/pnas.0408249102
Knecht, V., Muller, M., Bonn, M., Marrink, S-J., & Mark, A. E. (2005). Simulation studies of pore and domain formation in a phospholipid monolayer. Journal of Chemical Physics, 122(2), 24704 - 24713. [024704]. https://doi.org/10.1063/1.1825992
de Vries, A. H., Chandrasekhar, I., van Gunsteren, W. F., Hunenberger, P. H., & Chandrasekhar, N. V. (2005). Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time: Influence of artificial periodicity, system size, and simulation time. Journal of Physical Chemistry B, 109(23), 11643-11652. https://doi.org/10.1021/jp0507952

2004

de Vries, AH., Mark, AE., & Marrink, SJ. (2004). Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail. Journal of the American Chemical Society, 126(14), 4488-4489. https://doi.org/10.1021/ja0398417
Leontiadou, H., Mark, A. E., & Marrink, S. J. (2004). Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers. Biophysical Journal, 86(4), 2156-2164. https://doi.org/10.1016/S0006-3495(04)74275-7
de Vries, AH., Mark, AE., & Marrink, SJ. (2004). The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics study. Journal of Physical Chemistry B, 108(7), 2454-2463. https://doi.org/10.1021/jp0366926
Marrink, SJ., de Vries, AH., & Mark, AE. (2004). Coarse grained model for semiquantitative lipid simulations. Journal of Physical Chemistry B, 108(2), 750-760. https://doi.org/10.1021/jp036508g
Marrink, S. J. (2004). Molecular dynamics simulation of cholesterol nucleation in mixed micelles modelling human bile. In G. Adler, M. Fuchs, HE. Blum, & EF. Stange (Eds.), GALLSTONES: PATHOGENESIS AND TREATMENT (pp. 98-105 - 13). (FALK SYMPOSIUM; Vol. 139). DORDRECHT: Kluwer Academic Publishers.
Marrink, S. J., & Mark, A. E. (2004). Molecular view of hexagonal phase formation in phospholipid membranes. Biophysical Journal, 87(6), 3894 - 3900. https://doi.org/10.1529/biophysj.104.048710
Faller, R., & Marrink, S. J. (2004). Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir, 20(18), 7686 - 7693. https://doi.org/10.1021/la0492759
Folgering, J. H. A., Kuiper, J. M., Vries, A. H. D., Engberts, J. B. F. N., & Poolman, B. (2004). Lipid-Mediated Light Activation of a Mechanosensitive Channel of Large Conductance. Langmuir, 20(17), 6985 - 6987. https://doi.org/10.1021/la048942v
Bekker, H., Van den Berg, JP., & Wassenaar, TA. (2004). A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints. Journal of Computational Chemistry, 25(8), 1037-1046. https://doi.org/10.1002/jcc.20050

2003

Marrink, SJ., & Mark, AE. (2003). Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. Journal of the American Chemical Society, 125(49), 15233-15242. https://doi.org/10.1021/ja0352092
Marrink, SJ., & Mark, AE. (2003). The mechanism of vesicle fusion as revealed by molecular dynamics simulations. Journal of the American Chemical Society, 125(37), 11144-11145. https://doi.org/10.1021/ja036138+
Anezo, C., de Vries, AH., Holtje, HD., Tieleman, DP., & Marrink, SJ. (2003). Methodological issues in lipid bilayer simulations. Journal of Physical Chemistry B, 107(35), 9424-9433. https://doi.org/10.1021/jp0348981
Tieleman, DP., Leontiadou, H., Mark, AE., & Marrink, SJ. (2003). Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. Journal of the American Chemical Society, 125(21), 6382-6383. https://doi.org/10.1021/ja029504i
Colombo, G., Marrink, S. J., & Mark, A. E. (2003). Simulation of MscL Gating in a bilayer under stress. Biophysical Journal, 84(4), 2331-2337. https://doi.org/10.1016/S0006-3495(03)75038-3
de Vries, AH., Hozoi, L., & Broer, R. (2003). Origin of the chemical shift in X-ray absorption near-edge spectroscopy at the Mn K-Edge in manganese oxide compounds. International Journal of Quantum Chemistry, 91(1), 57-61. https://doi.org/10.1002/qua.10370
Bekker, H., van den Berg, J. P., & Wassenaar, T. A. (2003). Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions. In EPRINTS-BOOK-TITLE Springer.

2002

van Eijk, MCP., Bergsma, M., & Marrink, SJ. (2002). Association behaviour of glucitol amine gemini surfactants - Self-consistent-field theory and molecular-dynamics simulations. European Physical Journal E, 7(4), 317-324. https://doi.org/10.1140/epje/i2002-10012-6
Marrink, S. J., & Tieleman, D. P. (2002). Molecular dynamics simulation of spontaneous membrane fusion during a cubic-hexagonal phase transition. Biophysical Journal, 83(5), 2386 - 2392. https://doi.org/10.1016/S0006-3495(02)75252-1
Marrink, S. J., & Mark, A. E. (2002). Molecular dynamics simulations of mixed micelles modeling human bile. Biochemistry, 41(17), 5375 - 5382. https://doi.org/10.1021/bi015613i
de Vries, A. H., Hozoi, L., Broer, R., & Bagus, P. S. (2002). Importance of interatomic hole screening in core-level spectroscopy of transition metal oxides: Mn 3s hole states in MnO. Physical Review B, 66(3), [035108]. https://doi.org/10.1103/PhysRevB.66.035108
van Duijnen, P. T., de Vries, A. H., Swart, M., & Grozema, F. C. (2002). Polarizabilities in the condensed phase and the local fields problem: A direct reaction field formulation. Journal of Chemical Physics, 117(18), 8442 - 8453. https://doi.org/10.1063/1.1512278
Hozoi, L., de Vries, A. H., van Oosten, A. B., Broer-Braam, H. B., Cabrero, J., & Graaf, de, C. (2002). Theoretical characterization of the ground and optically excited states of alpha '-NaV2O5. Physical Review Letters, 89(7), [076407]. https://doi.org/10.1103/physrevlett.89.076407

2001

Marrink, S. J., & Mark, A. E. (2001). Effect of Undulations on Surface Tension in Simulated Bilayers. The Journal of Physical Chemistry B, 105(26), 6122 - 6127. https://doi.org/10.1021/jp0103474
Knackstedt, M. A., Marrink, S. J., Sheppard, A. P., Pinczewski, W. V., & Sahimi, M. (2001). Invasion Percolation on Correlated and Elongated Lattices: Implications for the Interpretation of Residual Saturations in Rock Cores. Transport in Porous Media, 44(3). https://doi.org/10.1023/A:1010770010309
Marrink, S. J., & Tieleman, D. P. (2001). Molecular dynamics simulation of a lipid diamond cubic phase. Journal of the American Chemical Society, 123(49), 12383 - 12391. https://doi.org/10.1021/ja016012h
Marrink, S-J., & Marčelja, S. (2001). Potential of Mean Force Computations of Ions Approaching a Surface. Langmuir, 17(25). https://doi.org/10.1021/la015526r
Marrink, S. J., Lindahl, E., Edholm, O., & Mark, A. E. (2001). Simulation of the spontaneous aggregation of phospholipids into bilayers. Journal of the American Chemical Society, 123(35), 8638 - 8639. https://doi.org/10.1021/ja0159618
Hozoi, L., Vries, A. H. D., & Broer, R. (2001). X-ray spectroscopy at the Mn K edge in LaMnO3: An ab initio study. Physical Review B, 64(16). https://doi.org/10.1103/PhysRevB.64.165104
Hozoi, L., de Vries, A. H., & Broer-Braam, H. B. (2001). X-ray spectroscopy at the MnK edge in LaMnO3: An ab initio study. Physical Review B, 6416(16), [165104]. https://doi.org/10.1103/PhysRevB.64.165104

2000

Marrink, S. J., Paterson, L., & Knackstedt, M. A. (2000). Definition of percolation thresholds on self-affine surfaces. Physica A: Statistical Mechanics and its Applications, 280(3). https://doi.org/10.1016/S0378-4371(99)00608-1
Marrink, S. J., & Knackstedt, M. A. (2000). Finite size scaling for percolation on elongated lattices in two and three dimensions. Physical Review E, 62(3). https://doi.org/10.1103/PhysRevE.62.3205
Marrink, S. J., Tieleman, D. P., & Mark, A. E. (2000). Molecular dynamics simulation of the kinetics of spontaneous micelle formation. Journal of Physical Chemistry B, 104(51), 12165 - 12173. https://doi.org/10.1021/jp001898h

1999

Marrink, S. J., & Knackstedt, M. A. (1999). Percolation thresholds on elongated lattices. Journal of Physics A%3A Mathematical and General, 32(44). https://doi.org/10.1088/0305-4470/32/44/101
de Vries, A. H., Sherwood, P., Collins, S. J., Rigby, A. M., Rigutto, M., & Kramer, G. J. (1999). Zeolite structure and reactivity by combined quantum-chemical- classical calculations. Journal of Physical Chemistry B, 103(29), 6133 - 6141. https://doi.org/10.1021/jp9913012

1998

Marrink, S-J., Berger, O., Tieleman, P., & Jähnig, F. (1998). Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophysical Journal, 74(2), 931-943. https://doi.org/10.1016/s0006-3495(98)74016-0

1997

Tieleman, D. P., Marrink, S. J., & Berendsen, H. J. C. (1997). A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochimica et Biophysica Acta-Reviews on Biomembranes, 1331(3), 235-270. https://doi.org/10.1016/S0304-4157(97)00008-7
deVries, AH., vanDuijnen, PT., Zijlstra, RWJ., & Swart, M. (1997). Thole's interacting polarizability model in computational chemistry practice. Journal of Electron Spectroscopy and Related Phenomena, 86(1-3), 49-55.

1996

Marrink, S. J., & Berendsen, H. J. C. (1996). Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations. Journal of Physical Chemistry, 100(41), 16729 - 16738. https://doi.org/10.1021/jp952956f
Marrink, S. J., Jähnig, F., & Berendsen, H. J. C. (1996). Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophysical Journal, 71(2), 632 - 647. https://doi.org/10.1016/S0006-3495(96)79264-0
Marrink, S. J., Sok, R. M., & Berendsen, H. J. C. (1996). Free volume properties of a simulated lipid membrane. Journal of Chemical Physics, 104(22), 9090 - 9099. https://doi.org/10.1063/1.471442
López Cascales, J. J., García de la Torre, J., Marrink, S. J., & Berendsen, H. J. C. (1996). Molecular dynamics simulation of a charged biological membrane. Journal of Chemical Physics, 104(7), 2713 - 2720. https://doi.org/10.1063/1.470992
Marrink, S. J., Tieleman, D. P., Buuren , van, A. R., & Berendsen, H. J. C. (1996). Membranes and water: An interesting relationship. Faraday Discussions, 103(3), 191-201. https://doi.org/10.1039/fd9960300191
Duijnen , van, P. T., & de Vries, A. H. (1996). Direct reaction field force field: A consistent way to connect and combine quantum-chemical and classical descriptions of molecules. International Journal of Quantum Chemistry, 60(6), 1111-1132.
Zijlstra, R. W. J., van Duijnen, P. T., & de Vries, A. (1996). Polarization of the excited states of twisted ethylene in a non-symmetrical environment. Chemical Physics, 204(2-3), 439-446.
De Vries, A. H., & Van Duijnen, P. T. (1996). Solvatochromism of the π* ← n transition of acetone by combined quantum mechanical—classical mechanical calculations. International Journal of Quantum Chemistry, 57(6), 1067-1076. https://doi.org/10.1002/(sici)1097-461x(1996)57:6<1067::aid-qua5>3.0.co;2-r

1995

Buuren, A. R. V., Marrink, S-J., & Berendsen, H. J. C. (1995). Characterisation of aqueous interfaces with different hydrophobicities by molecular dynamics. Colloids and Surfaces A-Physicochemical and Engineering Aspects, 102(41). https://doi.org/10.1016/0927-7757(95)03227-5
De Vries, A. H., Van Duijnen, P. T., Juffer, A. H., Rullmann, J. A. C., Dijkman, J. P., Merenga, H., & Thole, B. T. (1995). Erratum: Implementation of reaction field methods in quantum chemistry computer codes (Vol 16, Pg 37, 1995). Journal of Computational Chemistry, 16(11), 1445-1446. https://doi.org/10.1002/jcc.540161113
De Vries, A. H., Van Duijnen, P. T., Juffer, A. H., Rullmann, J. A. C., Dijkman, J. P., MERENGA, H., & Thole, B. T. (1995). Implementation of reaction field methods in quantum chemistry computer codes. Journal of Computational Chemistry, 16(1), 37-55. https://doi.org/10.1002/jcc.540160105
de Vries, A. H. (1995). Modelling condensed-phase systems: from quantum chemistry to molecular models. Groningen: s.n.
Van Duijnen, P. T., & De Vries, A. H. (1995). Utopia dielectrica. International Journal of Quantum Chemistry, 56(S29), 523-531. https://doi.org/10.1002/qua.560560855

1994

Marrink, S-J., & Berendsen, H. J. C. (1994). Simulation of Water Transport through a Lipid Membrane. The Journal of Physical Chemistry, 98(15), 4155-4168. https://doi.org/10.1021/j100066a040
Egberts, E., Marrink, S-J., & Berendsen, H. J. C. (1994). Molecular dynamics simulation of a phospholipid membrane. European biophysics journal with biophysics letters, 22(6), 423-436. https://doi.org/10.1007/BF00180163
Marrink, S. J. (1994). Permeation of small molecules across lipid membranes. A molecular dynamics study. s.n.

1993

BERENDSEN, HJC., & MARRINK, SJ. (1993). Molecular-dynamics of water transport through membranes - water from solvent to solute. Pure and Applied Chemistry, 65(12), 2513-2520. https://doi.org/10.1351/pac199365122513
Buuren, A. R. V., Marrink, S-J., & Berendsen, H. J. C. (1993). A Molecular Dynamics Study of the Decane/Water Interface. The Journal of Physical Chemistry, 97(36). https://doi.org/10.1021/j100138a023
Marrink, S-J., Berkowitz, M., & Berendsen, H. J. C. (1993). Molecular Dynamics Simulation of a Membrane/Water Interface: The Ordering of Water and Its Relation to the Hydration Force. Langmuir, 9(11). https://doi.org/10.1021/la00035a062
DEVRIES, AH., VANDUIJNEN, PT., & JUFFER, AH. (1993). SUCCESS AND PITFALLS OF THE DIELECTRIC CONTINUUM MODEL IN QUANTUM-CHEMICAL CALCULATIONS. International Journal of Quantum Chemistry, 451-466.

1992

Berendsen, H., Egberts, B., Marrink, S., & Ahlstroem, P. (1992). Molecular Dynamics Simulations of Phospholipid Membranes and Their Interaction with Phospholipase A2. In A. Pullman, J. Jortner, & B. Pullman (Eds.), Membrane Proteins: Structures, Interactions and Models (1 ed., Vol. 1, pp. 457-470). ( The Jerusalem Symposia on Quantum Chemistry and Biochemistry; Vol. 25). Springer International Publishing. https://doi.org/10.1007/978-94-011-2718-9_37
de Vries, A. H., & van Duijnen, P. T. (1992). Theoretical calculation of tautomer equilibria of 4-substituted imidazoles in the gas phase and in solution. Biophysical Chemistry, 43(2), 139-147. https://doi.org/10.1016/0301-4622(92)80028-4
Last modified:14 November 2018 12.22 p.m.