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Research GBB Molecular Dynamics Group Publications

Publications

2021

Nemchinova, M., Melcr, J., Wassenaar, T., Marrink, S., & Guskov, A. (2021). Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. Journal of chemical information and modeling. https://doi.org/10.1021/acs.jcim.1c00261
Kobauri, P., Szymanski, W., Cao, F., Thallmair, S., Marrink, S. J., Witte, M. D., Dekker, F. J., & Feringa, B. L. (2021). Biaryl sulfonamides as cisoid azosteres for photopharmacology. Chemical Communications, 57(34), 4126-4129. https://doi.org/10.1039/d1cc00950h
Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., Kroon, P. C., Melcr, J., Nieto, V., Corradi, V., Khan, H. M., Domański, J., Javanainen, M., Martinez-Seara, H., Reuter, N., ... Marrink, S. J. (2021). Martini 3: A general purpose force field for coarse-grained molecular dynamics. Nature Methods, 18, 382-388. https://doi.org/10.1038/s41592-021-01098-3
Souza, P. C. T., Limongelli, V., Wu, S., Marrink, S. J., & Monticelli, L. (2021). Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Frontiers in Molecular Biosciences, 8, [657222]. https://doi.org/10.3389/fmolb.2021.657222
Grünewald, F., Kroon, P. C., Souza, P. C. T., & Marrink, S. J. (2021). Protocol for Simulations of PEGylated Proteins with Martini 3. In Y. W. Chen , & CP. B. Yiu (Eds.), Structural Genomics (pp. 315-335). (Methods in Molecular Biology; Vol. 2199). Humana Press. https://doi.org/10.1007/978-1-0716-0892-0_18
Yakovlieva, L., Ramírez-Palacios, C., Marrink, S. J., & Walvoort, M. T. C. (2021). Semiprocessive Hyperglycosylation of Adhesin by Bacterial Protein N-Glycosyltransferases. ACS chemical biology, 16(1), 165-175. https://doi.org/10.1021/acschembio.0c00848
Pezeshkian, W., & Marrink, S. J. (2021). Simulating realistic membrane shapes. Current Opinion in Cell Biology, 71, 103-111. [j.ceb.2021.02.009]. https://doi.org/10.1016/j.ceb.2021.02.009
Alessandri, R., Grünewald, F., & Marrink, S. J. (2021). The Martini Model in Materials Science. Advanced materials, [e2008635]. https://doi.org/10.1002/adma.202008635

2020

Bruininks, B. M., Souza, P. C., Ingolfsson, H., & Marrink, S. J. (2020). A molecular view on the escape of lipoplexed DNA from the endosome. eLife, 9, [e52012]. https://doi.org/10.7554/eLife.52012
Dong, L., Meng, Q., Ramirez-Palacios, C., Wijma, H. J., Marrink, S. J., & Janssen, D. B. (2020). Asymmetric synthesis of optically pure aliphatic amines with an engineered robust ω-transaminase. Catalysts, 10(11), 1-14. [1310]. https://doi.org/10.3390/catal10111310
Pezeshkian, W., König, M., Wassenaar, T. A., & Marrink, S. J. (2020). Backmapping triangulated surfaces to coarse-grained membrane models. Nature Communications, 11(1), [2296]. https://doi.org/10.1038/s41467-020-16094-y
Khan, H. M., Telles de Souza, P. C., Thallmair, S., Barnoud, J., De Vries, A. H., Marrink, S. J., & Reuter, N. (2020). Capturing Choline–Aromatics Cation−π Interactions in the MARTINI Force Field. Journal of Chemical Theory and Computation, 16(4), 2550-2560. https://doi.org/10.1021/acs.jctc.9b01194
Maity, S., Ottelé, J., Santiago, G. M., Frederix, P. W. J. M., Kroon, P., Markovitch, O., Stuart, M. C. A., Marrink, S. J., Otto, S., & Roos, W. H. (2020). Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization. Journal of the American Chemical Society, 142(32), 13709-13717. https://doi.org/10.1021/jacs.0c02635
Schroer, C. F. E., Baldauf, L., van Buren, L., Wassenaar, T. A., Melo, M. N., Koenderink, G. H., & Marrink, S. J. (2020). Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers. Proceedings of the National Academy of Sciences of the United States of America, 117(11), 5861-5872. [pnas.1914884117]. https://doi.org/10.1073/pnas.1914884117
Marrink, S. J., & Levental, I. (2020). Computational and Experimental Advances in Biomembranes: Resolving Their Complexity. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 124(45), 9975-9976. https://doi.org/10.1021/acs.jpcb.0c09401
Liu, Y., Pezeshkian, W., Barnoud, J., De Vries, A. H., & Marrink, S. J. (2020). Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. Journal of Chemical Theory and Computation, 16(8), 5313-5322. [acs.jctc.0c00429]. https://doi.org/10.1021/acs.jctc.0c00429
Liu, Y., De Vries, A. H., Barnoud, J., Pezeshkian, W., Melcr, J., & Marrink, S. J. (2020). Dual Resolution Membrane Simulations Using Virtual Sites. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 124(19), 3944-3953. https://doi.org/10.1021/acs.jpcb.0c01842
Su, J., Marrink, S. J., & Melo, M. N. (2020). Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains. Frontiers in Cell and Developmental Biology, 8, [350]. https://doi.org/10.3389/fcell.2020.00350
Vazquez-Salazar, L. I., Selle, M., de Vries, A. H., Marrink, S. J., & Souza, P. C. T. (2020). Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid-liquid extraction. Green Chemistry, 22(21), 7376-7386. https://doi.org/10.1039/d0gc01823f
Faustino, I., Abdizadeh, H., Souza, P. C. T., Jeucken, A., Stanek, W. K., Guskov, A., Slotboom, D., & Marrink, S. (2020). Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nature Communications, 11(1), [1763]. https://doi.org/10.1038/s41467-020-15554-9
Liguori, N., Croce, R., Marrink, S. J., & Thallmair, S. (2020). Molecular dynamics simulations in photosynthesis. Photosynthesis Research, 144(2), 273-295. https://doi.org/10.1007/s11120-020-00741-y
Sun, F., Schroer, C. F. E., Palacios, C. R., Xu, L., Luo, S-Z., & Marrink, S. J. (2020). Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2. PLoS Computational Biology, 16(4), [e1007777]. https://doi.org/10.1371/journal.pcbi.1007777
Kriete, B., Bondarenko, A. S., Alessandri, R., Patmanidis, I., Krasnikov, V. V., Jansen, T. L. C., Marrink, S. J., Knoester, J., & Pshenichnikov, M. S. (2020). Molecular versus excitonic disorder in individual artificial light-harvesting systems. Journal of the American Chemical Society, 142(42), 18073-18085. [jacs.0c07392]. https://doi.org/10.1021/jacs.0c07392
Bondarenko, A. S., Patmanidis, I., Alessandri, R., Souza, P. C. T., Jansen, T. L. C., de Vries, A. H., Marrink, S. J., & Knoester, J. (2020). Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates. Chemical Science, 11(42), 11514-11524. https://doi.org/10.1039/d0sc03110k
Liu, J., van der Zee, B., Alessandri, R., Sami, S., Dong, J., Nugraha, M. I., Barker, A. J., Rousseva, S., Qiu, L., Qiu, X., Klasen, N., Chiechi, R. C., Baran, D., Caironi, M., Anthopoulos, T. D., Portale, G., Havenith, R. W. A., Marrink, S. J., Hummelen, J. C., & Koster, L. J. A. (2020). N-type organic thermoelectrics: demonstration of ZT > 0.3. Nature Communications, 11(1), [5694]. https://doi.org/10.1038/s41467-020-19537-8
Buyan, A., Cox, C. D., Barnoud, J., Li, J., Chan, H. S. M., Martinac, B., Marrink, S. J., & Corry, B. (2020). Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol. Biophysical Journal, 119(8), 1683-1697. [j.bpj.2020.07.043]. https://doi.org/10.1016/j.bpj.2020.07.043
Souza, P. C. T., Thallmair, S., Conflitti, P., Ramírez-Palacios, C., Alessandri, R., Raniolo, S., Limongelli, V., & Marrink, S. J. (2020). Protein-ligand binding with the coarse-grained Martini model. Nature Communications, 11(1), [3714]. https://doi.org/10.1038/s41467-020-17437-5
Alessandri, R., Sami, S., Barnoud, J., de Vries, A. H., Marrink, S. J., & Havenith, R. W. A. (2020). Resolving Donor-Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains. Advanced Functional Materials, 30(46), [2004799]. https://doi.org/10.1002/adfm.202004799
Patmanidis, I., de Vries, A. H., Wassenaar, T. A., Wang, W., Portale, G., & Marrink, S. J. (2020). Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS. PPCP : Physical Chemistry Chemical Physics, 22(37), 21083-21093. [D0CP03282D]. https://doi.org/10.1039/d0cp03282d
Grünewald, F., Souza, P. C. T., Abdizadeh, H., Barnoud, J., de Vries, A. H., & Marrink, S. J. (2020). Titratable Martini model for constant pH simulations. The Journal of Chemical Physics, 153(2), [024118]. https://doi.org/10.1063/5.0014258
Zhou, Q., Chen, J., Luan, Y., Vainikka, P. A., Thallmair, S., Marrink, S. J., Feringa, B. L., & van Rijn, P. (2020). Unidirectional rotating molecular motors dynamically interact with adsorbed proteins to direct the fate of mesenchymal stem cells. Science Advances, 6(5), [eaay2756]. https://doi.org/10.1126/sciadv.aay2756
Draper, E. R., Dietrich, B., McAuluy, K., Brasnett, C., Abdizadeh, H., Patmanidis, I., Marrink, S., Su, H., Cui, H., Schweins, R., Seddon, A., & Adams, D. J. (2020). Using Small-Angle Scattering and Contrast Matching to Understand Molecular Packing in Low Molecular Weight Gels. Matter, 2(3), 764-778. https://doi.org/10.1016/j.matt.2019.12.028
Gopal, S. M., Pawar, A. B., Wassenaar, T. A., & Sengupta, D. (2020). Lipid-dependent conformational landscape of the ErbB2 growth factor receptor dimers. Chemistry and physics of lipids, 230, [104911]. https://doi.org/10.1016/j.chemphyslip.2020.104911

2019

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
Bruininks, B. M. H., Souza, P. C. T., & Marrink, S. J. (2019). A Practical View of the Martini Force Field. In M. Bonomi, & C. Camilloni (Eds.), Biomolecular Simulations: Methods in Molecular Biology (pp. 105-127). (Methods in Molecular Biology; Vol. 2022). SPRINGER. https://doi.org/10.1007/978-1-4939-9608-7_5
Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S-J., Montalban-Lopez, M., de Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B., & 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
Souza, P. C. T., Thallmair, S., Marrink, S. J., & Mera-Adasme, R. (2019). An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10(24), 7740-7744. https://doi.org/10.1021/acs.jpclett.9b02868
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
Dadsena, S., Bockelmann, S., Mina, J. G. M., Hassan, D. G., Korneev, S., Razzera, G., Jahn, H., Niekamp, P., Müller, D., Schneider, M., Tafesse, F. G., Marrink, S. J., Melo, M. N., & 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
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
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. https://doi.org/10.1021/acs.chemrev.8b00460
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
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
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
Piskorz, T. K., Gobbo, C., Marrink, S. J., De Feyter, S., de Vries, A. H., & van Esch, J. H. (2019). Nucleation Mechanisms of Self-Assembled Physisorbed Monolayers on Graphite. Journal of Physical Chemistry C, 123(28), 17510-17520. https://doi.org/10.1021/acs.jpcc.9b01234
Alessandri, R., Souza, P. C. T., Thallmair, S., Melo, M. N., De Vries, A. H., & Marrink, S. J. (2019). Pitfalls of the Martini Model. Journal of Chemical Theory and Computation, 15(10), 5448-5460. [acs.jctc.9b00473]. https://doi.org/10.26434/chemrxiv.8113172
Newe, A., Rzeniewicz, K., Konig, M., Schroer, C. F. E., Joachim, J., Rey-Gallardo, A., Marrink, S. J., Deka, J., Parsons, M., & 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
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
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
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
Molenaar, M. R., Jeucken, A., Wassenaar, T. A., van de Lest, C. H. A., Brouwers, J. F., & Helms, J. B. (2019). LION/web: a web-based ontology enrichment tool for lipidomic data analysis. Gigascience, 8(6), [061]. https://doi.org/10.1093/gigascience/giz061

2018

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
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
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
Liu, J., Qiu, L., Alessandri, R., Qiu, X., Portale, G., Dong, J., Talsma, W., Ye, G., Sengrian, A. A., Souza, P. C. T., Loi, M. A., Chiechi, R. C., Marrink, S. J., Hummelen, J. C., & 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
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
Corradi, V., Mendez-Villuendas, E., Ingólfsson, H. I., Gu, R-X., Siuda, I., Melo, M. N., Moussatova, A., DeGagné, L. J., Sejdiu, B. I., Singh, G., Wassenaar, T. A., Delgado Magnero, K., Marrink, S. J., & 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
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
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
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
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
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
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
Su, J., Thomas, A. S., Grabietz, T., Landgraf, C., Volkmer, R., Marrink, S. J., Williams, C., & 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
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
Friedman, R., Khalid, S., Aponte-Santamaría, C., Arutyunova, E., Becker, M., Boyd, K. J., Christensen, M., Coimbra, J. T. S., Concilio, S., Daday, C., van Eerden, F. J., Fernandes, P. A., Gräter, F., Hakobyan, D., Heuer, A., Karathanou, K., Keller, F., Lemieux, M. J., Marrink, S. 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
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., Faustino, I., Meng, Z., Szymanski, W., Herrmann, A., & 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
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
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

2017

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
Groves, M. R., Schroer, C. F. E., Middleton, A. J., Lunev, S., Danda, N., Ali, A. M., Marrink, S. J., & 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
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
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
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
Hsu, P-C., Bruininks, B. M. H., Jefferies, D., Cesar Telles de Souza, P., Lee, J., Patel, D. S., Marrink, S. J., Qi, Y., Khalid, 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
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
Arnarez, C., & Marrink, S. J. (2017). Computational microscopy of mitochondrial membranes. In Computer Design for New Drugs and Materials: Molecular Dynamics of Nanoscale Phenomena (pp. 1-20). Nova Science Publishers, Inc, Hauppauge, NY, USA.
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
Qiu, L., Liu, J., Alessandri, R., Qiu, X., Koopmans, M., Havenith, R. W. A., Marrink, S. J., Chiechi, R. C., Koster, L. J. 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
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
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
Melo, M. N., Arnarez, C., Sikkema, H., Kumar, N., Walko, M., Berendsen, H. J. C., Kocer, A., Marrink, S. J., & 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
Swier, L. J. Y. M., Monjas, L., Reeßing, F., Oudshoorn, R. C., Aisyah, A., Primke, T., Bakker, M. M., Van Olst, E., Ritschel, T., Faustino, I., Marrink, S. J., Hirsch, A. K. H., & 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
Venable, R. M., Ingólfsson, H. I., Lerner, M. G., Perrin, B. S., Camley, B. A., Marrink, S. J., Brown, F. L. H., & 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
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
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
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
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
Frederix, P. W. J. M., Idé, J., Altay, Y., Schaeffer, G., Surin, M., Beljonne, D., Bondarenko, A. S., Jansen, T. L. C., Otto, S., & 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
Kanduc, M., Schlaich, A., de Vries, A. H., Jouhet, J., Marechal, E., Deme, B., Netz, R. R., & Schneck, E. (2017). Tight cohesion between glycolipid membranes results from balanced water-headgroup interactions. Nature Communications, 8, [14899]. https://doi.org/10.1038/ncomms14899
Capoferri, L., van Dijk, M., Rustenburg, A. S., Wassenaar, T. A., Kooi, D. P., Rifai, E. A., Vermeulen, N. P. E., & Geerke, D. P. (2017). eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. Journal of cheminformatics, 9, [58]. https://doi.org/10.1186/s13321-017-0243-x

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
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., McLaughlin, J., Sinke, R. J., Marrink, S-J., Reits, E., & 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
Antillón, A., De Vries, A. H., Espinosa-caballero, M., Falcón-gonzález, J. M., Flores Romero, D., González–damián, J., Jiménez-montejo, F. E., León-buitimea, A., López-ortiz, M., Magaña, R., Marrink, S. J., Morales-nava, R., Periole, X., Reyes-esparza, J., Rodríguez Lozada, J., Santiago-angelino, T. M., Vargas González, M. C., Regla, I., Carrillo-tripp, M., ... 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
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
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., Tieleman, D. P., & 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
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
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
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

2015

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
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
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
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.
Arnarez, C., Uusitalo, J. J., Masman, M. F., Ingolfsson, H. I., de Jong, D. H., Melo, M. N., Periole, X., de Vries, A. H., & 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
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
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

2014

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
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
Ingólfsson, H. I., Melo, M. N., van Eerden, F. J., Arnarez, C., Lopez, C. A., Wassenaar, T. A., Periole, X., de Vries, A. H., Tieleman, D. P., & Marrink, S. J. (2014). Lipid organization of the plasma membrane. Journal of the American Chemical Society, 136(41), 14554-14559. https://doi.org/10.1021/ja507832e
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
Boscia, A. L., Treece, B. W., Mohammadyani, D., Klein-Seetharaman, J., Braun, A. R., Wassenaar, T., Kloesgen, B., & 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

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
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
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
Gobbo, C., Beurroies, I., de Ridder, D., Eelkema, R., Marrink, S. J., De Feyter, S., van Esch, J. H., & 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
de Jong, D. H., Singh, G., Bennett, W. F. D., Arnarez, C., Wassenaar, T. A., Schafer, L. V., Periole, X., Tieleman, D. P., & 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
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

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
Goga, N., Rzepiela, A., de Sousa Pereira Simoes de Melo, M., de Vries, A., Hadar, A., Markvoort, A. J., Nedea, S., & 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., 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
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

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
Schaefer, L. V., de Jong, D. H., Holt, A., Rzepiela, A. J., de Vries, A. H., Poolman, B., Killian, J. A., & 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
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

2010

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
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
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
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

2009

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
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
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
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
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
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

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
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, 70(2), 333-343. https://doi.org/10.1002/prot.21541

2007

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
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
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
Baron, R., de Vries, A. H., Hunenberger, PH., & van Gunsteren, W. F. (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
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
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
Wassenaar, T. A. (2006). Molecular dynamics of sense and sensibility in processing and analysis of data. s.n.

2005

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
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

2004

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
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
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
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
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

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
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 Computational Science ― ICCS 2003: International Conference, Melbourne, Australia and St. Petersburg, Russia, June 2–4, 2003. Proceedings (Vol. 3). Springer.

2002

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

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

1999

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

1997

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

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

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. 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

1993

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

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.