Skip to ContentSkip to Navigation
Research GBB Molecular Dynamics Group Publications

Publications

2024

Diamanti, E., Souza, P. C. T., Setyawati, I., Bousis, S., Monjas, L., Swier, L. J. Y. M., Shams, A., Tsarenko, A., Stanek, W. K., Jäger, M., Marrink, S. J., Slotboom, D. J., & Hirsch, A. K. H. (2024). Author Correction: Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications biology, 7, Article 70. https://doi.org/10.1038/s42003-024-05770-0
Ozturk, T. N., König, M., Carpenter, T. S., Pedersen, K. B., Wassenaar, T. A., Ingólfsson, H. I., & Marrink, S. J. (2024). Building complex membranes with Martini 3. Methods in Enzymology. Advance online publication. https://doi.org/10.1016/bs.mie.2024.03.010
Brown, C. M., & Marrink, S. J. (2024). Modeling membranes in situ. Current Opinion in Structural Biology, 87, Article 102837. Advance online publication. https://doi.org/10.1016/j.sbi.2024.102837
van der Sleen, L., Stevens, J. A., Marrink, S. J., Poolman, B., & Tych, K. (2024). Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers. Cell reports, 43(4), Article 114110. https://doi.org/10.1016/j.celrep.2024.114110
Vilachã, J. F., Wassenaar, T. A., & Marrink, S. J. (2024). Structural Aspects of the ROS1 Kinase Domain and Oncogenic Mutations. Crystals, 14(2), Article 106. https://doi.org/10.3390/cryst14020106
Park, P., Matsubara, D. K., Barzotto, D. R., Lima, F. S., Chaimovich, H., Marrink, S. J., & Cuccovia, I. M. (2024). Vesicle protrusion induced by antimicrobial peptides suggests common carpet mechanism for short antimicrobial peptides. Scientific Reports, 14(1), Article 9701. https://doi.org/10.1038/s41598-024-60601-w

2023

van Tilburg, M. P. A., Marrink, S. J., König, M., & Grünewald, F. (2024). Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. Journal of Chemical Theory and Computation, 20, Article 3c00961. https://doi.org/10.1021/acs.jctc.3c00961
Empereur-Mot, C., Pedersen, K. B., Capelli, R., Crippa, M., Caruso, C., Perrone, M., Souza, P. C. T., Marrink, S. J., & Pavan, G. M. (2023). Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG. Journal of chemical information and modeling, 63(12), 3827–3838. https://doi.org/10.1021/acs.jcim.3c00530
Ramírez-Palacios, C., & Marrink, S. J. (2023). Computational prediction of ω-transaminase selectivity by deep learning analysis of molecular dynamics trajectories. QRB Discovery, 4, Article e1. https://doi.org/10.1017/qrd.2022.22
Stępień, P., Świątek, S., Robles, M. Y. Y., Markiewicz-Mizera, J., Balakrishnan, D., Inaba-Inoue, S., De Vries, A. H., Beis, K., Marrink, S. J., & Heddle, J. G. (2023). CRAFTing Delivery of Membrane Proteins into Protocells using Nanodiscs. ACS Applied Materials & Interfaces, 15, 56689–56701. https://doi.org/10.1021/acsami.3c11894
Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023). Dynamics of chromosome organization in a minimal bacterial cell. Frontiers in Cell and Developmental Biology, 11, Article 1214962. https://doi.org/10.3389/fcell.2023.1214962
Thangaratnarajah, C., Nijland, M., Borges-Araújo, L., Jeucken, A., Rheinberger, J., Marrink, S. J., Souza, P. C. T., Paulino, C., & Slotboom, D. J. (2023). Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nature Communications, 14(1), Article 4484. https://doi.org/10.1038/s41467-023-40266-1
Hilpert, C., Beranger, L., Souza, P. C. T., Vainikka, P. A., Nieto, V., Marrink, S. J., Monticelli, L., & Launay, G. (2023). Facilitating CG Simulations with MAD: The MArtini Database Server. Journal of chemical information and modeling, 63(3), 702–710. Article 9. https://doi.org/10.1021/acs.jcim.2c01375
Diamanti, E., Souza, P. C. T., Setyawati, I., Bousis, S., Gómez, L. M., Swier, L. J. Y. M., Shams, A., Tsarenko, A., Stanek, W. K., Jäger, M., Marrink, S. J., Slotboom, D. J., & Hirsch, A. K. H. (2023). Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications biology, 6(1), Article 1182. https://doi.org/10.1038/s42003-023-05555-x
Melcrová, A., Maity, S., Melcr, J., de Kok, N. A. W., Gabler, M., van der Eyden, J., Stensen, W., Svendsen, J. S. M., Driessen, A. J. M., Marrink, S. J., & Roos, W. H. (2023). Lateral membrane organization as target of an antimicrobial peptidomimetic compound. Nature Communications, 14(1), Article 4038. https://doi.org/10.1038/s41467-023-39726-5
Borges-Araújo, L., Borges-Araújo, A. C., Ozturk, T. N., Ramirez-Echemendia, D. P., Fábián, B., Carpenter, T. S., Thallmair, S., Barnoud, J., Ingólfsson, H. I., Hummer, G., Tieleman, D. P., Marrink, S. J., Souza, P. C. T., & Melo, M. N. (2023). Martini 3 Coarse-Grained Force Field for Cholesterol. Journal of Chemical Theory and Computation, 19(20), 7387–7404. https://doi.org/10.1021/acs.jctc.3c00547
Vainikka, P., & Marrink, S. J. (2023). Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches. Journal of Chemical Theory and Computation, 19, 596-604. Article 00796. https://doi.org/10.1021/acs.jctc.2c00796
Tharmasothirajan, A., Melcr, J., Linney, J., Gensch, T., Krumbach, K., Ernst, K. M., Brasnett, C., Poggi, P., Pitt, A. R., Goddard, A. D., Chatgilialoglu, A., Marrink, S. J., & Marienhagen, J. (2023). Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis. Nature Communications, 14(1), Article 5619. https://doi.org/10.1038/s41467-023-40947-x
Pezeshkian, W., Grünewald, F., Narykov, O., Lu, S., Arkhipova, V., Solodovnikov, A., Wassenaar, T. A., Marrink, S. J., & Korkin, D. (2023). Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling. Structure, 31(4), 492-503. Article 202302006. https://doi.org/10.1016/j.str.2023.02.006
Ren, M., Zhao, L., Ma, Z., An, H., Marrink, S. J., & Sun, F. (2023). Molecular Basis of PIP2-dependent Conformational Switching of Phosphorylated CD44 in binding FERM. Biophysical Journal, 2675-2685. https://doi.org/10.1016/j.bpj.2023.05.021
Stevens, J. A., Grünewald, F., van Tilburg, P. A. M., König, M., Gilbert, B. R., Brier, T. A., Thornburg, Z. R., Luthey-Schulten, Z., & Marrink, S. J. (2023). Molecular dynamics simulation of an entire cell. Frontiers in Chemistry, 11, Article 1106495. https://doi.org/10.3389/fchem.2023.1106495
Blanco-González, A., Marrink, S. J., Piñeiro, Á., & García-Fandiño, R. (2023). Molecular insights into the effects of focused ultrasound mechanotherapy on lipid bilayers: Unlocking the keys to design effective treatments. Journal of Colloid and Interface Science, 650(Pt B), 1201-1210. Article 07077. https://doi.org/10.1016/j.jcis.2023.07.077
Ingólfsson, H. I., Rizuan, A., Liu, X., Mohanty, P., Souza, P. C. T., Marrink, S. J., Bowers, M. T., Mittal, J., & Berry, J. (2023). Multiscale simulations reveal TDP-43 molecular level interactions driving condensation. Biophysical Journal, 122(22), 4370-4381. https://doi.org/10.1016/j.bpj.2023.10.016
Chiariello, M. G., Grünewald, F., Zarmiento-Garcia, R., & Marrink, S. J. (2023). pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 14, 905-911. https://doi.org/10.1021/acs.jpclett.2c03760
Waclawiková, B., Cesar Telles de Souza, P., Schwalbe, M., Neochoritis, C. G., Hoornenborg, W., Nelemans, S. A., Marrink, S. J., & El Aidy, S. (2023). Potential binding modes of the gut bacterial metabolite, 5-hydroxyindole, to the intestinal L-type calcium channels and its impact on the microbiota in rats. Gut Microbes, 15(1), Article 2154544. https://doi.org/10.1080/19490976.2022.2154544
Borges-Araújo, L., Patmanidis, I., Singh, A. P., Santos, L. H. S., Sieradzan, A. K., Vanni, S., Czaplewski, C., Pantano, S., Shinoda, W., Monticelli, L., Liwo, A., Marrink, S. J., & Souza, P. C. T. (2023). Pragmatic Coarse-Graining of Proteins: Models and Applications. Journal of Chemical Theory and Computation, 19(20), 7112-7135. Article e00733. https://doi.org/10.1021/acs.jctc.3c00733
Sami, S., & Marrink, S. J. (2023). Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 19(13), 4040-4046. https://doi.org/10.1021/acs.jctc.2c01186
Abraham Versloot, R. C., Arias-Orozco, P., Tadema, M. J., Rudolfus Lucas, F. L., Zhao, X., Marrink, S. J., Kuipers, O. P., & Maglia, G. (2023). Seeing the Invisibles: Detection of Peptide Enantiomers, Diastereomers, and Isobaric Ring Formation in Lanthipeptides Using Nanopores. Journal of the American Chemical Society, 145(33), 18355-18365. Article 4076. https://doi.org/10.1021/jacs.3c04076
Ramírez-Palacios, C., & Marrink, S. J. (2023). Super High-Throughput Screening of Enzyme Variants by Spectral Graph Convolutional Neural Networks. Journal of Chemical Theory and Computation, 19(14), 4668–4677. Article 1227. https://doi.org/10.1021/acs.jctc.2c01227
Manrho, M., Krishnaswamy, S. R., Kriete, B., Patmanidis, I., de Vries, A. H., Marrink, S. J., Jansen, T. L. C., Knoester, J., & Pshenichnikov, M. S. (2023). Watching Molecular Nanotubes Self-Assemble in Real Time. Journal of the American Chemical Society, 145(41), 22494–22503. https://doi.org/10.1021/jacs.3c07103
Bruininks, B. M. H., Wassenaar, T. A., & Vattulainen, I. (2023). Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries. Journal of chemical information and modeling, 63(11), 3448–3452. https://doi.org/10.1021/acs.jcim.2c01574

2022

De Franceschi, N., Pezeshkian, W., Fragasso, A., Bruininks, B. M. H., Tsai, S., Marrink, S. J., & Dekker, C. (2023). Synthetic Membrane Shaper for Controlled Liposome Deformation. Acs Nano, 17(2), 966–978. https://doi.org/10.1021/acsnano.2c06125
Marrink, S. J., Monticelli, L., Melo, M. N., Alessandri, R., Tieleman, D. P., & Souza, P. C. T. (2023). Two decades of Martini: Better beads, broader scope. Wiley Interdisciplinary Reviews: Computational Molecular Science, 13(1), Article e1620. https://doi.org/10.1002/wcms.1620
Grünewald, F., Punt, M. H., Jefferys, E. E., Vainikka, P. A., König, M., Virtanen, V., Meyer, T. A., Pezeshkian, W., Gormley, A. J., Karonen, M., Sansom, M. S. P., Souza, P. C. T., & Marrink, S. J. (2022). Martini 3 Coarse-Grained Force Field for Carbohydrates. Journal of Chemical Theory and Computation, 18(12), 7555–7569. https://doi.org/10.1021/acs.jctc.2c00757
Frallicciardi, J., Melcr, J., Siginou, P., Marrink, S. J., & Poolman, B. (2022). Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. Nature Communications, 13(1), Article 1605. https://doi.org/10.1038/s41467-022-29272-x
Patmanidis, I., Souza, P. C. T., Sami, S., Havenith, R. W. A., de Vries, A. H., & Marrink, S. J. (2022). Modelling structural properties of cyanine dye nanotubes at coarse-grained level. Nanoscale advances, 4(14), 3033-3042. https://doi.org/10.1039/d2na00158f
Losa, J., Leupold, S., Alonso-Martinez, D., Vainikka, P., Thallmair, S., Tych, K. M., Marrink, S. J., & Heinemann, M. (2022). Perspective: A stirring role for metabolism in cells. Molecular Systems Biology, 18(4), Article e10822. https://doi.org/10.15252/msb.202110822
Grünewald, F., Alessandri, R., Kroon, P. C., Monticelli, L., Souza, P. C. T., & Marrink, S. J. (2022). Polyply: A python suite for facilitating simulations of macromolecules and nanomaterials. Nature Communications, 13(1), Article 68. https://doi.org/10.1038/s41467-021-27627-4
Versloot, R. C. A., Lucas, F. L. R., Yakovlieva, L., Tadema, M. J., Zhang, Y., Wood, T. M., Martin, N. I., Marrink, S. J., Walvoort, M. T. C., & Maglia, G. (2022). Quantification of Protein Glycosylation Using Nanopores. Nano Letters, 22(13), 5357-5364. Article 2c10338. https://doi.org/10.1021/acs.nanolett.2c01338
Sami, S., Alessandri, R., Jeff, J. B., Grünewald, F., De Vries, A. H., Marrink, S. J., Broer, R., & Havenith, R. W. A. (2022). Strategies for Enhancing the Dielectric Constant of Organic Materials. Journal of Physical Chemistry C, 126(45), 19462-19469. Article 2c05682. https://doi.org/10.1021/acs.jpcc.2c05682
Thallmair, V., Schultz, L., Zhao, W., Marrink, S. J., Oliver, D., & Thallmair, S. (2022). Two cooperative binding sites sensitize PI(4,5)P2 recognition by the tubby domain. Science Advances, 8(36), Article eabp9471. https://doi.org/10.1126/sciadv.abp9471
Krishnaswamy, S. R., Gabrovski, I. A., Patmanidis, I., Stuart, M. C. A., de Vries, A. H., & Pshenichnikov, M. S. (2022). Cryogenic TEM imaging of artificial light harvesting complexes outside equilibrium. Scientific Reports, 12(1), Article 5552. https://doi.org/10.1038/s41598-022-09496-z
Appukutti, N., de Vries, A. H., Gudeangadi, P. G., Claringbold, B. R., Garrett, M. D., Reithofer, M. R., & Serpell, C. J. (2022). Sequence-complementarity dependent co-assembly of phosphodiester-linked aromatic donor-acceptor trimers. Chemical communications (Cambridge, England), 58(87), 12200-12203. https://doi.org/10.1039/d2cc00239f

2021

Machado, N., Bruininks, B. M. H., Singh, P., Dos Santos, L., Dal Pizzol, C., Dieamant, G. D. C., Kruger, O., Martin, A. A., Marrink, S. J., Souza, P. C. T., & Favero, P. P. (2022). Complex nanoemulsion for vitamin delivery: Droplet organization and interaction with skin membranes. Nanoscale, 14(2), 506-514. https://doi.org/10.1039/d1nr04610a
Alessandri, R., Barnoud, J., Gertsen, A. S., Patmanidis, I., de Vries, A. H., Souza, P. C. T., & Marrink, S. J. (2022). Martini 3 Coarse-Grained Force Field: Small Molecules. Advanced theory and simulations, 5(1), Article 2100391. https://doi.org/10.1002/adts.202100391
Azadi-Chegeni, F., Thallmair, S., Ward, M. E., Perin, G., Marrink, S. J., Baldus, M., Morosinotto, T., & Pandit, A. (2022). Protein dynamics and lipid affinity of monomeric, zeaxanthin-binding LHCII in thylakoid membranes. Biophysical Journal, 121(3), 396-409. Article bpj.2021.12.039. https://doi.org/10.1016/j.bpj.2021.12.039
Stehantsev, P., Stetsenko, A., Nemchinova, M., Aduri, N. G., Marrink, S., Gati, C., & Guskov, A. (2021). A structural view onto disease-linked mutations in the human neutral amino acid exchanger ASCT1. Computational and Structural Biotechnology Journal, 19, 5246-5254. https://doi.org/10.1016/j.csbj.2021.09.015
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, 61(5), 2407-2417. 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
Zhang, S., Huang, G., Versloot, R. C. A., Bruininks, B. M. H., de Souza, P. C. T., Marrink, S.-J., & Maglia, G. (2021). Bottom-up fabrication of a proteasome-nanopore that unravels and processes single proteins. Nature Chemistry, 13(12), 1192–1199. https://doi.org/10.1038/s41557-021-00824-w
Liu, Y., de Vries, A. H., Pezeshkian, W., & Marrink, S. J. (2021). Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 17(9), 5876-5884. Article 00151. https://doi.org/10.1021/acs.jctc.1c00151
Tsanai, M., Frederix, PW. J. M., Schroer, C. F. E., Souza, P. C. T., & Marrink, S. J. (2021). Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chemical Science, 12(24), 8521-8530. https://doi.org/10.1039/d1sc00374g
Patmanidis, I., Alessandri, R., de Vries, A. H., & Marrink, S. J. (2021). Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields. Molecules, 26(19), Article 6069. https://doi.org/10.3390/molecules26196069
Ramírez-Palacios, C., Wijma, H. J., Thallmair, S., Marrink, S. J., & Janssen, D. B. (2021). Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. Journal of chemical information and modeling, 61(11), 5569–5580. https://doi.org/10.1021/acs.jcim.1c00617
Meng, Q., Ramírez-Palacios, C., Capra, N., Hooghwinkel, M. E., Thallmair, S., Rozeboom, H. J., Thunnissen, A. M. W. H., Wijma, H. J., Marrink, S. J., & Janssen, D. B. (2021). Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines. ACS Catalysis, 11(17), 10733-10747. https://doi.org/10.1021/acscatal.1c02053
Dong, J., Sami, S., Balazs, D. M., Alessandri, R., Jahani, F., Qiu, L., Marrink, S. J., Havenith, R. W. A., Hummelen, J. C., Loi, M. A., & Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C, 9(45), 16217-16225. https://doi.org/10.1039/d1tc02753k
Kjølbye, L. R., De Maria, L., Wassenaar, T. A., Abdizadeh, H., Marrink, S. J., Ferkinghoff-Borg, J., & Schiøtt, B. (2021). General Protocol for Constructing Molecular Models of Nanodiscs. Journal of chemical information and modeling, 61(6), 2869-2883. Article acs.jcim.1c00157. https://doi.org/10.1021/acs.jcim.1c00157
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
Vainikka, P., Thallmair, S., Souza, P. C. T., & Marrink, S. J. (2021). Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties. ACS Sustainable Chemistry and Engineering, 9(51), 17338-17350. https://doi.org/10.1021/acssuschemeng.1c06521
Thallmair, S., Javanainen, M., Fábián, B., Martinez-Seara, H., & Marrink, S. J. (2021). Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations. Journal of Physical Chemistry B, 125(33), 9537-9546. https://doi.org/10.1021/acs.jpcb.1c03665
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, Article 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
Bruininks, B. M. H., Thie, A. S., Souza, P. C. T., Wassenaar, T. A., Faraji, S., & Marrink, S. J. (2021). Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies. Journal of Chemical Theory and Computation, 17(12), 7873–7885. https://doi.org/10.1021/acs.jctc.1c00446
Pezeshkian, W., & Marrink, S. J. (2021). Simulating realistic membrane shapes. Current Opinion in Cell Biology, 71, 103-111. Article j.ceb.2021.02.009. https://doi.org/10.1016/j.ceb.2021.02.009
Liaci, A. M., Steigenberger, B., Telles de Souza, P. C., Tamara, S., Gröllers-Mulderij, M., Ogrissek, P., Marrink, S. J., Scheltema, R. A., & Förster, F. (2021). Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Molecular Cell, 81(19), 3934-3948.e11. https://doi.org/10.1016/j.molcel.2021.07.031
Alessandri, R., Grünewald, F., & Marrink, S. J. (2021). The Martini Model in Materials Science. Advanced materials, 33(24), Article e2008635. https://doi.org/10.1002/adma.202008635
Marjanovic, A., Ramírez-Palacios, C. J., Masman, M. F., Drenth, J., Otzen, M., Marrink, S.-J., & Janssen, D. B. (2021). Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase. Protein Engineering, Design & Selection, 34, Article gzab016. https://doi.org/10.1093/protein/gzab016
Piskorz, T. K., de Vries, A. H., & van Esch, J. H. (2022). How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers. Journal of Chemical Theory and Computation, 18(1), 431-440. Article acs.jctc.1c00257. https://doi.org/10.1021/acs.jctc.1c00257
Yildirim, A., Tekpinar, M., & Wassenaar, T. A. (2021). Competing Roles of Ca2+and Nonmuscle Myosin IIA on the Dynamics of the Metastasis-Associated Protein S100A4. Journal of Physical Chemistry B, 125(36), 10059-10071. Article 02096. https://doi.org/10.1021/acs.jpcb.1c02096
Molenaar, M. R., Yadav, K. K., Toulmay, A., Wassenaar, T. A., Mari, M. C., Caillon, L., Chorlay, A., Lukmantara, I. E., Haaker, M. W., Wubbolts, R. W., Houweling, M., Vaandrager, A. B., Prieur, X., Reggiori, F., Choudhary, V., Yang, H., Schneiter, R., Thiam, A. R., Prinz, W. A., & Helms, J. B. (2021). Retinyl esters form lipid droplets independently of triacylglycerol and seipin. The Journal of Cell Biology, 220(10), Article 202011071. https://doi.org/10.1083/jcb.202011071

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, Article 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. Article 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), Article 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. Article 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. Article 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, Article 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), Article 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), Article 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. Article 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), Article 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. Article 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), Article 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), Article 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. Article 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), Article 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), Article 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, Article 104911. https://doi.org/10.1016/j.chemphyslip.2020.104911

2019

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), Article 15. https://doi.org/10.1186/s12862-018-1331-x
Pezeshkian, W., König, M., Marrink, S. J., & Ipsen, J. H. (2019). A Multi-Scale Approach to Membrane Remodeling Processes. Frontiers in Molecular Biosciences, 6, Article 59. https://doi.org/10.3389/fmolb.2019.00059
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
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
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, Article 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), Article 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). Article 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. Article j.bpj.2019.03.009. https://doi.org/10.1016/j.bpj.2019.03.009
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
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. https://doi.org/10.1021/acs.jctc.9b00473
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), Article 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
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. Article 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), Article 1006229. https://doi.org/10.1371/journal.pcbi.1006229
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
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), Article 144111. https://doi.org/10.1063/1.5041835
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. Article 370. https://doi.org/10.1016/j.bpj.2017.11.440

2017

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. Article jacs.6b11717. https://doi.org/10.1021/jacs.6b11717
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. Article jpcb.6b07142. https://doi.org/10.1021/acs.jpcb.6b07142
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, Article 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, Article 58. https://doi.org/10.1186/s13321-017-0243-x

2016

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), Article e0162171. https://doi.org/10.1371/journal.pone.0162171
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
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), Article 1005169. https://doi.org/10.1371/journal.pcbi.1005169

2015

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, Article 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), Article 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. Article 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.
Wassenaar, T. A., & Mark, A. E. (2006). The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. Journal of Computational Chemistry, 27(3), 316-325. https://doi.org/10.1002/jcc.20341

2005

de Vries, A. H., Chandrasekhar, I., van Gunsteren, W. F., & Hunenberger, P. H. (2005). Molecular Dynamics Simulations of Phospholipid Bilayers: 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), Article 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), Article 076407. https://doi.org/10.1103/physrevlett.89.076407

2001

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, 64(16), Article 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

1998

Sinclair, P. E., De Vries, A., Sherwood, P., Catlow, C. R. A., & Van Santen, R. A. (1998). Quantum-chemical studies of alkene chemisorption in chabazite: A comparison of cluster and embedded-cluster models. Journal of the Chemical Society - Faraday Transactions, 94(22), 3401-3408. https://doi.org/10.1039/a805616a

1997

Sherwood, P., De Vries, A. H., Collins, S. J., Greatbanks, S. P., Burton, N. A., Vincent, M. A., & Hillier, I. H. (1997). Computer simulation of zeolite structure and reactivity using embedded cluster methods. Faraday Discussions, 106, 79-92. https://doi.org/10.1039/a701790a
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. [Thesis fully internal (DIV), University of 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

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:09 June 2023 8.36 p.m.