Publications

Complete list of articles featuring the Martini Force Field Initiative.

  • Bartender: Martini 3 Bonded Terms via Quantum Mechanics-based Molecular Dynamics
    Gilberto P Pereira, Riccardo Alessandri, Moisés Domínguez, Rocío Araya-Osorio, Linus Grünewald, Luís Borges-Araújo, Sangwook Wu, Siewert J Marrink, Paulo Cesar Telles de Souza, and Raul Mera-Adasme
    chemRxiv (2024)
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  • Benchmarking coarse-grained simulation methods for investigation of transport tunnels in enzymes
    Nishita Mandal, Jan A. Stevens, Adolfo B. Poma, Bartlomiej Surpeta, Carlos Sequeiros-Borja, Aravind Selvaram Thirunavukarasu, Siewert-Jan Marrink, and Jan Brezovsky.
    bioRxiv (2024)
    Details DOI
  • Building complex membranes with Martini 3
    Tugba Nur Ozturk, Melanie König, Timothy S Carpenter, Kasper B Pedersen, Tsjerk A Wassenaar, Helgi I Ingólfsson, and Siewert J Marrink
    Methods in Enzymology (2024)
    Details DOI
  • Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations
    Christopher Brasnett, Armin Kiani, Selim Sami, Sijbren Otto & Siewert J. Marrink
    Communications Chemistry (2024)
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  • GōMartini 3: From large conformational changes in proteins to environmental bias corrections
    Paulo CT Souza, Luis P Borges Araujo, Chris Brasnett, Rodrigo A Moreira, Fabian Grunewald, Peter Park, Liguo Wang, Hafez Razmazma, Ana C Borges-Araujo, Luis F Cofas-Vargas, Luca Monticelli, Raul Mera-Adasme, Manuel N Melo, Sangwook Wu, Siewert J Marrink, Adolfo B Poma, and Sebastian Thallmair
    bioRxiv (2024)
    Details DOI Preprint
  • Hybrid lipid-block copolymer membranes enable stable reconstitution of a wide range of nanopores and robust sampling of serum
    Edo Vreeker, Fabian Grunewald, Nieck van der Heide, Siewert-Jan Marrink, Katarzyna Tych, and Giovanni Maglia
    bioRxiv (2024)
    Details DOI Preprint
  • Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis
    Maria Gabriella Chiariello, Rubi Zarmiento-Garcia and Siewert-Jan Marrink
    International Journal of Molecular Sciences (2024)
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  • Martini 3 OliGo̅mers: A Scalable Approach for Multimers and Fibrils in GROMACS
    Ksenia Korshunova, Julius Kiuru, Juho Liekkinen, Giray Enkavi, Ilpo Vattulainen and Bart M. H. Bruininks
    Journal of Chemical Theory and Computation (2024)
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  • Modeling membranes in situ
    Chelsea M. Brown, and Siewert J. Marrink
    Current Opinion in Structural Biology (2024)
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  • OLIVES: A Go-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field
    Kasper B Pedersen, Luís Borges-Araújo, Amanda D Stange, Paulo CT Souza, Siewert-Jan Marrink, and Birgit Schiøtt
    Journal of Chemical Theory and Computation (2024)
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  • Oxygen partitioning into biomolecular condensates is governed by excluded volume
    Ankush Garg, Christopher Brasnett, Siewert J Marrink, Klaus Koren, and Magnus Kjaergaard
    bioRxiv (2024)
    Details DOI Preprint
  • Probing the stability and interdomain interactions in the ABC transporter OpuA, using single-molecule optical tweezers
    Lyan van der Sleen, Jan Stevens, Siewert J Marrink, Bert Poolman, and Katarzyna Tych
    Cell Reports (2024)
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  • Shocker-a molecular dynamics protocol and tool for accelerating and analyzing the effects of osmotic shocks
    Marco PA van Tilburg, Siewert J Marrink, Melanie König, and Fabian Grünewald
    Journal of Chemical Theory and Computation (2024)
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  • There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning
    Julie Cornet, Nelly Coulonges, Weria Pezeshkian, Maël Penissat-Mahaut, Siewert-Jan Marrink, Nicolas Destainville, Matthieu Chavent, and Manoel Manghi
    Soft Matter (2024)
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  • Vesicle protrusion induced by antimicrobial peptides suggests common carpet mechanism for short antimicrobial peptides
    Peter Park, Danilo Kiyoshi Matsubara, Domenico R Barzotto, Filipe S Lima, Hernan Chaimovich, Siewert Jan Marrink, and Iolanda M Cuccovia
    Scientific Reports (2024)
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  • A Guide to Titratable Martini Simulations
    Selim Sami, Fabian Grünewald, Paulo C. T. Souza and Siewert J. Marrink
    A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules (2023)
    Details DOI
  • A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations
    Riccardo Alessandri, Sebastian Thallmair, Cristina Gil Herrero, Raúl Mera-Adasmem, Siewert J. Marrink and Paulo C. T. Souza
    A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules (2023)
    Details DOI
  • Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG
    Charly Empereur-mot, Kasper B. Pedersen, Riccardo Capelli, Martina Crippa, Cristina Caruso, Mattia Perrone, Paulo C. T. Souza, Siewert J. Marrink and Giovanni M. Pavan
    Journal of chemical information and modeling (2023)
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  • CRAFTing Delivery of Membrane Proteins into Protocells using Nanodiscs
    Piotr Stępień, Sylwia Świątek, Manuel Yamil Yusef Robles, Joanna Markiewicz-Mizera, Dhanasekaran Balakrishnan, Satomi Inaba-Inoue, Alex H De Vries, Konstantinos Beis, Siewert J Marrink, and Jonathan G Heddle
    ACS Applied Materials & Interfaces (2023)
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  • Curvature-induced lipid sorting beyond the critical packing parameter
    Melanie Konig, Reinier de Vries, Fabian Grunewald, Siewert-Jan Marrink, and Weria Pezeshkian
    bioRxiv (2023)
    Details DOI Preprint
  • Dynamics of chromosome organization in a minimal bacterial cell
    Benjamin R. Gilbert, Zane R. Thornburg, Troy A. Brier, Jan A. Stevens, Fabian Grünewald, John E. Stone, Siewert J. Marrink and Zaida Luthey-Schulten
    Frontiers in Cell and Developmental Biology (2023)
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  • Expulsion mechanism of the substrate-translocating subunit in ECF transporters
    Chancievan Thangaratnarajah, Mark Nijland, Luís Borges-Araújo, Aike Jeucken, Jan Rheinberger, Siewert J. Marrink, Paulo C. T. Souza, Cristina Paulino & Dirk J. Slotboom
    Nature Communications (2023)
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  • Facilitating CG Simulations with MAD: The MArtini Database Server
    Cécile Hilpert, Louis Beranger, Paulo C. T. Souza, Petteri A. Vainikka, Vincent Nieto, Siewert J. Marrink, Luca Monticelli and Guillaume Launay
    Journal of chemical information and modeling (2023)
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  • Identification of inhibitors targeting the energy-coupling factor (ECF) transporters
    Eleonora Diamanti, Paulo C. T. Souza, Inda Setyawati, Spyridon Bousis, Leticia Monjas, Lotteke J.Y.M. Swier, Atanaz Shams, Aleksei Tsarenko, Weronika K. Stanek, Manuel Jäger, Siewert J. Marrink, Dirk J. Slotboom & Anna K. H. Hirsch
    Communications biology (2023)
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  • Lateral membrane organization as target of an antimicrobial peptidomimetic compound
    Adéla Melcrová, Sourav Maity, Josef Melcr, Niels A. W. de Kok, Mariella Gabler, Jonne van der Eyden, Wenche Stensen, John S. M. Svendsen, Arnold J. M. Driessen, Siewert J. Marrink & Wouter H. Roos
    Nature Communications (2023)
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  • Martini 3 Coarse-Grained Force Field for Cholesterol
    Luís Borges-Araújo, Ana C. Borges-Araújo, Tugba Nur Ozturk, Daniel P. Ramirez-Echemendia, Balázs Fábián, Timothy S. Carpenter, Sebastian Thallmair, Jonathan Barnoud, Helgi I. Ingólfsson, Gerhard Hummer, D. Peter Tieleman, Siewert J. Marrink, Paulo C. T. Souza, and Manuel N. Melo
    Journal of Chemical Theory and Computation (2023)
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  • Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches
    Petteri Vainikka and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2023)
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  • Martinize2 and Vermouth: Unified Framework for Topology Generation
    Peter C. Kroon, Fabian Grünewald, Jonathan Barnoud, Marco van Tilburg, Paulo C. T. Souza, Tsjerk A. Wassenaar, Siewert-Jan Marrink
    eLife (2023)
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  • Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis
    Apilaasha Tharmasothirajan, Josef Melcr, John Linney, Thomas Gensch, Karin Krumbach, Karla Marlen Ernst, Christopher Brasnett, Paola Poggi, Andrew R. Pitt, Alan D. Goddard, Alexandros Chatgilialoglu, Siewert J. Marrink & Jan Marienhagen
    Nature Communications (2023)
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  • Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling
    Weria Pezeshkian, Fabian Grünewald, Oleksandr Narykov, Senbao Lu, Valeria Arkhipova, Alexey Solodovnikov, Tsjerk A. Wassenaar, Siewert J. Marrink and Dmitry Korkin
    Structure (2023)
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  • Molecular basis of PIP2-dependent conformational switching of phosphorylated CD44 in binding FERM
    Meina Ren, Lina Zhao, Ziyi Ma, Hailong An, Siewert Jan Marrink and Fude Sun
    Biophysical Journal (2023)
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  • Molecular dynamics simulation of an entire cell
    Jan A. Stevens, Fabian Grünewald, P. A. Marco van Tilburg, Melanie König, Benjamin R. Gilbert, Troy A. Brier, Zane R. Thornburg, Zaida Luthey-Schulten and Siewert J. Marrink
    Frontiers in Chemistry (2023)
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  • Molecular insights into the effects of focused ultrasound mechanotherapy on lipid bilayers: Unlocking the keys to design effective treatment
    Alexandre Blanco-González, Siewert J. Marrink, Ángel Piñeiro, Rebeca García-Fandiño
    Journal of Colloid and Interface Science (2023)
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  • Multiscale simulations reveal TDP-43 molecularlevel interactions driving condensation
    Helgi I. Ingólfsson, Azamat Rizuan, Xikun Liu, Priyesh Mohanty, Paulo C.T. Souza, Siewert J. Marrink, Michael T. Bowers, Jeetain Mittal, Joel Berry
    Biophysical Journal (2023)
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  • 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
    Barbora Waclawiková, Paulo Cesar Telles de Souza, Markus Schwalbe, Constantinos G. Neochoritis, Warner Hoornenborg, Sieger A. Nelemans, Siewert J. Marrink & Sahar El Aidy
    Gut microbes (2023)
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  • Pragmatic Coarse-Graining of Proteins: Models and Applications
    Luís Borges-Araújo, Ilias Patmanidis, Akhil P. Singh, Lucianna H. S. Santos, Adam K. Sieradzan, Stefano Vanni, Cezary Czaplewski, Sergio Pantano, Wataru Shinoda, Luca Monticelli, Adam Liwo, Siewert J. Marrink, and Paulo C. T. Souza
    Journal of Chemical Theory and Computation (2023)
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  • Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations
    Selim Sami and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2023)
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  • Synthetic Membrane Shaper for Controlled Liposome Deformation
    Nicola De Franceschi, Weria Pezeshkian, Alessio Fragasso, Bart M. H. Bruininks, Sean Tsai, Siewert J. Marrink, and Cees Dekker
    ACS nano (2023)
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  • Two decades of Martini: Better beads, broader scope
    Siewert J. Marrink, Luca Monticelli, Manuel N. Melo, Riccardo Alessandri, D. Peter Tieleman and Paulo C. T. Souza
    Wiley Interdisciplinary Reviews: Computational Molecular Science (2023)
    Details DOI
  • Watching Molecular Nanotubes Self-Assemble in Real Time
    Marìck Manrho, Sundar Raj Krishnaswamy, Björn Kriete, Ilias Patmanidis, Alex H. de Vries, Siewert J. Marrink, Thomas L. C. Jansen, Jasper Knoester, and Maxim S. Pshenichnikov
    Journal of the American Chemical Society (2023)
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  • pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer
    Maria Gabriella Chiariello, Fabian Grünewald, Rubi Zarmiento-Garcia, and Siewert J. Marrink
    The Journal of Physical Chemistry Letters (2023)
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  • Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes
    Neila Machado, Bart M. H. Bruininks, Priyanka Singh, Laurita dos Santos, Carine Dal Pizzol, Gustavo de C. Dieamant, Odivania Kruger, Airton A. Martin, Siewert J. Marrink, Paulo C. T. Souza and Priscila P. Favero
    Nanoscale (2022)
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  • Martini 3 Coarse-Grained Force Field for Carbohydrates
    Fabian Grünewald, Mats H. Punt, Elizabeth E. Jefferys, Petteri A. Vainikka, Melanie König, Valtteri Virtanen, Travis A. Meyer, Weria Pezeshkian, Adam J. Gormley, Maarit Karonen, Mark S. P. Sansom, Paulo C. T. Souza and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2022)
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  • Martini 3 Coarse-Grained Force Field: Small Molecules
    Riccardo Alessandri, Jonathan Barnoud, Anders S. Gertsen, Ilias Patmanidis, Alex H. deVries, Paulo C. T. Souza, and Siewert J. Marrink
    Advanced Theory and Simulations (2022)
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  • Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes
    Jacopo Frallicciardi, Josef Melcr, Pareskevi Siginou, Siewert J. Marrink & Bert Poolman
    Nature communications (2022)
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  • Modelling structural properties of cyanine dye nanotubes at coarse-grained level
    Ilias Patmanidis, Paulo C. T. Souza, Selim Sami, Remco W. A. Havenith, Alex H. de Vries and Siewert J. Marrink
    Nanoscale advances (2022)
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  • Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials
    Fabian Grünewald, Riccardo Alessandri, Peter C. Kroon, Luca Monticelli, Paulo C. T. Souza & Siewert J. Marrink
    Nature communications (2022)
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  • Protein dynamics and lipid affinity of monomeric, zeaxanthin-binding LHCII in thylakoid membranes
    Fatemeh Azadi-Chegeni, Sebastian Thallmair, Meaghan E. Ward, Giorgio Perin, Siewert J. Marrink, Marc Baldus, Tomas Morosinotto, Anjali Pandit
    Biophysical journal (2022)
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  • Two cooperative binding sites sensitize PI(4,5)P2 recognition by the tubby domain
    Veronika Thallmair, Lea Schultz, Wencai Zhao, Siewert J. Marrink, Dominik Oliver and Sebastian Thallmair
    Science advances (2022)
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  • Asymmetric CorA gating mechanism as observed by molecular dynamics simulations
    Mariia Nemchinova, Josef Melcr, Tsjerk A. Wassenaar, Siewert J. Marrink, and Albert Guskov
    Journal of chemical information and modeling (2021)
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  • Bottom-up fabrication of a proteasome–nanopore that unravels and processes single proteins
    Shengli Zhang, Gang Huang, Roderick Corstiaan Abraham Versloot, Bart Marlon Herwig Bruininks, Paulo Cesar Telles de Souza, Siewert-Jan Marrink & Giovanni Maglia
    Nature chemistry (2021)
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  • Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations
    Yang Liu, Alex H. de Vries, Weria Pezeshkian, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2021)
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  • Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model
    Maria Tsanai, Pim WJM Frederix, Carsten FE Schroer, Paulo CT Souza, Siewert J Marrink
    Chemical Science (2021)
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  • Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies
    Filipe M Sousa, Luís MP Lima, Clément Arnarez, Manuela M Pereira, Manuel N Melo
    Journal of Chemical Information and Modeling (2021)
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  • Development of Martini 2.2 parameters for N-glycans: A case study of the HIV-1 Env glycoprotein dynamics
    Srirupa Chakraborty, Kshitij Wagh, S Gnanakaran, Cesar A López
    Glycobiology (2021)
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  • Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field
    Luís Borges-Araújo, Paulo C. T. Souza, Fábio Fernandes, and Manuel N. Melo
    Journal of Chemical Theory and Computation (2021)
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  • Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties
    Petteri Vainikka, Sebastian Thallmair, Paulo Cesar Telles Souza, Siewert J Marrink
    ACS Sustainable Chemistry & Engineering (2021)
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  • Martini 3: a general purpose force field for coarse-grained molecular dynamics
    Paulo CT Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grünewald, Ilias Patmanidis, Haleh Abdizadeh, Bart MH Bruininks, Tsjerk A Wassenaar, Peter C Kroon, Josef Melcr, Vincent Nieto, Valentina Corradi, Hanif M Khan, Jan Domański, Matti Javanainen, Hector Martinez-Seara, Nathalie Reuter, Robert B Best, Ilpo Vattulainen, Luca Monticelli, Xavier Periole, D Peter Tieleman, Alex H de Vries, Siewert J Marrink
    Nature Methods (2021)
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  • Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations
    Sebastian Thallmair, Matti Javanainen, Balázs Fábián, Hector Martinez-Seara, and Siewert J. Marrink
    The Journal of Physical Chemistry B (2021)
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  • Perspectives on high-throughput ligand/protein docking with martini MD simulations
    Paulo C. T. Souza, Vittorio Limongelli, Sangwook Wu, Siewert J. Marrink and Luca Monticelli
    Frontiers in Molecular Biosciences (2021)
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  • Protocol for Simulations of PEGylated Proteins with Martini 3
    Fabian Grünewald, Peter C Kroon, Paulo CT Souza, Siewert J Marrink
    Structural Genomics: Methods in Molecular Biology (2021)
    Details DOI
  • Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies
    Bart M. H. Bruininks*, Albert S. Thie, Paulo C. T. Souza, Tsjerk A. Wassenaar, Shirin Faraji, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2021)
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  • Simulating realistic membrane shapes
    Weria Pezeshkian and Siewert J. Marrink
    Current opinion in cell biology (2021)
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  • Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage
    A. Manuel Liaci, Barbara Steigenberger, Paulo Cesar Telles de Souza, Sem Tamara, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert J. Marrink, Richard A. Scheltema and Friedrich Förster
    Molecular cell (2021)
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  • The Martini model in materials science
    Riccardo Alessandri, Fabian Grünewald, Siewert J Marrink
    Advanced Materials (2021)
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  • A molecular view on the escape of lipoplexed DNA from the endosome
    Bart MH Bruininks, Paulo CT Souza, Helgi Ingolfsson and Siewert J Marrink
    Elife (2020)
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  • Backmapping triangulated surfaces to coarse-grained membrane models
    Weria Pezeshkian, Melanie König, Tsjerk A Wassenaar, Siewert J Marrink
    Nature communications (2020)
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  • Capturing Choline–Aromatics Cation− π Interactions in the MARTINI Force Field
    Hanif M Khan, Paulo CT Souza, Sebastian Thallmair, Jonathan Barnoud, Alex H De Vries, Siewert J Marrink, Nathalie Reuter
    Journal of Chemical Theory and Computation (2020)
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  • Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization
    Sourav Maity, Jim Ottelé, Guillermo Monreal Santiago, Pim W. J. M. Frederix, Peter Kroon, Omer Markovitch, Marc C. A. Stuart, Siewert J. Marrink, Sijbren Otto, and Wouter H. Roos
    Journal of the American Chemical Society (2020)
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  • Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers
    Carsten F. E. Schroer, Lucia Baldauf, Lennard van Buren, Tsjerk A. Wassenaar, Manuel N. Melo, Gijsje H. Koenderink, and Siewert J. Marrink
    Proceedings of the National Academy of Sciences (2020)
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  • Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange
    Yang Liu, Weria Pezeshkian, Jonathan Barnoud, Alex H de Vries, Siewert J Marrink
    Journal of chemical theory and computation (2020)
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  • Dual Resolution Membrane Simulations Using Virtual Sites
    Yang Liu, Alex H De Vries, Jonathan Barnoud, Weria Pezeshkian, Josef Melcr, Siewert J Marrink
    The Journal of Physical Chemistry B (2020)
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  • Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains
    Juanjuan Su, Siewert J. Marrink and Manuel N. Melo
    Frontiers in cell and developmental biology (2020)
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  • Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid-liquid extraction
    Luis Itza Vazquez-Salazar, Michele Selle, Alex H De Vries, Siewert-Jan Marrink, Paulo CT Souza
    Green Chemistry (2020)
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  • Membrane mediated toppling mechanism of the folate energy coupling factor transporter
    Ignacio Faustino, Haleh Abdizadeh, Paulo C. T. Souza, Aike Jeucken, Weronika K. Stanek, Albert Guskov, Dirk J. Slotboom & Siewert J. Marrink
    Nature Communications (2020)
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  • Molecular dynamics simulations in photosynthesis
    Nicoletta Liguori, Roberta Croce, Siewert J. Marrink and Sebastian Thallmair
    Photosynthesis research (2020)
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  • Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2
    Fude Sun, Carsten F. E. Schroer, Carlos R. Palacios, Lida Xu, Shi-Zhong Luo and Siewert J. Marrink
    PLoS Computational Biology (2020)
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  • Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol
    Amanda Buyan, Charles D. Cox, Jonathan Barnoud, Jinyuan Li, Hannah S.M. Chan, Boris Martinac, Siewert J. Marrink, Ben Corry
    Biophysical journal (2020)
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  • Protein–ligand binding with the coarse-grained Martini model
    Paulo CT Souza, Sebastian Thallmair, Paolo Conflitti, Carlos Ramírez-Palacios, Riccardo Alessandri, Stefano Raniolo, Vittorio Limongelli, Siewert J Marrink
    Nature communications (2020)
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  • Resolving Donor–Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains
    Riccardo Alessandri, Selim Sami, Jonathan Barnoud, Alex H. de Vries, Siewert J. Marrink and Remco W. A. Havenith
    Advanced Functional Materials (2020)
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  • Titratable Martini model for constant pH simulations
    Fabian Grünewald, Paulo CT Souza, Haleh Abdizadeh, Jonathan Barnoud, Alex H de Vries, Siewert J Marrink
    The Journal of Chemical Physics (2020)
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  • A Multi-Scale Approach to Membrane Remodeling Processes
    Weria Pezeshkian, Melanie König, Siewert J. Marrink and John H. Ipsen
    Frontiers in molecular biosciences (2019)
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  • A Practical View of the MARTINI Force Field
    Bart MH Bruininks, Paulo CT Souza, Siewert J Marrink
    Biomolecular Simulations (2019)
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  • An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation
    Paulo C. T. Souza, Sebastian Thallmair, Siewert J. Marrink, and Raúl Mera-Adasme
    The journal of physical chemistry letters (2019)
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  • Ceramides bind VDAC2 to trigger mitochondrial apoptosis
    Shashank Dadsena, Svenja Bockelmann, John G. M. Mina, Dina G. Hassan, Sergei Korneev, Guilherme Razzera, Helene Jahn, Patrick Niekamp, Dagmar Müller, Markus Schneider, Fikadu G. Tafesse, Siewert J. Marrink, Manuel N. Melo & Joost C. M. Holthuis
    Nature Communications (2019)
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  • Computational Modeling of Realistic Cell Membranes
    Siewert J. Marrink, Valentina Corradi, Paulo C.T. Souza, Helgi I. Ingólfsson, D. Peter Tieleman, and Mark S.P. Sansom
    Chemical Reviews (2019)
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  • Emerging Diversity in Lipid–Protein Interactions
    Valentina Corradi, Besian I. Sejdiu, Haydee Mesa-Galloso, Haleh Abdizadeh, Sergei Yu. Noskov, Siewert J. Marrink, and D. Peter Tieleman
    Chemical reviews (2019)
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  • Gangliosides Destabilize Lipid Phase Separation in Multicomponent Membranes
    Yang Liu, Jonathan Barnoud, and Siewert J. Marrink
    Biophysical Journal (2019)
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  • Lipid Fingerprints and Cofactor Dynamics of Light Harvesting Complex II in Different Membranes
    Sebastian Thallmair, Petteri A. Vainikka, and Siewert J. Marrink
    Biophysical journal (2019)
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  • Nucleation Mechanisms of Self-Assembled Physisorbed Monolayers on Graphite
    Tomasz K. Piskorz, Cristian Gobbo, Siewert J. Marrink, Steven De Feyter, Alex H. de Vries, and Jan H. van Esch
    The Journal of Physical Chemistry C (2019)
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  • Pitfalls of the MARTINI Model
    Riccardo Alessandri, Paulo Cesar Telles de Souza, Sebastian Thallmair, Manuel N Melo, Alex H De Vries, Siewert J Marrink
    Journal of Chemical Theory and Computation (2019)
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  • SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids
    Julija Zavadlav, Siewert J Marrink, Matej Praprotnik
    Interface focus (2019)
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  • Serine Phosphorylation of L-Selectin Regulates ERM Binding, Clustering, and Monocyte Protrusion in Transendothelial Migration
    Abigail Newe, Karolina Rzeniewicz, Melanie König, Carsten F. E. Schroer, Justin Joachim, Angela Rey-Gallardo, Siewert J. Marrink, Jürgen Deka, Maddy Parsons and Aleksandar Ivetic
    (2019)
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  • Two distinct anionic phospholipid-dependent events involved in SecA-mediated protein translocation
    Sabrina Koch, Marten Exterkate, Cesar A. López, Megha Patro, Siewert J. Marrink and Arnold J.M. Driessen
    Biochimica et Biophysica Acta (BBA)-Biomembranes (2019)
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  • Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models
    Sebastian Thallmair, Helgi I. Ingólfsson, and Siewert J. Marrink
    The journal of physical chemistry letters (2018)
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  • Curvature-Induced Sorting of Lipids in Plasma Membrane Tethers
    Svetlana Baoukina, Helgi I. Ingólfsson, Siewert J. Marrink and D. Peter Tieleman
    Advanced Theory and Simulations (2018)
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  • Enhancing Molecular n-Type Doping of Donor–Acceptor Copolymers by Tailoring Side Chains
    Jian Liu, Li Qiu, Riccardo Alessandri, Xinkai Qiu, Giuseppe Portale, JingJin Dong, Wytse Talsma, Gang Ye, Aprizal Akbar Sengrian, Paulo C. T. Souza, Maria Antonietta Loi, Ryan C. Chiechi, Siewert J. Marrink, Jan C. Hummelen, and L. Jan Anton Koster
    Advanced Materials (2018)
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  • Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins
    Valentina Corradi, Eduardo Mendez-Villuendas, Helgi I. Ingólfsson, Ruo-Xu Gu, Iwona Siuda, Manuel N. Melo, Anastassiia Moussatova, Lucien J. DeGagné, Besian I. Sejdiu, Gurpreet Singh, Tsjerk A. Wassenaar, Karelia Delgado Magnero, Siewert J. Marrink, and D. Peter Tieleman
    ACS Central Science (2018)
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  • Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2
    Fude Sun, Carsten F.E. Schroer, Lida Xu, Huiwei Yin, Siewert J. Marrink, and Shi-Zhong Luo
    Biophysical journal (2018)
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  • Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers
    Minmin Xue, Lisheng Cheng, Ignacio Faustino, Wanlin Guo, and Siewert J. Marrink
    Biophysical journal (2018)
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  • Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments
    Pim W. J. M. Frederix, Ilias Patmanidis and Siewert J. Marrink
    Chemical Society Reviews (2018)
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  • Role of Charge and Hydrophobicity in Liprotide Formation: A Molecular Dynamics Study with Experimental Constraints
    Jannik Nedergaard Pedersen, Pim Wilhelmus Johannes Maria Frederix, Jan Skov Pedersen, Siewert Jan Marrink, and Daniel E. Otzen
    ChemBioChem (2018)
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  • The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission
    Juanjuan Su, Ann S. Thomas, Tanja Grabietz, Christiane Landgraf, Rudolf Volkmer, Siewert J. Marrink, Chris Williams, and Manuel N. Melo
    Biochimica et Biophysica Acta (BBA)-Biomembranes (2018)
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  • Transferable MARTINI Model of Poly (ethylene Oxide)
    Fabian Grunewald, Giulia Rossi, Alex H de Vries, Siewert J Marrink, Luca Monticelli
    The Journal of Physical Chemistry B (2018)
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  • Alcohol Interactions with Lipid Bilayers
    Tomáš Kondela, Jana Gallová, Thomas Hauß, Jonathan Barnoud, Siewert-J. Marrink and Norbert Kučerka
    Molecules (2017)
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  • Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations
    Riccardo Alessandri, Jaakko J. Uusitalo, Alex H. de Vries, Remco W. A. Havenith, and Siewert J. Marrink
    Journal of the American Chemical Society (2017)
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  • CHARMM‐GUI MARTINI Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides
    Pin‐Chia Hsu, Bart MH Bruininks, Damien Jefferies, Paulo Cesar Telles de Souza, Jumin Lee, Dhilon S Patel, Siewert J Marrink, Yifei Qi, Syma Khalid, Wonpil Im
    Journal of Computational Chemistry (2017)
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  • Computational Lipidomics of the Neuronal Plasma Membrane
    Helgi I. Ingólfsson, Timothy S. Carpenter, Harsh Bhatia, Peer-Timo Bremer, Siewert J. Marrink, and Felice C. Lightstone
    Biophysical journal (2017)
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  • Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding
    Boqun Liu, Christoffer Åberg, Floris J. van Eerden, Siewert J. Marrink, Bert Poolman, and Arnold J. Boersma
    Biophysical journal (2017)
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  • Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics
    Li Qiu, Jian Liu, Riccardo Alessandri, Xinkai Qiu, Marten Koopmans, Remco W. A. Havenith, Siewert J. Marrink, Ryan C. Chiechi, L. Jan Anton Koster and Jan C. Hummelen
    Journal of materials chemistry A (2017)
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  • Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex
    Floris J. Van Eerden, Manuel N. Melo, Pim W. J. M. Frederix, Xavier Periole & Siewert J. Marrink
    Nature Communications (2017)
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  • Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations
    Ruo-Xu Gu, Helgi I. Ingólfsson, Alex H. de Vries, Siewert J. Marrink, and D. Peter Tieleman
    The Journal of Physical Chemistry B (2017)
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  • Lipid and Peptide Diffusion in Bilayers: The Saffman–Delbrück Model and Periodic Boundary Conditions
    Richard M. Venable, Helgi I. Ingólfsson, Michael G. Lerner, B. Scott Perrin, Jr., Brian A. Camley, Siewert J. Marrink, Frank L. H. Brown, and Richard W. Pastor
    The Journal of Physical Chemistry B (2017)
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  • MARTINI coarse-grained force field: extension to RNA
    Jaakko J Uusitalo, Helgi I Ingólfsson, Siewert J Marrink, Ignacio Faustino
    Biophysical journal (2017)
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  • Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane
    Floris J. van Eerden, Tom van den Berg, Pim W. J. M. Frederix, Djurre H. de Jong, Xavier Periole, and Siewert J. Marrink
    The Journal of Physical Chemistry B (2017)
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  • Parameterization of palmitoylated cysteine, farnesylated cysteine, geranylgeranylated cysteine, and myristoylated glycine for the martini force field
    Yoav Atsmon-Raz, D Peter Tieleman
    The Journal of Physical Chemistry B (2017)
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  • Prediction of Thylakoid Lipid Binding Sites on Photosystem II
    Floris J. Van Eerden, Manuel N. Melo, Pim W.J.M. Frederix, and Siewert J. Marrink
    Biophysical journal (2017)
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  • Stability and dynamics of membrane-spanning DNA nanopores
    Vishal Maingi, Jonathan R. Burns, Jaakko J. Uusitalo, Stefan Howorka, Siewert J. Marrink & Mark S. P. Sansom
    Nature Communications (2017)
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  • cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations
    Ignacio Faustino, and S J Marrink
    Bioinformatics (2017)
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  • Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles
    Julija Zavadlav, Siewert J. Marrink, and Matej Praprotnik
    Journal of chemical theory and computation (2016)
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  • Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution
    J. Zavadlav, R. Podgornik, M.N. Melo, S.J. Marrink & M. Praprotnik
    The European Physical Journal Special Topics (2016)
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  • Computational ‘microscopy’ of cellular membranes
    Helgi I. Ingólfsson, Clément Arnarez, Xavier Periole, and Siewert J. Marrink
    Journal of cell science (2016)
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  • MARTINI straight: Boosting performance using a shorter cutoff and GPUs
    Djurre H De Jong, Svetlana Baoukina, Helgi I Ingólfsson, Siewert J Marrink
    Computer Physics Communications (2016)
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  • Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes
    C. Arnarez, S. J. Marrink and X. Periole
    Chemical Science (2016)
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  • Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
    Julija Zavadlav, Manuel N. Melo, Siewert J. Marrink, and Matej Praprotnik
    The Journal of Chemical Physics (2015)
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  • Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex
    Djurre H. de Jong, Nicoletta Liguori, Tom van den Berg, Clement Arnarez, Xavier Periole, and Siewert J. Marrink
    The Journal of Physical Chemistry B (2015)
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  • Benchmark of Schemes for Multiscale Molecular Dynamics Simulations
    N. Goga, M. N. Melo, A. J. Rzepiela, A. H. de Vries†, A. Hadar, S. J. Marrink, and H. J. C. Berendsen
    Journal of Chemical Theory and Computation (2015)
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  • CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
    Yifei Qi, Helgi I. Ingólfsson, Xi Cheng, Jumin Lee, Siewert J. Marrink, and Wonpil Im
    Journal of Chemical Theory and Computation (2015)
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  • Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations
    Floris J. van Eerden, Djurre H. de Jong, Alex H. de Vries, Tsjerk A. Wassenaar, and Siewert J. Marrink
    Biochimica et Biophysica Acta (BBA)-Biomembranes (2015)
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  • Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
    Tsjerk A. Wassenaar, Helgi I. Ingólfsson, Rainer A. Böckmann, D. Peter Tieleman, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2015)
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  • Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent
    Clément Arnarez, Jaakko J. Uusitalo, Marcelo F. Masman, Helgi I. Ingólfsson, Djurre H. de Jong, Manuel N. Melo, Xavier Periole, Alex H. de Vries, and Siewert J. Marrink
    Journal of chemical theory and computation (2015)
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  • High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach
    Tsjerk A. Wassenaar, Kristyna Pluhackova, Anastassiia Moussatova, Durba Sengupta, Siewert J. Marrink, D. Peter Tieleman, and Rainer A. Böckmann
    Journal of Chemical Theory and Computation (2015)
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  • Martini Coarse-Grained Force Field: Extension to DNA
    Jaakko J. Uusitalo, Helgi I. Ingólfsson, Parisa Akhshi, D. Peter Tieleman, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2015)
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  • Parameters for MARTINI sterols and hopanoids based on a virtual-site description
    MN Melo, HI Ingólfsson, SJ Marrink
    The Journal of Chemical Physics (2015)
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  • Adaptive Resolution Simulation of MARTINI Solvents
    Julija Zavadlav, Manuel N. Melo, Ana V. Cunha, Alex H. de Vries, Siewert J. Marrink, and Matej Praprotnik
    Journal of Chemical Theory and Computation (2014)
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  • Adaptive resolution simulation of an atomistic protein in MARTINI water
    Julija Zavadlav, Manuel Nuno Melo, Siewert J. Marrink, and Matej Praprotnik
    The Journal of chemical physics (2014)
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  • Disaccharides Impact the Lateral Organization of Lipid Membranes
    Gemma Moiset, Cesar A. López, Rianne Bartelds, Lukasz Syga, Egon Rijpkema, Abhishek Cukkemane, Marc Baldus, Bert Poolman, and Siewert J. Marrink
    Journal of the American Chemical Society (2014)
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  • Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry
    Albert Konijnenberg, Duygu Yilmaz, Helgi I. Ingólfsson, Anna Dimitrova, Siewert J. Marrink, Zhuolun Li, Catherine Vénien-Bryan, Frank Sobott, and Armağan Koçer
    Proceedings of the National Academy of Sciences (2014)
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  • Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
    Tsjerk A. Wassenaar, Kristyna Pluhackova, Rainer A. Böckmann, Siewert J. Marrink, and D. Peter Tieleman
    Journal of Chemical Theory and Computation (2014)
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  • Helfrich model of membrane bending: From Gibbs theory of liquid interfaces to membranes as thick anisotropic elastic layers
    Felix Campelo, Clement Arnarez, Siewert J. Marrink, and Michael M. Kozlov
    Advances in colloid and interface science (2014)
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  • Hydrophobic Compounds Reshape Membrane Domains
    Jonathan Barnoud, Giulia Rossi, Siewert J. Marrink, and Luca Monticelli
    PLoS Computational Biology (2014)
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  • Lipid Organization of the Plasma Membrane
    Helgi I. Ingólfsson, Manuel N. Melo, Floris J. van Eerden, Clément Arnarez, Cesar A. Lopez, Tsjerk A. Wassenaar, Xavier Periole, Alex H. de Vries, D. Peter Tieleman, and Siewert J. Marrink
    Journal of the American Chemical Society (2014)
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  • MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers
    César A. López, Giovanni Bellesia, Antonio Redondo, Paul Langan, Shishir P. S. Chundawat, Bruce E. Dale, Siewert J. Marrink, and S. Gnanakaran
    The Journal of Physical Chemistry B (2014)
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  • Phytochemicals Perturb Membranes and Promiscuously Alter Protein Function
    Helgi I. Ingólfsson, Pratima Thakur, Karl F. Herold, E. Ashley Hobart, Nicole B. Ramsey, Xavier Periole, Djurre H. de Jong, Martijn Zwama, Duygu Yilmaz, Katherine Hall, Thorsten Maretzky, Hugh C. Hemmings, Jr., Carl Blobel, Siewert J. Marrink, Armağan Koçer, Jon T. Sack, and Olaf S. Andersen
    ACS Chemical Biology (2014)
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  • Simulation of polyethylene glycol and calcium-mediated membrane fusion
    Martina Pannuzzo, Djurre H. De Jong, Antonio Raudino, and Siewert J. Marrink
    The Journal of Chemical Physics (2014)
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  • The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension-induced gating
    Nobina Mukherjee, Mac Donald Jose, Jan Peter Birkner, Martin Walko, Helgi I. Ingólfsson, Anna Dimitrova, Clément Arnarez, Siewert J. Marrink, and Armağan Koçer
    The FASEB Journal (2014)
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  • The power of coarse graining in biomolecular simulations
    Helgi I. Ingólfsson, Cesar A. Lopez, Jaakko J. Uusitalo, Djurre H. de Jong, Srinivasa M. Gopal, Xavier Periole, and Siewert J. Marrink
    Wiley Interdisciplinary Reviews: Computational Molecular Science (2014)
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  • Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: A theoretical and computational study
    Antonio Raudino, Siewert J. Marrink, and Martina Pannuzzo
    The Journal of Chemical Physics (2013)
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  • Coarse-grain modelling of protein–protein interactions
    Marc Baaden, Siewert J Marrink
    Current Opinion in Structural Biology (2013)
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  • Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes
    Cesar A. López, Alex H. de Vries & Siewert J. Marrink
    Scientific reports (2013)
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  • Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc1
    Clement Arnarez, Jean-Pierre Mazat, Juan Elezgaray, Siewert-J Marrink, and Xavier Periole
    Journal of the American Chemical Society (2013)
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  • Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model
    Mingyang Hu, Djurre H. de Jong, Siewert J. Marrink and Markus Deserno
    Faraday Discussions (2013)
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  • Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels
    Clement Arnarez, Siewert-J Marrink, and Xavier Periole
    Scientific Reports (2013)
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  • Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations
    Monica Bulacu, Nicolae Goga, Wei Zhao, Giulia Rossi, Luca Monticelli, Xavier Periole, D. Peter Tieleman, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2013)
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  • Improved Parameters for the Martini Coarse-Grained Protein Force Field
    Djurre H. de Jong, Gurpreet Singh, W. F. Drew Bennett, Clement Arnarez, Tsjerk A. Wassenaar, Lars V. Schäfer, Xavier Periole, D. Peter Tieleman, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2013)
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  • Interbilayer repulsion forces between tension-free lipid bilayers from simulation
    Yuliya G. Smirnova, Sebastian Aeffner, Herre Jelger Risselada, Tim Salditt, Siewert-Jan Marrink, Marcus Müller, and Volker Knecht
    Soft Matter (2013)
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  • MARTINI Model for Physisorption of Organic Molecules on Graphite
    Cristian Gobbo, Isabelle Beurroies, David de Ridder, Rienk Eelkema, Siewert J. Marrink, Steven De Feyter, Jan H. van Esch, and Alex H. de Vries
    The Journal of Physical Chemistry C (2013)
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  • Martini Force Field Parameters for Glycolipids
    César A. López, Zofie Sovova, Floris J. van Eerden, Alex H. de Vries, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2013)
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  • Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic–Coarse-Grained Biomolecular Simulations
    Tsjerk A. Wassenaar, Helgi I. Ingólfsson, Marten Prieß, Siewert J. Marrink, and Lars V. Schäfer
    The Journal of Physical Chemistry B (2013)
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  • Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors
    Djurre H. de Jong, Cesar A. Lopez and Siewert J. Marrink
    Faraday Discussions (2013)
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  • Perspective on the Martini model
    Siewert J. Marrink and D. Peter Tieleman
    Chemical Society Reviews (2013)
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  • The Martini Coarse-Grained Force Field
    Xavier Periole & Siewert-Jan Marrink
    Biomolecular simulations: Methods and protocols (2013)
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  • Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields
    Djurre H. de Jong, Xavier Periole, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2012)
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  • In Silico Design of Robust Bolalipid Membranes
    Monica Bulacu, Xavier Périole, and Siewert J. Marrink
    Biomacromolecules (2012)
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  • Line-Tension Controlled Mechanism for Influenza Fusion
    Herre Jelger Risselada, Giovanni Marelli, Marc Fuhrmans, Yuliya G. Smirnova, Helmut Grubmüller, Siewert Jan Marrink, and Marcus Müller
    PLoS One (2012)
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  • Molecular Structure of Membrane Tethers
    Svetlana Baoukina, Siewert J. Marrink, and D. Peter Tieleman
    Biophysical journal (2012)
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  • Molecular View of the Role of Fusion Peptides in Promoting Positive Membrane Curvature
    Marc Fuhrmans and Siewert J. Marrink
    Journal of the American Chemical Society (2012)
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  • Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers
    Xavier Periole, Adam M. Knepp, Thomas P. Sakmar, Siewert J. Marrink, and Thomas Huber
    Journal of the American Chemical Society (2012)
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  • Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations
    Evelyne Deplazes, Martti Louhivuori, Dylan Jayatilaka, Siewert J. Marrink, and Ben Corry
    PLoS Computational Biology (2012)
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  • Transmembrane helices can induce domain formation in crowded model membranes
    Jan Domański, Siewert J. Marrink, and Lars V. Schäfer
    Biochimica et Biophysica Acta (BBA)-Biomembranes (2012)
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  • Curvature-Dependent Elastic Properties of Liquid-Ordered Domains Result in Inverted Domain Sorting on Uniaxially Compressed Vesicles
    H. Jelger Risselada, Siewert Jan Marrink, and Marcus Müller
    Physical review letters (2011)
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  • Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites
    Andrzej J. Rzepiela, Martti Louhivuori, Christine Peter and Siewert J. Marrink
    Physical Chemistry Chemical Physics (2011)
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  • Lipid Acrobatics in the Membrane Fusion Arena
    Albert J. Markvoort, and Siewert J. Marrink
    Current Topics in Membranes (2011)
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  • Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes
    Lars V. Schäfer, Djurre H. de Jong, Andrea Holt, Andrzej J. Rzepiela, Alex H. de Vries, Bert Poolman, J. Antoinette Killian, and Siewert J. Marrink
    Proceedings of the National Academy of Sciences (2011)
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  • Low density lipoprotein: structure, dynamics, and interactions of apoB-100 with lipids
    Teemu Murtola, Timo A. Vuorela, Marja T. Hyvönen, Siewert-Jan Marrink, Mikko Karttunenf and Ilpo Vattulainen
    Soft Matter (2011)
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  • Protein Shape Change Has a Major Effect on the Gating Energy of a Mechanosensitive Channel
    O.H. Samuli Ollila, Martti Louhivuori, Siewert J. Marrink, and Ilpo Vattulainen
    Biophysical journal (2011)
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  • Protofibrillar Assembly Toward the Formation of Amyloid Fibrils
    Jesper Sørensen, Xavier Periole, Katrine K. Skeby, Siewert-J. Marrink, and Birgit Schiøtt
    The Journal of Physical Chemistry Letters (2011)
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  • Sphere-to-Rod Transitions of Nonionic Surfactant Micelles in Aqueous Solution Modeled by Molecular Dynamics Simulations
    Maria Velinova, Durba Sengupta, Alia V. Tadjer, and Siewert-Jan Marrink
    Langmuir (2011)
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  • The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles — A small-angle neutron scattering and molecular dynamics study
    M. Klacsová, M. Bulacu, N. Kučerka, D. Uhríková, J. Teixeira, S.J. Marrink, and P. Balgavý
    Biochimica et Biophysica Acta (BBA)-Biomembranes (2011)
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  • Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane
    Anton A. Polyansky, Rajesh Ramaswamy, Pavel E. Volynsky, Ivo F. Sbalzarini, Siewert J. Marrink, and Roman G. Efremov
    The Journal of Physical Chemistry Letters (2010)
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  • Cholesterol in Bilayers with PUFA Chains: Doping with DMPC or POPC Results in Sterol Reorientation and Membrane-Domain Formation
    Norbert Kučerka, Drew Marquardt, Thad A. Harroun, Mu-Ping Nieh, Stephen R. Wassall, Djurre H. de Jong, Lars V. Schäfer, Siewert J. Marrink, and John Katsaras
    Biochemistry (2010)
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  • 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
    Siewert J. Marrink,a Xavier Periole,a D. Peter Tielemanb and Alex H. de Vriesa
    Physical Chemistry Chemical Physics (2010)
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  • Concerted diffusion of lipids in raft-like membranes
    Touko Apajalahti, Perttu Niemelä, Praveen Nedumpully Govindan, Markus S. Miettinen, Emppu Salonen, Siewert-Jan Marrink and Ilpo Vattulainen
    Faraday discussions (2010)
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  • Effects of bundling on the properties of the SPC water model
    Marc Fuhrmans, Barbara P. Sanders, Siewert-Jan Marrink & Alex H. de Vries
    Theoretical Chemistry Accounts (2010)
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  • Immobilization of the Plug Domain Inside the SecY Channel Allows Unrestricted Protein Translocation
    Jelger A. Lycklama a Nijeholt, Monica Bulacu, Siewert Jan Marrink, and Arnold J.M. Driessen
    Journal of biological chemistry (2010)
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  • Influence of Hydrophobic Mismatch and Amino Acid Composition on the Lateral Diffusion of Transmembrane Peptides
    Sivaramakrishnan Ramadurai, Andrea Holt, Lars V. Schäfer, Victor V. Krasnikov, Dirk T.S. Rijkers, Siewert J. Marrink, J. Antoinette Killian, and Bert Poolman
    Biophysical journal (2010)
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  • Lateral pressure profiles in lipid monolayers
    Svetlana Baoukina, Siewert J. Marrink and D. Peter Tieleman
    Faraday discussions (2010)
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  • Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes
    Durba Sengupta and Siewert J. Marrink
    Physical Chemistry Chemical Physics (2010)
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  • Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions
    Andrzej J. Rzepiela, Durba Sengupta, Nicolae Goga and Siewert J. Marrink
    Faraday discussions (2010)
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  • Partitioning of Lipids at Domain Boundaries in Model Membranes
    Lars V. Schäfer and Siewert J. Marrink
    Biophysical journal (2010)
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  • Polarizable Water Model for the Coarse-Grained MARTINI Force Field
    Semen O. Yesylevskyy, Lars V. Schäfer, Durba Sengupta, and Siewert J. Marrink
    PLoS computational biology (2010)
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  • Reconstruction of atomistic details from coarse-grained structures
    Andrzej J. Rzepiela, Lars V. Schäfer, Nicolae Goga, H. Jelger Risselada, Alex H. De Vries, and Siewert J. Marrink
    Journal of computational chemistry (2010)
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  • Release of content through mechano-sensitive gates in pressurized liposomes
    Martti Louhivuori, H. Jelger Risselada, Erik van der Giessen, and Siewert J. Marrink
    Proceedings of the National Academy of Sciences (2010)
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  • Role of Lipids in Spheroidal High Density Lipoproteins
    Timo Vuorela, Andrea Catte, Perttu S. Niemelä, Anette Hall, Marja T. Hyvönen, Siewert-Jan Marrink, Mikko Karttunen, and Ilpo Vattulainen
    PLoS Computational Biology (2010)
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  • Solvent-Exposed Tails as Prestalk Transition States for Membrane Fusion at Low Hydration
    Yuliya G. Smirnova, Siewert-Jan Marrink, Reinhard Lipowsky, and Volker Knecht
    Journal of the American Chemical Society (2010)
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  • 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes
    O. H. Samuli Ollila, H. Jelger Risselada, Martti Louhivuori, Erik Lindahl, Ilpo Vattulainen, and Siewert J. Marrink
    Physical review letters (2009)
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  • A Coarse-Grained Model for Polyethylene Oxide and Polyethylene Glycol: Conformation and Hydrodynamics
    Hwankyu Lee, Alex H. de Vries, Siewert-Jan Marrink, and Richard W. Pastor
    The Journal of Physical Chemistry B (2009)
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  • A Single Bicontinuous Cubic Phase Induced by Fusion Peptides
    Marc Fuhrmans, Volker Knecht, and Siewert J. Marrink
    Journal of the American Chemical Society (2009)
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  • Areas of Monounsaturated Diacylphosphatidylcholines
    Norbert Kučerka, Jana Gallová, Daniela Uhríková, Pavol Balgavý, Monica Bulacu, Siewert-Jan Marrink, and John Katsaras
    Biophysical Journal (2009)
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  • Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition
    Xavier Periole, Marco Cavalli, Siewert-Jan Marrink, and Marco A. Ceruso
    Journal of Chemical Theory and Computation (2009)
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  • Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations
    H. Jelger Risselada and Siewert J. Marrink
    Physical Chemistry Chemical Physics (2009)
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  • Location, Tilt, and Binding: A Molecular Dynamics Study of Voltage-Sensitive Dyes in Biomembranes
    Marlon J. Hinner, Siewert-J. Marrink, and Alex H. de Vries
    The Journal of Physical Chemistry B (2009)
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  • Martini Coarse-Grained Force Field: Extension to Carbohydrates
    Cesar A. López, Andrzej J. Rzepiela, Alex H. de Vries, Lubbert Dijkhuizen, Philippe H. Hünenberger, and Siewert J. Marrink
    Journal of Chemical Theory and Computation (2009)
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  • Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments
    W. F. Drew Bennett, Justin L. MacCallum, Marlon J. Hinner, Siewert J. Marrink, and D. Peter Tieleman
    Journal of the American Chemical Society (2009)
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  • Simulations of the c-subunit of ATP-synthase reveal helix rearrangements
    Durba Sengupta, Aldo Rampioni & Siewert-Jan Marrink
    Molecular Membrane Biology (2009)
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  • The freezing process of small lipid vesicles at molecular resolution
    H. Jelger Risselada and Siewert J. Marrink
    Soft Matter (2009)
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  • The structural basis for peptide selection by the transport receptor OppA
    Ronnie P‐A Berntsson, Mark K Doeven, Fabrizia Fusetti, Ria H Duurkens, Durba Sengupta, Siewert‐Jan Marrink, Andy‐Mark W H Thunnissen, Bert Poolman, and Dirk‐Jan Slotboom
    The EMBO Journal (2009)
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  • Application of Mean Field Boundary Potentials in Simulations of Lipid Vesicles
    H. Jelger Risselada, Alan E. Mark, and Siewert J. Marrink
    The Journal of Physical Chemistry B (2008)
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  • Cholesterol Shows Preference for the Interior of Polyunsaturated Lipid Membranes
    Siewert J. Marrink, Alex H. de Vries, Thad. A. Harroun, John Katsaras, and Stephen R. Wassall
    Journal of the American Chemical Society (2008)
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  • Gating Motions in Voltage-Gated Potassium Channels Revealed by Coarse-Grained Molecular Dynamics Simulations
    Werner Treptow, Siewert-J Marrink, and Mounir Tarek
    The Journal of Physical Chemistry B (2008)
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  • Mechanosensitive Membrane Channels in Action
    Serge Yefimov, Erik van der Giessen, Patrick R. Onck, and Siewert J. Marrink
    Biophysical Journal (2008)
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  • Structure of Spheroidal HDL Particles Revealed by Combined Atomistic and Coarse-Grained Simulations
    Andrea Catte, James C. Patterson, Denys Bashtovyy, Martin K. Jones, Feifei Gu, Ling Li, Aldo Rampioni, Durba Sengupta, Timo Vuorela, Perttu Niemelä, Mikko Karttunen, Siewert Jan Marrink, Ilpo Vattulainen, and Jere P. Segrest
    Biophysical journal (2008)
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  • The MARTINI Coarse-Grained Force Field: Extension to Proteins
    Luca Monticelli, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, and Siewert-Jan Marrink
    Journal of Chemical Theory and Computation (2008)
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  • The MARTINI force field
    Siewert J. Marrink, Marc Fuhrmans, H. Jelger Risselada, and Xavier Periole
    Coarse graining of condensed phase and biomolecular systems (2008)
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  • The molecular face of lipid rafts in model membranes
    H. Jelger Risselada and Siewert J. Marrink
    Proceedings of the National Academy of Sciences (2008)
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  • The molecular mechanism of lipid monolayer collapse
    Svetlana Baoukina, Luca Monticelli, H. Jelger Risselada, Siewert J. Marrink, and D. Peter Tieleman
    Proceedings of the National Academy of Sciences (2008)
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  • Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models
    Riccardo Baron, Daniel Trzesniak, Alex H. de Vries, Andreas Elsener, Siewert J. Marrink, and Wilfred F. van Gunsteren
    ChemPhysChem (2007)
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  • G Protein-Coupled Receptors Self-Assemble in Dynamics Simulations of Model Bilayers
    Xavier Periole, Thomas Huber, Siewert-Jan Marrink, and Thomas P. Sakmar
    Journal of the American Chemical Society (2007)
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  • Pressure−Area Isotherm of a Lipid Monolayer from Molecular Dynamics Simulations
    Svetlana Baoukina, Luca Monticelli, Siewert J. Marrink, and D. Peter Tieleman
    Langmuir (2007)
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  • The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
    Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, and Alex H. de Vries
    The Journal of Physical Chemistry B (2007)
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  • Comparison of Atomic-Level and Coarse-Grained Models for Liquid Hydrocarbons from Molecular Dynamics Configurational Entropy Estimates
    Riccardo Baron, Alex H. de Vries, Philippe H. Hünenberger, and Wilfred F. van Gunsteren
    The Journal of Physical Chemistry B (2006)
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  • Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model
    Siewert J. Marrink, Jelger Risselada, and Alan E. Mark
    Chemistry and Physics of Lipids (2005)
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  • Coarse Grained Model for Semiquantitative Lipid Simulations
    Siewert J. Marrink, Alex H. de Vries, and Alan E. Mark
    The Journal of Physical Chemistry B (2004)
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  • Molecular View of Hexagonal Phase Formation in Phospholipid Membranes
    Siewert-Jan Marrink and Alan E. Mark
    Biophysical journal (2004)
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  • Simulation of Domain Formation in DLPC−DSPC Mixed Bilayers
    Roland Faller and Siewert-Jan Marrink
    Langmuir (2004)
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  • Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles
    Siewert J. Marrink and Alan E. Mark
    Journal of the American Chemical Society (2003)
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  • The Mechanism of Vesicle Fusion as Revealed by Molecular Dynamics Simulations
    Siewert J. Marrink and Alan E. Mark
    Journal of the American Chemical Society (2003)
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