Siewert-Jan Marrink (Siewert J Marrink)

Researcher ID ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 98

Top Topics

Molecular Dynamics

Structural Basis

Mesenchymal Stem Cells

Top Venues

Journal of chemical theory and computation

Nature communications

The journal of physical chemistry. B

Journal of chemical information and modeling

This page only lists publications with an associated author ORCID identifier.

Publications

Julie Cornet, Nelly Coulonges, Weria Pezeshkian, Maël Penissat-Mahaut, Hermes Desgrez-Dautet, Siewert-Jan Marrink, Nicolas Destainville, Matthieu Chavent, Manoel Manghi
There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning. Soft matter (2024)
Maria Gabriella Chiariello, Rubi Zarmiento-Garcia, Siewert-Jan Marrink
Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis. International journal of molecular sciences 25 (14) (2024)
Eleonora Diamanti, Paulo Cesar Telles de Souza, Inda Setyawati, Spyridon Bousis, Leticia Monjas, Lotteke J Y M Swier, Atanaz Shams, Aleksei Tsarenko, Weronika K Stanek, Manuel Jäger, Siewert-Jan Marrink, Dirk Jan Slotboom, Anna Katharina Herta Hirsch
Author Correction: Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications biology 7 (1) (2024)
Julie Cornet, Nelly Coulonges, Weria Pezeshkian, Maël Penissat-Mahaut, Hermes Desgrez-Dautet, Siewert-Jan Marrink, Nicolas Destainville, Matthieu Chavent, Manoel Manghi
There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning. Soft matter 20 (25) (2024)
Anna M Borowska, Maria Gabriella Chiariello, Alisa A Garaeva, Jan Rheinberger, Siewert-Jan Marrink, Cristina Paulino, Dirk Jan Slotboom
Structural basis of the obligatory exchange mode of human neutral amino acid transporter ASCT2. Nature communications 15 (1) (2024)
Maria Gabriella Chiariello, Rubi Zarmiento-Garcia, Siewert-Jan Marrink
Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis. International journal of molecular sciences 25 (14) (2024)
Maria Gabriella Chiariello, Rubi Zarmiento-Garcia, Siewert-Jan Marrink
Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis. International journal of molecular sciences 25 (14) (2024)
Eleonora Diamanti, Paulo Cesar Telles de Souza, Inda Setyawati, Spyridon Bousis, Leticia Monjas, Lotteke J Y M Swier, Atanaz Shams, Aleksei Tsarenko, Weronika K Stanek, Manuel Jäger, Siewert-Jan Marrink, Dirk Jan Slotboom, Anna Katharina Herta Hirsch
Author Correction: Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications biology 7 (1) (2024)
Mariia Nemchinova, Gea K Schuurman-Wolters, Jacob J Whittaker, Valentina Arkhipova, Siewert-Jan Marrink, Bert Poolman, Albert Guskov
Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ. The journal of physical chemistry. B 128 (32) (2024)
Gilberto P Pereira, Riccardo Alessandri, Moisés Domínguez, Rocío Araya-Osorio, Linus Grünewald, Luís Borges-Araújo, Sangwook Wu, Siewert-Jan Marrink, Paulo Cesar Telles de Souza, Raul Mera-Adasme
Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics. Journal of chemical theory and computation 20 (13) (2024)
Mariia Nemchinova, Gea K Schuurman-Wolters, Jacob J Whittaker, Valentina Arkhipova, Siewert-Jan Marrink, Bert Poolman, Albert Guskov
Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ. The journal of physical chemistry. B 128 (32) (2024)
Kasper B Pedersen, Luís Borges-Araújo, Amanda Dyrholm Stange, Paulo Cesar Telles de Souza, Siewert-Jan Marrink, Birgit Schiøtt
OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field. Journal of chemical theory and computation (2024)
Christopher Brasnett, Armin Kiani, Selim Sami, Sijbren Otto, Siewert-Jan Marrink
Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations. Communications chemistry 7 (1) (2024)
Eleonora Diamanti, Paulo Cesar Telles de Souza, Inda Setyawati, Spyridon Bousis, Leticia Monjas, Lotteke J Y M Swier, Atanaz Shams, Aleksei Tsarenko, Weronika K Stanek, Manuel Jäger, Siewert-Jan Marrink, Dirk Jan Slotboom, Anna Katharina Herta Hirsch
Author Correction: Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications biology 7 (1) (2024)
Anna M Borowska, Maria Gabriella Chiariello, Alisa A Garaeva, Jan Rheinberger, Siewert-Jan Marrink, Cristina Paulino, Dirk Jan Slotboom
Structural basis of the obligatory exchange mode of human neutral amino acid transporter ASCT2. Nature communications 15 (1) (2024)
Anna M Borowska, Maria Gabriella Chiariello, Alisa A Garaeva, Jan Rheinberger, Siewert-Jan Marrink, Cristina Paulino, Dirk Jan Slotboom
Structural basis of the obligatory exchange mode of human neutral amino acid transporter ASCT2. Nature communications 15 (1) (2024)
Christopher Brasnett, Armin Kiani, Selim Sami, Sijbren Otto, Siewert-Jan Marrink
Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations. Communications chemistry 7 (1) (2024)
Christopher Brasnett, Armin Kiani, Selim Sami, Sijbren Otto, Siewert-Jan Marrink
Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations. Communications chemistry 7 (1) (2024)
Mariia Nemchinova, Gea K Schuurman-Wolters, Jacob J Whittaker, Valentina Arkhipova, Siewert-Jan Marrink, Bert Poolman, Albert Guskov
Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ. The journal of physical chemistry. B (2024)
Gilberto P Pereira, Riccardo Alessandri, Moisés Domínguez, Rocío Araya-Osorio, Linus Grünewald, Luís Borges-Araújo, Sangwook Wu, Siewert-Jan Marrink, Paulo Cesar Telles de Souza, Raul Mera-Adasme
Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics. Journal of chemical theory and computation (2024)
Mariia Nemchinova, Gea K Schuurman-Wolters, Jacob J Whittaker, Valentina Arkhipova, Siewert-Jan Marrink, Bert Poolman, Albert Guskov
Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ. The journal of physical chemistry. B 128 (32) (2024)
Mariia Nemchinova, Gea K Schuurman-Wolters, Jacob J Whittaker, Valentina Arkhipova, Siewert-Jan Marrink, Bert Poolman, Albert Guskov
Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ. The journal of physical chemistry. B 128 (32) (2024)
Petteri A Vainikka, Siewert-Jan Marrink
Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches. Journal of chemical theory and computation (2023)
Marco P A van Tilburg, Siewert-Jan Marrink, Melanie König, Fabian Grünewald
Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. Journal of chemical theory and computation 20 (1) (2023)
Roderick Corstiaan Abraham Versloot, Patricia Arias-Orozco, Matthijs Jonathan Tadema, Florian Leonardus Rudolfus Lucas, Xinghong Zhao, Siewert-Jan Marrink, Oscar Paul Kuipers, Giovanni Maglia
Seeing the Invisibles: Detection of Peptide Enantiomers, Diastereomers, and Isobaric Ring Formation in Lanthipeptides Using Nanopores. Journal of the American Chemical Society (2023)
Cécile Hilpert, Louis Beranger, Paulo Cesar Telles de Souza, Petteri A Vainikka, Vincent Nieto, Siewert-Jan Marrink, Luca Monticelli, Guillaume Launay
Facilitating CG Simulations with MAD: The MArtini Database Server. Journal of chemical information and modeling 63 (3) (2023)
Cécile Hilpert, Louis Beranger, Paulo Cesar Telles de Souza, Petteri A Vainikka, Vincent Nieto, Siewert-Jan Marrink, Luca Monticelli, Guillaume Launay
Facilitating CG Simulations with MAD: The MArtini Database Server. Journal of chemical information and modeling 63 (3) (2023)
Marco P A van Tilburg, Siewert-Jan Marrink, Melanie König, Fabian Grünewald
Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. Journal of chemical theory and computation 20 (1) (2023)
Marco P A van Tilburg, Siewert-Jan Marrink, Melanie König, Fabian Grünewald
Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. Journal of chemical theory and computation 20 (1) (2023)
Chancievan Thangaratnarajah, Mark Nijland, Luís Borges-Araújo, Aike Jeucken, Jan Rheinberger, Siewert-Jan Marrink, Paulo Cesar Telles de Souza, Cristina Paulino, Dirk Jan Slotboom
Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nature communications 14 (1) (2023)
Petteri A Vainikka, Siewert-Jan Marrink
Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches. Journal of chemical theory and computation (2023)
Maria Gabriella Chiariello, Fabian Grünewald, Rubi Zarmiento-Garcia, Siewert-Jan Marrink
pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. The journal of physical chemistry letters 14 (4) (2023)
Marìck Manrho, Sundar Raj Krishnaswamy, Björn Kriete, Ilias Patmanidis, Alex H de Vries, Siewert-Jan Marrink, Thomas la Cour Jansen, Jasper Knoester, Maxim S Pshenichnikov
Watching Molecular Nanotubes Self-Assemble in Real Time. Journal of the American Chemical Society (2023)
Piotr Stępień, Sylwia Świątek, Manuel Yamil Yusef Robles, Joanna Markiewicz-Mizera, Dhanasekaran Balakrishnan, Satomi Inaba-Inoue, Alex H De Vries, Konstantinos Beis, Siewert-Jan Marrink, Jonathan Gardiner Heddle
CRAFTing Delivery of Membrane Proteins into Protocells using Nanodiscs. ACS applied materials & interfaces (2023)
Selim Sami, Siewert-Jan Marrink
Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. Journal of chemical theory and computation (2023)
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-Jan Marrink, Jan Marienhagen
Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis. Nature communications 14 (1) (2023)
Maria Gabriella Chiariello, Fabian Grünewald, Rubi Zarmiento-Garcia, Siewert-Jan Marrink
pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. The journal of physical chemistry letters 14 (4) (2023)
Petteri A Vainikka, Siewert-Jan Marrink
Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches. Journal of chemical theory and computation (2023)
Eleonora Diamanti, Paulo Cesar Telles de Souza, Inda Setyawati, Spyridon Bousis, Leticia M Gómez, Lotteke J Y M Swier, Atanaz Shams, Aleksei Tsarenko, Weronika K Stanek, Manuel Jäger, Siewert-Jan Marrink, Dirk Jan Slotboom, Anna Katharina Herta Hirsch
Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications biology 6 (1) (2023)
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, Jozef Adam Liwo, Siewert-Jan Marrink, Paulo Cesar Telles de Souza
Pragmatic Coarse-Graining of Proteins: Models and Applications. Journal of chemical theory and computation (2023)
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-Jan Marrink, Paulo Cesar Telles de Souza, Manuel N Melo
Martini 3 Coarse-Grained Force Field for Cholesterol. Journal of chemical theory and computation (2023)
Adéla Melcrová, Sourav Maity, Josef Melcr, Niels A W de Kok, Mariella Gabler, Jonne van der Eyden, Wenche Stensen, John Sigurd Mjøen Svendsen, Arnold J M Driessen, Siewert-Jan Marrink, Wouter H Roos
Lateral membrane organization as target of an antimicrobial peptidomimetic compound. Nature communications 14 (1) (2023)
Marco P A van Tilburg, Siewert-Jan Marrink, Melanie König, Fabian Grünewald
Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. Journal of chemical theory and computation (2023)
Maria Gabriella Chiariello, Fabian Grünewald, Rubi Zarmiento-Garcia, Siewert-Jan Marrink
pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. The journal of physical chemistry letters 14 (4) (2023)
Carlos J Ramírez-Palacios, Siewert-Jan Marrink
Super High-Throughput Screening of Enzyme Variants by Spectral Graph Convolutional Neural Networks. Journal of chemical theory and computation (2023)
Cécile Hilpert, Louis Beranger, Paulo Cesar Telles de Souza, Petteri A Vainikka, Vincent Nieto, Siewert-Jan Marrink, Luca Monticelli, Guillaume Launay
Facilitating CG Simulations with MAD: The MArtini Database Server. Journal of chemical information and modeling 63 (3) (2023)
Maria Gabriella Chiariello, Fabian Grünewald, Rubi Zarmiento-Garcia, Siewert-Jan Marrink
pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. The journal of physical chemistry letters (2023)
Petteri A Vainikka, Siewert-Jan Marrink
Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches. Journal of chemical theory and computation (2023)
Charly Empereur-Mot, Kasper B Pedersen, Riccardo Capelli, Martina Crippa, Cristina Caruso, Mattia Perrone, Paulo Cesar Telles de Souza, Siewert-Jan Marrink, Giovanni M Pavan
Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG . Journal of chemical information and modeling (2023)
Marco P A van Tilburg, Siewert-Jan Marrink, Melanie König, Fabian Grünewald
Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. Journal of chemical theory and computation 20 (1) (2023)
Maria Gabriella Chiariello, Fabian Grünewald, Rubi Zarmiento-Garcia, Siewert-Jan Marrink
pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. The journal of physical chemistry letters 14 (4) (2023)
Cécile Hilpert, Louis Beranger, Paulo Cesar Telles de Souza, Petteri A Vainikka, Vincent Nieto, Siewert-Jan Marrink, Luca Monticelli, Guillaume Launay
Facilitating CG Simulations with MAD: The MArtini Database Server. Journal of chemical information and modeling (2023)
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, Siewert-Jan Marrink
Martini 3 Coarse-Grained Force Field for Carbohydrates. Journal of chemical theory and computation (2022)
Veronika Thallmair, Lea Schultz, Wencai Zhao, Siewert-Jan Marrink, Dominik Oliver, Sebastian Thallmair
Two cooperative binding sites sensitize PI(4,5)P 2 recognition by the tubby domain. Science advances 8 (36) (2022)
Roderick Corstiaan Abraham Versloot, Florian Leonardus Rudolfus Lucas, Liubov Yakovlieva, Matthijs Jonathan Tadema, Yurui Zhang, Thomas M Wood, Nathaniel I Martin, Siewert-Jan Marrink, Marthe T C Walvoort, Giovanni Maglia
Quantification of Protein Glycosylation Using Nanopores. Nano letters 22 (13) (2022)
Neila Machado, Bart Marlon Herwig Bruininks, Priyanka Singh, Laurita Dos Santos, Carine Dal Pizzol, Gustavo de C Dieamant, Odivania Kruger, Airton Abraão Martins, Siewert-Jan Marrink, Paulo Cesar Telles de Souza, Priscila P Favero
Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes. Nanoscale 14 (2) (2022)
Ilias Patmanidis, Paulo Cesar Telles de Souza, Selim Sami, Remco W A Havenith, Alex H de Vries, Siewert-Jan Marrink
Modelling structural properties of cyanine dye nanotubes at coarse-grained level. Nanoscale advances 4 (14) (2022)
Nicola de Franceschi, Weria Pezeshkian, Alessio Fragasso, Bart Marlon Herwig Bruininks, Sean Tsai, Siewert-Jan Marrink, Cees Dekker
Synthetic Membrane Shaper for Controlled Liposome Deformation. ACS nano (2022)
Fabian Grünewald, Riccardo Alessandri, Peter C Kroon, Luca Monticelli, Paulo Cesar Telles de Souza, Siewert-Jan Marrink
Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials. Nature communications 13 (1) (2022)
Selim Sami, Riccardo Alessandri, Jeff B W Wijaya, Fabian Grünewald, Alex H de Vries, Siewert-Jan Marrink, Ria Broer, Remco W A Havenith
Strategies for Enhancing the Dielectric Constant of Organic Materials. The journal of physical chemistry. C, Nanomaterials and interfaces 126 (45) (2022)
Carlos J Ramírez-Palacios, Siewert-Jan Marrink
Computational prediction of ω-transaminase selectivity by deep learning analysis of molecular dynamics trajectories. QRB discovery 4 (2022)
Jacopo Frallicciardi, Josef Melcr, Pareskevi Siginou, Siewert-Jan Marrink, Bert Poolman
Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. Nature communications 13 (1) (2022)
José Losa, Simeon Leupold, Diego Alonso-Martinez, Petteri A Vainikka, Sebastian Thallmair, Katarzyna M Tych, Siewert-Jan Marrink, Matthias Heinemann
Perspective: a stirring role for metabolism in cells. Molecular systems biology 18 (4) (2022)
Mariia Nemchinova, Josef Melcr, Tsjerk A Wassenaar, Siewert-Jan Marrink, Albert Guskov
Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. Journal of chemical information and modeling 61 (5) (2021)
Bart Marlon Herwig Bruininks, Albert S Thie, Paulo Cesar Telles de Souza, Tsjerk A Wassenaar, Shirin Faraji, Siewert-Jan Marrink
Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies. Journal of chemical theory and computation (2021)
Ilias Patmanidis, Riccardo Alessandri, Alex H de Vries, Siewert-Jan Marrink
Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields. Molecules (Basel, Switzerland) 26 (19) (2021)
Piermichele Kobauri, Wiktor Szymanski, Fangyuan Cao, Sebastian Thallmair, Siewert-Jan Marrink, Martin D Witte, Frank J Dekker, Ben L Feringa
Biaryl sulfonamides as cisoid azosteres for photopharmacology. Chemical communications (Cambridge, England) 57 (34) (2021)
Siewert-Jan Marrink, Ilya Levental
Computational and Experimental Advances in Biomembranes: Resolving Their Complexity. The journal of physical chemistry. B 124 (45) (2021)
Riccardo Alessandri, Fabian Grünewald, Siewert-Jan Marrink
The Martini Model in Materials Science. Advanced materials (Deerfield Beach, Fla.) 33 (24) (2021)
Maria Tsanai, Pim Wilhelmus Johannes Maria Frederix, Carsten F E Schroer, Paulo Cesar Telles de Souza, Siewert-Jan Marrink
Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chemical science 12 (24) (2021)
Liubov Yakovlieva, Carlos Ramírez-Palacios, Siewert-Jan Marrink, Marthe T C Walvoort
Semiprocessive Hyperglycosylation of Adhesin by Bacterial Protein N-Glycosyltransferases. ACS chemical biology 16 (1) (2021)
Qinglong Meng, Carlos J Ramírez-Palacios, Nikolas Capra, Mattijs E Hooghwinkel, Sebastian Thallmair, Henriëtte J Rozeboom, Andy-Mark W H Thunnissen, Hein J Wijma, Siewert-Jan Marrink, Dick B Janssen
Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines. ACS catalysis 11 (17) (2021)
Shengli Zhang, Gang Huang, Roderick Corstiaan Abraham Versloot, Bart Marlon Herwig Bruininks, Paulo Cesar Telles de Souza, Siewert-Jan Marrink, Giovanni Maglia
Bottom-up fabrication of a proteasome-nanopore that unravels and processes single proteins. Nature chemistry 13 (12) (2021)
Yang Liu, Alex H de Vries, Weria Pezeshkian, Siewert-Jan Marrink
Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. Journal of chemical theory and computation 17 (9) (2021)
Sebastian Thallmair, Matti Javanainen, Balázs Fábián, Hector Martinez-Seara, Siewert-Jan Marrink
Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations. The journal of physical chemistry. B 125 (33) (2021)
Carlos J Ramírez-Palacios, Hein J Wijma, Sebastian Thallmair, Siewert-Jan Marrink, Dick B Janssen
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. Journal of chemical information and modeling 61 (11) (2021)
Lisbeth R Kjølbye, Leonardo De Maria, Tsjerk A Wassenaar, Haleh Abdizadeh, Siewert-Jan Marrink, Jesper Ferkinghoff-Borg, Birgit Schiøtt
General Protocol for Constructing Molecular Models of Nanodiscs. Journal of chemical information and modeling 61 (6) (2021)
Jingjin Dong, Selim Sami, Daniel M Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert-Jan Marrink, Remco W A Havenith, Jan C Hummelen, Maria Antonietta Loi, Giuseppe Portale
Fullerene derivatives with oligoethylene-glycol side chains: an investigation on the origin of their outstanding transport properties. Journal of materials chemistry. C 9 (45) (2021)
Sourav Maity, Jim Ottelé, Guillermo Monreal Santiago, Pim Wilhelmus Johannes Maria Frederix, Peter Kroon, Omer Markovitch, Marc C A Stuart, Siewert-Jan Marrink, Sijbren Otto, Wouter H Roos
Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization. Journal of the American Chemical Society 142 (32) (2020)
Bart Marlon Herwig Bruininks, Paulo Ct Souza, Helgi Ingolfsson, Siewert-Jan Marrink
A molecular view on the escape of lipoplexed DNA from the endosome. eLife 9 (2020)
Weria Pezeshkian, Melanie König, Tsjerk A Wassenaar, Siewert-Jan Marrink
Backmapping triangulated surfaces to coarse-grained membrane models. Nature communications 11 (1) (2020)
Yang Liu, Weria Pezeshkian, Jonathan Barnoud, Alex H de Vries, Siewert-Jan Marrink
Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. Journal of chemical theory and computation 16 (8) (2020)
Yang Liu, Alex H De Vries, Jonathan Barnoud, Weria Pezeshkian, Josef Melcr, Siewert-Jan Marrink
Dual Resolution Membrane Simulations Using Virtual Sites. The journal of physical chemistry. B 124 (19) (2020)
Anna S Bondarenko, Ilias Patmanidis, Riccardo Alessandri, Paulo Cesar Telles de Souza, Thomas la Cour Jansen, Alex H de Vries, Siewert-Jan Marrink, Jasper Knoester
Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates. Chemical science 11 (42) (2020)
Hanif M Khan, Paulo Cesar Telles de Souza, Sebastian Thallmair, Jonathan Barnoud, Alex H de Vries, Siewert-Jan Marrink, Nathalie Reuter
Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field. Journal of chemical theory and computation 16 (4) (2020)
Ignacio Faustino, Haleh Abdizadeh, Paulo C T Souza, Aike Jeucken, Weronika K Stanek, Albert Guskov, Dirk Jan Slotboom, Siewert-Jan Marrink
Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nature communications 11 (1) (2020)
Paulo Cesar Telles de Souza, Sebastian Thallmair, Paolo Conflitti, Carlos J Ramírez-Palacios, Riccardo Alessandri, Stefano Raniolo, Vittorio Limongelli, Siewert-Jan Marrink
Protein-ligand binding with the coarse-grained Martini model. Nature communications 11 (1) (2020)
Fabian Grünewald, Paulo Cesar Telles de Souza, Haleh Abdizadeh, Jonathan Barnoud, Alex H de Vries, Siewert-Jan Marrink
Titratable Martini model for constant pH simulations. The Journal of chemical physics 153 (2) (2020)
Qihui Zhou, Jiawen Chen, Yafei Luan, Petteri A Vainikka, Sebastian Thallmair, Siewert-Jan Marrink, Ben L Feringa, Patrick van Rijn
Unidirectional rotating molecular motors dynamically interact with adsorbed proteins to direct the fate of mesenchymal stem cells. Science advances 6 (5) (2020)
Carsten F E Schroer, Lucia Baldauf, Lennard van Buren, Tsjerk A Wassenaar, Manuel N Melo, Gijsje Hendrika Koenderink, Siewert-Jan Marrink
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) (2020)
Björn Kriete, Anna S Bondarenko, Riccardo Alessandri, Ilias Patmanidis, Victor V Krasnikov, Thomas la Cour Jansen, Siewert-Jan Marrink, Jasper Knoester, Maxim S Pshenichnikov
Molecular versus Excitonic Disorder in Individual Artificial Light-Harvesting Systems. Journal of the American Chemical Society 142 (42) (2020)
Nicoletta Liguori, Roberta Croce, Siewert-Jan Marrink, Sebastian Thallmair
Molecular dynamics simulations in photosynthesis. Photosynthesis research 144 (2) (2020)
Jian Liu, Bas van der Zee, Riccardo Alessandri, Selim Sami, Jingjin Dong, Mohamad I Nugraha, Alex J Barker, Sylvia Rousseva, Li Qiu, Xinkai Qiu, Nathalie Klasen, Ryan C Chiechi, Derya Baran, Mario Caironi, Thomas D Anthopoulos, Giuseppe Portale, Remco W A Havenith, Siewert-Jan Marrink, Jan C Hummelen, L Jan Anton Koster
N-type organic thermoelectrics: demonstration of ZT > 0.3. Nature communications 11 (1) (2020)
Paulo Cesar Telles de Souza, Sebastian Thallmair, Siewert-Jan Marrink, Raul Mera-Adasme
An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation. The journal of physical chemistry letters 10 (24) (2019)
Siewert-Jan Marrink, Valentina Corradi, Paulo C T Souza, Helgi I Ingólfsson, D Peter Tieleman, Mark S P Sansom
Computational Modeling of Realistic Cell Membranes. Chemical reviews 119 (9) (2019)
Riccardo Alessandri, Paulo Cesar Telles de Souza, Sebastian Thallmair, Manuel N Melo, Alex H de Vries, Siewert-Jan Marrink
Pitfalls of the Martini Model. Journal of chemical theory and computation 15 (10) (2019)
Valentina Corradi, Besian I Sejdiu, Haydee Mesa-Galloso, Haleh Abdizadeh, Sergei Yu Noskov, Siewert-Jan Marrink, D Peter Tieleman
Emerging Diversity in Lipid-Protein Interactions. Chemical reviews 119 (9) (2019)
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