Martini straight: Boosting performance using a shorter cutoff and GPUs
de Jong, Djurre H., Baoukina, Svetlana, Ingólfsson, Helgi I., Marrink, Siewert J.
Published in Computer physics communications (01.02.2016)
Published in Computer physics communications (01.02.2016)
Get full text
Journal Article
Improved Parameters for the Martini Coarse-Grained Protein Force Field
de Jong, Djurre H, Singh, Gurpreet, Bennett, W. F. Drew, Arnarez, Clement, Wassenaar, Tsjerk A, Schäfer, Lars V, Periole, Xavier, Tieleman, D. Peter, Marrink, Siewert J
Published in Journal of chemical theory and computation (08.01.2013)
Published in Journal of chemical theory and computation (08.01.2013)
Get full text
Journal Article
The power of coarse graining in biomolecular simulations
Ingólfsson, Helgi I., Lopez, Cesar A., Uusitalo, Jaakko J., de Jong, Djurre H., Gopal, Srinivasa M., Periole, Xavier, Marrink, Siewert J.
Published in Wiley interdisciplinary reviews. Computational molecular science (01.05.2014)
Published in Wiley interdisciplinary reviews. Computational molecular science (01.05.2014)
Get full text
Journal Article
Phytochemicals Perturb Membranes and Promiscuously Alter Protein Function
Ingólfsson, Helgi I, Thakur, Pratima, Herold, Karl F, Hobart, E. Ashley, Ramsey, Nicole B, Periole, Xavier, de Jong, Djurre H, Zwama, Martijn, Yilmaz, Duygu, Hall, Katherine, Maretzky, Thorsten, Hemmings, Hugh C, Blobel, Carl, Marrink, Siewert J, Koçer, Armağan, Sack, Jon T, Andersen, Olaf S
Published in ACS chemical biology (15.08.2014)
Published in ACS chemical biology (15.08.2014)
Get full text
Journal Article
Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes
Schäfer, Lars V., de Jong, Djurre H., Holt, Andrea, Rzepiela, Andrzej J., de Vries, Alex H., Poolman, Bert, Killian, J. Antoinette, Marrink, Siewert J., Klein, Michael L.
Published in Proceedings of the National Academy of Sciences - PNAS (25.01.2011)
Published in Proceedings of the National Academy of Sciences - PNAS (25.01.2011)
Get full text
Journal Article
Simulation of polyethylene glycol and calcium-mediated membrane fusion
Pannuzzo, Martina, De Jong, Djurre H, Raudino, Antonio, Marrink, Siewert J
Published in The Journal of chemical physics (28.03.2014)
Published in The Journal of chemical physics (28.03.2014)
Get more information
Journal Article
Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent
Arnarez, Clément, Uusitalo, Jaakko J, Masman, Marcelo F, Ingólfsson, Helgi I, de Jong, Djurre H, Melo, Manuel N, Periole, Xavier, de Vries, Alex H, Marrink, Siewert J
Published in Journal of chemical theory and computation (13.01.2015)
Published in Journal of chemical theory and computation (13.01.2015)
Get full text
Journal Article
Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations
van Eerden, Floris J., de Jong, Djurre H., de Vries, Alex H., Wassenaar, Tsjerk A., Marrink, Siewert J.
Published in Biochimica et biophysica acta (01.06.2015)
Published in Biochimica et biophysica acta (01.06.2015)
Get full text
Journal Article
Imidazolium-Based Lipid Analogues and Their Interaction with Phosphatidylcholine Membranes
Wang, Da, de Jong, Djurre H, Rühling, Andreas, Lesch, Volker, Shimizu, Karina, Wulff, Stephanie, Heuer, Andreas, Glorius, Frank, Galla, Hans-Joachim
Published in Langmuir (06.12.2016)
Published in Langmuir (06.12.2016)
Get full text
Journal Article
Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex
de Jong, Djurre H, Liguori, Nicoletta, van den Berg, Tom, Arnarez, Clement, Periole, Xavier, Marrink, Siewert J
Published in The journal of physical chemistry. B (25.06.2015)
Published in The journal of physical chemistry. B (25.06.2015)
Get full text
Journal Article
Cholesterol in Bilayers with PUFA Chains: Doping with DMPC or POPC Results in Sterol Reorientation and Membrane-Domain Formation
Kučerka, Norbert, Marquardt, Drew, Harroun, Thad A, Nieh, Mu-Ping, Wassall, Stephen R, de Jong, Djurre H, Schäfer, Lars V, Marrink, Siewert J, Katsaras, John
Published in Biochemistry (Easton) (07.09.2010)
Published in Biochemistry (Easton) (07.09.2010)
Get full text
Journal Article
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations
De Jong, Djurre H., Schäfer, Lars V., De Vries, Alex H., Marrink, Siewert J., Berendsen, Herman J. C., Grubmüller, Helmut
Published in Journal of computational chemistry (15.07.2011)
Published in Journal of computational chemistry (15.07.2011)
Get full text
Journal Article
P3HT:DiPBI bulk heterojunction solar cells: morphology and electronic structure probed by multiscale simulation and UV/vis spectroscopy
Winands, Thorsten, Böckmann, Marcus, Schemme, Thomas, Ly, Phong-Minh Timmy, de Jong, Djurre H, Wang, Zhaohui, Denz, Cornelia, Heuer, Andreas, Doltsinis, Nikos L
Published in Physical chemistry chemical physics : PCCP (17.02.2016)
Published in Physical chemistry chemical physics : PCCP (17.02.2016)
Get full text
Journal Article
Correction to “Atomistic and Coarse Grain Topologies for the Cofactors Associated with the PhotoSystem II Core Complex”
de Jong, Djurre H, Liguori, Nicoletta, van den Berg, Tom, Arnarez, Clement, Periole, Xavier, Marrink, Siewert J
Published in The journal of physical chemistry. B (13.08.2015)
Published in The journal of physical chemistry. B (13.08.2015)
Get full text
Journal Article
Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide
Oktaviani, Nur Alia, Risør, Michael W., Lee, Young-Ho, Megens, Rik P., de Jong, Djurre H., Otten, Renee, Scheek, Ruud M., Enghild, Jan J., Nielsen, Niels Chr, Ikegami, Takahisa, Mulder, Frans A. A.
Published in Journal of biomolecular NMR (01.06.2015)
Published in Journal of biomolecular NMR (01.06.2015)
Get full text
Journal Article