Publications

• Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. J. Frallicciardi, J. Melcr, P. Siginou, S. J. Marrink and B. Poolman. Nature communications, 2022. DOI: 10.1038/s41467-022-29272-x, Preprint on BioRxiv since 2021.

• Inverse conformational selection in lipid-protein binding. A. Bacle, P. Buslaev, R. Garcia-Fandino, F. Favela-Rosales, T. Mendes Ferreira, P. Fuchs, I. Gushchin, M. Javanainen, A. Kiirikki, J. Madsen, J. Melcr, P. Milán Rodríguez, M. Miettinen, S. O. H. Ollila, C. Papadopoulos, A. Peon, T. Piggot, A. Pineiro, S. Virtanen. Journal of American Chemical Society, 2021. DOI: 10.1021/jacs.1c05549, preprint at GitHub.

• Adaptive response to wine selective pressures shapes the genome of a Saccharomyces interspecies hybrid. M. Lairón-Peris; G. L. Castiglioni; S. J. Routledge; J. Alonso del Real; J. A Linney; A. R. Pitt; J. Melcr; A. D. Goddard; E. Barrio; A. Querol. Microbial Genomics, 2021. DOI: 10.1099/mgen.0.000628

• Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. Mariia Nemchinova, Josef Melcr, Tsjerk A. Wassenaar, Siewert J. Marrink, and Albert Guskov. J. Chem. Inf. Model, 2021. DOI: 10.1021/acs.jcim.1c00261.

• Martini 3.0: A General Purpose Force Field for Coarse-Grained Molecular Dynamics. Paulo C. T. Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grünewald, Ilias Patmanidis, Haleh Abdizadeh, Bart M. H. 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 and Siewert J. Marrink, Nature Methods, 2021. DOI: 10.1038/s41592-021-01098-3.

• Quantitative Linear Dichroism Imaging of Molecular Processes in Living Cells Made Simple by Open Software Tools. Alexey Bondar, Olga Rybakova, Josef Melcr, Jan Dohnálek, Petro Khoroshyy, Ondrej Tichacek, Štěpán Timr, Paul Miclea, Alina Sakhi, Josef Lazar, Communications Biology 4, 2021. DOI: 10.1038/s42003-021-01694-1, preprint and a related blog post.

• Dual Resolution Membrane Simulations Using Virtual Sites. Liu, Y., De Vries, A. H., Barnoud, J., Pezeshkian, W., Melcr, J., and Marrink, S. J., The Journal of Physical Chemistry B, 124, 2020. DOI: 10.1021/acs.jpcb.0c01842

• Accurate biomolecular simulations account for electronic polarization. Josef Melcr and Jean-Philip Piquemal, Frontiers in Molecular Biosciences, 4, 2019. DOI: 10.3389/fmolb.2019.00143, arXiv preprint and a related blog post.

• Improved Cation Binding to Lipid Bilayer with Negatively Charged POPS by Effective Inclusion of Electronic Polarization. Melcr, J., Mendes Ferreira, T., Jungwirth, P. & Ollila, O. H. S., Journal of Chemical Theory and Computation, 16 (1), 738-748, 2020. DOI: 10.1021/acs.jctc.9b00824, preprint at GitHub.

• Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers. Hanne S. Antila, Pavel Buslaev, Fernando Favela-Rosales, Tiago Mendes Ferreira, Ivan Gushchin, Matti Javanainen, Batuhan Kav, Jesper J. Madsen, Josef Melcr, Markus Sakari Miettinen, Jukka Määttä, Ricky Nencini, O.H. Samuli Ollila, Thomas J. Piggot, The Journal of Physical Chemistry B, 123(43), 9066-9079, 2019. DOI: 10.1021/acs.jpcb.9b06091, preprint at GitHub, part of NMRlipids project.

• Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization. Josef Melcr, Hector Martinez-Seara, Ricky Nencini, Jiri Kolafa, Pavel Jungwirth, and O.H. Samuli Ollila, The Journal of Physical Chemistry B, 122 (16), 4546-4557, 2018. DOI: 10.1021/acs.jpcb.7b12510, preprint at GitHub.

• The electrometer concept and binding of cations to phospholipid bilayers. Andrea Catte, Mykhailo Girych, Matti Javanainen, Claire Loison, Josef Melcr, Markus S. Miettinen, Luca Monticelli, Jukka Määttä, Vasily S. Oganesyan, O. H. Samuli Ollila, Joona Tynkkynen and Sergey Vilov, Phys. Chem. Chem. Phys., 18, 32560, 2016. DOI: 10.1039/C6CP04883H, preprint at GitHub, part of NMRlipids project.

• Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance. Josef Melcr, Daniel Bonhenry. Štěpán Timr and Pavel Jungwirth, Journal of Chemical Theory and Computation, 12 (5), 2016. DOI: 10.1021/acs.jctc.5b01202

• Estimation of transition-metal empirical parameters for molecular mechanical force fields. Filip Šebesta, Vladislav Sláma, Josef Melcr, Zdeněk Futera and Jaroslav V Burda. Journal of chemical theory and computation, 12 (8), 2016. DOI: 10.1021/acs.jctc.6b00416

Awards

• PRACE Tier-0 project award at Curie-HN supercomputer
• Juelich Supercomputing Centre project award at JUROPA and JURECA supercomputers
• Best poster award at CECAM Conference “Understanding function of proteins in membrane by atomistic and multiscale simulations”, Lugano, Switzerland, November 2015