Ilias Patmanidis

Ilias
Postdoc
Involved in projects
Modelling membrane-embedded systems
Universität Oldenburg
Institut für Physik
Carl-von-Ossietzky-Str. 9-11
26129 Oldenburg, Germany
email: ilias.patmanidis@uni-oldenburg.de
room: W16A-1-116




 

 

Background:
2015-2019: Ph.D. in Computational Chemistry at the University of Groningen
2020-2022: Post-doc in Molecular Dynamics group at the University of Groningen
2022-2023: Post-doc in Biomodelling group at the Aarhus University
 
Research interest:
My main expertise lies on all-atom simulations, coarse-grained models, force field optimisation and small molecule parameterization, and my research interests could be summarised as simulating properties of nanomaterials and different biomolecules. At the QuantumBio group, I am contributing in the development of the VIKING suite (an online platform for computational modelling), and I am supporting the group on projects that require multi-scale modelling approaches.

Publications

Watching Molecular Nanotubes Self-Assemble in Real Time, Maríck Manrho, Sundar Raj Krishnaswamy, Björn Kriete, Ilias Patmanidis, Alex H. de Vries, Siewert J. Marrink, Thomas L. C. Jansen, Jasper Knoester, Maxim S. Pshenichnikov, Journal of the American Chemical Society, 145, 22494-22503, (2023)
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, Siewert J. Marrink, Nanoscale Advances, 4, 3033-3042, (2022)
Martini 3: 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 Doma\'nski, 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 Medicine, 18, 382-388, (2021)
Martini 3 Coarse-Grained Force Field: Small Molecules, Riccardo Alessandri, Jonathan Barnoud, Anders S. Gertsen, Ilias Patmanidis, Alex H. de Vries, Paulo C. T. Souza, Siewert J. Marrink, Advanced Theory and Simulations, 5, 2100391, (2021)
Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS, Ilias Patmanidis, Alex H. de Vries, Tsjerk A. Wassenaar, Wenjun Wang, Giuseppe Portale, Siewert J. Marrink, Physical Chemistry - Chemical Physics, 22, 21083-21093, (2020)