Date: 18 March 2025
Time: 15:00 CET
Abstract
This talk will provide the state of the art on the use of the latest version of the coarse-grained Martini model to simulate complex systems, including the possibility to capture chemical reactions and to reach the whole cell level.
Presenter
Siewert-Jan Marrink, University of Groningen
As trained physical chemist (PhD in 1994), Siewert-Jan Marrink specialized in the use of computational modelling. Central aims of his research are: i) to unravel the lateral organization principles of biological membranes, and ii) to develop efficient computational models to simulate molecular processes. Marrink’s group is well known for the development of the Martini model, a coarse-grained force field for biomolecular simulations, and has contributed fundamental understanding of membrane related processes such as fusion, domain formation, and membrane protein activity (‘simulating is believing’). Marrink is also credited with several methodological advances to improve the computational microscope, including development of pioneering multi-scale simulation algorithms and high-throughput tools.
His main current research areas include:
- Cell membrane complexity: elucidation of the impact of complexity and crowdedness on the functioning of cell membranes
- Whole-cell modelling: integrating various sources of experimental data into near-atomic dynamic models of entire cells and cell organelles
- Computational microscopy: establishing efficient multi-resolution models to simulate and visualize cellular processes across large spatio-temporal scales
- Self-assembling materials: computational design of self-assembling bio-inspired materials. His ambition is to use the computational microscope to provide an unprecedented detailed view on the molecular processes that underlie the functioning of (synthetic) cells.
Marrink is one of the recognized world leaders and pioneer in the field of coarse-grain (CG) simulations. The Martini model developed by him is the most popular CG force field available, with ten thousands of users around the globe. Marrink has published >330 peer-reviewed papers that received >55,000 citations (Google Scholar); He received various (personal) grants from NWO and the EU, including three NWO TOP (2004, 2008, 2014) and two ERC Advanced grants (2015, 2022). He is chair of the board of the GBB institute, director and founder of the Berendsen Centre for Multiscale Modeling and Material Design, is an elected Member of the Royal Netherlands Academy of Arts and Sciences, and has been granted an honorary doctorate of the Polytechnic University Bucharest (Romania). He serves on the editorial board of Biophysical Journal, and is on the advisory board of a variety of computation-oriented journals.
Selected key publications:
P.C.T. Souza, R. Alessandri, J. Barnoud, S. Thallmair, I. Faustino, … S.J. Marrink. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods 18:382–388, 2021.
Pezeshkian, M. Konig, T.A. Wassenaar, S.J. Marrink. Backmapping triangulated surfaces to coarse-grained membrane models. Nature Commun. 11:2296, 2020.
P.C.T. Souza, S. Thallmair, P. Conflitti, C. Ramírez-Palacios, R. Alessandri, S. Raniolo, V. Limongelli, S.J. Marrink. Protein–ligand binding with the coarse-grained Martini model. Nature Commun. 11:3714, 2020.
S.J. Marrink, V. Corradi, P.C.T. Souza, H.I. Ingolfsson, D.P. Tieleman, M.S.P. Sansom. Computational Modeling of Realistic Cell Membranes. Chem. Review, 119:6184–6226, 2019.
H.I. Ingólfsson, M.N. Melo, F.J. van Eerden, C. Arnarez, C.A. López, T.A. Wassenaar, X. Periole, A.H. De Vries, D.P. Tieleman, S.J. Marrink. Lipid organization of the plasma membrane. JACS, 136:14554-14559, 2014.
Social media:
X: @CG_Martini
Bluesky: @cg-martini.bsky.social
