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Research GBB Molecular Dynamics Group

ERC Advanced Grant for Siewert-Jan Marrink

28 April 2022

The University of Groningen has a long history in computer simulations of molecules and atoms. The Gromacs simulation software which was created here is one of the leading packages for molecular dynamics research. Siewert-Jan Marrink inherited this and has developed a dedicated and widely used force field, the Martini model, to achieve a significant speedup of the simulations (see Another Martini for better simulations)

These simulations have to span different scales, from atoms to molecules to larger structures. The Martini model is especially designed to simulate lipid membranes, like those that surround living cells. Simulations can show processes that are not visible in experiments, such as the interactions between molecules in a cell membrane. This is called ‘computational microscopy’. The ultimate goal of Marrink is to simulate a cell organelle and even an entire cell.

In his ERC project, Marrink aims to set a large step towards this goal. This will require challenging methodological innovations at the crossroads of biology, physics, and chemistry. To simulate a realistic biological structure, the Martini model must be able to handle interactions between a large variety of biomolecules. The computational microscope must be able to zoom in on details and zoom out to ‘see’ the entire object, which requires simulations at very different scales. Marrink is confident that he will pull this off. One of the aims stated in his ERC project is to simulate − for the first time − a complete cell at molecular resolution: the JCVI- syn3A minimal cell derived from mycobacteria.

See also:

The ultimate microscope: a computer

Last modified:28 April 2022 2.09 p.m.

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