Cholesterol artefacts

Be aware of using proper mdp settings when simulating cholesterol, as it might cause artificial phase separation if you don't, according to Javanainen et al: arXiv:2009.07767

Organic semiconductors

bhj-martini.jpgMartini is not only suitable to simulate biomolecular processes, but also increasingly to study material properties. Check the latest paper from our group on resolving the impact of polar side chains on electronic and structural properties of donor-acceptor (DA) interfaces of organic semiconductors:

Alessandri et al., Advanced Funct. Materials, 2020, online.

Piezo lipid fingerprints

piezo-martini.jpgInterested in mechosensitive channels or protein-lipid interplay ?

Read about specific protein-lipid interactions of Piezo1, a mechanically gated  ion channel, combining electrophysiology and mutagenesis experiments with CG simulations:

Buyan et al., Biophys. J., 2020, online

Druggable Martini

Tpathways.pnghe forthcoming Martini 3.0 forcefield opens the way to high-throughput drug screening. Unbiased simulations show reversible binding of a large variety of ligands to both soluble and membrane-embedded proteins, reproducing known pathways and binding sites, as well as correct binding free energies.

For details, see: Souza et al., "Protein–ligand binding with the coarse-grained Martini model", Nature Commun. 11, 3714, 2020. doi:10.1038/s41467-020-17437-5

Titratable Martini


Even protons do not escape our coarse-graining strategy! See how Martini protons hop around in a pH dependent way, protonating amino acids, fatty acids, or titratable groups of dendrimers.

F. Grunewald et al., Titratable Martini Model for Constant pH Simulations. J. Chem. Phys, 2020. doi:10.1063/5.0014258

PhD and post-doc positions available

We currently have two positions open in our group:

(1) A PhD position (4yr) on resolving the molecular driving forces behind the switching behavior of light harvesting complexes. Together with experimental colleagues, we would like to unravel the role of PsbS, an important protein that is involved in the switching (which occurs under high light conditions). If you are not afraid of teaming up with experimentalists (these are nice ones, I promise) and running large scale simulations, this is your chance. We might even end up modeling a whole chloroplast !

(2) A post-doc position (2yr) on development of titratable Martini, aimed at improving the model and extending the application range. Our recently introduced method to enable constant pH Martini simulations opens the way to extend Martini into unknown territories, including reactive-Martini. If you would like to be the main explorer, then consider applying.

For both positions, a solid background in computational modeling is required. Interested ? Apply by sending an email to This email address is being protected from spambots. You need JavaScript enabled to view it. including CV, motivation letter, and contact details of at least two references. Application deadline: Sept 1st, 2020. Both positions are available right away, and ideally start before the end of the year.

Read more: PhD and post-doc positions available