DNA nanopores

DNA origami pore in bilayer

A nice application of the Martini DNA model in assessing properties of membrane spanning DNA-based nanopores:

Maingi et al., Nature Comm. 14784 (2017). doi:10.1038/ncomms14784

Intoxicated MscL (too many Martinis ?)

MscL opened in silico

Membrane mediated effects of alcohols on MscL function revealed using
high throughput, 600+, Martini simulations.

M.N. Melo, C. Arnarez, H. Sikkema, N. Kumar, M. Walko, H.J.C. Berendsen, A. Kocer, S.J. Marrink, H.I. Ingólfsson. High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating. JACS, 139:2664–2671, 2017. open access

Martini Solar Cells

Martini is also suited for non-biological applications. Check out our latest work on bulk heterojunction morphologies for organic solar cells. Mixtures of poly(3-hexyl-thiophene) (P3HT) and phenyl-C61-butyric acid methyl ester (PCBM), solvated in chlorobenzene, slowly dried and cooked to perfection !

R. Alessandri, J.J. Uusitalo, A.H. De Vries, R.W.A. Havenith, S.J. Marrink. Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations. JACS, 139:3697–3705, 2017. open access

NEW ! Want to get a more concrete idea of what this is about? Check the associated ACS LiveSlides presentation !

TIP ! Check the newest downloads if you want to try the simulations yourself !

Polarizable water model

A refined polarizable water model is now available, developed by the group of Jens Smiatek. The new model improves the behavior of Martini with long range electrostatic interactions. Available from the download section. See: J. Michalowsky, L.V. Schäfer, C. Holm, J. Smiatek. http://dx.doi.org/10.1063/1.4974833 for details.

CNT mediated membrane fusion

Joining a Martini workshop can pave the way to cool simulations and a nice paper:
R.M. Bhaskara, S.M. Linker, M. Vögele, J. Köfinger, G. Hummer. Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS Nano, Article ASAP. DOI:10.1021/acsnano.6b05434

STiRreD Martini

Cool stuff! Dry Martini coupled to stochastic rotational dynamics to account for solvent hydrodynamics:

A. Zgorski, E. Lyman. Toward Hydrodynamics with Solvent Free Lipid Models: STRD Martini. Biophys. J. 111:2689–2697, 2016. doi:10.1016/j.bpj.2016.11.010