Siewert-Jan Marrink
Editor, Computational Biophysics
Biophysical Journal

What are you currently working on that excites you?

When I was a PhD student in the early nineties, molecular dynamics simulations of lipid membranes was an upcoming area of research. We struggled getting our force fields to the point that a bilayer configuration was actually stable. And once we achieved this, we could simulate a small patch of only 64 lipids over a very limited (100 ps) time period. Nowadays we are pushing simulations of entire cells (admittedly: one of the smallest cells known, JCVI-syn3A), comprising millions of lipids together with 1000s of membrane proteins and a crowded cytoplasm inside, totaling close to a billion particles. Remarkably, those early days simulations took months to complete on the most powerful computers of that era (Cyber 205) and once completed, analysis of the resulting data took only a few afternoons. On the contrary, nowadays we generate terabytes of data overnight even on our local desktop machines, but analysis of these huge multi-component systems requires months of work. This ongoing increase in the time and length scales that we can simulate, together with the associated challenges how to deal with complex data, excites me, and pushes me to continue exploring the frontiers of computational modeling.

At a cocktail party of non-scientists, how would you explain what you do?

I would start pouring them a Martini, my favorite cocktail and the name-giver of the force field we have developed in my group (together with many others). Then I would explain how we, like making a cocktail, mix different ingredients together that allow us to simulate what happens inside a cell. Most likely they will already be lost at this point, so I will pour them another Martini. In fact, I will mix them our special prize-winning liquid-liquid phase separated (LLPS) Martini, giving me the opportunity to explain how LLPS is of fundamental importance for providing the final answer to everything. They might want to know what the actual question is, so I simply refer to the hitchhiker’s guide. After shaking another round of Martinis, I will reiterate that working in science is fun, as you get to mix a lot of Martinis and you can even publish the recipes in respected scientific journals (true! have a look at the end of the SI material of our Nature Methods paper on the Martini force field, doi:10.1038/s41592-021-01098-3).