Open Positions: Motivated and molecular simulations inclined Ph.D. and M.Sc. students always welcome!


We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time.

[ T. S. Eliot ]


December 12, 2019

Congratulations to the winners of the 2019 Martina Roeselova Memorial Fellowship!

With the help of all the private donors and IOCB Tech we are happy to support four bright young scientists/parents and their families - Lenka Ťupová from the Charles University, Faculty of Pharmacy in Hradec Králové, Jaroslava Nováková from the Charles University, Faculty of Mathematics and Physics in Prague, Aneta Ledererová from the Masaryk University, Faculty of Medicine in Brno, and Miroslav Dvorský (first ever father to be awarded!) from the Institute of Botany of the Academy in Třeboň. Big thanks to all who contributed with their money, time, and advice!


December 5, 2019

There are no free lunches...well, maybe except when including electronic polarization effects into nominally non-polarizable force field molecular dynamics simulations via charge scaling. Feel free to taste this free lunch and have a look at our Charge Scaling Manifesto, where we outline with Brian Kirby from Cornell University the basic physics behind charge scaling and point to recent successes and pitfalls. And of course feel free to join the ever growing crowd of charge scaling simulators!


December 3, 2019

Congratulations to the winners of the Dream Chemistry Award 2019!

This year's TOP 5 Dream Chemistry Awards go to Yujia Qing (Oxford U) - who is the absolute winner of the competition organized jointly by IOCB Prague and IPC Warsaw, as well as to Hannes Mikula (TU Wien), Jeffrey Martell (U Wisconsin), Yoeri van de Burgt (TU Eindhoven), and Emiliano Cortes (LMU Munich). Congrats to all and big thanks to Bara and her team for organization, to Robert and all jury members for evaluation work, and to IOCB and IOCB Tech managment for support!



April 9, 2019

Our group is inspecting the newly installed computer cluster - the biggest in IOCB so far with over 240 nodes - all fresh from the owen. Thank you very much European Union for grant support of 2 M € from the Structural Funds!


March 9, 2019

Thanks to everybody for making our annual group seminar/teambuilding at the top of the highest Czech mountain Sněžka a success - meaning we did not loose anybody despite the hurricane up there :). When we passed the group with Tibetian flags commemorating the 60th anniversary of the failed uprising against Chinese rule it really felt like we were in the Himalayas!


December 17, 2018

Big congratulations to the four winners of the 2018 Martina Roeselová Memorial Fellowship!

Support to young scientists raising small kids goes to Sylvie Rimpelová, Barbora Melkes, Petra Šedová, and Klára Frydrýsková! The award ceremony at the Christmas party of the Institute on December 14 was great fun and big thanks to all that helped - the small donors, the Institute and IOCB Tech, member of the selection comittee, and the Memorial Fund!


December 10, 2018

Last year around this time we presented here an artistic Christmas movie showing the beauties of solvated electrons in ammonia. Well, now we've actually managed to measure their photoelectron spectra in a cool liquid ammonia microjet going from the blue regime of (di)electrons all the way to the golden/bronze metallic state. This has been a massive collective effort together with our buddies - Steve Bradforth's group at USC, Bernd Winter's group at the Fritz Haber Institute in Berlin, and Robert Seidel and his people at the BESSY synchrotron. Big thanks to everybody on the picture, which also shows the first spotting of the photoelectron signature of an ammoniated electron! Turns out this is a shy nocturnal animal, which usually shows up only late at night and stinks a lot...


November 8, 2018

Our latest study on cell penetrating peptides, combining molecular simulations with fluorescence and electron microscopy of model vesicles and cells, has just been published in PNAS. After a long march through journals (thank you Russell in Nature Chemistry and all the critical anonymous reviewers for helping to make the study better) we are coming out with a suggestion that the passive cell penetration mechanism of arginine-rich peptides may not be a simple opening of a transition pore but rather involves complex membrane bifurcation and fusion processes, the latter being analogous to the well known calcium induced membrane fusion. Passive cell penetration and membrane fusion may thus be two sides of the same coin!


October 29, 2018

Happy birthday JACS!

JACS is turning 140 and as a part of the birthday celebration the editors selected representative papers from recent years. We are happy that our colleague Paul Cremer selected our joint paper dealing with the effect of guanidinium on stability of boiomacromolecules for the year 2017. Thanks Paul!


May 7, 2018

Big congratulations and thanks to everybody on the picture, in particular to Tillmann and Phil, for producing after a year of work in the lab the first ever liquid ammonia microjet! Not a simple task given the fact that it all has to be cooled down to about -50 °C. This allows us to measure at the Berlin synchrotron BESSY II the photoelectron spectra of liquid ammonia and hopefully eventually to characterize the solvated electrons therein, in what should become a new twist of our never-ending "throwing sodium into something" story.



March 6, 2018

The American Institute of Physics has highlighted in an editorial our new article in the Journal of Chemical Physics on developing a simple but accurate model of calcium for biological simulations. Sweet, since this is certainly not a breakthrough discovery but rather an incremental results of a tedious down-to-the-earth work, which will hopefully be useful to the community. If you are modeling calcium signaling or any other process involving this lovely but difficult ion, feel free to use our new parameterization and let us know how it works for you!


A standard calcium model overestimates how strongly calcium binds, leading to clumps of ion pairs (left). An intermediate model shows less clumping (middle),
and a refined charge-scale model correctly predicts a weak association with carboxylic groups in water (not shown) (right).

Martinek T., Duboué-Dijon E., Timr Š., Mason P.E., Baxová K., Fischer H.E., Schmidt B., Pluhařová E., Jungwirth P.:
Calcium Ions in Aqueous Solutions: Accurate Force Field Description Aided by Ab Initio Molecular Dynamics and Neutron Scattering.
Journal of Chemical Physics 148 : 222813 (2018).