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


  • "One should not increase, beyond what is necessary, the number of entities required to explain anything."
    [ Occam's razor ]
  • "For every phenomenon, however complex, someone will eventually come up with a simple and elegant theory. This theory will be wrong."
    [ Rothchild's rule ]
  • "The "reductionism" of evolutionary science is purely tactical. We do what we can do in the face of an awsome amount of diversity and complexity."
    [ Tactical reductionism by Richerson and Boyd ]


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).

February 23, 2018

Congratulations Ondra!

Ondřej Ticháček got for his work on a computational model of the inner ear and the auditory nerve the Werner von Siemens prize for the third best master thesis in sciences and engineering in 2017. It was a fun party, we both dressed sharp, got a free dinner and a tiny part of the whole sum.


February 10, 2018

Our latest JPC B article on interactions of divalent cations with insulin has been selected as Editor's Choice among papers published in all ACS journals. Possibly, the editors were as intrigued as we were by the disagreement between our results obtained by capillary electrophoresis vs. those from our molecular dynamics simulations. Or, maybe, they liked our hand-waving argument potentially blaming restructuring and/or aggregation of insulin molecules upon ion binding for the disagreement.


January 5, 2018

Throughout the year 2017, I participated, as (maybe) an expert on memory of water, on a Statement on homeopathy by the European Academies Science Advisory Council (EASAC). The whole report with a typical Brussels language title "Homeopatic products and practices: assessing the evidence and ensuring consistency in regulating medical claims in the EU" can be downloaded here. The common language title of our report may be something like "Hey guys, do not even try to use the memory-of-water explanation, homeopathy is placebo at best, so why don't you call it like this?". We are far from calling for a ban on homeopatic products since we fully respect the freedom of customers choice. At the same time, patients have the right for evidence-based information and should be protected from false advertisement. Therefore, we make the following recommendations (citing from our report):

  1. There should be consistent regulatory requirements to demonstrate efficacy, safety and quality of all products for human and veterinary medicine, to be based on verifiable and objective evidence, commensurate with the nature of the claims being made. In the absence of this evidence, a product should be neither approvable nor registrable by national regulatory agencies for the designation medicinal product.
  2. Evidence-based public health systems should not reimburse homeopathic products and practices unless they are demonstrated to be efficacious and safe by rigorous testing.
  3. The composition of homeopathic remedies should be labelled in a similar way to other health products available: that is, there should be an accurate, clear and simple description of the ingredients and their amounts present in the formulation.
  4. Advertising and marketing of homeopathic products and services must conform to established standards of accuracy and clarity. Promotional claims for efficacy, safety and quality should not be made without demonstrable and reproducible evidence.

There has been a surprising surge of interest in our report by the media recently, but only time will tell what impact on the public and policy makers it's gonna have. At the very least, I learnt a lot about placebo...and found on the web this nice cartoon on memory of water.