Kolář lab at UCT Prague

Students intake

published 2020-02-13

Three new undergraduate students want to learn some of Python and Gromacs, and will study how biomolecules move. Welcome Hugo, Jan and Petr.

Special relativity and the halogen bonding

published 2020-01-29

In 1905, Albert Einstein formulated the theory of relativity which described the motion of objects with speeds close to the speed of light. The theory postulated that no object can move faster than light, so no process can be instataneous. About twenty years later, Paul Dirac merged the theory of relativity with the quantum mechanics and formulated what is today known as Dirac equation. The equation directly yields the spin, as a property of electron, and adjusts our understanding of chemistry of heavy elements such as gold or thallium. In our lates contribution we investigate, how the special relativity contributes to properties of halogen boding.

Special relativity and the halogen bonding.

Welcome new group members

published 2019-11-29

Two PhD students are joining our group in Prague to study biomolecular dynamics. Warmest welcome to Michaela from Slovakia and Felipe from Brazil who will hopefully spend a few years with atomistic simulations, python and Dejvice district. While Michaela has a background in molecular biology, Felipe studied bioinformatics. Wish them a steep learning curve, great discoveries, and smooth studies at UCT. Both will work on the project recently approved by the Czech Funging Agency (aka GAČR) about allosteric regulation of large biomolecules, of the ribosome in particular.

#NaPhdVen Workshop

published 2019-09-05

The culture of academic mobility is still latent in Czechia and many students feel OK staying in the same lab throughout all their studies. It was my case as well, although 10 years ago, and I view it as a sort of missed opportunity. With UCT Prague and Czexpats in Science, an NGO which connects Czech scientists working all over the world, we organize a workshop for undergraduate students about pros and cons of studying abroad.

Save the date and find out more (in Czech only): NaPhdVen.CzexpatsInScience.cz.

October 10, 2019 at UCT Prague.

#NaPhdVen: A workshop about studies abroad.

EMBO Workshop in Nové Hrady

published 2019-06-25

The workshop was about integration of experimental data to (mostly) molecular simulations and I attended it during the last week of June. Here I put a few thoughts, mixed scientific and personal.

There was a roof in front of the window in my room.

A Blog Post for Czexpats in Science

published 2019-05-22

This is a blog post about a blog post. After joining the Twitter, funny things started to happen. Through several independent routes I got in touch with a group of Czech scientists living abroad. They felt disconnected (personal opinion) from the wild Czech academic system, so they established an organization Czexpats in Science, which aims at curing their disconnection.

Czech scientists tend to discuss "science" rather than science.

We Are on Twitter

published 2019-03-27

There's not much more to say. It happened once upon a time in a train from České Budějovice to Prague, on a way from a panel discussion about perspectives of young researchers in the wild Czech academic environment.

Follow us on https://twitter.com/mhkoscience.

15th Open Call of IT4I: Our Second Project Got Approved

published 2019-02-05

With a three-week delay, the Czech supercomputing center IT4I in Ostrava has announced the results of the 15th Open Call for the computing time. I applied with a project which deals with a ribosome-regulatory peptide VemP. By a set of non-equilibrium simulations we will extend our previous simulation project, where we studied VemP and a few of its mutants.

I analyzed the result page. There are only 3 (three!) female PIs out of 71 projects. Is there anything wrong with the supercomputing community in the Czech Republic? The 8 largest projects consume almost one half of the total allocation available, while the smallest projects (half of the total number) received only about 14% of the total allocation. Hover over the bars for details.

New Publication in Vesmír: A Thin Line of Authorship

published 2019-01-08

An interesting text about authorship appeared in Nature by the end of the last year. It presented a study of researchers from Palo Alto and Philadelphia, USA about hyperproductive authors of scientific literature. With Petr Slavíček from UCT Prague we discuss its main findings and put them into a broader context of the complicated issues around scientific authorship.

A thin line of authorship. In Vesmír 2019/01.

A Few Thoughts on GAČR Grants

published 2018-12-18

The Czech Science Foundation has recently published a list of projects, which will receive its support. The Foundation does it once a year, so there are quite some of them. I've had a look on the list trying to answer, who the winners actually are.