Kolář lab at UCT Prague

Rubber Stamp

I've just received a rubber stamp.

published 2017-05-20

Emotional Arcs and Random Diffusion

published 2017-05-14

This week I gave a seminar in our group on principal component analysis (PCA). It is a standard computational/mathematical technique to process complex data. During my preparation, I came across an article that uses the PCA to analyze text. The results are somewhat contradicting to what I've learned from PCA of biomolecules, and here I want to mention what I find suspicious.

Fellowship of the RNA Society

published 2017-03-22

In May, I'll be traveling to Prague to a big conference about RNA. Good news has arrived: the registration fee will be reimbursed thanks to a travel fellowship I've received from the RNA Society. This is the first academic society I'm member of and it's just started paiyng off. I'm looking forward to visiting the city, where I spent ten wonderful years.

RNA Society

Web of Science Hot Paper

published 2017-03-11

Great news! In December 2016, our review on sigma-hole calculations was ranked by Thomson Reuters Web of Science in the top 0.1 % of the academic field of chemistry.

Hot paper

Reaction Path Averaging

published 2017-02-13

The DNA is one of the best-known biomolecules. Upon electromagnetic radiation, an electron may be released from a nucleobase, resulting in a positive electron hole. The hole may travel across the nucleobases turning the DNA into a sort of nanowire. This is a rather established fact. The shape of the DNA is so classic that it is natural to ask how the DNA distorts upon the electron transfer. With Tom Kubař we've recently attempted to answer. We used a computational approach, which we called Reaction Path Averaging (RPA).

Reaction Path Averaging

Text about Biophysics in Vesmír

published 2017-02-11

In October 2016, Klaus Schulten passed away. He was a professor at the University of Illinois, USA, and a pioneer of computer simulations in biophysics. I've met him just once, but that episode left strong memories. In a recent article for Vesmír, I put Klaus' life into context with the progress in computational biophysics. Written in Czech, available for subscribers.

HTML5 in Bratislava

published 2016-12-09

Michal Pitonak invited me to Bratislava to give a talk on sigma-holes. The Department of physical and theoretical chemistry at the Comenius University in Bratislava is world-renowned for the accurate quantum chemical calculations. They develop, benchmark and apply perhaps the highest quantum chemistry one can imagine.

Ribosome Meeting in Heidelberg

published 2016-11-25

Last week, I attended a meeting on ribosomes. All the german experts on all aspects of ribosome research at one place. I gave a talk on the simulations I'm trying to establish. Given that there were like only two more simulation guys in the audience, the feedback that I got was in general quite positive.

Ribosome meeting in Heidelberg

This is what I saw in the morning from the hotel window, after a dreamless night of rendering the last videos for my talk.

CPU-Time Granted

published 2016-10-28

Our computational proposal with Helmut and others has just been approved! We will receive 67 million core-hours to study RNA-protein interactions within a prokaryotic ribosome. Thanks to the Leibniz Rechnenzentrum in Munich, Germany, our simulations of more than 2 million atoms will not take ages and I'll bring some news soon, hopefully.

Ribosomal exit tunnel

The figure shows the tRNA at the catalytic center of the ribosome (yellow), the exit tunnel for newly synthesized proteins (gray surface), and two ribosomal proteins (red and blue). The lines with dots are chemical bonds between atoms, just to put it all into context.

Highly Cited Paper

published 2016-10-21

Good news! In June 2016, our review on sigma-hole calculations was ranked by Thomson Reuters Web of Science in the top 1 % of the academic field of chemistry. No matter that the paper has received 10 citations so far...

Highly cited paper