Kolář lab at UCT Prague

Computer modeling of halogen bonds and other sigma-hole interactions: tag cloud

My recent Chemical Reviews article in its 150 most frequent words. Appreciation to python and Inkscape...

published 2016-02-19

Review on Modeling of Sigma-Holes

published 2016-02-04

I've been involved in computer calculations of halogen bonding for quite some time. In fact, a large part of my doctoral thesis was about halogen bonds and their sigma-holes. I was asked to contribute with a paper into a special issue of Chemical Reviews about noncovalent interactions, and finally - the first week in February - it appeared online. No doubts it is the most extensive article I've written so far and I'm trying to hold back being proud.

Computer modeling of halogen bonds and other sigma-hole interactions

Farewell Jülich

published 2016-01-04

My Humboldt fellowship is over. After two years I'm leaving Jülich to face new challenges. It's time for some statistics. During that time the following were "produced!":

1 daughter born
6 peer-reviewed articles published
9 conferences or workshops visited
56 postcards received
156 analog photographs taken
1470 EUR spent in Seekasino FZJ
3180 digital photographs taken
4894 km ridden to FZJ and back
many TB of data generated and analyzed
many CPU-hours consumed

Klaus Schulten

"I can convince you in a picosecond that this molecule is important."
Klaus Schulten about ATP, Physics Colloquium at RWTH Aachen.

published 2015-12-15

1000 PDFs

published 2015-12-09

I've just added the 1000th article to my pdf library. The anniversary article is from Bouvignies et al. and it deals with residual dipolar couplings of a protein backbone. My reference manager (so far CiteULike) offers some statistics. So the top three authors are Pavel Hobza (not surprising, the person I did my Ph.D. with), Peter Politzer (halogen bonding expert), and Peter Kollmann (pioneer of all-atom MD) and the top three keywords/tags are molecular dynamics (27%), halogen bonding (17%), and drug design (16.5%). Another one would be nucleic acid (21%) if I wouldn't have separated DNA and RNA into two tags. Looking forward to the next thousand.

GRS building

Here I work. The building was build in 2010 and has received several awards since then. Personally, I like the interior much more than its external look. It has circular-sector s hape and it is orange also from outside. Strangly, one of its sides has no windows at all.

published 2015-09-02

Polar flattening in JCTC

published 2015-08-10

Isolated atoms are spheres. One can view them as soft balls which attract each other on long distances and repel each other on short distance. In molecules, however, the shape of atoms is distorted. In fact, it is somewhat difficult to distinguish particular atoms in molecules. The most visible distortion is a flattening of the sphere in the elongation of the covalent bond.

Polar flattening on a dihalogen

Information embargo (un)broken

published 2015-07-21

As soon as our article was accepted for publication in Plos ONE last week (by the way, my first article in an open access journal), I found out that I'm not allowed to share my positive mood. Or more precisely not my positive mood but the science. The company reserved jus primaenoctis with our article, so sorry guys, I can't share any details about what we've done. Just make sure I'm really happy.

Science Fair

published 2015-05-26

I spent one week in Prague as a committee member in the Open Science Project. My task was to evaluate scientific posters of high-school and university students. They worked for one year in a scientific group in a university or a research institute of their choice.

"Science is observation and experiment followed by appeal to theory and a return to experiment."

Richard F. W. Bader

published 2015-09-26