New Publication in a Munich Supercomputer Book
published 2018-11-18
The Leibniz Supercomputing Center in Munich has recently published a book of project reports. To me, it is a quite impressive list of top-class computational projects, easy to digest by non-experts. We contributed with a short text about nascent peptides in the ribosome exit tunnel.
Visiting the National Supercomputing Center in Ostrava
published 2018-11-07
I'm just visiting the Supercomputing center in Ostrava, which operates the largest Czech supercomputers. (Actually, I'm not sure about that because the data about private-company supercomputers are not available.) In Ostrava, there is the 2nd User Meeting with bunch of astrophysicists, material chemists, and software developers. I've contributed with a structural biology talk about ribosomes and VemP. In the end of my talk, couldn't stand comparing the nascent peptide with a baby leaving the mum's vagina.
Some of the presentations I really enjoyed. Prime numbers in 2D by Alberto Fraile, Nitride superlattices by Miroslav Černý, Star formation by Richard Wünsch.
Yet Another Text About Chemistry Olympiad
published 2018-10-26
Would you like to know how the International Chemistry Olympiad was founded? How hard and funny it can be to get there and what role Běstvina plays? Do you know some Czech language? If yes, a brand new article published online on vesmir.cz is right for you. This time written together with Petr Slavíček.
It's always nice to return back to Göttingen. I still have many connections there and enjoy discussions with my former group mates. This time, I stayed in a guesthouse, where Max von Laue lived after the World War II. Inspiring.
published 2018-10-13
Jiří - a colleague of mine, who I share my office with - has just turned 60. It was a great opportunity to eat some extra-chocolate cake and drink sparkling wine. We wish him all the best. (Motivated by Solvay conferences, we took a picture of us. Just in case...)
published 2018-09-25
50th International Chemistry Olympiad
published 2018-07-31
This year, the International Chemistry Olympiad (IChO) has celebrated its 50th anniversary. The first IChO took place in Prague, Czechoslovakia in 1968, and, although it is usually not emphasized, it pop up during the period known as Prague spring. Slovak and Czech republics were also the organizing countries of this year issue. It was my pleasure to be a part of Scientific committee, and with Tom Kubař to prepare and evaluate one of the eight theoretical exam problems. It was all about DNA, and part of our motivation stemmed from the work of Prof. Jan Svoboda, a famous Czech virologist in the picture below. It is just coincidence that his surname means "freedom".
New Publication in Vesmír: Göttingen Cemetery
published 2018-07-20
Living in Göttingen for a couple of years, I had to visit the Town cemetery. The cemetery is famoust because of many prominent scientific figures including eight Nobel prize laureates and it is worth seeing. With Tom Kubař from Karlsruhe, we put together a text about the buried and their rich relationships when still alived. A sort of longer reading fits nicely to a summer double issue of the Vesmír journal. Just thinking, where to go next...
MPIbpc NEWS
published 2018-06-26
MPIbpc NEWS is a non-peer reviewed magazine, which highlights research of the MPI Biophysical Chemistry in Göttingen. Our contribution on ribosome simulations has recently been published and featured on the journal cover page.
The figure shows dynamics of a macrolide antibiotic (in red) bound in the ribosome exit tunnel. In bacteria, the molecule interacts with certain nascent peptides and causes ribosome stalling. No surprise that bacteria don't like it.
New Publication in Vesmír: How Are Proteins Born?
published 2018-05-02
Birth - this is a fascinating topic in many areas of humanity. How it is with proteins, biomolecules that define the life as we know it? Protein are produced in ribosomes in a process called translation. According to an RNA blueprint, ribosomes catalyze peptide bond formation between amino acids and, what is more, they can regulate how proteins are produced.
Last year, I joined a conference in Cambridge, UK about so called co-translational events. A large variety of things may happen to the nascent protein before it is released from translating ribosome. Many excellent talks in Cambridge motivated me to sum up the key ideas in a popular-science article. The article has just been published in a Czech magazine Vesmír (which has tradition since 1871!). The editorial board selected it for free-of-charge access, so you can enjoy it online without any paywall (in Czech only though).
Running Proteasome on Hazel Hen
published 2018-04-27
Hazel Hen, one of the largest supercomputers in Europe, has just "opened its processors" to our simulations. Our large-scale computational project has been awarded 40 million core-hours, which is a nice chunk of the supercomputing power. For comparison, it is equivalent to almost 70% of the power, which was provided for the whole Czech computational community by IT4I in its last call.
So in the next 12 months, we will run all-atom molecular dynamics simulations of the human proteasome. It is a large biomolecular complex responsible for protein degradation. Interestingly, a few drugs and drug candidates act through affecting proteasome function. We will try to uncover, how these drug affect proteasome choreography.