600k hours for collapse kinetics of PNIPAM

615 000 CPU hours were granted in 12th IT4I call for our project entitled: “Collapse kinetics of themoresponsive polymer chain and hydration dynamics”. Denis and Vladimir will be investigating how does the PNIPAM chain collapse, and how does the properties of interfacial water changes near the critical temperature.

More details about projects supported in this IT4I call in Ostrava – link.

Bottom-up and Top-down Coarse-Grained model for poly-ethylene-oxide polymers

We have developed a temperature T-dependent coarse-grained Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution, which may be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range.

Our approach combined bottom-up approach, i.e., large scale atomistic MD simulations, and top-down closure, when explicitly targeting macroscopic experimental properties, such as scaling of polymer chain length and osmotic pressure equation of state.

Happy reading and employing!!! link

Positively charged poly-arginine chains are very special


First publication in PNAS!
Very thorough joint experimental (NMR, SAXS) & theoretical (umbrella-sampling, MD, mean field modeling) work of a group around Mikael Lund and his collaborators provided strong support on unusual self-association of highly charged poly-arginine chains. Note that like-charged species normally repel each other. This behavior is unique for arginine, and diminishes upon mutation to lysine (another positively charged amino acid). On the other end, purely poly-lysine chains behave as standard polyelectrolytes.

Long poly-arginine segment are found in many cell penetrating peptides, also known as arginine-rich peptides (RRPs), which can spontaneously traverse biological membranes in so called direct mode. Therefore this unusual binding motif may have a potential biological role.

Note that the rare like-charge attraction has its origin already on the level of guanidinium cations. link1, link2, research

The origin of this story goes back to 2012, to Pavel Jungwirth‘s group in Prague, when Mario Vazdar did first MD simulations of many deca-arginine and deca-lysine chains, and we have quantified the observed like-charged association. The motivation was the obsess by guanidinium and arginine systems, and a talk of Robin Curtis (University of Manchester) on his DLS experiments from around 2010.

Experiments in light in MD simulations and theory (seminar N403049)

In 2017, we will follow topics of bachelor thesis of the participating students.

  • Modeling of chromatography via MD simulation
  • Efficient sampling of rare events
  • Generic modeling of a salting out effect
  • Basics of the Lattice Boltzmann method

PS: In 2016 we investigated concepts of Kirkwood-Buff theory, and in 2015, we were dealing with special techniques of free energy calculation.

14 junior researcher positions at UCT

University of Chemistry and Technology, Prague, offers 14 2-year fellowships within EU program MOBILITY (MSCA-IF concept). The salary is very decent, 3 000 Euro/month brutto ~ 2.200 Euro netto.

The application deadline is November 27. And the positions start at April, May, June 2018.
For more details and application, please, visit: https://www.vscht.cz/research/chemjets

In a nutshell, we are looking for 14 postdoc and/or junior researchers with high degree of independence (the fellowship contain also ~15 000 Euro for consumables). The researcher  will be supported by the mentor of his/her choice.

Broad spectrum of chemistry/physics/engineering in application/experiment/theory is covered by our experienced mentors.

Heyda Jan  Soft Matter Chemistry – I would like to attract to Prague experimentalist with experience in spectroscopy of soft matter (neutron, Xray, NMR, IR, …) who will be able to take advantage of newly opened Czech (CEITEC, ELI) or EU facilities (Grenoble, etc.). I can offer my support from the computer simulations, theory and thermodynamic experiments (DSC, ITC, phase-equilibria). 

Other mentors:
Pumera Martin
Inorganic Chemistry
Lhoták Pavel  Organic Chemistry
Švorčík Václav  Chemistry & Technology of Materials
Svozil Daniel  Chemoinformatics – Computational Drug Design
Bouzek Karel Chemistry & Chemical Technology
Novák Pavel  Chemistry & Technology of Materials
Jeníček Pavel  Environmental Chemistry
Hajšlová Jana Food Chemistry & Analysis
Ruml Tomáš  Biochemistry
Patáková Petra & Moucha Tomáš & Ondřej Vopička  Biotechnology & Chemical Engineering & Physical Chemistry
Štěpánek František  Chemical Engineering – Particle Technology
Slavíček Petr Physical Chemistry
Kosek Juraj Chemical Engineering

Welcome new students: Anezka, Denis and Emil

We are pleased that three new bachelor students, Anezka, Denis and Emil, joined our group. They will strengthen the theoretical&computation part of the group. Denis is dealing with Transition Path Sampling and large-scale simulations of pNIPAM, Emil will focus on Kirkwood-Buff theory of model systems, and Anezka contributes the simulation support of the GACR chromatography project (Dr. Katerina Uselova) at the Faculty of Science, Charles University.
See the group web page for more details.


1 Megahour for phase-separations

model-FES1 080 000 CPU hours were granted in 10th IT4I call for our project entitled: “From single chain collapse to phase separation”. Denis and Vladimir will be in charge of modeling and revealing another from many peculiarities which are observed for PNIPAM.

More details about this IT4I call in Ostrava – link.