Open Positions: Motivated and molecular simulations inclined Ph.D. and M.Sc. students always welcome!
We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time.
[ T. S. Eliot ]
November 8, 2023
Coming out! After 12 years of work we are coming out with my extraordinarily talented and hard-working student Ondřej Ticháček and our friendly collaborator Pavel Mistrík at MED-EL Austria with a complete bottom-up computer model of the peripheral auditory system. In normal language this means that we can now model mammalian (yes, including human) hearing from the outer ear all the way to the auditory nerve. In other words, our model describes in a physically justified way and with physiologically relevant parameters how incoming sound translates to mechanical excitation in the middle and inner ear, followed by electrical excitation of the outer and inner hair cells and finally, via action of neurotransmitters to spikes in the auditory nerve, to be translated to the central nervous system. Why did I in 2011 start this project which seems totally out of the scope of research in our group? Mixture of craziness and personal reasons – a hard of hearing family member, as well as realization that at an atomistic level hearing is based on flows of ions like potassium and calcium, modelling of which is our daily bread. True, the present model does not go down to the atomistic level explicitly, but wherever possible builds in parameters reflecting the actual ionic flows in the inner ear. Our MATLAB-based model is now open for use to general public. So, whoever of you wants to play with it and, e.g., model various types of hearing impairment and in the future versions also model their compensation by hearing aids or cochlear implants, is welcome!
Graphical input/output of the model simulating a person saying the word "greasy" (don't ask me why this particular word).
Ticháček O., Mistrík P., Jungwirth P.:
From the outer ear to the nerve: A complete computer model of the peripheral auditory system.
Hearing Research 440: 108900, 2023.
September 12, 2023
Couple photos from our informal ERC Advanced Grant kick off meeting & debriefing. The project Q-SCALING (Doing Charges Right: Modelling Ion-Controlled Biological Processes with the Correct Toolbox) starts officially on October 1. Nevertheless, we are already putting together our research team for developing de novo a charge scaled force field for biomolecular simulations, including group members as well as external collaborators, most notably Elise Duboue-Dijon (IBPC Paris), Matti Javanainen (University of Helsinki), and Christoph Alolio (Charles University). May the properly scaled charges be with you soon!
December 9, 2022
In our combined experimental and computational study done in collaboration with an IOCB colleague Tomáš Slanina and his group we characterize the key intermediates of the Birch reduction process in liquid ammonia, i.e., the solvated electron, dielectron, and the benzene radical anion using two complementary approaches – synchrotron X-ray photoelectron spectroscopy in liquid microjets and cyclic voltammetry. First, this has allowed us to extract mutually consistent values of electron binding energies/redox potentials of these species, whichare in quantitative agreement with our electronic structure calculations. Second, this case study showed what are the pitfalls when attempting to bridge the two experimental techniques and how careful one has to be when relating results of photoelectron spectroscopy measured with respect to the vacuum level to cyclic voltammetry employing a standard electrode.
Nemirovich T., Košťál V., Copko J., Schewe H.Ch., Boháčová S., Martinek T., Slanina T., Jungwirth P.:
Bridging Electrochemistry and Photoelectron Spectroscopy in the Context of Birch Reduction: Detachment Energies and Redox Potentials of Electron, Dielectron, and Benzene Radical Anion in Liquid Ammonia.
Journal of the American Chemical Society 144 (48): 22093–22100, 2022.
August 3, 2022
In our JPCB Perspective Article we propose with our collaborators in Finland, Norway, and Germany a practical path employing automated parameterization tools to systematically building up physically well-justifed models for biomembrane systems in native aqueous environments, which effectively account for electronic polarization via charge scaling. This work has been already initiated within the open collaboration NMRlipids project (nmrlipids.blogspot.com) and benefits from creation of databanks of molecular dynamics simulations with enforced quality control. The ultimate goal is to provide the scientific community a consistent charge-scaled biomolecular force field allowing to obtain in a computationally efficient way "the right results for the right reasons" and you are most welcome to participate on this collaborative project.
Antila H.S., Kav B., Miettinen M.S., Martinez-Seara H., Jungwirth P., Samuli Ollila O.H.:
Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks.
Journal of Physical Chemistry B 126: 4169, 2022.
July 29, 2021
The idea of using high pressure to make metal out of water is nothing new. However, the required pressure of 50 Mbar may exist in the cores of large planets, but not at terrestrial conditions. In collaboration with colleagues and friends (thank you Steve, Bernd, Robert, Tillmann,…) from the University of Southern California, the Fritz Haber Institute, the BESSY II synchrotron, and other institutes, our group (thank you Phil, Christian, Vojta, Marco,…) developed a method that allowed us to a prepare metallic water solution while completely sidestepping the need for high pressure. Inspired by work with alkali metal-liquid ammonia solutions, which at high concentrations behave like a metal, we decided to attempt formation of a conduction band not by compressing water molecules but rather by massive dissolution of electrons released from the alkali metal. In doing so, however, we had to overcome a fundamental obstacle, namely that on introduction to water, alkali metals tend to explode.
The successful way around the explosive chemistry was in exposing (inside a vacuum chamber) a drop of liquid sodium-potassium alloy to a small amount of water vapor, which began to condense on its surface. Electrons liberated from the alkali metal dissolved in the layer of water on the surface of the drop faster than the chemical reaction that results in the explosion proceeds. Moreover, there was a sufficient number of them to overcome the critical limit for the formation of a conduction band, giving thus rise to a beautiful golden metallic water solution, which we then characterized using optical reflectance and synchrotron X-ray photoelectron spectroscopies.
Mason P.E., Schewe Ch.H., Buttersack T., Košťál V., Vitek M., McMullen R.S., Ali H., Trinter F., Lee Ch., Neumark D.M., Thürmer S., Seidel R., Winter B., Bradforth S.E., Jungwirth P.:
Spectroscopic Evidence for a Gold-Coloured Metallic Water Solution.
Nature 595: 673, 2021.
April 6, 2021
Ordinary pure water has no distinct taste, but how about heavy water – does it taste sweet, as anecdotal evidence going back to 1930s may have indicated? And if yes – why, when D2O is chemically practically identical to H2O, of which it is a stable naturally-occurring isotope? These questions arose shortly after heavy water was isolated almost 100 years ago, but they had not been satisfactorily answered until now. Together with the group of Masha Niv at the Hebrew University and Maik Behrens at the Technical University of Munich, we have now found answers to these questions using molecular dynamics simulations, cell-based experiments, mouse models, and human subjects. In our article published in Communications Biology, we show conclusively that, unlike ordinary water, heavy water tastes mildly sweet to humans but not to mice, with this effect being mediated by the human sweet taste receptor. But why does it taste sweet and not, e.g., salty or bitter, remains to be established...
Abu N.B., Mason P.E., Klein H., Dubovski N., Shoshan-Galeczki Y.B., Malach E., Pražienková V., Maletínská L., Tempra C., Chamorro V.C., Cvačka J., Behrens M., Niv M.Y., Jungwirth P.:
Sweet taste of heavy water.
Communications Biology 4: 440, 2021.
April 1, 2021
This may look like April Fools but it's actually a serious study where we used molecular simulations with charge scaling to resolve the following puzzle - why are the experimental number densities of aqueous solutions of LiCl and NaCl practically the same at equal concentrations? Normally, one would assume that the number density of NaCl(aq) should be lower than that of LiCl(aq) since sodium cationsare larger than lithium cations. The trick is that lithium tightly orients four H2O molecules in its first solvation shell, such that these waters cannot make good hydrogen bonds with neighboring molecules. As a result, voids occur in the solvation environment of Li+ which compensate the tight first solvation shell, yielding an overall number density equal to the more regular sodium chloride solution.
Nguyen M.T.H., Ticháček O., Martinez-Seara H., Mason P.E., Jungwirth P.:
Resolving the Equal Number Density Puzzle: Molecular Picture from Simulations of LiCl(aq) and NaCl(aq).
Journal of Physical Chemistry B 125: 3153, 2021.