164 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Scuola Internazionale Superiore di Studi AvanzatiIT7 papers
- Czech Academy of SciencesCZ6 papers
- Palacký University OlomoucCZ5 papers
- Regional Centre of Advanced Technologies and MaterialsCZ5 papers
- Centre National de la Recherche ScientifiqueFR3 papers
- Central European Institute of Technology – Masaryk UniversityCZ2 papers
- Czech Academy of Sciences, Heyrovsky InstituteCZ2 papers
- Heidelberg UniversityDE2 papers
- InsermFR2 papers
- Lyon 1 UniversitéFR2 papers
- Masaryk UniversityCZ2 papers
- Technical University of MunichDE2 papers
16 papers
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
Valerio Piomponi, Miroslav Krepl, Jiri Sponer +1
N6-methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT…
RNA Dynamics from Experimental and Computational Approaches
Giovanni Bussi, Massimiliano Bonomi, Paraskevi Gkeka +16
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining…
Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment
Andrey V. Solov'yov, Alexey V. Verkhovtsev, Nigel J. Mason +20
This paper reviews the new highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The paper highlights several relevant exa…
Foundational Competencies and Responsibilities of a Research Software Engineer: Current State and Suggestions for Future Directions
Florian Goth, Renato Alves, Matthias Braun +20
The term Research Software Engineer, or RSE, emerged a little over 10 years ago as a way to represent individuals working in the research community but focusing on software develop…
Do conformational changes contribute to the surface plasmon resonance signal?
Daniel Dobrovodský, Carmelo Di Primo
Surface plasmon resonance (SPR)-based biosensors are widely used instruments for characterizing molecular interactions. In theory the SPR signal depends only on mass changes for in…
Automatic learning of hydrogen-bond fixes in an AMBER RNA force field
Thorben Fröhlking, Vojtěch Mlýnský, Michal Janeček +5
The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enfor…
Silver Amalgam Nanoparticles and Microparticles: A Novel Plasmonic Platform for Spectroelectrochemistry
Filip Ligmajer, Michal Horák, Tomáš Šikola +2
Plasmonic nanoparticles from unconventional materials can improve or even bring some novel functionalities into the disciplines inherently related to plasmonics such as photochemis…
Dust Motions in Magnetized Turbulence: Source of Chemical Complexity
Giuseppe Cassone, Franz Saija, Jiri Sponer +6
Notwithstanding manufacture of complex organic molecules from impacting cometary and icy planet surface analogues is well-established, dust grain-grain collisions driven by turbule…
Solvation Effects Alter the Photochemistry of 2-Thiocytosine
Mikołaj J. Janicki, Rafał Szabla, Jiří Šponer +1
Radiationless deactivation channels of 2-thiocytosine in aqueous environment are revisited by means of quantum-chemical simulations of excited-state absorption spectra, and investi…
Folding of guanine quadruplex molecules -- funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies
Jiří Šponer, Giovanni Bussi, Petr Stadlbauer +6
Background: Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural stud…
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
Petra Kührová, Robert B. Best, Sandro Bottaro +4
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motif…
Free Energy Landscape of GAGA and UUCG RNA Tetraloops
Sandro Bottaro, Pavel Banáš, Jiri Sponer +1
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the fol…
Hairpins Participating in Folding of Human Telomeric Sequence Quadruplexes Studied by Standard and T-REMD Simulations
Petr Stadlbauer, Petra Kührová, Pavel Banáš +5
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting…
Limit-cycle-based control of the myogenic wingbeat rhythm in the fruit fly Drosophila
Jan Bartussek, A. Kadir Mutlu, Martin Zapotocky +1
In many animals, rhythmic motor activity is governed by neural limit cycle oscillations under the control of sensory feedback. In the fruit fly Drosophila melanogaster, the wingbea…
Bonding distances as Exact Sums of the Radii of the Constituent Atoms in Nanomaterials - Boron Nitride and Coronene
Raji Heyrovska
This paper presents for the first time the exact structures at the atomic level of two important nanomaterials, boron nitride and coronene. Both these compounds are hexagonal layer…
Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii
Raji Heyrovska
The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of ade…