For several years, the distributed computing of the ATLAS experiment at the LHC has been granted opportunistic use of computing resources of the Czech national HPC centre, IT4Innovations. With the introduction of Karolina HPC, resources provided to ATLAS significantly increased, but with lower efficiency. The inefficiency arose because ATLAS jobs, designed for 8 cores, have a rather short...
Common-envelope evolution is arguably the most crucial major process in binary stars evolution, but also the least-well-constrained and more generally one of the most important unsolved challenge in stellar evolution.
Great efforts and progress have been made to confront numerical simulations outcomes to observational constraints over the last few decades. However, because of the wide range...
Ribosomes are the biomolecular factories in charge of protein synthesis and are thus essential for life as we know it. In order to better understand proteosynthesis it is important to understand the ways in which it is regulated. The regulatory mechanisms may involve conformational changes of the ribosome induced by external factors possibly transferred over large distances. The principles of...
The non-uniform Local Fourier Basis (LFB) method is designed to optimize memory consumption and increase the performance of strongly heterogeneous simulations. A crucial part of this modification is spatial resampling at resolution interfaces. The performance and accuracy of the simulation are closely tied to the performance and accuracy of resampling. In practice, these two aspects are...
Guanine-rich DNA sequences are capable to form non-canonical four-stranded secondary structures called G-quadruplexes (GQs). They are prevalent in gene promoters or telomeres, where they play role in key biological functions, such as maintenance of genome integrity, transcription, replication or epigenetic regulation. GQ formation is involved in development of genomic diseases such as some...
Polymorphism of elements or compounds means that these substances can exist in more than
one crystalline form. Due to the different mutual arrangement of molecules in these
polymorphs, both their static electron energies and their dynamic degrees of freedom vary.
As a result, different polymorphs of the same substance exhibit different physical properties.
Pharmaceutically active...
Diamond as a material of extreme properties has already proved to be a very promising candidate to build nanoengineered devices with a vast variety of applications such as in nanophotonics, optomechanics, photovoltaics and electronics. To harness diamond properties in an optimal way, it is then crucial to understand how its entangled electronic and geometric properties determine the width and...
The shaping of a time profile of the high-intensity laser pulse can substantially influence
electron and ion dynamics in the irradiated target. It was shown that a steep time profile could
mitigate the development of transverse short-wavelength instabilities with Rayleigh-Taylor-like
features to use long-wavelength corrugation of the target for quasi-monoenergetic ion accel-
eration [1]....
On-surface chemistry complemented with scanning probe microscopy (SPM) opens a completely new area of single-molecular organic synthesis and nano-fabrication. But this unparalleled level of atomic control and insight can be achieved only by close collaboration between SPM experiments with simulations. Currently these simulations are often unnecessarily costly and laborious due to lack of...
Lipid nanoparticles (LNPs) as the carrier systems of pharmacologically active compounds have entered the spotlight during the Covid19 pandemics in the mRNA containing vaccines. However, the technology of nanoparticle drug delivery has been also studied as a tool for cancer or rare disease therapy. The advantage of LNPs comprised of ionizable lipids (ILs) is in the tunability of the IL...
Designed for use with transcranial ultrasound stimulation (TUS) techniques, k-Plan is an advanced modelling tool for the precision planning of TUS procedures. k-Plan uses a streamlined and intuitive workflow that allows users to select an ultrasound device, position the device using a template or medical image, and specify the sonication parameters.
High-resolution calculations of the...
The so-called smart materials are unique for their ability to rapidly and fully reversibly change physical or chemical properties upon exposure to external stimuli, such as temperature, light, pH, or solvent quality.
In this contribution, we have taken under focus the prominent example of thermoresponsive polymer, which conformation can be near critical temperature modulated by the addition...
While the elastic properties of a composite microstructure are relatively straightforward in obtaining (e.g., using the resonance ultrasound spectroscopy), the features of a single grain are not directly measured. Here, we show our approach to determine these properties by employing large-scale ab-initio modeling techniques. Furthermore, we quantitatively reproduce the observed values of the...
The Ni-Mn-Ga ferromagnetic shape memory alloys have exceptional magneto-deformational properties, such as giant magnetic field induced strain (MFIS) in martensitic phase [1]. This effect originates in the high mobility of twin boundaries combined with large magneto-crystalline anisotropy [1,2]. MFIS allows use of the alloy in applications such as micro-sensors and actuators [3] or as...
Acid forms of zeolites have been used in industry for several decades but scaling the strength of their acid centers is still an unresolved and intensely debated issue. The Brønsted acidity strength in aluminosilicates measured by their deprotonation energy was investigated for FAU, CHA, IFR, MOR, FER, MFI, and TON zeolites by means of periodic and cluster calculations at the density...
P. Dwivedi$^{1}$, A. Fraile$^{2}$, G. Bonny$^{3}$, T. Polcar$^{1}$
$^{1}$Department of Control Engineering, Faculty of Electrical Engineering, Czech Technical
University in Prague, Karlovo náměstí 13, 121 35, Czech Republic
$^{2}$Nuclear Futures Institute, Bangor University, Gwynedd, LL57 2DG, United Kingdom
$^{3}$Nuclear Materials Science Institute, SCK CEN, Boeretang 200, B-2400 Mol,...
The contribution focuses on the parallel numerical solution of partial differential equations. The original problem is transformed into the system of ordinary differential equations using the method of lines. The resulting system of ordinary differential equations is solved by a higher-order numerical method based on the Taylor series. The numerical solution is compared with the...
Proteins are the most ubiquitous biomolecules in nature. In the first seconds of their existence, proteins are confined to the exit tunnel of the ribosome, the cell’s protein assembler. Under confinement, proteins behave differently than when free in aqueous solution. The principles of protein translocation through the confined space have been the target of previous studies. The difference of...
Monika Všianská$^{1}$, Iva Rambousková$^{1}$, Aneta Benešová$^{1}$, Jana Pavlů$^{1}$* and Mojmír Šob$^{1,2}$
$^{1}$ Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 753/5,
CZ-625 00 Brno, Czech Republic
$^{2}$ Institute of Physics of Materials CAS, v. v. i., Žižkova 513/22,
CZ-616 00 Brno, Czech Republic
An ab initio analysis of MoSi$_2$-XSi$_2$ (X = Nb,...
Photo-active nanomaterials are receiving increasing attention due to their prospects for light-driven applications. However, to exploit the properties of photoactive materials and access their enhanced capabilities require a fine-tuning between their topology-dependent electronic structure and the ability to integrate them into photoreactors or to deposit them on large surfaces. Subsequently,...
Motivated by their efficient charge-transfer capabilities over long-range distances, redox-active proteins have been recently incorporated into various nanobioelectronic devices in view of interesting applications like accurate biocompatible sensors or multi-state biomemristors. However, rather non-expected physical phenomena were observed when the proteins were connected to metal contacts....
Heterostructures made up of two-dimensional materials are excellent platforms to achieve twist-angle-independent ultra-low friction due to their weak interlayer van der Waals interactions and natural lattice mismatches. However, for finite-size interfaces, the domain edges can still play a role on the friction process, and their overall effect remains still unclear. In a recent publication[1],...
