Jožef Stefan Institute
  • Ljubljana, Slovenia
Recent publications
The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton–proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run 2 (2015–2018), there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of sampling the inelastic interactions and adding their energy deposits to a hard-scatter interaction one-by-one, the inelastic interactions are presampled, independent of the hard scatter, and stored as combined events. Consequently, for each hard-scatter interaction, only one such presampled event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.
The ATLAS experiment at the Large Hadron Collider has a broad physics programme ranging from precision measurements to direct searches for new particles and new interactions, requiring ever larger and ever more accurate datasets of simulated Monte Carlo events. Detector simulation with Geant4 is accurate but requires significant CPU resources. Over the past decade, ATLAS has developed and utilized tools that replace the most CPU-intensive component of the simulation—the calorimeter shower simulation—with faster simulation methods. Here, AtlFast3, the next generation of high-accuracy fast simulation in ATLAS, is introduced. AtlFast3 combines parameterized approaches with machine-learning techniques and is deployed to meet current and future computing challenges, and simulation needs of the ATLAS experiment. With highly accurate performance and significantly improved modelling of substructure within jets, AtlFast3 can simulate large numbers of events for a wide range of physics processes.
Low-temperature solid-state reactions between Ni and Si were studied using in situ transmission electron microscopy (TEM). In the experiments thin amorphous silicon (a-Si) films were laid on Ni micro-grids and heated up to 973 K. In our approach the supporting Ni-grid serves as an unlimited source of nickel to successively form the whole range of Ni-silicide phases while diffusing into amorphous silicon. Unlike other thin film experiments where Ni and Si are layered on top of each other, our arrangement enables lateral diffusion of Ni along the Si layer and therefore enables the formation and study of successive Ni-Si phases side by side. That allowed us to observe in situ α-NiSi2 as the first reaction product, in contrast to most studies that had reported either δ-Ni2Si or θ-Ni2Si as the first phase to form. α-NiSi2 was continuously present at the reaction front propagating into the a-Si film. The phase sequence followed the increasing Ni concentration from a-Si towards the Ni-grid: α-NiSi2, NiSi, Ni3Si2, δ-Ni2Si, γ-Ni31Si12 and Ni3Si. Almost all known Ni-silicide phases were found to form at relatively low temperatures except the θ-Ni2Si, β-NiSi2 and β3-Ni3Si. The dominant phase was γ-Ni31Si12 which appeared in three structural modifications, differing in lattice periodicity along the c-axis. The periodicity of the basic γ-Ni31Si12 structure along the c-axis is ~12 Å (c0 = 12.288 Å) and that of the other two modifications were ~18 Å and ~36 Å, denoted by S12, S18 and S36 respectively. Of the three, only S12 has a structural model, S18 had been previously observed by Chen, but S36 had not been documented in previous works. During our in situ heating experiments, in addition to the Ni-silicide layer formation a new phenomenon was observed, namely the appearance, growth and transformation of Ni-silicide whiskers which was attributed to the accumulation of compressive stress in the thin layer.
An extensive study on using plant waste aqueous extracts as natural chemicals for in-situ synthesis of zinc oxide (ZnO) on cotton is presented. Reducing agents were prepared from green tea leaves (GT), pomegranate peels (PG), and staghorn sumac leaves (SsL) and drupes (SsD), and the alkaline medium from discarded wood ash. Zinc acetate was found to be more appropriate precursor than zinc nitrate. Formation of ZnO on cotton was confirmed by energy dispersive spectroscopy, X-ray photoelectron spectroscopy and X-ray diffraction analysis (XRD). The inductively coupled plasma mass spectrometry and X-ray fluorescence results showed the highest amount of ZnO on cotton was formed using PG and SsL extracts, which was also confirmed with scanning electron microscopy and UV/visible spectroscopy. The ZnO-functionalised samples exhibited excellent UV-blocking ability and different wetting properties (hydrophilic or hydrophobic) depending on the reducing agent used due to their different total phenolic content. This study shows that by choosing the plant waste source as a reducing agent for ZnO formation directly on cotton, the properties of cotton can be designed to be hydrophilic or hydrophobic with excellent UV-blocking properties. The XRD results of ex-situ synthesis prove that the short reaction time enables the formation of ZnO.
Layered double oxide (LDO) photocatalyst microparticles were synthetized with special radial lamellar orientation. We presented that the 25.31 ± 2.34 μm LDO particles with rough surface can incorporated in fluoropolymer solution and resulted a composite layer with dual superhydrophobic and photocatalytic properties with high bacterial adhesion and inactivation ability. Next the LDO content in the composite layers were systematically increased (0, 20, 40, 60, 80 and 100 wt% LDO) which facilitated the surface adhesion of bacteria by electrostatic interactions. The structure of the initial LDO and LDO/fluoropolymer composites was verified by small angle X-ray scattering (SAXS), XRD and SEM measurements. We showed that the surface roughness and hydrophobicity increase with increasing LDO loading. At 80/20 wt% LDO/fluoropolymer ratio the apparent surface energy was low enough to obtain a superhydrophobic surface (θw= 156.3° and γstot= 2.7 mJ/m²). The bacterial adhesion extent on LDO/fluoropolymer composite layers increases with increasing LDO content because the adhesion takes place preferentially to LDO lamellae. The reason for this pronounced adhesion of negatively charged and hydrophilic bacteria onto positively charged and hydrophilic LDO surfaces is the electrostatic attraction between oppositely charged surfaces. The bacterial adhesion was detected by scanning electron and fluorescence microscopy and crystal violet staining assay. Finally, the adhered bacteria were inactivated by the LED-light illumination due to photoreactivity of LDO particles containing 12 wt% of ZnO phase.
Yttrium manganite, YMnO3, was doped with different concentrations of titanium (x = 0, 0.04, 0.08, 0.10, 0.15, 0.20) in order to improve the microstructural and multiferroic properties. The powders were prepared using sol-gel polymerization complex method from citrate precursors. Depending on the titanium concentration, the hexagonal structure and/or the rhombohedral superstructure are present in the sintered samples. The YMn1–xTixO3+δ (x = 0.10, 0.15, 0.20) ceramic samples showed significantly reduced density of microcracks, and of inter- and intragranular pores, and relative densities greater than 90%. The structural parameters for YMn1–xTixO3+δ (x = 0, 0.10, 0.15) were correlated with the results of magnetic and ferroelectric measurements. The most of titanium-doped samples showed a reduction of the leakage current density in comparison with undoped YMnO3, and their ferroelectric responses were slightly improved. The modifications in structural arrangement resulted in partial suppression of ideal antiferromagnetic ordering visible through decrease of the Néel temperature and Weiss parameter, as well as the appearance of weak ferromagnetism and increase of magnetization (especially, in samples x = 0.08, 0.10, 0.15). These changes in physical quantities most likely originated from incorporation of the uncompensated magnetic moments and possible spin canting induced by enhanced symmetry break of the superexchange bridges. Graphical abstract
The aim of this work is to develop a novel π-coordination compound with unusual architecture using allylcytisine (Acyt) as a suitable scaffold. The synthesis and structural characterization of {Acyt(H⁺)}[Cu8{Acyt(H⁺)}Cl10] (1) and Acyt itself have been performed, accompanied by quantum chemical studies. A distinctive feature of structure 1 is the formation of H-bonded pairs of two {Acyt(H⁺)} cations, showing the non-equivalent participation of its allyl group regarding to Cu⁺ coordination, thus forcing the organization of the acentric structure 1 with the unusually organized anionic copper(I) halide 1D-coordination polymer.
We numerically study the relaxation of correlation functions in weakly perturbed integrable XXZ chain. The decay of the spin-current and the energy-current correlations at zero magnetization are well described by single, but quite distinct, relaxation rates governed by the square of the perturbation strength g g . However, at finite magnetization a single correlation function reveals multiple relaxation rates. The result can be understood in terms of multi-scale relaxation scenario, where various relaxation times are linked with various quantities which are conserved in the reference integrable system. On the other hand, the correlations of non-commuting quantities, being conserved at particular anisotropies \Delta Δ , decay non-exponentially with characteristic time scale linear in g g .
Decarbonylation reactions of acetyl metal carbonyls, in particular of organocobalt compounds, and of amides are discussed in view of stabilization/resonance energies. It is found that the archetypal acetylcobalt tetracarbonyl, CH3C(O)Co(CO)4, has ca. 25 kJ mol⁻¹ stabilization, while the corresponding phthalimido- and phenoxy-substituted species have inexplicable destabilization of ca. 8 kJ mol⁻¹. By comparison, the archetypal N,N-dimethylacetamide, CH3C(O)N(CH3)2, has a resonance energy of 71 kJ mol⁻¹.
We aimed to identify potential physiological and performance differences of trained cross-country skiers (V˙o2max=60±4 ml ∙ kg–1 ∙ min–1) following two, 3-week long altitude modalities: 1) training at moderate altitudes (600–1700 m) and living at 1500 m (LMTM;N=8); and 2) training at moderate altitudes (600–1700 m) and living at 1500 m with additional nocturnal normobaric hypoxic exposures (FiO2 =0.17;LHTM; N=8). All participants conducted the same training throughout the altitude training phase and underwent maximal roller ski trials and submaximal cyclo-ergometery before, during and one week after the training camps. No exercise performance or hematological differences were observed between the two modalities. The average roller ski velocities were increased one week after the training camps following both LMTM (p=0.03) and LHTM (p=0.04) with no difference between the two (p=0.68). During the submaximal test, LMTM increased the Tissue Oxygenation Index (11.5±6.5 to 1.0±8.5%; p=0.04), decreased the total hemoglobin concentration (15.1±6.5 to 1.7±12.9 a.u.;p=0.02), and increased blood pH (7.36±0.03 to 7.39±0.03;p=0.03). On the other hand, LHTM augmented minute ventilation (76±14 to 88±10 l·min−1;p=0.04) and systemic blood oxygen saturation by 2±1%; (p=0.02) with no such differences observed following the LMTM. Collectively, despite minor physiological differences observed between the two tested altitude training modalities both induced comparable exercise performance modulation.
This paper reports three exploratory empirical studies with older adults that had little or no prior experience with interactive technologies. The participants were introduced to interactive technology by playing games on touchscreens, playing in pairs with the assistance of a mentor. We focus on two principle aspects, the peer-to-peer interaction during these sessions, and the role of the mentor in progressing the sessions. In the case of peer-to-peer interaction we looked for ways in which players supported each other during interaction to assess the role of peer interaction in this context. In the case of mentoring, we examined the efficacy of a minimalist approach where verbal encouragement, suggestions or (in the last resort) intervention are used to provide support to learners. The sessions showed that learners typically could play and learn basic manipulations independently after initial help and guidance from mentors. We also found that peer interaction, both in verbal and non-verbal communication and cooperative action was broadly a positive influence within sessions, suggesting that there is a significant value in building confidence as well as in learning.
The increasing use of Liquefied Natural Gas (LNG) in shipping has led to an increased interest in marine bunkering safety in ports. The main tool for risk management and siting of bunkering facilities is quantitative risk assessment. This paper addresses the uncertainties in the available data on bunker equipment (loading and unloading arms and hoses), safety system failure rates, and ignition probabilities required for risk assessment. Using the search engines Scopus and Google, a literature search was conducted for studies and papers on the risk assessment of LPG bunkering. Analysis of the relevant studies revealed that different sources of data were used for equipment failure rates and ignition probabilities. The analysis of failure rates for leaks and ruptures of arms and hoses revealed that there are several problems with comparability, but also that there is a high degree of uncertainty, with data ranging from two to four orders of magnitude. The analysis of ignition probabilities showed that the uncertainty is about two orders of magnitude for small releases and within one order of magnitude for large releases. The failure rates of the emergency shutdown systems are within one order of magnitude. A wide range of arm and hose failure rates represents a large uncertainty for a reliable risk assessment. The way forward appears to be a transparent data collection system that describes the scope and the various assumptions.
Construction and demolition waste are one of the largest waste streams generated in the EU by volume. They consist of materials such as concrete, bricks, gypsum, wood, glass, metals, foams, plastics, solvents, asbestos, asphalt, and excavated soil. Nowadays, many of them can be recycled, some even endlessly. This research attempts to contribute to the non-destructive characterization of such a waste with a novel method using terahertz radiation. By combining terahertz imaging and spectroscopy, we performed analytical characterization of selected building materials. The results demonstrate that terahertz technology allows an inside view into some of the non-conducting building materials. THz imaging can detect and visualize the organic solvents in the insulation material, which are often disposed of together with construction and demolition waste. It can also visualize the content of foreign objects or hazardous and toxic substances, which is important for their separation in the recyclate according to the type of the material. Furthermore, THz spectra reveal some spectral lines that can differentiate between different plastics and polymers within the frequency range of 1.0–4.5 THz due to different material structures and chemical compositions. Such results significantly contribute to the decision of which product meets all the standards, which can be returned to the production process due to irregularities or may be disposed of as waste. The only way to reduce construction and demolition waste in the future is to encourage the adoption of innovative technologies like terahertz spectroscopy in combination with traditional methods. This approach can bring some changes also to the construction design philosophy toward more sustainable buildings with minimum end-of-life demolition.
Purpose To evaluate visual function parameters during and after an acute central serous chorioretinopathy (CSC) episode. Methods A prospective study included 19 fovea involving acute CSC patients with episode resolution within 3 months from the episode onset. Optical coherence tomography, best corrected visual acuity (BCVA), contrast sensitivity (CS), microperimetry (MP), and multifocal electroretinography (mfERG) were performed at baseline, 3 and 6 months from the episode onset. In a sub analysis, patients were divided into groups with greater (gMV, N = 9) and lower (lMV, N = 10) macular volume at presentation, and functional outcomes were observed. Results BCVA (p < 0.001), average CS (CS-A) (p < 0.001), average retinal sensitivity (MP-A) (p < 0.001), mfERG amplitude densities in the first and second ring (mfERG-A1, p < 0.001; mfERG-A2, p = 0.017), and implicit times in the first, second, and third ring (mfERG-IT1, p = 0.024; mfERG-IT2, p = 0.002; mfERG-IT3, p = 0.018) improved with episode resolution 3 months after the episode onset. From 3 to 6 months after the episode onset, only CS-A (p = 0.045) continued to improve. Patients in the gMV group had lower mfERG-A1 (p = 0.017) and central retinal sensitivity (MP-C, p = 0.05) 6 months from the episode onset. Conclusions Although all functional parameters mostly improve with CSC episode resolution, only CS continues to improve thereafter. Patients with greater MV at presentation have worse functional outcomes. Visual function impairment in acute CSC patients is confined to the topographical area of subretinal fluid detachment.
Coupled antiferromagnetic–ferromagnetic bilayers have been intensively investigated as low-dimensional memory materials. However, the connection between their architecture and emergent hysteresis loop phenomena remains elusive. Here, we revealed this relation through low-temperature simulations of the field-driven Ising spin reversal dynamics in heterostructures of coupled ferromagnetic and antiferromagnetic layers of varied thicknesses and a weak random-field disorder. The hysteresis loop exhibits the fractional-magnetisation plateaus, where their number, the height of the central loop, and the structure of side sub-loops strictly depend on the antiferromagnetic layer thickness. Meanwhile, the interlayer coupling chiefly determines the coercive field values, modified by the magnetic disorder, the thickness of the ferromagnetic layer and the system size, in agreement with the derived theoretical formula. The magnetisation fluctuations are modulated with peaks at the transitions between successive plateaus, reflecting the active groups of spins with different levels of (anti)ferromagnetic couplings arising at the interplay of antiferromagnetic sublattices and disorder. The cyclic trend drives the magnetisation fluctuations within limited time intervals; multifractal fluctuations occur on larger time scales. These findings shed new light on the tuneable hysteresis loop properties and the related magnetisation fluctuations in thin antiferromagnetic–ferromagnetic bilayers. The described hysteresis-loop phenomena are not limited to these model systems but should be present in different antiferromagnetic materials with complex morphology.
A theoretical simulation model of solid particles behaviour inside a scrubbing pool was developed, with the purpose to evaluate the particles decontamination factor. A three-step approach to describe pool scrubbing on the local instantaneous scale, using Computational Fluid Dynamics, is proposed. A subgrid model for particle decontamination, based on simulation of particle flow within individual bubbles of different sizes, is introduced first. Experimental data from the literature were then used to first validate the used open-source numerical solver's gas-liquid flow part with the implemented drag model, and then to assess the results of pool scrubbing simulations using the implemented decontamination model.
We report on the dynamics of a magnetic-field-driven antiferromagnetic-to-paramagnetic quantum phase transition in monocrystalline Ce3Al via transverse-field muon spin rotation (TF-µSR) experiments down to low temperature of ∼ 80 mK. The quantum phase transition is of a spin-flip type and takes place on the Ce–Al magnetic chains as a result of competition between the indirect exchange and the Zeeman interaction of the Ce moments with the external field, applied along the chain direction (also the direction of the antiferromagnetic axis). The Ce moments are not static at T→ 0, but fluctuate in their direction due to the Heisenberg uncertainty principle. Upon applying the magnetic field sweep, the fluctuations exhibit the largest amplitude at the quantum critical point, manifested in a maximum of the muon transverse relaxation rate at the critical field. The quantum nature of fluctuations observed in the TF-µSR experiments is reflected in the temperature independence of the average local magnetic field component along the external magnetic field at the muon stopping site(s) and the muon transverse relaxation rate within the investigated temperature range 1.5 K–80 mK. Quantum fluctuations are fast on the muon Larmor frequency scale, τ0< 10–10 s.
The three-dimensional conformation of RNA is important in the function and fate of the molecule. The common conformation of mRNA is formed based on the closed-loop structure and internal base pairings with the activity of the ribosome movements. However, recent reports suggest that the closed-loop structure might not be formed in many mRNAs. This implies that mRNA can be considered as a single polymer in the cell. Here, we introduce the Three-dimensional RNA Illustration Program TRIP, to model the three-dimensional RNA folding shape based on single-chain models and angle restriction of each bead component from previously reported single-molecule FISH (smFISH) experimental data. This simulation method was able to recapitulate the mRNA conformation change of the translation activity and three-dimensional positional interaction between organelle and its localized mRNAs as end-to-end distances. Within the analyzed cases base-pairing interactions only have minor effects on the three-dimensional mRNA conformation, and instead single-chain polymer characteristics have a more significant impact on the conformation. This top-down method will be used to interpret the aggregation mechanism of mRNA under different cellular conditions such as nucleolus and phase-separated granules.
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916 members
Boris Turk
  • Department of Biochemistry, Molecular and Structural Biology
Eva Zerovnik
  • Department of Biochemistry, Molecular and Structural Biology
Matjaz Gams
  • Department of Intelligent Systems
Jamova 39, 1000, Ljubljana, Slovenia
Head of institution
Prof. dr. Boštjan Zalar