Jožef Stefan Institute
  • Ljubljana, Slovenia
Recent publications
To theoretically investigate atmosphere mixing in an enclosure, three experiments of interaction of a vertical air jet with a helium-rich layer performed in SPARC, PANDA and MiniPanda experimental facilities, were simulated using the URANS approach. For the purposes of this work, firstly, a local Froude number is introduced, which can be directly used in computational fluid dynamics calculations to specify the regions with possible occurrence of Kelvin-Helmholtz instability. Namely, it is shown that in these regions, turbulent diffusion is underpredicted and turbulence model fails to replicate some phenomena. Secondly, a model for dynamically prescribe turbulent Schmidt and Prandtl numbers is proposed. The proposed model improves the results in isothermal case with possible occurrence of Kelvin-Helmholtz instability, while its effects are negligible in cases with higher temperature jets with lower local Froude number values, where the conditions for the Kelvin-Helmholtz instability are not established.
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.
Liquid crystals with high electro-optical responses play significant roles in optics and photonics. Providing a simple method for increasing the electro-optical behaviors of liquid crystals can be considered one of the most important and challenging research areas. In this work, left-handed chiral dopants and temperature effects on the electro-optical properties of pure and doped nematic liquid crystals with different percentages of chiral dopants were investigated. Despite decreasing the Kerr constant by increasing the percentage of chiral dopants, and temperature, the maximum values were observed for 4% of chiral dopants near the transition temperature. In this case, the value of Kerr constant is approximately 20 times that of a pure liquid crystal sample. This interesting result can be related to the changes in molecular polarizability due to molecular interactions. Hence, doped liquid crystals with high and controllable responses can be a good candidate for designing optoelectronic devices.
The cross section averaged over ²³⁵U thermal-neutron induced fission spectrum is a fundamental quantity that can be used in evaluation and validation of nuclear data. Many experiments focused on the determination of Spectrum Averaged Cross Sections (SACS) in ²³⁵U(nth,f) Prompt Fission Neutron Spectrum (PFNS) in light water reactors using enriched uranium fuel. In these reactors, there is already some amount of water moderator between the uranium fuel and the irradiated sample. Due to the decrease of hydrogen cross-section with neutron energy, the high energy tail of the reactor spectrum in cores with water moderator may be harder than the pure PFNS. This paper aims to compare the shape of the actual reactor spectrum in various core positions of a research light-water reactor differing each from other by the effective water thickness. The spectrum shape is determined both by calculations and experimentally using various high energy threshold reactions. The impact of the photo-nuclear reactions (γ,n) competing with (n,2n) in production of the same residual nucleus was shown to be less than a percent for most of studied dosimeters. An important exception was found for ¹⁹⁷Au(n,2n)¹⁹⁶Au dosimeter irradiated in the outcore channel where a notable photo-neutron contribution to the production of ¹⁹⁶Au is caused by the neutron production from the high energy γ-rays from thermal-neutron capture in ⁵⁴Fe. The corresponding ENDF/B-VIII.0 data turned out to underestimate such γ-yield by 40 % in comparison with ENDF/B-VI.8. This has improved but however not resolved the disagreement between our measurement and calculations. The remaining deficiency was attributed to the underestimation of the evaluated cross section IAEA/PD-2019 for the ¹⁹⁷Au(γ,n) cross section near the reaction threshold. The later was confirmed by comparison with existing measured data.
The main purpose of this work was to assess the potential of using temperature-programmed desorption coupled to quadrupole mass spectrometry to study the mercury partitioning in the cement production. This information is of significance to understanding mercury's migration and partitioning in the production process. In conventional raw materials—limestone, mercury is matrix-bound, but with the introduction of other mineral components, this stability is variable. In raw mills, mercury exhibits three distinct fractions that remain until the raw meal is dispatched in the preheater. Mercury collected in dust from fabric filters was desorbed at 200–250 °C, indicating the presence of chloro-containing mercury compounds to be the predominant form. Clinker had a low content of mercury primarily present as a very stable fraction. These results add to the current knowledge of mercury behavior in the cement production process and can be used to support the development of control technologies.
Bio-monitoring of mercury (Hg) in air using transplanted and in-situ lichens was conducted at three locations in Slovenia: (I) the town of Idrija in the area of the former Hg mine, where Hg contamination is well known; (II) Anhovo, a settlement with a cement production plant, which is a source of Hg pollution, and (III) Pokljuka, a part of a national park. Lichens from Pokljuka were transplanted to different sites and sampled four times—once per season, from January 2020 to February 2021. Lichens were set on tree branches, fences, and under cover, allowing them to be exposed to different environmental conditions (e.g., light and rain). The in-situ lichens were sampled at the beginning and the end of the sampling period. The highest concentrations were in the Idrija area, which was consistent with previous research. Significant mass-dependent fractionation has been observed in transplanted lichens during summer period. The δ²⁰²Hg changed from −3.0‰ in winter to −1.0‰ in summer and dropped again to the same value in winter the following year. This trend was observed in all samples, except those from the most polluted Idrija sampling site, which was in the vicinity of the former Hg ore-smelting plant. This was likely due to large amounts of Hg originating from polluted soil close to the former smelting plant with a distinct isotopic fingerprint in this local area. The Δ¹⁹⁹Hg in transplanted lichens ranged from −0.5‰ to −0.1‰ and showed no seasonal trends. These findings imply that seasonality, particularly in summer months, may affect the isotopic fractionation of Hg and should be considered in the sampling design and data interpretation. This trend was thus described in lichens for the first time. The mechanism behind such change is not yet fully understood.
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.
The CO2 absorption method is applicable for analyzing radiocarbon content in environmental samples. Since this method is characterized with low accuracy and sensitivity, optimization and improvement are needed. In the Laboratory for Liquid Scintillation Spectrometry at Jožef Stefan Institute, internal method validation was performed. The main aim of this validation was to set optimal and controlled conditions that would improve the total uncertainty. For that purpose, we investigated the effect of three parameters on the final results: size of the trap, flow rate and combination of trapping mediums. All measurements were performed on ultra-low level liquid scintillation counter Quantulus™ 1220. The counting efficiency was determined with the use of the external standard method (SQP(E)) and standard addition method. We recognized the use of a big trap, thus use of a balance with a readability of 0.01 g, as the most significant contributor to the total uncertainty. A small trap, flow rate of 0.1 L/min and a mixture of CarbonCount™ and CarbonTrap™ proved to be the most suitable parameters. Using a small trap instead of a big one lowered the relative uncertainty from 2.4% to 0.01%, causing a decrease in the total uncertainty from 4.7% to 3.2%.
The high design luminosity of the SuperKEKB electron–positron collider will result in challenging levels of beam-induced backgrounds in the interaction region. Understanding and mitigating these backgrounds is critical to the success of the Belle II experiment. We report on the first background measurements performed after roll-in of the Belle II detector, a period known as SuperKEKB Phase 2, utilizing both the BEAST II system of dedicated background detectors and the Belle II detector itself. We also report on first revisions to the background simulation made in response to our findings. Backgrounds measured include contributions from synchrotron radiation, beam-gas, Touschek, and injection backgrounds. At the end of Phase 2, single-beam backgrounds originating from the 4 GeV positron Low Energy Ring (LER) agree reasonably well with simulation, while backgrounds from the 7 GeV electron High Energy Ring (HER) are approximately one order of magnitude higher than simulation. We extrapolate these backgrounds forward and conclude it is safe to install the Belle II vertex detector.
Andean Patagonian catchments comprise large freshwater networks along a sharp west-to-east bioclimatic gradient. The Nahuel Huapi National Park (Argentina) includes the headwaters of the largest fluvial network of North Patagonia characterized by mountain and piedmont aquatic systems draining toward the Atlantic and Pacific oceans. Several studies in the region have recorded moderate to high mercury (Hg) levels in different environmental compartments of Andean catchments. Lake sediment sequences have revealed that the departure of Hg concentrations from background levels, attributable to global circulation of this toxic metal, is connected to frequent disturbances caused by active volcanoes of the Andean belt (Southern Volcanic Zone of South America) and wildfires. Freshwaters of the region are oligo- to ultraoligotrophic, with extremely low concentrations of dissolved organic matter, displaying high total Hg to dissolved organic carbon ratios which reflect in high Hg availability. This work reviews the evidence from different studies performed in Nahuel Huapi lake catchment, which explored the sources of Hg, the terrestrial and aquatic pathways of its biogeochemical cycling, as well as its circulation in lake food webs. Moreover, potential changes in the cycle of Hg in Andean Patagonian catchments are discussed in the context of the global and regional climate trends. In this regard, changes in Hg cycling in ecosystems of the region are expected to be manyfold because different components influencing this process (Hg stored in ecosystems, processing rates, the lateral transport to aquatic end points, methylation, etc.) are climate-sensitive.KeywordsPatagonian catchments Mercury Mercury sources Freshwater Mercury trophodynamics
Post-hazard rapid response has emerged as a promising pathway towards resilient critical infrastructure systems (CISs). Nevertheless, it is challenging to scheme the optimal plan for those rapid responses, given the enormous search space and the hardship of assessment on the spatiotemporal status of CISs. We now present a new approach to post-shock rapid responses of road networks (RNs), based upon lookahead searches supported by machine learning. Following this approach, we examined the resilience-oriented rapid response of a real-world RN across Luchon, France, under destructive earthquake scenarios. Our results show that the introduction of one-step lookahead searches can effectively offset the lack of adaptivity due to the deficient heuristic of rapid responses. Furthermore, the performance of rapid responses following such a strategy is far surpassed, when a series of deep neural networks trained based solely on machine learning, without human interventions, are employed to replace the heuristic and guide the searches.
Packing problems are abundant in nature and have been researched thoroughly both experimentally and in numerical models. In particular, packings of anisotropic, elliptical particles often emerge in models of liquid crystals, colloids, and granular and jammed matter. While most theoretical studies on anisotropic particles have thus far dealt with packings in Euclidean geometry, there are many experimental systems where anisotropically-shaped particles are confined to a curved surface, such as Pickering emulsions stabilized by ellipsoidal particles or protein adsorbates on lipid vesicles. Here, we study random close packing configurations in a two-dimensional model of spherical geodesic ellipses. We focus on the interplay between finite-size effects and curvature that is most prominent at smaller system sizes. We demonstrate that on a spherical surface, monodisperse ellipse packings are inherently disordered, with a non-monotonic dependence of both their packing fraction and the mean contact number on the ellipse aspect ratio, as has also been observed in packings of ellipsoids in both 2D and 3D flat space. We also point out some fundamental differences with previous Euclidean studies and discuss the effects of curvature on our results. Importantly, we show that the underlying spherical surface introduces frustration and results in disordered packing configurations even in systems of monodispersed particles, in contrast to the 2D Euclidean case of ellipse packing. This demonstrates that closed curved surfaces can be effective at introducing disorder in a system and could facilitate the study of monodispersed random packings.
  • Samo GregorčičSamo Gregorčič
  • Jaka HrovatJaka Hrovat
  • Neli BizjakNeli Bizjak
  • [...]
  • Damjan OsredkarDamjan Osredkar
Objectives The aim of this study was to analyse the characteristics of typical absence seizures (AS), myoclonic AS and AS with eyelid myoclonia in children and to find associations between these characteristics and difficult to treat absence seizures (DTAS). Methods This was a single-center retrospective study. Electronic health records of pediatric patients with a clinical diagnosis of AS treated at a single tertiary epilepsy center between January 2013 and June 2020 were reviewed. Clinical characteristics, seizure information, ASM, and therapeutic response of patients were recorded. All patients were followed up for at least 1 year. DTAS were defined as failure to achieve remission after treatment with at least 2 anti-seizure medications (ASM), regardless of whether remission was achieved eventually in the study period. Results Data from 131 patients were available for analysis. Remission was achieved after the first ASM treatment in 81 (61.8%) patients, and eventually in 120 (91.6%) during the study period. Epilepsy was classified as DTAS in 18 (13.7%) patients. AS were more often difficult to treat in patients with myoclonic AS and AS with eyelid myoclonia (40.0%), compared with patients with typical AS (11.4%; p = 0.012, 95% CI 1.480–25.732). A positive family history of epilepsy ( p = 0.046; 95% CI 1.021–8.572), a higher seizure frequency ( p = 0.023, 95% CI 1.009–1.126) prior to ASM treatment, and longer time between seizure onset and treatment onset ( p = 0.026; 95% CI 1.006–1.099) were also associated with DTAS. Significance Our study suggests that several clinical characteristics of AS are associated with DTAS. One of these was the time between onset of AS and initiation of ASM treatment, which can be shortened with better care, suggesting that early diagnosis and treatment may improve prognosis in pediatric patients with AS. These findings remain to be confirmed in larger prospective studies.
Unwanted oscillations are common source of problems in industrial processes that contain rotational elements. The procedures for detecting and isolating such periodic disturbances are often based on the application of FFT and subsequent analysis in the frequency domain. The approach presented here modifies this procedure: all rotating elements in the system are assumed to produce unwanted oscillations, and the resulting hypothetical power spectral density is continuously compared to the real power spectrum generated by the main process variable. When the real oscillations occur, the results of the comparison indicate their probable source(s). The approach is first demonstrated and tested on simulated data and then verified on real recorded data. The method is primarily intended for inspection of a cold rolling mill whose data were used for verification.
The crystals of the first copper(II) ethylenediamine complex containing citrate anion have been prepared and characterized. Despite the archetypical character of the copper(II) ethylenediamine complexes, some structural peculiarities were found to be interesting since they are quite rare even among the mentioned type of the complex compounds i.e. a presence of both mono and diaqua-bis(ethylenediamine)copper(II) cations together in the same crystal structure, intramolecular hydrogen bonding of the citric anion, cis,trans-configuration of the citric anion and the disordered C-C bond of the ethylenediamine molecule in the monoaqua-bis(ethylenediamine)copper(II) cation, which in fact is a co-existence of two energetically close δδ and δλ conformers. The Raman as well as FTIR spectra were recorded and discussed. Finally, the magnetic measurements have shown paramagnetic behavior of the prepared complex in a wide range of temperatures.
Patients infected with SARS-CoV-2 risk co-infection with Gram-positive bacteria, which severely affects their prognosis. Antimicrobial drugs with dual antiviral and antibacterial activity would be very useful in this setting. Although glycopeptide antibiotics are well-known as strong antibacterial drugs, some of them are also active against RNA viruses like SARS-CoV-2. It has been shown that the antiviral and antibacterial efficacy can be enhanced by synthetic modifications. We here report the synthesis and biological evaluation of seven derivatives of teicoplanin bearing hydrophobic or superbasic side chain. All but one teicoplanin derivatives were effective in inhibiting SARS-CoV-2 replication in VeroE6 cells. One lipophilic and three perfluoroalkyl conjugates showed activity against SARS-CoV-2 in human Calu-3 cells and against HCoV-229E, an endemic human coronavirus, in HEL cells. Pseudovirus entry and enzyme inhibition assays established that the teicoplanin derivatives efficiently prevent the cathepsin-mediated endosomal entry of SARS-CoV-2, with some compounds inhibiting also the TMPRSS2-mediated surface entry route. The teicoplanin derivatives showed good to excellent activity against Gram-positive bacteria resistant to all approved glycopeptide antibiotics, due to their ability to dually bind to the bacterial membrane and cell-wall. To conclude, we identified three perfluoralkyl and one monoguanidine analog of teicoplanin as dual inhibitors of Gram-positive bacteria and SARS-CoV-2.
Electronic transport in transition metal spinel oxides is associated with small polaron hopping, either nearest-neighbor, resulting in Arrhenius activated conductivity, or variable energy, leading to a sub-Arrhenius relationship, with the conductivity logarithm being a convex function of inverse temperature. For the case of manganese spinel oxides alloyed with zinc and nickel, instances of super-Arrhenius behavior are measured, with the conductivity logarithm functional dependence on temperature deviating quadratically. Here, we study the transport in Zn 0.5 Ni x Mn 2.5−x O 4 ternary oxide pellets, as a function of Ni content in the range 0 ≤ x ≤ 1.25, in combination with structural characterization and theoretical investigations of their electronic and structural properties using density functional theory. The coexistence of cubic spinel and tetragonal Hausmannite structures is revealed along with the presence of various magnetic conformations that are metastable at room temperature. For systems where metastable structures exist, having similar formation energy but different electronic structures, conductivity is a non-trivial function of temperature. Considering nearest-neighbor polaron transfer in such an energetically inhomogeneous landscape, a new hopping mechanism model is proposed which consistently describes the temperature dependence of conductivity in this ternary alloy spinel oxide system. Understanding the underlying physical transport mechanism is vital for sensor, electrochemical, and catalytic applications.
Circular RNAs (circRNAs) have been shown to play an important role in the pathogenesis of hepatocellular carcinoma (HCC). By implementing available transcriptomic analyses of HCC patients, we identified an upregulated circRNA hsa_circ_0062682. Stable perturbations of hsa_circ_0062682 in Huh-7 and SNU-449 cell lines influenced colony formation, migration, cell proliferation, sorafenib sensitivity, and additionally induced morphological changes in cell lines, indicating an important role of hsa_circ_0062682 in oncogenesis. Pathway enrichment analysis and gene set enrichment analysis of the transcriptome data from hsa_circ_0062682 knockdown explained the observed phenotypes and exposed transcription factors E2F1, Sp1, HIF-1α, and NFκB1 as potential downstream targets. Biotinylated oligonucleotide pulldown combined with proteomic analyses identified protein interaction partners of which YBX1, a known oncogene, was confirmed by RNA immunoprecipitation. Furthermore, we discovered a complex cell-type-specific phenotype in response to the oncogenic potential of hsa_circ_0062682. This finding is in line with different classes of HCC tumours, and more studies are needed to shed a light on the molecular complexity of liver cancer.
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921 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