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The conformational plasticity of the selectivity filter methionines controls the in-cell Cu(I) uptake through the CTR1 transporter
Pavel Janoš, Jana Aupič, Sharon Ruthstein , Alessandra Magistrato, 2022, izvirni znanstveni članek

Opis: Copper is a trace element vital to many cellular functions. Yet its abnormal levels are toxic to cells, provoking a variety of severe diseases. The high affinity copper transporter 1 (CTR1), being the main in-cell copper [Cu(I)] entry route, tightly regulates its cellular uptake via a still elusive mechanism. Here, all-atoms simulations unlock the molecular terms of Cu(I) transport in eukaryotes disclosing that the two methionine (Met) triads, forming the selectivity filter, play an unprecedented dual role both enabling selective Cu(I) transport and regulating its uptake rate thanks to an intimate coupling between the conformational plasticity of their bulky side chains and the number of bound Cu(I) ions. Namely, the Met residues act as a gate reducing the Cu(I) import rate when two ions simultaneously bind to CTR1. This may represent an elegant autoregulatory mechanism through which CTR1 protects the cells from excessively high, and hence toxic, in-cell Cu(I) levels. Overall, our outcomes resolve fundamental questions in CTR1 biology and open new windows of opportunity to tackle diseases associated with an imbalanced copper uptake.
Ključne besede: copper, membrane transporter, molecular dynamics, QM/MM, free energy
Objavljeno v RUNG: 15.09.2022; Ogledov: 757; Prenosov: 0
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1/x distribution in a close proximity of the Bak-Tang-Wiesenfeld sandpile
Alexander Shapoval, druga izvedena dela

Ključne besede: sandpile, scale-free distribution, power-law
Objavljeno v RUNG: 09.07.2021; Ogledov: 1474; Prenosov: 0
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An Overview of the Characteristics of Free Market Economies
Andi Jamšek, 2021, magistrsko delo

Opis: In this work we are collecting and processing basic information that allows us a general overview of the five most popular global, free market economies which are: the exchange of currency (foreign exchange), rare metals, stocks, residential real estate and the cryptocurrency markets. By having more in-depth knowledge about the possibilities that each separate financial instrument or asset offers we are devising a strategy suited for different types of investors. Any economical system in its most natural state will create some sort of dynamic; it is possible to draw parallels between the free-economy and the Lotka-Volterra predator behaviour equations, which can help us to better visualise the behaviour of such systems. We try to compare the model with real life scenarios that had greatly affected some of the economies, one of them being the popularization of cryptocurrencies in 2017 and the other being the most recent Coronavirus epidemic. By having a rough comparison we can see a clearer picture of the practical uses and the necessities of having an increased and better selection of such models.
Ključne besede: free market, investing, cryptocurrency, stocks, foreign exchange, Lotka-Volterra predator/prey equations
Objavljeno v RUNG: 28.06.2021; Ogledov: 2148; Prenosov: 80
.pdf Celotno besedilo (1,93 MB)

Molekularna karakterizacija lebdećih čestica slobodne troposfere sa Opservatorija Pico planine
Katja Džepina, Claudio Mazzoleni, Paulo Fialho, Swarup China, B. Zhang, R. Chris Owen, D. Helmig, J. Hueber, Sumit Kumar, J. A. Perlinger, 2017, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: Long-range transported free tropospheric aerosol was sampled at the PMO (38°28’15’’N, 28°24’14’’W; 2225 m amsl) on Pico Island of the Azores in the North Atlantic. Filter-collected aerosol during summer 2012 was analysed for organic and elemental carbon, and inorganic ions. The average aerosol ambient concentration was 0.9 µg m-3. Organic aerosol contributed the majority of mass (57%), followed by sulphate (21%) and nitrate (17%). Filter-collected aerosol was positively correlated with on-line aerosol measurements of black carbon, light scattering and number concentration. Water-soluble organic compounds (WSOC) from 9/24 and 9/25 samples collected during a pollution event were analysed with ultrahigh-resolution FT-ICR MS. FLEXPART analysis showed the air masses were very aged (>12 days). ~4000 molecular formulas were assigned to each of the mass spectra between m/z 100-1000. The majority of the assigned molecular formulas have unsaturated structures with CHO and CHNO elemental compositions. WSOC have an average O/C of ~0.45, relatively low compared to O/C of other aged aerosol, which might be the result of evaporation and fragmentation during long-range transport. The increase in aerosol loading during 9/24 was linked to biomass burning emissions from North America by FLEXPART and MODIS fire counts. This was confirmed with WSOC biomass burning markers and with the morphology and mixing state of particles as determined by SEM. The presence of markers characteristic of aqueous-phase reactions of biomass burning phenolic species suggests that the aerosol collected at Pico had undergone cloud processing. The air masses on 9/25 were more aged (~15 days) and influenced by marine emissions, as indicated by organosulphates and species characteristic for marine aerosol (e.g. fatty acids). The change in air masses for the two samples was corroborated by the changes in ozone, ethane, propane, morphology of particles, as well as by FLEXPART. In this presentation we will presents the first detailed molecular characterization of free tropospheric aged aerosol intercepted at the PMO.
Ključne besede: Atmospheric aerosol, Free troposphere, Mass spectrometry, Pico mountain observatory
Objavljeno v RUNG: 26.05.2021; Ogledov: 1886; Prenosov: 0
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Morphology and mixing state of aged soot particles at a remote marine free troposphere site : implications for optical properties
Swarup China, Barbara Scarnato, Robert C. Owen, Bo Zhang, MarianT. Ampadu, Sumit Kumar, Katja Džepina, Michael P. Dziobak, Paulo Fialho, Judith A. Perlinger, 2015, izvirni znanstveni članek

Opis: The radiative properties of soot particles depend on their morphology and mixing state, but their evolution during transport is still elusive. Here we report observations from an electron microscopy analysis of individual particles transported in the free troposphere over long distances to the remote Pico Mountain Observatory in the Azores in the North Atlantic. Approximately 70% of the soot particles were highly compact and of those 26% were thinly coated. Discrete dipole approximation simulations indicate that this compaction results in an increase in soot single scattering albedo by a factor of <= 2.17. The top of the atmosphere direct radiative forcing is typically smaller for highly compact than mass-equivalent lacy soot. The forcing estimated using Mie theory is within 12% of the forcing estimated using the discrete dipole approximation for a high surface albedo, implying that Mie calculations may provide a reasonable approximation for compact soot above remote marine clouds.
Ključne besede: atmospheric aerosol, soot, long-range transport, free troposphere, single scattering albedo
Objavljeno v RUNG: 11.04.2021; Ogledov: 1607; Prenosov: 0
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Measuring free word order: Some empirical and modeling perspectives
Artur Stepanov, predavanje na tuji univerzi

Opis: Languages manifesting flexibility of word order (within the sentence's compositional meaning) have always presented a challenge for modern theories of syntax requiring any deviation from the canonical word order to be grammatically motivated. Parasyntactic motivations such as information structural or stylistic requirements may account for some portion of this flexibility, but not all of it. In addition, native speakers do not necessarily accept canonical and non-canonical word orders to an equal extent. In fact, the latter typically receive lower acceptability scores than the former, albeit above the subjective threshold for what would count as "ungrammatical". Some of the combinatorially possible word orders are not acceptable at all. In this experimental study we scrutinize different word order sequences in a free word order language (Serbo-Croatian) and attempt to isolate independent displacement factors responsible for various elements of the sentence appearing away from their canonical structural positions. We explore differential and cumulative effects of these independent factors to predict speakers' acceptability scores.
Ključne besede: Free word order, experimental syntax, Serbo-Croatian, sentence acceptability task
Objavljeno v RUNG: 11.02.2021; Ogledov: 2053; Prenosov: 0
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Advantages and disadvantages of experiments with ultrashort two-color pulses
Matija Stupar, 2020, doktorska disertacija

Opis: Advances in the development of lasers have led to a new class of radiation sources generating coherent, tunable, ultrashort light pulses in the spectral region ranging from infrared to soft X-rays. This includes high-order harmonics generation in gas (HHG), on which relies the CITIUS facility at University of Nova Gorica (Slovenia), and free-electron lasers (FELs), such as the facility FERMI at Elettra-Sincrotrone Trieste (Italy). The distinctive structure of HHG and FEL radiation paved the way to time-resolved experiments, which are performed to investigate events occurring on a short, or very short, temporal scale, from picoseconds to femtoseconds. This work focuses on the advantages and disadvantages of some experimental techniques based on using these novel light sources to investigate the microscopic and/or ultrafast dynamics of matter samples, which have been previously driven out of equilibrium. Advantages rely on the implementation of various applications based on two-color schemes and, more specifically, include the possibility of acquiring two-dimensional frequency maps, measuring electrons’ effective masses, or investigating electronic properties decoupled from the influence of the lattice. Particular focus will be put on experimental methods relying on photoelectric effect and photoelectron spectroscopy. In all experiments, we took advantage of one or more specific properties of HHG and FEL sources, such as controllable chirp, to study laser dressed states in helium, variable polarization, to study electronic properties of iron-based pnictides and ultrashort pulses (< 10 fs) to study the purely electronic dynamics in transition metal dichalcogenides. On the other hand, the study of the interface between a molecule and a topological insulator revealed some intrinsic limitations and physical drawbacks of the technique, such as spurious effects originating from the high power pulses, like multiphoton absorption and the space charge effect, or the reduction of experimental resolution when pushing for shorter and shorter pulse durations. Some disadvantages are also connected to the current state-of-the-art in the field of ultrashort laser systems, where a trade-off needs to be found between repetition rate and laser power. Finally, state-of-the-art experiments based on the ability to generate ultrashort pulses carrying orbital angular momentum in visible, near-infrared as well as extreme UV range will be presented. The use of these pulses opens the door to the investigation of new physical phenomena, such as probing magnetic vortices using extreme ultraviolet light from a free-electron laser or imprinting the spatial distribution of an ultrashort infrared pulse carrying orbital angular momentum onto a photoelectron wave packet.
Ključne besede: ultrafast lasers, two-color experiments, photoemission, high-order harmonic generation, free-electron lasers, hot-electrons dynamics, surface science, pump-probe photoemission, ultraviolet photoemission, orbital angular momentum
Objavljeno v RUNG: 02.12.2020; Ogledov: 3031; Prenosov: 108
.pdf Celotno besedilo (19,78 MB)

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