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Differential scanning calorimetry of proteins and the two-state model : comparison of two formulas
Knarik Yeritsyan, Artem Badasyan, 2024, izvirni znanstveni članek

Opis: Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. In order to connect the measured profile to the properties of a particular protein, a model is required to fit. We discuss here the application of an exact two-state formula with its approximation and process the DSC experimental data on protein folding in water. The approximate formula relies on the smallness of the transition interval, which is different for each protein. With an example of the set of 33 different proteins, we show the practical validity of the approximation and the equivalence of exact and approximate two-state formulas for processing DSC data.
Ključne besede: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Objavljeno v RUNG: 21.05.2024; Ogledov: 372; Prenosov: 3
.pdf Celotno besedilo (380,96 KB)
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Integrating in situ measurements and city scale modelling to assess the COVID–19 lockdown effects on emissions and air quality in Athens, Greece
Georgios Grivas, Eleni Athanasopoulou, Anastasia Kakouri, Jennifer Bailey, Eleni Liakakou, Iasonas Stavroulas, Panayiotis Kalkavouras, Aikaterini Bougiatioti, Dimitris G. Kaskaoutis, Michel Ramonet, 2020, izvirni znanstveni članek

Opis: The lockdown measures implemented worldwide to slow the spread of the COVID–19 pandemic have allowed for a unique real-world experiment, regarding the impacts of drastic emission cutbacks on urban air quality. In this study we assess the effects of a 7-week (23 March–10 May 2020) lockdown in the Greater Area of Athens, coupling in situ observations with estimations from a meteorology-atmospheric chemistry model. Measurements in central Athens during the lockdown were compared with levels during the pre- and post-lockdown 3-week periods and with respective levels in the four previous years. We examined regulatory pollutants as well as CO2, black carbon (BC) and source-specific BC components. Models were run for pre-lockdown and lockdown periods, under baseline and reduced-emissions scenarios. The in-situ results indicate mean concentration reductions of 30–35% for traffic-related pollutants in Athens (NO2, CO, BC from fossil fuel combustion), compared to the pre-lockdown period. A large reduction (53%) was observed also for the urban CO2 enhancement while the reduction for PM2.5 was subtler (18%). Significant reductions were also observed when comparing the 2020 lockdown period with past years. However, levels rebounded immediately following the lift of the general lockdown. The decrease in measured NO2 concentrations was reproduced by the implementation of the city scale model, under a realistic reduced-emissions scenario for the lockdown period, anchored at a 46% decline of road transport activity. The model permitted the assessment of air quality improvements on a spatial scale, indicating that NO2 mean concentration reductions in areas of the Athens basin reached up to 50%. The findings suggest a potential for local traffic management strategies to reduce ambient exposure and to minimize exceedances of air quality standards for primary pollutants.
Ključne besede: pandemic, urban air pollution, traffic, chemical transport model, TAPM, mapping
Objavljeno v RUNG: 10.05.2024; Ogledov: 308; Prenosov: 2
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Constraints on upward-going air showers using the Pierre Auger Observatory data
Emanuele De Vito, Andrej Filipčič, Jon Paul Lundquist, Shima Ujjani Shivashankara, Samo Stanič, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, 2023, objavljeni znanstveni prispevek na konferenci

Opis: The fluorescence detector (FD) of the Pierre Auger Observatory is sensitive to upward-going air showers with energies above 1017 eV. Given its operation time and wide field of view, the FD has the potential to support or constrain the “anomalous” observations by the ANITA detector, interpreted as upward-going air showers that would be indicative of Beyond Standard Model (BSM) physics. To this end, a search for upward-going air showers with the FD has been performed applying selection criteria that were optimized using 10% of FD data. Dedicated background simulations (downward-going events) have been performed to estimate our capability to distinguish candidates from false positives. Also dedicated signal simulations (upward-going events) have been used to estimate our sensitivity to such showers with a focus on the energy region close to the ANITA observations. Improved and updated results of the Pierre Auger Observatory exposure to upward-going showers will be presented after the unblinding of 14 years of FD data. Extensive simulations allow the FD exposure to be obtained at lower energies which are particularly relevant for the comparison with the ANITA results. A refinement of the method for signal discrimination and background rejection has also been applied. The implications are discussed under the assumption that the ANITA events were due to upward-going events.
Ključne besede: Pierre Auger Observatory, ultra-high energy cosmic rays, air showers, beyond standard model, fluorescence detectors, ANITA
Objavljeno v RUNG: 23.01.2024; Ogledov: 603; Prenosov: 6
.pdf Celotno besedilo (2,95 MB)
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The second knee in the cosmic ray spectrum observed with the surface detector of the Pierre Auger Observatory
Gabriel Brichetto Orquera, Andrej Filipčič, Jon Paul Lundquist, Shima Ujjani Shivashankara, Samo Stanič, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, 2023, objavljeni znanstveni prispevek na konferenci

Opis: The determination of the energy spectrum features with low systematic uncertainty is crucial for interpreting the nature of cosmic rays. In this study, we conducted a measurement of the energy spectrum at the Pierre Auger Observatory using a surface detector with a calorimetric energy scale indirectly set by a fluorescence detector. The surface detector consists of an array of water-Cherenkov detectors that extends over 3000 km^2 with 1500m spacing. Additionally, two nested arrays of the same kind with 750m and 433m spacing were utilized to lower the energy threshold of the measurements. This contribution presents, for the first time, the spectrum measured with the 433m array, which reduces the energy threshold down to 63 PeV, nearly half the energy at which we previously published a steepening using the 750m array. Our measurements include a characterization of the spectral features of the flux steepening around 230 PeV, known as the second-knee. The study benefits from a nearly 100% duty cycle and geometrical exposure. Notably, this is the first simultaneous measurement of the second knee energy and spectral indexes before and after the break, using a surface detector with an energy scale predominantly independent of air shower simulations and assumptions regarding hadronic interaction models.
Ključne besede: ultra-high energy cosmic rays, Pierre Auger Observatory, hadronic interaction model, water-Cherenkov detectors
Objavljeno v RUNG: 23.01.2024; Ogledov: 578; Prenosov: 4
.pdf Celotno besedilo (1,48 MB)
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Modelling water for calorimetry of proteins
Knarik Yeritsyan, Artem Badasyan, 2023, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: Differential Scanning Calorimetry (DSC) is a powerful technique used to study the thermal stability and unfolding of proteins. DSC provides the excess heat capacity profile and is used to study the thermodynamics of a given protein. By fitting DSC data to the model, researchers can obtain valuable information about the thermodynamics of protein folding and unfolding, which can help them better understand protein structure, stability, and function. Based on Hamiltonian representation of ZB model and using the solvent effects we derived an expression for heat capacity in proteins and successfuly fit it to experimental data. As we show, our model provides a better fit to experimental data, as compared to the 2-state model. The model we propose takes into account also water effects and we show that it fits better to experimental data giving inter- and intra-molecular H-bonding energies instead of reporting only one total enthalpy.
Ključne besede: Zimm-Bragg model, water model, helix-coil transition, protein folding, differential scanning calorimetry
Objavljeno v RUNG: 18.10.2023; Ogledov: 958; Prenosov: 0
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The Cherenkov Telescope Array. Science Goals and Current Status
Rene A. Ong, Christopher Eckner, Gašper Kukec Mezek, Samo Stanič, Serguei Vorobiov, Lili Yang, Gabrijela Zaharijas, Danilo Zavrtanik, Marko Zavrtanik, Lukas Zehrer, 2019, objavljeni znanstveni prispevek na konferenci (vabljeno predavanje)

Opis: The Cherenkov Telescope Array (CTA) is the major ground-based gamma-ray observatory planned for the next decade and beyond. Consisting of two large atmospheric Cherenkov telescope arrays (one in the southern hemisphere and one in the northern hemisphere), CTA will have superior angular resolution, a much wider energy range, and approximately an order of magnitude improvement in sensitivity, as compared to existing instruments. The CTA science programme will be rich and diverse, covering cosmic particle acceleration, the astrophysics of extreme environments, and physics frontiers beyond the Standard Model. This paper outlines the science goals for CTA and covers the current status of the project.
Ključne besede: very-high-energy gamma-ray astronomy, Cherenkov Telescope Array (CTA), cosmic particle acceleration, astrophysics of extreme environments, physics beyond the Standard Model
Objavljeno v RUNG: 11.10.2023; Ogledov: 797; Prenosov: 7
.pdf Celotno besedilo (3,28 MB)
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Collaborative lessons in a cross-border space : learning each other's language, literature and history on the basis of the CoBLaLT model
Ivana Zajc, 2023, objavljeni znanstveni prispevek na konferenci

Opis: In the paper we propose a new paradigm for teaching literature, language and history in cross-border territories from the point of view of cross-border didactics and cross-curricular collaboration at the higher elementary school level. Based on the CoBLaLT model, we propose interdisciplinar activities for students of two cross-border classes on both sides of the Slovenian-Italian border, who, while studying picture books written in Slovenian, meet via online platforms and live. They get to know each other, learn the languages of other students, experience literature and the art of illustration, and above all experience the complex history of the area where they live.
Ključne besede: foreign language, CoBlaLT model, border spaces, teaching, literature
Objavljeno v RUNG: 02.10.2023; Ogledov: 975; Prenosov: 3
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Expected exclusion limits to TeV dark matter from the perseus cluster with the Cherenkov Telescope Array
Rémi Adam, Saptashwa Bhattacharyya, Judit Pérez Romero, Samo Stanič, Veronika Vodeb, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, Miha Živec, 2023, objavljeni znanstveni prispevek na konferenci

Opis: Clusters of galaxies are the largest gravitationally-bound structures in the Universe. They are composed of galaxies and gas (approximately 15% of the total mass) mostly dark matter (DM, accounts up to 85% of the total mass). If the DM is composed of Weakly Interacting Massive Particles (WIMPs), galaxy clusters represent one of the best targets to search for gamma-ray signals induced by the decay of WIMPs, with masses around the TeV scale. Due to its sensitivity and energy range of operation (from 20 GeV to 300 TeV), the Cherenkov Telescope Array (CTA) Observatory has a unique opportunity to test WIMPs with masses close to the unitarity limit. This will complement the searches for DM from other gamma-ray observatories as well as direct and collider experiments. The CTA Observatory is planning to search for gamma-ray emission, either its origin may be cosmic-ray (CR) or DM related, in the Perseus galaxy cluster during the first years of operation. In this poster, we will present the software created to perform the analysis using the ctools software and the corresponding results.
Ključne besede: Cherenkov Telescope Array, CTA, dark matter, standard model, dwarf spheroidal galaxies
Objavljeno v RUNG: 26.09.2023; Ogledov: 828; Prenosov: 4
.pdf Celotno besedilo (1,33 MB)
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Variability studies of active galactic nuclei from the long-term monitoring program with the Cherenkov Telescope Array
G. Grolleron, Saptashwa Bhattacharyya, Judit Pérez Romero, Samo Stanič, Veronika Vodeb, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, Miha Živec, 2023, objavljeni znanstveni prispevek na konferenci

Opis: Blazars are active galactic nuclei (AGN) with a relativistic jet oriented toward the observer. This jet is composed of accelerated particles which can display emission over the entire electromagnetic spectrum. Spectral variability has been observed on short- and long-time scales in AGN, with a power spectral density (PSD) that can show a break at frequencies below the well-known red-noise process. This break frequency in the PSD has been observed in X-rays to scale with the accretion regime and the mass of the central black hole. It is expected that a break could also be seen in the very-high-energy gamma rays, but constraining the shape of the PSD in these wavelengths has not been possible with the current instruments. The Cherenkov Telescope Array (CTA) will be more sensitive by a factor of five to ten depending on energy than the current generation of imaging atmospheric Cherenkov telescopes, therefore it will be possible with CTA to reconstruct the PSD with a high accuracy, bringing new information about AGN variability. In this work, we focus on the AGN long-term monitoring program planned with CTA. The program is proposed to begin with early-start observing campaigns with CTA precursors. This would allow us to probe longer time scales on the AGN PSD.
Ključne besede: Cherenkov Telescope Array, CTA, dark matter, standard model, dwarf spheroidal galaxies
Objavljeno v RUNG: 26.09.2023; Ogledov: 993; Prenosov: 7
.pdf Celotno besedilo (3,48 MB)
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