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Modelling water for calorimetry of proteins
Knarik Yeritsyan, Artem Badasyan, 2023, published scientific conference contribution abstract

Abstract: 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.
Keywords: Zimm-Bragg model, water model, helix-coil transition, protein folding, differential scanning calorimetry
Published in RUNG: 18.10.2023; Views: 302; Downloads: 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, published scientific conference contribution (invited lecture)

Abstract: 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.
Keywords: very-high-energy gamma-ray astronomy, Cherenkov Telescope Array (CTA), cosmic particle acceleration, astrophysics of extreme environments, physics beyond the Standard Model
Published in RUNG: 11.10.2023; Views: 261; Downloads: 7
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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, published scientific conference contribution

Abstract: 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.
Keywords: Literature, Language, History, Cross-Border Didactics, CoBLaLT Model, Emotions in the Classroom
Published in RUNG: 02.10.2023; Views: 351; Downloads: 2
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Dark matter searches in dwarf spheroidal galaxies with the Cherenkov Telescope Array
Francesco Gabriele Saturni, Saptashwa Bhattacharyya, Judit PÉREZ ROMERO, Samo Stanič, Veronika VODEB, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, Miha Živec, 2023, published scientific conference contribution

Abstract: Dark matter (DM) is one of the major components in the Universe. However, at present its existence is still only inferred through indirect astronomical observations. DM particles can annihilate or decay, producing final-state Standard Model pairs that subsequently annihilate into high-energy �-rays. The dwarf spheroidal galaxies (dSphs) in the Milky Way DM halo have long been considered optimal targets to search for annihilating DM signatures in GeV-to-TeV �-ray spectra due to their high DM densities (hence high astrophysical factors), as well as the expected absence of intrinsic �-ray emission of astrophysical origin. For such targets, it is important to compute the amount of DM in their halos in a consistent way to optimize the �-ray data analysis. Such estimates directly affect the observability of DM signals in dSphs, as well as the DM constraints that can be derived in case of null detection. In this contribution, we present the results on the sensitivity of the Cherenkov Telescope Array (CTA) for DM annihilation and decay searches using planned observations of the Milky Way dSphs. We select the most promising targets among all presently known dwarf satellites, providing new determinations of their expected DM signal. This study shows an improvement of approximately an order of magnitude in sensitivity compared to current searches in similar targets. We also discuss the results in terms of cuspy and cored DM models, and investigate the sensitivity obtained by the combination of observations from different dSphs. Finally, we explore the optimal strategies for CTA observations of dSphs.
Keywords: Cherenkov Telescope Array, CTA, Dark matter, Standard Model, dwarf spheroidal galaxies
Published in RUNG: 26.09.2023; Views: 282; Downloads: 4
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Constraints on BSM particles from the absence of upward-going air showers in the Pierre Auger Observatory
Baobiao Yue, Andrej Filipčič, Jon Paul Lundquist, Shima Ujjani Shivashankara, Samo Stanič, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, 2023, published scientific conference contribution

Abstract: The Fluorescence Detector (FD) of the Pierre Auger Observatory has a large exposure to search for upward-going showers. Constraints have been recently obtained by using 14 years of FD data searching for upward-going showers in the zenith angle range [110◦, 180◦]. In this work, we translate these bounds to upper limits of a possible flux of ultra high energy tau-leptons escaping from the Earth into the atmosphere. Such a mechanism could explain the observation of "anomalous pulses" made by ANITA, that indicated the existence of upward-going air showers with energies above 10[sup]17 eV. As tau neutrinos would be absorbed within the Earth at the deduced angles and energies, a flux of upward-going taus could only be resulted from an unknown type of ultra high energy Beyond Standard Model particle penetrating the Earth with little attenuation, and then creating tau-leptons through interactions within a maximum depth of about 50 km before exiting. We test classes of such models in a generic way and determine upper flux limits of ultra high energy BSM particles as a function of their unknown cross section with matter.
Keywords: Ultra-high energy cosmic rays, Pierre Auger Observatory, Fluorescence Detector, upward-going air showers, Beyond Standard Model particles
Published in RUNG: 26.09.2023; Views: 248; Downloads: 5
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CTA sensitivity for probing cosmology and fundamental physics with gamma rays
Ievgen Vovk, Saptashwa Bhattacharyya, Barbara MARČUN, Judit PÉREZ ROMERO, Samo Stanič, Veronika VODEB, Serguei Vorobiov, Gabrijela Zaharijas, Marko Zavrtanik, Danilo Zavrtanik, Miha Živec, 2021, published scientific conference contribution

Abstract: The Cherenkov Telescopic Array (CTA), the next-generation ground-based gamma-ray observatory, will have unprecedented sensitivity, providing answers to open questions in gamma-ray cosmology and fundamental physics. Using simulations of active galactic nuclei observations foreseen in the CTA Key Science Program, we find that CTA will measure gamma-ray absorption on the extragalactic background light with a statistical error below 15% up to the redshift of 2 and detect or establish limits on gamma halos induced by the intergalactic magnetic field of at least 0.3 pG. Extragalactic observations using CTA also demonstrate the potential for testing physics beyond the Standard Model. The best state-of-the-art constraints on the Lorentz invariance violation from astronomical gamma-ray observations will be improved at least two- to threefold. CTA will also probe the parameter space where axion-like particles can represent a significant proportion – if not all – of dark matter. Joint multiwavelength and multimessenger observations, carried out together with other future observatories, will further foster the growth of gamma-ray cosmology.
Keywords: Cherenkov Telescopic Array, ground-based gamma-ray observatory, beyond the Standard Model, extragalactic observations
Published in RUNG: 19.09.2023; Views: 214; Downloads: 5
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Mikroplastika v kraških ekosistemih in njen vpliv na kakovost pitne vode
Lara Valentić, 2023, doctoral dissertation

Abstract: Namen doktorske disertacije je bil opredeliti mikroplastiko (MP) ter izboljšati razumevanje o onesnaženju z MP v kraških ekosistemih in njenem vplivu na kakovost pitne vode, saj je to področje raziskav še v povojih. Obenem je bil namen doktorske disertacije določiti vire onesnaženja z MP in določiti transportne poti onesnaženja v kraških ekosistemih, da bi se preprečilo ali zmanjšalo onesnaževanje okolja, saj so kraški vodonosniki v sušnih območjih pogosto edini in najpomembnejši viri pitne vode za lokalno prebivalstvo. Izbrane so bile različne lokacije vzorčenja, s čimer smo zagotovili širok pregled nad različnimi ekosistemi (zrak, voda, deževnica in sediment). Izbrana sta bila dva od najpomembnejših kraških izvirov (Malni in Rižana, ki skupaj zagotavljata pitno vodo za celotno obalo z zaledjem in za več kot 20.000 lokalnih prebivalcev v občinah Postojna in Pivka). Nadalje so bila izbrana tri vzorčna mesta v Alpah kot referenčne točke z najbolj neokrnjenim okoljem v Sloveniji (Bohinjsko jezero, Blejsko jezero in ob Domu na Komni) ter v Lescah kot referenčni točki najbolj onesnažene lokacije, ki je hkrati tudi najbližje proučevanemu kraškemu ekosistemu. V okviru doktorske naloge so bile uporabljene različne metode vzorčenja, saj smo poskušali določiti protokol, ki je najboljši za posamezno kraško okolje. Tako so bili izviri in jezera vzorčeni z vzorčevalno mrežo, sedimenti so bili vzorčeni z uporabo sedimentnega stratigrafskega vzorčevalnika Uwitec, vzorčenje zraka je bilo izvedeno z uporabo sekvenčnega vzorčevalnika prahu Giano PMx, deževnica pa je bila vzorčena z 20-litrsko steklenico in lijem iz nerjavnega jekla. Vsi vzorci so bili filtrirani s steklenimi filtri, pregledani pod stereomikroskopom za določitev potencialnih MP-delcev in analizirani z mikroskopom Lumos II FTIR-ATR za določitev plastičnih polimerov. Kasneje smo uporabo posamezne metode vzorčenja in analize kritično ocenili. Pri vzorcih, ki so bili vzeti na izviru Malni, so rezultati pokazali, da je najvišja koncentracija MP v prvem vodnem pulzu po daljšem sušnem obdobju, medtem ko za Rižano iz dobljenih rezultatov ne moremo razbrati trendov transporta MP. Pri vzorcih deževnice in zraka je bilo pričakovano, da bodo imeli vzorci iz Lesc najvišje koncentracije MP-delcev zaradi bližine glavnih prometnih povezav: avtoceste proti Salzburgu (Avstrija) in Nemčiji, glavne železniške povezave in manjšega športnega letališča. Izkazalo se je, da so bile najvišje vrednosti MP v vzorcih deževnice na Komni, medtem ko so vsi vzorci zraka imeli zelo majhne količine MP-delcev. Vzorci sedimenta so bili odvzeti samo v Bohinjskem in Blejskem jezeru in niso vsebovali večjih količin MP-delcev, kar bi lahko bil vpliv hitrega transporta MP-delcev z vodnimi tokovi, zaradi česar delci nimajo časa za posedanje. Prav tako se celotna masa vode v obeh jezerih razmeroma hitro zamenja – v Bohinjskem jezeru se celotni volumen vode zamenja trikrat na leto, medtem ko se v Blejskem jezeru volumen vode zamenja vsako leto in pol. V splošnem je bilo mogoče sklepati na dva vira onesnaženja z MP: plastični čolni in kajaki lokalnih prebivalcev in turistov na obeh jezerih ter oblačila pomembno prispevajo k onesnaženju. To smo določili na podlagi najdenih plastičnih polimerov (v obeh jezerih) in na podlagi oblike delcev (največkrat smo našli različno debela vlakna in nitke). V vzorcih smo sicer našli veliko delcev, vendar je bila le majhna količina identificirana kot vir plastike, kar je tudi ena od ugank v tej raziskavi. Pripravili smo tudi konceptualni model za boljše razumevanje transportnih poti MP v kraškem okolju. V modelu smo združili rezultate iz doktorske disertacije in raziskave Valentić (2018). Še vedno je veliko neznank, vendar lahko z gotovostjo trdimo, da so viri onesnaženja zelo pomembni. Najvišje koncentracije MP so bile najdene v vodi iz ponvic turističnih jam in v deževnici na Komni. Koncentracije so visoke tudi v vzorcih sedimenta iz turističnih delov jam in iz alpskih jezer.
Keywords: mikroplastika (MP), Slovenija, alpski kras, dinarski kras, kraški vodonosnik, alpska jezera, izviri, deževnica, zrak, sedimenti, konceptualni model
Published in RUNG: 14.09.2023; Views: 330; Downloads: 14
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Artem Badasyan, Knarik Yeritsyan, 2023, published scientific conference contribution abstract

Abstract: The presence of several distinct minima in nearest-neighbor potentials in polymers makes it possible to describe polymer conformations in terms of discrete isomeric states, naturally leading to spin language. Using this general approach, a decade ago we have suggested the Hamiltonian formulation for the Zimm and Bragg model of protein conformations [1,2]. Later we have augmented the model by an oversimplified spin model for water, resulting in both cold and hot denaturations [3]. We construct the Statistical Mechanics for the model and get access to its Thermodynamics. Resulting order parameter and specific heat expressions are successfully fit to available experimental data [4]. Thanks to solid and traceable theoretical foundations, the procedure provides better quality fits as compared to the state-of-the-art two-state model, routinely used to process protein folding experiments.
Published in RUNG: 04.09.2023; Views: 339; Downloads: 2
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Teaching literature and foreign language through the CoBlaLT model
Ivana Zajc, 2023, published scientific conference contribution abstract

Keywords: foreign language, CoBlaLT model, border spaces, teaching, literature
Published in RUNG: 04.08.2023; Views: 359; Downloads: 2
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