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1.
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, published scientific conference contribution

Abstract: 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.
Keywords: ultra-high energy cosmic rays, Pierre Auger Observatory, hadronic interaction model, water-Cherenkov detectors
Published in RUNG: 23.01.2024; Views: 259; Downloads: 4
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2.
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: 625; Downloads: 0
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3.
Spin model of water and post-processing of protein folding experiments
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.
Keywords: spin model, water, protein folding
Published in RUNG: 04.09.2023; Views: 702; Downloads: 3
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4.
5.
Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins
Artem Badasyan, Sh. A. Tonoyan, Matjaž Valant, Jože Grdadolnik, 2021, original scientific article

Abstract: Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra- molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold dena- turation and thus clarifies its absence in some proteins.
Keywords: protein folding, cold denaturation, water, Zimm-Bragg model
Published in RUNG: 06.05.2021; Views: 2026; Downloads: 13
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