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1.
Modeling of solvent role in protein folding experiments : dissertation
Knarik Yeritsyan, 2025, doctoral dissertation

Abstract: The Zimm-Bragg (ZB) model serves as a fundamental framework for elucidating conformational transitions in biopolymers, offering simplicity and efficacy in processing experimental data. This study provides a comprehensive review of the Zimm-Bragg model and its Hamiltonian formulation, with particular emphasis on incorporating water interactions and chain size effects into the computational framework. We propose a modified ZB model that accounts for water-polypeptide interactions, demonstrating its ability to describe phenomena such as cold denaturation and helix-coil transitions. In the realm of NanoBioTechnologies, the manipulation of short polypeptide chains is commonplace. Experimental investigation of these chains in vitro often relies on techniques like Circular Dichroism (CD) and timeresolved infrared spectroscopy. Determining interaction parameters necessitates processing the temperature dependence of the normalized degree of helicity through model fitting. Leveraging recent advancements in the Hamiltonian formulation of the Zimm and Bragg model, we explicitly incorporate chain length and solvent effects into the theoretical description. The resulting expression for helicity degree adeptly fits experimental data, yielding hydrogen bonding energies and nucleation parameter values consistent with field standards. Differential Scanning Calorimetry (DSC) stands as a potent tool for measuring the specific heat profile of materials, including proteins. However, relating the measured profile to microscopic properties requires a suitable model for fitting. We propose a novel algorithm for processing DSC experimental data based on the ZB theory of protein folding in water. This approach complements the classical two-state paradigm and provides insights into protein-water and intraprotein hydrogen bonding energies. An analytical expression for heat capacity, considering water interaction, is derived and successfully applied to fit numerous DSC experimental datasets reported in the literature. Additionally, we compare this approach with the classical two-state model, demonstrating its efficacy in fitting DSC data. Furthermore, we have developed and launched a free online tool for processing CD and DSC experimental data related to protein folding, aiming to support scientific research.
Keywords: Zimm-Bragg model, conformational transitions, helix-coil transitions, cold denaturation, circular dichroism, differential scanning calorimetry, protein folding, water-protein interaction, hydrogen bonding energy, degree of helicity, short polypeptide chains, protein heat capacity, protein data analysis, dissertations
Published in RUNG: 27.01.2025; Views: 266; Downloads: 9
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2.
Data and data analysis : aktivnosti v okviru Tedna Univerze v Novi Gorici, TUNG 2023, 4. 10. 2023, Vipava
Ahmad Hosseini, 2023, other performed works

Abstract: In contemporary times, the words "Data" and "Data Analysis" are commonly encountered. This seminar offers an opportunity to understand the concept of Data Analysis and witness some applications in real-world scenarios pertaining to some industrial problems.
Keywords: Data, Data Analysis
Published in RUNG: 06.01.2025; Views: 215; Downloads: 1
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3.
A short introduction to some basic statistical tests using SPSS : seminar, 9. 5. 2024, Vipava
Ahmad Hosseini, 2024, other performed works

Abstract: This short 1-hour seminar aims to provide a gentle introduction to quantitative analysis using the statistical software SPSS. It is designed to assist individuals who wish to familiarize themselves with using SPSS as a tool for data manipulation and conducting some basic statistical tests. The seminar is ideal for students and practitioners who have a solid understanding of various statistical tests (such as GLM methods) and theoretical quantitative data analysis methodologies and are interested in exploring their application in SPSS. Additionally, it caters to students and researchers who have completed courses in Applied Statistics and Methodology but have not had significant exposure to statistical analysis software.
Keywords: Quantitative Analysis, Statistical Software SPSS, Statistical Tests, GLM Methods, Applied Statistics
Published in RUNG: 06.01.2025; Views: 236; Downloads: 2
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4.
Initial ZEB benchmarks based on cost-optimal study
Marjana Šijanec-Zavrl, Henrik Gjerkeš, Luka Zupančič, 2024, published scientific conference contribution

Abstract: Revised EPBD (EU/2024/1275) has introduced zero energy buildings (ZEB) and foreseen operational carbon and whole life cycle carbon (GWP) as benchmarks supporting setting minimum requirements in future building codes, building renovation plan and a national roadmap for progressive reducing GWP values for decarbonization of buildings by 2050. Starting from 2023 cost-optimal analysis this study proposed the method for assessment of initial ZEB benchmarks (in operational carbon) and emphasised the urgent need for the national database of GWP (operational and embodied carbon emissions).
Keywords: zero energy buildings, global warming potential, cost-optimal analysis, life cycle assesment
Published in RUNG: 11.12.2024; Views: 410; Downloads: 3
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5.
Uncertainty modeling and stability assessment of minimum spanning trees in network design
Ahmad Hosseini, 2024, original scientific article

Abstract: The Minimum Spanning Tree (MST) problem in networks focuses on finding efficient routes, with applications in transportation, logistics, telecommunications, and more. However, catastrophes can make these networks uncertain, requiring robust computational models for decision-making. This paper introduces an uncertainty theory-based model to analyze the stability of MSTs in uncertain networks. By incorporating reliability and risk variables, we assess the robustness of uncertain MSTs (UMSTs) and address the challenge of computing link tolerances, which define the range within which network links can vary without compromising MST optimality. This study proposes computational formulations to systematically calculate these tolerances, offering a more efficient alternative to traditional re-optimization methods.
Keywords: operations research, transportation, sensitivity analysis, uncertainty, reliability
Published in RUNG: 03.12.2024; Views: 498; Downloads: 4
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6.
Large-scale cosmic-ray anisotropies with 19 yr of data from the Pierre Auger Observatory
A. Abdul Halim, P. Abreu, M. Aglietta, Ingo Allekotte, K. Almeida Cheminant, Jon Paul Lundquist, Shima Ujjani Shivashankara, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, 2024, original scientific article

Abstract: We present results of the measurement of large-scale anisotropies in the arrival directions of ultra–high-energy cosmic rays detected at the Pierre Auger Observatory during 19 yr of operation, prior to AugerPrime, the upgrade of the observatory. The 3D dipole amplitude and direction are reconstructed above 4 EeV in four energy bins. Besides the established dipolar anisotropy in right ascension above 8 EeV, the Fourier amplitude of the 8–16 EeV energy bin is now also above the 5σ discovery level. No time variation of the dipole moment above 8 EeV is found, setting an upper limit to the rate of change of such variations of 0.3% per year at the 95% confidence level. Additionally, the results for the angular power spectrum are shown, demonstrating no other statistically significant multipoles. The results for the equatorial dipole component down to 0.03 EeV are presented, using for the first time a data set obtained with a trigger that has been optimized for lower energies. Finally, model predictions are discussed and compared with observations, based on two source emission scenarios obtained in the combined fit of spectrum and composition above 0.6 EeV.
Keywords: ultra–high-energy cosmic rays, UHECRs, UHECR anisotropies, Pierre Auger Observatory, dipolar anisotropy in right ascension, Fourier amplitude analysis, angular power spectrum, equatorial dipole component, UHECR source emission scenarios
Published in RUNG: 26.11.2024; Views: 502; Downloads: 1
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7.
8.
Exhaled volatile organic compounds and respiratory disease : recent progress and future outlook
Maria Chiara Magnano, Waqar Ahmed, Ran Wang, Martina Bergant Marušič, Stephen J. Fowler, Iain R. White, 2024, review article

Abstract: The theoretical basis of eVOCs as biomarkers for respiratory disease diagnosis is described, followed by a review of the potential biomarkers that have been proposed as targets from in vitro studies. The utility of these targets is then discussed based on comparison with results from clinical breath studies. The current status of breath research is summarised for various diseases, with emphasis placed on quantitative and targeted studies. Potential for bias highlights several important concepts related to standardization, including practices adopted for compound identification, correction for background inspired VOC levels and computation of mixing ratios. The compiled results underline the need for targeted studies across different analytical platforms to understand how sampling and analytical factors impact eVOC quantification. The impact of environmental VOCs as confounders in breath analysis is discussed alongside the potential that eVOCs have as biomarkers of air pollution exposure and future perspectives on clinical breath sampling are provided.
Keywords: breath analysis, disease diagnosis, exhaled volatile organic compounds, respiratory disease, environmental exposure analysis, breath analysis
Published in RUNG: 06.05.2024; Views: 1841; Downloads: 9
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9.
Synthesis of helional by hydrodechlorination reaction in the presence of mono- and bimetallic catalysts supported on alumina
Oreste Piccolo, Iztok Arčon, Das Gangadhar, Giuliana Aquilanti, Andrea Prai, Stefano Paganelli, Manuela Facchin, Valentina Beghetto, 2024, original scientific article

Abstract: Hydrodechlorination reaction of 3-(benzo-1,3-dioxol-5-yl)-3-chloro-2-methylacrylaldehyde in the presence of different low metal content heterogeneous mono- or bimetallic catalysts was tested for the synthesis of the fragrance Helional® (3-[3,4-methylendioxyphenyl]-2-methyl-propionaldehyde). In particular, mono Pd/Al2O3, Rh/Al2O3 or bimetallic Pd-Cu/Al2O3, Rh-Cu/Al2O3 catalysts were tested in different reaction conditions from which it emerged that mono-Rh/Al2O3 was the best performing catalyst, allowing achievement of 100% substrate conversion and 99% selectivity towards Helional® in 24 h at 80 °C, p(H2) 1.0 MPa in the presence of a base. To establish correlations between atomic structure and catalytic activity, catalysts were characterized by Cu, Rh and Pd K-edge XANES, EXAFS analysis. These characterizations allowed verification that the formation of Pd-Cu alloys and the presence of Cu oxide/hydroxide species on the surface of the Al2O3 support are responsible for the very low catalytic efficiency of bimetallic species tested.
Keywords: selective hydrodechlorination, heterogeneous catalysis, XANES analysis, EXAFS analysis
Published in RUNG: 25.04.2024; Views: 2086; Downloads: 9
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10.
Complex network based Fourier analysis for signal processing
Vijayan Vijesh, K. Satheesh Kumar, Mohanachandran Nair Sindhu Swapna, Sankaranarayana Iyer Sankararaman, 2024, published scientific conference contribution

Keywords: fourier analysis, complex network, signal processing
Published in RUNG: 15.04.2024; Views: 1770; Downloads: 3
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