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1.
Two-dimensional BC tracer model to distinguish between primary and secondary OC : lecture at The European Aerosol Conference 2024, 25. 8.-30. 8. 2024, Tampere, Finland
Matic Ivančič, Asta Gregorič, Gašper Lavrič, Bálint Alföldy, Irena Ježek, Iasonas Stavroulas, Martin Rigler, 2024, unpublished conference contribution

Abstract: In this work, we propose an extension of this method. Using the Aethalometer model (Sandradewi et al., 2008), BC as a tracer for primary emitted aerosols can be successfully divided into two components – BCff related to the usage of fossil fuels and BCbb emitted from biomass burning. Because the OC/BC ratio is expected to be different for fossil fuels and biomass burning, we can similarly introduce the two components of POC – a fossil fuel-related POCff and a biomass-burning-related POCbb.
Keywords: BC tracer model, secondary organic carbon, black carbon
Published in RUNG: 14.11.2024; Views: 273; Downloads: 1
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2.
Catalytic hydro(deoxy)genation of furfural and modelling of its reaction kinetics : dissertation
Rok Šivec, 2024, doctoral dissertation

Abstract: In recent decades, there has been a growing interest in producing biofuels and biochemicals from renewable sources. Furfural stands as one of the ligno(hemi)cellulosic biomass derived platform chemical, which can be transformed into numerous value-added products. The goal of this PhD was to systematically study hydrotreatment reactions of furfural under varying operating conditions and to gain insights into the reaction mechanism and kinetics. An extensive experimental and computational study of hydrogenation, hydrodeoxygenation, oligomerisation and etherification of furfural in a three-phase batch reactor was performed. The goals were divided into three consecutive objectives. In the first part, hydrotreatment of furfural over Pd/C catalyst under various reaction conditions, including the solvent selection (solventless conditions, tetrahydrofuran, isopropanol), atmosphere (nitrogen, hydrogen), temperature (100–200 °C), pressure (25–75 bar) and stirring speed, was studied. A reaction pathway network and a micro-kinetic model were developed, incorporating thermodynamics (hydrogen solubility), mass transfer, adsorption, desorption, and surface reactions. These phenomena and their contribution to the surface coverages, TOF’s and global reaction rates were studied. The hydrogen presence on the catalyst surface was found to influence the main reaction pathway, leading to ring, aldehyde group or full hydrogenation. In the second part, various monometallic catalysts (Pd/C, Pt/C, Re/C, Ru/C, Rh/C, Ni/C, Cu/C) were tested at 100 -200 °C with 60 bar of hydrogen and tetrahydrofuran as solvent. A generalized reaction pathway network was developed. H2 temperature-programmed reduction (H2-TPR) and CO temperature-programmed desorption (CO-TPD) were conducted, and a regression analysis of the results was subsequently performed by numerical modelling and optimisation. The obtained adsorption and desorption kinetic parameters for active metallic sites were further used in a generalized micro-kinetic model, applicable to all tested catalysts. Pd/C exhibited high activity and non-selective hydrogenation of furfural, while other catalysts showed selective aldehyde group hydrogenation followed by deoxygenation, consistent with density functional theory (DFT) calculations. Ru/C uniquely produced 2 methyltetrahydrofuran and ring-opening products at 200 °C. In silico optimization of reaction conditions for promising catalysts ((Pd/C, Pt/C, Re/C, Ni/C) aimed to maximize the yield of the target product. In the third part, the influence of support on catalytic activity was studied. Hydrotreatment of furfural over Pd/Al2O3, Pd/SiO2, Ru/Al2O3, Ru/SiO2, Ni/Al2O3, and Ni/SiO2 was performed between 150 - 200 °C, using 60 bar of hydrogen and tetrahydrofuran as solvent. The strength and rate of adsorption and desorption to/from acidic, metallic and interface site structures were determined, using H2-TPR, CO-TPD and NH3-TPD and subsequent regression analysis of the results by numerical modelling and optimisation. The resulting parameters were sequentially used in the generalized micro-kinetic model to quantify the contribution of the active metal (Ni, Pd, or Ru), support (Al2O3 or SiO2), interphase sites and their relationship on catalyst activity and selectivity. Evaluation of morphological and structural characteristics, adsorption/desorption and intrinsic reaction kinetics has indicated that the coverage of acidic sites (on alumina or silica) facilitated yielding ring hydrogenation and inhibited deoxygenation, decarbonylation and cyclic compound opening. The rates for aromatics or aldehyde functional groups were, nonetheless, affected in a different order. The used and developed methods and findings of this PhD offer useful guidelines for transforming furfural into high-value chemicals through catalytic hydrotreatment, with significant implications for future research and industrial applications.
Keywords: lignocellulosic biomass, furfural, catalytic hydrogenation, micro-kinetic mass transfer model, reaction kinetics, first-principle methods, furfuryl alcohol, tetrahydrofurfuryl alcoholv, dissertations
Published in RUNG: 08.11.2024; Views: 268; Downloads: 4
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3.
Reaction mechanism and microkinetics of heterogeneously catalysed lignin depolymerisation and (de)functionalization : dissertation
Tina Ročnik, 2024, doctoral dissertation

Abstract: Lignin, a complex aromatic polymer derived from lignocellulosic biomass, is a renewable resource for the production of aromatic-like chemicals and materials. However, its complex nature, depolymerisation and valorisation remain a major challenge for the bio-based community within biorefinery concepts. For this reason, lignin model compounds have been used to understand and design lignin depolymerisation, but insufficient attention has been paid to linking knowledge between simpler systems and applying it to a more complex problem. The objectives of this thesis were formulated accordingly to address the aforementioned gap in the literature. The objectives included a systematic approach correlating studies of lignin model compounds with lignin. Hydrodeoxygenation, cleavage of the β-O-4 bond and depolymerisation were investigated to evaluate the process- and structure-dependent correlations, effects on product distribution and kinetic parameters. The catalytic reactions were carried out in batch reactor and the conditions were applied and intensified according to the knowledge gained during the experimental work. The liquid samples for monomer yield evaluation were analysed by GC-MS, while the structural characteristics of lignin and oligomeric fragments, e.g. molecular weight, functionality/reactivity and structural features, were examined by SEC, quantitative 31P and 2D-HSQC NMR. Kinetic modelling was performed to determine the kinetic parameters (e.g. kinetic constants and activation energies) describing defunctionalisation, β-O-4 bond cleavage and depolymerisation. The study with monomeric lignin compounds contributed to the understanding of the key parameters leading to condensation during hydrotreatment. The unsaturated alkyl side-chain of eugenol and the reactive hydroxyl groups bound irreversibly and formed the carbonaceous species, while 4-propylphenol and 4-propylguaiacol provided important insights into the contribution of steric hindrances to a favourable reaction mechanism. An initial assessment of β-O-4 cleavage was performed with β-O-4-model compound, 2-phenoxy-1-phenylethanol, and linked to the lignin macromolecule by process- and structure-dependent correlations. Although the lignin model compound lacks the structural complexity of lignin, important insights into possible reaction processes were gained and accurate kinetic parameters were determined. Furthermore, lignin isolated in 50 vol% EtOH/H2O solutions was depolymerised and the optimal reaction conditions were defined at a temperature of 275 °C and a pressure of 1.5 MPa with regard to the product distribution and the changes in the structural characteristics of the corresponding oligomeric fragments. Depolymerisation of lignins isolated in different EtOH/H2O solutions showed the importance of the structural features, especially ethoxylation degree and the content of β-O-4 or α-ethoxylated β-O-4 bonds. A higher ethoxylation degree of lignin reduced its potential to depolymerise and achieve the theoretical monomer yield. Therefore, the structural characteristics of lignin play the main role in designing and prediction of lignin depolymerisation. The thesis represents a systematic approach of increasing the complexity of structures exposed to hydrodeoxygenation and depolymerisation. The approach contributed to incorporating the knowledge gained from less complex model compounds to real lignin samples by tailoring and designing lignin depolymerisation to exploit the potential of lignin for biorefinery concepts.
Keywords: model compounds, hydrodeoxygenation, organosolv lignin, depolymerisation, structural characteristics, kinetic modelling, dissertations
Published in RUNG: 08.11.2024; Views: 266; Downloads: 3
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4.
Differential scanning calorimetry of proteins and Zimm–Bragg model in water
Knarik Yeritsyan, Artem Badasyan, 2019, original scientific article

Abstract: Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. Hydrogen bonds play a crucial role in stabilizing the three-dimensional structure of proteins. Naturally, information about the strength of hydrogen bonds is contained in the measured DSC profiles. Despite its obvious importance, there is no approach that would allow the extraction of such information from the heat capacity measurements. In order to connect the measured profile to microscopic properties of a polypeptide chain, a proper model is required to fit. Using recent advances in the Zimm–Bragg (ZB) theory of protein folding in water, we propose a new and efficient algorithm to process the DSC experimental data and to extract the H-bonding energy among other relevant constants. Thus, for the randomly picked set of 33 proteins, we have found a quite narrow distribution of hydrogen bonding energies from 1 to 8 kJ/mol with the average energy of intra-protein hydrogen bonds kJ/mol and the average energy of water–protein bonds as kJ/mol. This is an important illustration of a tiny disbalance between the water–protein and intraprotein hydrogen bonds. Fitted values of the nucleation parameter belong to the range from 0.001 to 0.01, as expected. The reported method can be considered as complementary to the classical two-state approach and together with other parameters provides the protein–water and intraprotein H-bonding energies, not accessible within the two-state paradigm.
Keywords: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Published in RUNG: 26.08.2024; Views: 718; Downloads: 4
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5.
Origins of fine structure in DNA melting curves
Arevik V. Asatryan, Albert S. Benight, Artem Badasyan, 2024, original scientific article

Abstract: With the help of the one-dimensional random Potts-like model, we study the origins of fine structures observed on differential melting profiles of double-stranded DNA. We theoretically assess the effects of sequence arrangement on DNA melting curves through the comparison of results for random, correlated, and block sequences. Our results re-confirm the smearing out of the fine structure with the increase in chain length for all types of sequence arrangements and suggest that the fine structure is a finite-size effect. We have found that the fine structures on melting curves of chains comprised of blocks with correlations in sequence are more persistent, probably because of increased sequence disorder the blocks introduce. Many natural DNAs show a well-expressed fine structure of melting profiles. Our results for block sequences may suggest the existence of such sequence motifs in natural DNA sequences.
Keywords: disordered systems, DNA melting, Potts model
Published in RUNG: 08.08.2024; Views: 876; Downloads: 3
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6.
Differential scanning calorimetry of proteins and the two-state model : comparison of two formulas
Knarik Yeritsyan, Artem Badasyan, 2024, original scientific article

Abstract: 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.
Keywords: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Published in RUNG: 21.05.2024; Views: 1187; Downloads: 7
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7.
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, original scientific article

Abstract: 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.
Keywords: pandemic, urban air pollution, traffic, chemical transport model, TAPM, mapping
Published in RUNG: 10.05.2024; Views: 1298; Downloads: 4
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8.
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, published scientific conference contribution

Abstract: 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.
Keywords: Pierre Auger Observatory, ultra-high energy cosmic rays, air showers, beyond standard model, fluorescence detectors, ANITA
Published in RUNG: 23.01.2024; Views: 1264; Downloads: 8
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9.
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: 1418; Downloads: 5
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10.
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