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Opis: 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.
Ključne besede: 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
Objavljeno v RUNG: 27.01.2025; Ogledov: 705; Prenosov: 13
Celotno besedilo (5,12 MB)

Opis: 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.
Ključne besede: lignocellulosic biomass, furfural, catalytic hydrogenation, micro-kinetic mass transfer model, reaction kinetics, first-principle methods, furfuryl alcohol, tetrahydrofurfuryl alcoholv, dissertations
Objavljeno v RUNG: 08.11.2024; Ogledov: 1078; Prenosov: 23
Celotno besedilo (9,22 MB)

Opis: 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.
Ključne besede: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Objavljeno v RUNG: 26.08.2024; Ogledov: 1335; Prenosov: 4
Celotno besedilo (645,94 KB)
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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: 1816; Prenosov: 11
Celotno besedilo (380,96 KB)
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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: 1808; Prenosov: 33
Celotno besedilo (2,95 MB)
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