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41.
42.
Water reveals non-Arrhenius kinetics in protein folding experiments
Artem Badasyan, 2020, objavljeni povzetek znanstvenega prispevka na konferenci (vabljeno predavanje)

Opis: Statistical theories describe systems in equilibrium, and cannot be used to study kinetics. However, the theo- ries are based on coarse-grained parameters, that include assumptions regarding the underlying kinetics. If such assumptions are incorrect, the theoretical expressions, used to process the experimental data, will not fit. I report on one such case we have met within the application of Zimm-Bragg [1] theory to process folding experiments, and discuss the reasons and consequences. Studies of relaxation phenomena in glass-forming liquids by default account for the shift in temperature by some value, corresponding to the glass formation temperature, .In particular, temperature shift appears in hydrated proteins because of the presence of partially glassy states giving rise to non- Arrhenius relaxation times log τ ~ [2]. A phenomenological approach was suggested by Adam and Gibbs as early as in 1965 to describe the sudden increase of viscosity and the slowing down of the collective modes in super-cooled liquids as the temperature is approaching[3]. The key idea of Adam-Gibbs theory was to consider the supercooled liquid as a set of clusters (cooperatively rearranging regions) of different sizes that change with temperature, giving rise to the shift in re- laxation time. The temperature shift factor is present in many theories describing properties of water. Thus, Truskett and Dill had to include the Adamm-Gibbs temperature shift into their simple analytical model of water to achieve the agreement with experimental data on the tem- perature dependence of self-diffusion coefficient [4]. Later, Schiro and Weik have summarised recent in vitro and in silico experimental results regarding the role of hydration water in the onset of protein structural dy- namics, and have reported the presence of super-Arrhenius relaxation region above the ”protein dynamic transition” temperature [4]. Recently, Mallamace et al have used the Adam-Gibbs theory in their NMR meas- urements of protein folding-unfolding in water [4] and to rationalise the complicated pressure-temperature diagrams in these glass-forming systems. Motivated by the considerations above, and taking into account the relationship between the unimolecular rate of folding in water and the relaxation time 45 , we introduce the tem- perature shift into the formulas used to fit experimental data on hydrated polypeptides. By doing so we resolve the paradox and complete the new method of processing the Circular Dichroism ex- perimental data on protein folding
Ključne besede: water, protein folding, non-Arrhenius kinetics
Objavljeno v RUNG: 20.07.2020; Ogledov: 2596; Prenosov: 111
.pdf Celotno besedilo (2,35 MB)

43.
Study of water adsorption on EDTA dealuminated zeolite Y
O. L. Pliekhov, Olena Pliekhova, Iztok Arčon, Federica Bondino, Elena Magnano, Gregor Mali, Nataša Zabukovec Logar, 2020, izvirni znanstveni članek

Opis: Zeolite Y was synthesized and modified with EDTA dealumination procedure. The modified zeolites were analyzed by X-ray diffraction, X-ray absorption spectroscopy, chemical analysis and water adsorption measurements. We demonstrated that dealumination with bulk organic acid such as EDTA is able to reduce the original intense water affinity. Furthermore, it was found that dealumination with EDTA, in contrast with steaming and HCl dealumination, provides fully controllable, predictable and secure process of Al removal from the zeolites’ frameworks. The shift of the adsorption isotherm in the low partial pressure range represents an interesting result for adsorption-based applications.
Ključne besede: Zeolite Y Water sorption Dealumination Al XANES EDTA treatment
Objavljeno v RUNG: 05.06.2020; Ogledov: 2907; Prenosov: 0
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44.
Mediterranean Coastal Lagoons: The Importance of Monitoring in Sediments the Biochemical Composition of Organic Matter
Monia Renzi, Francesca Provenza, Sara Pignattelli, Lucrezia Cilenti, Antonietta Specchiulli, Milva Pepi, 2019, izvirni znanstveni članek

Opis: Transitional water ecosystems are targeted by the European Union (EU) Water Framework Directive (WFD, CE 2000/60) monitoring programs in coastal zones. Concerning sediments, activities performed for the WFD focus on a few variables concerning the biochemical composition of organic matter. Our research reports the effects of oxygen availability on the biochemical composition of organic matter in sediments to highlight levels of targeted variables in time and, according to the depth of sediment layer, both under oxygenated and anoxic conditions in a mesocosm study on sediment cores. Results provide evidence that tested factors of interest (i.e., disturbance type, oxygenic versus anoxic conditions; persistence time of disturbance, 0–14 days; penetration through sedimentary layers, 0–10 cm depth) are able to significantly affect the biochemical composition of organic matter in sediments. Large part of the variables considered in this study (total organic carbon (TOC), total phosphorous (TP), total sulphur (TS), Fe, carbohydrates (CHO), total proteins (PRT), biopolymeric carbon (BPC), chlorophyll-a (Chl-a) are significantly affected and correlated to the oxygenation levels and could be good early indicators of important changes of environmental conditions. Monitoring activities performed under WFD guidelines and management strategies of Mediterranean coastal lagoon ecosystems shall include the biochemical composition of organic matter in sediment to provide an exhaustive picture of such dynamic ecosystems.
Ključne besede: decomposition, transitional water ecosystems, organic loads, mesocosm, monitoring programs
Objavljeno v RUNG: 20.04.2020; Ogledov: 2734; Prenosov: 0
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45.
Zr/Cu-TiO2 CATALYSTS FOR PHOTOCATALYTIC WATER TREATMENT
Olena Pliekhova, 2019, doktorska disertacija

Opis: This work entitled «Zr/Cu-TiO2 catalysts for photocatalytic water treatment» tackles a problem of tons of dyes discharged everyday mainly from textile industries. This is a huge concern because of dyes persistence, toxicity and potential to the bioaccumulation in living organisms. Here, a small contribution to overall problem is presented. The research work consists of three main parts: Theoretical background, Experimental and Results and discussion. In the Theoretical background chapter the overall problem is identified and discussed. The main water treatment techniques are presented briefly with their advantages and drawbacks. Photocatalysis assisted with TiO2 is shown as an alternative additional technique with its own pros and cons. Further, a cursory overview of TiO2 modification techniques is made and advantages in using copper and zirconium oxides for TiO2 modification are presented. The reason and possible positive effect of using of two oxides simultaneously for TiO2 modification is indicated. Additionally, a positive impact of solar light for overall rate of dyes degradation assisted with TiO2 is discussed. Within the framework of photosensitization effect, the problem of using dyes for assessment of photocatalytic properties of materials under the visible light is touched on. Photothermal methods as possible beneficial techniques for this purpose are proposed. In the Experimental chapter, all experimental techniques used in current research work with the technical details specific for the research work are presented. There are methods of materials preparation, photocatalytic tests under different conditions and varying model pollutants, and physico-chemical characterization techniques. The Results and discussion chapter is divided by three subchapters. Each chapter is dedicated to one hypothesis, which was checked and confirmed or disproved. The first hypothesis is about beneficial loading of copper and zirconium oxides to TiO2. After numerous experiments held, it was concluded that the pair of copper and zirconium oxides is beneficial for simultaneous application on TiO2 surface to promote its performance. The second subchapter is about zirconium distribution and its impact on the activity of studied materials towards the antraquinone dye Reactive Blue 19. Different techniques such as XRD, TEM, EXAFS and many others were used in order to characterize the materials and to understand the details of the processes taking place. The existence of upper limit of copper oxide loading for its beneficial effect on TiO2 performance was demonstrated. It was observed that zirconium species loading leads to improvement in performance of materials with higher copper loading, which otherwise lowers activity of TiO2 – this is in case when copper only above its optimal level is present. It was concluded that zirconium oxide containing species occupy rutile surface sites in mixed phase TiO2 and this way beneficially influence the material performance towards the dye removal. The third subchapter is about the visible light TiO2 assisted dye degradation. It is well known that photosensitization mechanism of dye degradation appears under the visible and as a consequence under the solar light irradiation. This leads to the overall enhancement of dyes degradation, which is positive and may be used as a benefit for faster pollutant destruction. However, this fact leads to mishmash in the determination of real photocatalytic activity of materials towards the dye. It was hypothesized that the impact of photosensitization mechanism on the overall material performance against Reactive blue 19 dye (RB19) descends with the dye concentration lowering. Thermal lens spectrometry (TLS) which is sensitive to chemicals at low concentrations was used for hypothesis evaluation. To summarize the research work achievements, the conclusions of the thesis are given at the end.
Ključne besede: titanium dioxide, photocatalysis, zirconium/copper, surface modification, water treatment, dyes
Objavljeno v RUNG: 03.12.2019; Ogledov: 5841; Prenosov: 136
.pdf Celotno besedilo (3,18 MB)

46.
47.
Mass composition of cosmic rays with energies from 10^17.2 eV to 10^20 eV using surface and fluorescence detectors of the Pierre Auger Observatory
Gašper Kukec Mezek, 2018, objavljeni znanstveni prispevek na konferenci

Opis: Ultra-high-energy cosmic rays (UHECRs) are highly energetic particles with EeV energies, exceeding the capabilities of man-made colliders. They hold information on extreme astrophysical processes that create them and the medium they traverse on their way towards Earth. However, their mass composition at such energies is still unclear, because data interpretation depends on our choice of high energy hadronic interaction models. With its hybrid detection method, the Pierre Auger Observatory has the possibility to detect extensive air showers with an array of surface water-Cherenkov stations (SD) and fluorescence telescopes (FD). We present recent mass composition results from the Pierre Auger Collaboration using observational parameters from SD and FD measurements. Using the full dataset of the Pierre Auger Observatory, implications on composition can be made for energies above 10^17.2 eV.
Ključne besede: astroparticle physics, ultra-high energy cosmic rays, extensive air showers, mass composition, Pierre Auger Observatory, fluorescence telescopes, water-Cherenkov stations
Objavljeno v RUNG: 24.05.2019; Ogledov: 3298; Prenosov: 110
.pdf Celotno besedilo (573,00 KB)

48.
A Biogenerated Polymetallic Catalyst from Society's Wastes
Oreste Piccolo, Stefano Paganelli, Petro Zanatta, Sebastiano Tieuli, Laura Sperni, Franco Baldi, Iztok Arčon, Michele Gallo, Katarina Vogel-Mikuš, 2019, izvirni znanstveni članek

Opis: Aims:Preparation of the new metals - polymeric composite, Met x-EPS (I), to be used as a green catalyst in water or in two-phase aqueous conditions. Study Design: Recovery and valorization of polymetallic wastes to obtain directly new catalysts using a microorganism to explore their application in removal of difficult and dangerous chemical pollutants present in aqueous environment
Ključne besede: Metals - polymeric composite, biogenerated polymetallic exopolysaccharide, new catalyst from metallic wastes, hydrodechlorination of PCBs in water
Objavljeno v RUNG: 06.05.2019; Ogledov: 3268; Prenosov: 0
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49.
The dissociation constant of water at extreme conditions: a molecular dynamics study
Rabi Khanal, 2012, diplomsko delo

Ključne besede: water, molecular dynamics, pK, dissociation, Bluemoon approach
Objavljeno v RUNG: 21.03.2019; Ogledov: 3373; Prenosov: 1
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50.
On spin description of water-biopolymer interactions: theory and experiment of reentrant order-disorder transition.
Artem Badasyan, predavanje na tuji univerzi

Opis: The experimental studies of biopolymer conformations have reached an unprecedented level of detailization during the past decade and allow now to study single molecules in vivo [1]. Processing of experimental data essentially relies on theoretical approaches to conformational transitions in biopolymers [2]. However, the models that are currently used, originate from the early 1960's and contain several unjustified assumptions, widely accepted at that time. Thus, the view on the conformational transitions in the polypeptides as a two-state process has very limited applicability because the all-or-none transition mechanism takes place only in short polypeptides with sizes comparable to the spatial correlation length; the original formulation of Zimm-Bragg model is phenomenological and does not allow for a microscopic model for water; the implicit consideration of the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy difference on temperature can only be justified through the assumption of an ideal gas with a constant heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation [3] of the Zimm-Bragg model [4] with the term describing the water-polypeptide interactions [5]. The analytical solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat and cold denaturation. On the example of several sets of experimental data we show, that our formula results in a significantly better fit, as compared to the existing approaches. Moreover, the application of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an information, inaccessible before.
Ključne besede: helix-coil transition, water-polypeptide interactions
Objavljeno v RUNG: 13.03.2019; Ogledov: 3113; Prenosov: 0
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