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11.
12.
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: 3368; Prenosov: 1
Gradivo ima več datotek! Več...

13.
Orbital-dependent electron dynamics in Fe-pnictide superconductors
Ganesh Adhikary, Barbara Ressel, Primož Rebernik Ribič, Jurij Urbančič, Giovanni De Ninno, Damjan Krizmancic, A. Thamizhavel, Kalobaran Maiti, Matija Stupar, 2018, izvirni znanstveni članek

Opis: We report on orbital-dependent quasiparticle dynamics in EuFe 2 As 2, a parent compound of Fe-based superconductors, and a way to experimentally identify this behavior using time-and angle-resolved photoelectron spectroscopy across the spin density wave transition. We observe two different relaxation timescales for photoexcited d x z/d y z and d x y electrons. While the itinerant d x z/d y z electrons relax faster through the electron-electron scattering channel, d x y electrons form a quasiequilibrium state with the lattice due to their localized character, and the state decays slowly. Our findings suggest that electron correlation in Fe pnictides is an important property, which should carefully be taken into account when describing the electronic properties of both parent and carrier-doped compounds, and therefore establish a strong connection with cuprates
Ključne besede: photoelectron dynamics, Fe based superconductors
Objavljeno v RUNG: 29.11.2018; Ogledov: 3469; Prenosov: 0
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14.
CONTRIBUTION TO DEVELOPMENT OF MESHLESS METHODS FOR FREE AND MOVING BOUNDARY PROBLEMS
NAZIA TALAT, 2018, doktorska disertacija

Ključne besede: Two-phase flow, free and moving boundaries, computational fluid dynamics, phasefield formulation, 2D problems, axisymmetric problems, diffuse approximate meshless method, Rayleigh-Taylor instability, Boussinesq approximation, variable density and viscosity, flow focusing, dripping, jetting
Objavljeno v RUNG: 11.09.2018; Ogledov: 4984; Prenosov: 178  (1 glas)
.pdf Celotno besedilo (4,24 MB)

15.
Energy enhancement of the target surface electron by using a 200 TW sub-picosecond laser
J. Y. Mao, 2018, izvirni znanstveni članek

Opis: One order of magnitude energy enhancement of the target surface electron beams with central energy at 11.5 MeV is achieved by using a 200 TW, 500 fs laser at an incident angle of 72° with a prepulse intensity ratio of 5×10−6. The experimental results demonstrate the scalability of the acceleration process to high electron energy with a longer (sub-picosecond) laser pulse duration and a higher laser energy (120 J). The total charge of the beam is 400±20 pC(
Ključne besede: Strong field laser physics, Plasmas, Particles, Femtosecond phenomena, Surface dynamics.
Objavljeno v RUNG: 07.08.2018; Ogledov: 4075; Prenosov: 0
Gradivo ima več datotek! Več...

16.
DISTRIBUTION OF ENTERIC VIRUSES IN THE GULF OF TRIESTE AND THEIR INTERACTIONS WITH ENVIRONMENTAL AND BIOLOGICAL PARAMETERS
José Manuel Carita Gonçalves, 2018, doktorska disertacija

Opis: The available classical diagnostic methods, due to many disadvantages, do not allow effective detection of pathogenic enteric viruses in environmental samples. Due to low concentrations of pathogenic viruses in the sea, it is important to develop an effective concentration procedure for their successful detection. In the first part of the doctoral thesis, we focused primarily on the development of a protocol for an effective concentration of pathogenic enteric viruses in coastal water samples. Monolithic chromatographic columns (BIAseparations) were used for the concentration of rotaviruses and noroviruses, prior to the detection with reverse transcription quantitative PCR in real time (RT-qPCR). We tested the efficiency of concentration using columns of various chemical properties and selected pathogenic enteric viruses (rotavirus and norovirus). Among them, hydrophobic interaction monolithic column (CIM® C4) was the most effective. CIM C4 was used to optimize the concentration step and tested in waters with different salinities. The presence of concentrated viruses was confirmed by RT-qPCR and transmission electron microscope. We have developed a protocol that enables rapid concentration of viruses in coastal waters of various salinities and can be used on-site. The presence of RoV and NoV was surveyed, using the developed concentration protocol, prior to one-step RT-qPCR molecular detection, in the inner part of the Bay of Koper, in mussel farming areas and a swimming area. Rotaviruses, noroviruses and fecal indicator bacteria were frequently detected in the inner part of the Bay of Koper. Rotaviruses and noroviruses were detected in the studied area, with higher rates close to the outfall of the wastewater treatment plant in the estuary of river Rižana and were also detected in the middle of the Bay of Koper and in areas used for recreation and mussel farming. The results show that water bodies, which are otherwise defined as suitable for bathing or mussel farming, based on the results of fecal indicator bacteria, still contain low concentrations of pathogenic enteric viruses. In addition to human pathogenic enteric viruses and faecal coliforms, changes in abundance of bacteria and virus particles were studied in relation to temperature, salinity, inorganic and organic nutrient concentrations in the organically polluted Rižana estuary. Preliminary results showed spatially and seasonally changes in bacterial and viral particles abundance, and bacterial composition spatially and seasonally. However, seasonality plays a greater role in bacterial dynamics.
Ključne besede: Concentration of viruses, Enteric viruses, Rotavirus, Norovirus, Feacal coliforms, Feacal contamination, qPCR, RT-qPCR, Monolithic columns, Sewage, Seasonal dynamics, Concentration, Coastal environment, Gulf of Trieste
Objavljeno v RUNG: 02.07.2018; Ogledov: 4767; Prenosov: 211
.pdf Celotno besedilo (1,95 MB)

17.
NADGRADNJA INFORMACIJSKEGA SISTEMA ZA UPRAVLJANJE STORITVENIH ZAHTEVKOV V PODJETJU INFORMACIJSKE DEJAVNOSTI
Adnan Omerčević, 2018, diplomsko delo

Opis: V večini podjetij, ki se ukvarjajo z informacijskimi tehnologijami, osnovna dejavnost temelji na storitvenih zahtevkih. Ustrezna informacijska podprtost tovrstnih procesov je ključnega pomena za obvladovanje le-teh v najširšem pomenu. V diplomskem smo razvili nadgradnjo obstoječega informacijskega podsistema za vodenje storitvenih zahtevkov v podjetju Business Solutions, d.o.o. Informacijski sistem teče na platformi Microsoft Dynamics NAV. Nadgradnja stremi predvsem k tehničnim in vsebinskim izboljšavam pri odpiranju novih zahtevkov, pregledu nad zahtevki, upravljanju nalog znotraj zahtevkov in lažjem vnosu opravljenih storitvenih ur, ki predstavljajo glavni vir prihodkov podjetja. Pomemben del nadgradnje predstavlja tudi realizacija funkcionalnosti, ki so osnova za integracijo rešitve s spletnim portalom. Uporabljena metodologija sestoji iz analize obstoječe rešitve, tehnične izvedbe s ključnimi koraki razvoja v okolju C/AL, dejanske operativne uvedbe sistema ter načrta uvedbe spletnega portala. Uspešna uvedba nadgradnje je v prvi vrsti prispevala k temu, da so zaposleni pri svojem delu bolj produktivni, stranke podjetja pa z učinkovitejšim reševanjem njihovih storitvenih zahtevkov bolj zadovoljne.
Ključne besede: Microsoft Dynamics NAV, storitveni zahtevek, nadgradnja informacijskega sistema
Objavljeno v RUNG: 01.06.2018; Ogledov: 4999; Prenosov: 350
.pdf Celotno besedilo (1,72 MB)

18.
Simulation Of Gas Focused Liquid Jets
Rizwan Zahoor, 2018, doktorska disertacija

Opis: The main aim of dissertation is to develop an experimentally verified computational fluid dynamic (CFD) model of micron-sized liquid jet, produced by an injection molded Gas Dynamic Virtual Nozzle (GDVN). In these nozzles, liquid jets are efficiently orientedly transporting mass and momentum. They are produced by intelligently projecting hydrodynamic focusing effect from a high-speed stream of a co-flowing lower density and lower viscosity gas on a stream of liquid from a feeding capillary. Liquid micro-jets are used for delivery of protein crystal samples in a hard X-ray beam in serial femtosecond crystallography experiments. The diffraction patterns of crystals are collected just before their destruction. The samples are hard to crystallize and very precious, so a thorough knowledge of the jet used in delivering them is required. The jet characteristics are analyzed as a function of operating parameters, geometry and material properties. The physical model is described by mixture formulation and Navier-Stokes equations for transient, Newtonian, two-phase, compressible flow. Multiphase flow problem is solved with finite volume method (FVM), where fluid-fluid interface tracking is obtained with volume of fluid (VOF). The implementation of FVM-VOF CFD model is available in open source codes OpenFOAM and Gerris. They are validated by performing a series of standard interface advection and multiphase flow test cases. Both open source codes are compared for their abilities in solving GDVN flow problem. Due to the compressible nature of the focusing gas flow, OpenFOAM was chosen for GDVN simulations, since Gerris has no compressible flow option. Constant effective material properties are used in the phases together with ideal gas density constitutive relation. A mixture model of the two-phase system is solved in axisymmetry. The discretization of the nozzle and chamber system uses approximately 300 000 finite volumes. Mesh independent results are obtained with the finite volumes of the size 0.25 µm in the vicinity of the jet and drops. The simulations are compared with experimental results according to the jet thickness and length for distilled water jet and helium focusing gas, discharging into low-pressure environment of 150 Pa. Reynolds numbers of the liquid and gas are in the range 413-3828 and 17-1222, respectively and Weber number in the range 3-353. A reasonably good agreement with experimental and scaling results is found for the range of nozzle operating parameters never tackled before. Subsequently, a numerical study of effects of nozzle geometry on stability, shape and flow characteristics of micron-sized liquid jets is performed. The jet characteristics are described as a function of (i) capillary-to-orifice distance, (ii) nozzle outlet orifice diameter and (iii) liquid feeding capillary angle. The study is performed for two sets of liquid flow rates while keeping the gas flow rate unchanged. It is observed that for each value of capillary-to-orifice distance and nozzle outlet diameter, there exists a minimum liquid flow rate below which the jet stability cannot be achieved. It is found that the changes in the nozzle outlet diameter have the biggest influence on the jet diameter, length and velocity, while the liquid capillary angle has no observable effect on the jet characteristic. Change in capillary-to-orifice distance does not affect the flow field around micro jet, so the jet stability and shape is found to be affected by the way liquid-gas interacts near meniscus. The same numerical model is used to additionally analyze the jet performance under the influence of Argon, Carbon dioxide and Nitrogen focusing gases. The study shows that the helium gas at the same mass flow rate provides twice the length of the jet compared to other gases. The jet focused with helium is also much thinner, faster and interestingly shows no considerable temperature drop at the nozzle outlet. This work for the first time discuss the computational model of an injection molded micron-sized nozzle and produces valuable information for their design.
Ključne besede: Microfluidics, gas dynamic virtual nozzle, flow focusing, micro-jet, convective instability, absolute instability, compressible multiphase flows, dripping, spurting, jetting, jet thickness, jet length, computational fluid dynamics, finite volume method, volume of fluid method
Objavljeno v RUNG: 27.03.2018; Ogledov: 6315; Prenosov: 170
.pdf Celotno besedilo (11,47 MB)

19.
Nanobodies: towards rational design of immune-reagents
Ario De Marco, 2017, objavljeni povzetek znanstvenega prispevka na konferenci (vabljeno predavanje)

Opis: Antibodies are irreplaceable reagents in both research and clinical practice. Despite their relevance, the structural complexity of conventional mono- and polyclonal antibodies (IgG) has always been a limit for their engineering towards reagents optimized for specific applications, such as in vivo diagnostics and therapy. Furthermore, their isolation is time consuming, their production expensive, and their functionalization results often in heterogeneous macromolecule populations. These drawbacks promoted the search for both innovative antibody isolation strategies and alternative scaffolds. In vitro panning of pre-immune collections of recombinant antibody fragments allows for the simple and fast recovery of binders. Since they did not undergo somatic maturation, their affinity for targets can be insufficient but on the other hand they can be rapidly mutated by standard molecular biology techniques to generate second-generation antibodies among which to identify clones with improved characteristics. Both stochastic and rational methods have been proposed for the optimization process. Random mutagenesis followed by panning at stringent conditions has been successful used to select binders with improved physical characteristics. Rational methods try to identify in silico key residues involved in the regulation of specific antibody features, such as stability or binding affinity. The accuracy of these methods usually depends on the calculation resources. In this perspective, smaller molecules can be analyzed “better” than larger because of their restricted number of residues. Nanobodies small dimensions have been long appreciated since enable better tissue penetration, shorter clearance time, higher yields. Now it becomes evident that this characteristic makes them also optimal objects for modeling.
Ključne besede: recombinant antibody modeling, nanobody engineering, molecular dynamics and docking
Objavljeno v RUNG: 21.03.2018; Ogledov: 4374; Prenosov: 0
Gradivo ima več datotek! Več...

20.
Ecological evaluation of aquatic and terrestrial subterranean fauna in a karst cave
Peter Kozel, 2018, doktorska disertacija

Opis: Studies on environmental parameters−subterranean fauna relationship and spatial and temporal patterns of subterranean fauna have dealt with either aquatic or terrestrial faunas. So far, no simultaneous ecological evaluation of aquatic and terrestrial faunas has been performed. To address this issue, we conducted a pilot study dealing in parallel with these two faunas in the cave Zguba jama near Postojna, Slovenia, applying monthly sampling over one year. Aquatic fauna was sampled from permanent water drips, and terrestrial fauna by visual inspection and advanced baited pitfall trapping, along with recording the main abiotic parameters. In percolating water, we recorded aquatic fauna, Copepoda being the dominant taxon, and species-rich troglobiotic fauna, which most probably coexist with aquatic species in a semi-aquatic epikarst environment. Analyses revealed that temperature, distance from the entrance and ceiling thickness are the most important parameters that influence the presence of stygobionts; higher values of these parameters result in a higher probability of the presence of stygobionts in percolation water. The recorded spatial distribution of stygobionts varied distinctly among the sampling sites. This indicates that fauna in sampled drips originated from aquatic or semiaquatic epikarst microhabitats, being completely or nearly completely separated from each other, and probably varied according to environmental characteristics. The temporal pattern of the stygobiotic fauna dynamics presumably occurred because of variable water flow rates and the specific physical and chemical characteristics of the water. The abundance of troglobionts showed distinctive spatial distribution pattern over the seasons. In spring and summer, the highest abundances and the highest probability of presence were found near the entrance. In autumn and winter, unfavorable conditions in the entrance zone most likely triggered the migration of troglobionts towards the climatically more stable deep cave zone, and from the cave into the adjacent fissure network. The highest abundance of troglobionts was found at 7–9°C and relatively high ground substrate moisture. Additionally, we found a higher probability of the presence of troglobionts in cave sections with a larger passage cross-section size, which is probably due to the greater variability of microhabitat types in spacious cave sections. In addition, the higher probability of presence relates to higher substrate pH. One potential explanation for this could be that the specific microorganism communities present in such conditions support the nutritional needs of troglobionts. Most troglobiotic species preferred the deep cave zone where the highest species richness and diversity were also observed. Species richness, abundance and diversity of troglophiles and trogloxenes were highest in the entrance zone and showed relatively similar patterns within the cave. However, troglophiles were more abundant in the transition zone and the initial part of the inner zone. The temporal pattern of trogloxenes and presumably of most troglophiles occurred because of migration between the surface and the cave. The probability of the presence of trogloxenes was highest in the entrance zone and in winter, owing to massive overwintering in the cave. A modified technique of pitfall trapping by placing traps in two parallel sets, a ground and an upper one along the cave, resulted in recording greater species diversity in comparison with the traditional method, i.e., ground pitfall trapping alone. It turned out that such sampling contributes at the same time to both more effective and less invasive inventory of subterranean fauna. The dynamics of relative abundance and species richness of stygobionts and troglobionts within the cave showed partly comparable annual patterns. Nevertheless, our findings point toward the need for a long-term and more detailed study in future to address this question properly.
Ključne besede: biological inventories, epikarst fauna, faunal dynamics, microhabitats, stygobionts, troglobionts, troglophiles, trogloxenes, Zguba jama
Objavljeno v RUNG: 16.02.2018; Ogledov: 4473; Prenosov: 313
.pdf Celotno besedilo (5,25 MB)

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