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System size dependence of the Zimm-Bragg model
Artem Badasyan, 2021, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: Zimm-Bragg model, final size effects
Objavljeno v RUNG: 27.09.2021; Ogledov: 1191; Prenosov: 0
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Vibrational spectra of am-Al 2 O 3 : tuning a parametric model. : Written report: in fulfillment of Diploma Seminar 1FAF29 requirements
Kurtović Jasmin, 2021, raz. nal. na višji ali visoki šoli

Opis: The present diploma seminar work has been dedicated first to the implementation of a procedure to calculate the vibrational density of states of two structural models of vitreous SiO 2 (v- SiO 2 ) and amorphous Al 2 O 3 (am-Al 2 O 3 ) models, and next to tune a parametric model for the calculation of the infrared (IR) spectra of am-Al 2 O 3 , in particular of the imaginary part of the dielectric function. The ground state of both structural models is obtained by relaxing the atomic structure by using the conjugate gradient method as implemented in the LAMMPS code. Vibrational frequencies and modes are obtained, in the harmonic approximation, by diagonalizing the dynamical matrices calculated for the given v-SiO 2 and am-Al 2 O 3 structural models. Dynamical matrices are obtained through a finite differences approach and vibrational density of states are plotted by applying Gaussian broadening. The calculation of the dielectric function requires the knowledge of the vibrational frequencies as well as the knowledge of the dynamical (or Born) charge tensors related to the atoms of the am-Al 2 O 3 structural model. For the latter model, a parametrization of the ab-initio Born charge tensors has been carried out with the purpose to allow for the fast calculation of the IR spectrum of any other am- Al 2 O 3 model without the need to calculate for it the Born charge tensors using expensive ab- initio methods. The parametrization of Born charge tensors takes into account, for aluminium atoms, only of the isotropic charge which depends on coordination number and average Al- O bond length of aluminium atoms, while for oxygen atoms coordinated to three Al atoms (75%), dynamical charges are parametrized also by the area bounded by aluminium atoms nearest neighbours of the 3-coordinated oxygen atom. Moreover for analyzing the dynamical charge tensors of 3-coordinated oxygen atoms a decomposition in terms of the representations of the spatial rotations was used. The IR spectrum obtained by means of the above described parametrization provides a good approximation to the IR spectrum obtained by using the ab- initio calculated dynamical charges, as it differs from it, on average, by around 5.1% which is much better (12%) than using a average isotropic charge model (i.e. diagonal Born charge tensors where each diagonal element is one third of the average isotropic charge).
Ključne besede: Vibrational spectra, am-Al 2 O 3, parametric model
Objavljeno v RUNG: 15.09.2021; Ogledov: 1472; Prenosov: 0
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Theoretical and experimental aspects of numerosity and quantification in Lebanese Arabic : dissertation
Ali Al Moussaoui, 2021, doktorska disertacija

Opis: A question that is receiving an increasing attention in linguistics research concerns the language components of counting. This topic is approached from syntactic, semantic and pragmatic points of view. While some accounts advocate for purely syntactic or semantic approaches of countability, other adopt hybrid accounts in which labor is divided between syntax and semantics. At the same time, research finds that there is a pragmatic component enriching the interpretation of countability and numerosity in language. This dissertation attempts to contribute into the lines of research concerned in the syntactic, semantic and pragmatic aspects of countability with a focus on Lebanese Arabic (Henceforth LA), a language that has received little attention in the literature of counting. In this dissertation, a broken agreement pattern in LA between the cardinal numerals and the post-numeral counted noun phrases is examined on the basis of a syntactic-semantic model of countability developed by Stepanov and Stateva (2018). We argue that the current existing model can be used to account for the countability broken agreement pattern in LA when necessary modifications are applied to it. The success of this model in accounting for the numeral-noun-phrase agreement in LA is added to its success in similar missions in countability in Russian (Stepanov and Stateva 2018) and previously in Japanese (Watanabe 2010). The pragmatic component of countability in LA is also examined from the angle of pragmatic strengthening. The traditional difference between singular nominals and plural nominals which makes a distinction between domains of atoms and domains of sums is seriously challenged by current semantic and pragmatic research. The plural is found to be more complex than a simplistic view of more than one, and its interpretation has a pragmatic component which involves enriching the meaning of plurality against singularity. In our dissertation, we intend to examine an enriching pragmatic process of plural against duality in LA, a language that still preserves special morphological marking for duality. So, our research investigates the pragmatic strengthening of the plural morphology in LA against the dual morphology which results in at-least-three meaning of the plural. On the assumption that pragmatic reasoning contributes to the interpretation of plural nominals, we extend our research to the area of bilingual LA speakers who can be an ideal environment to look into the cognitive processes involved in the interaction between two linguistic systems that have diverging features pertaining to a given linguistic phenomenon, which is countability in our study. We predict crosslinguistic variation in the interpretation of plural morphology. If languages like English associate plural with an at-least-two meaning as a result of pragmatic enrichment with an anti-singularity inference, then, in languages that morphologically differentiate among singular, plural and dual number, the morphological plural is predicted to correspond to an at-least-three meaning. In this study, we ask whether the predicted variation in the interpretation of plural morphology among the non-dual and dual-featuring languages is a locus of negative pragmatic transfer of features from LA as a mother tongue and English/ French as foreign languages.
Ključne besede: countability, numerosity, Lebanese Arabic, countability model, negative pragmatic transfer, and foreign language exposure
Objavljeno v RUNG: 16.07.2021; Ogledov: 2362; Prenosov: 117
.pdf Celotno besedilo (3,00 MB)
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System size dependence in the Zimm-Bragg model : partition function limits, transition temperature and interval
Artem Badasyan, 2021, izvirni znanstveni članek

Opis: Within the recently developed Hamiltonian formulation of the Zimm and Bragg model we re-evaluate several size dependent approximations of model partition function. Our size analysis is based on the comparison of chain length N with the maximal correlation (persistence) length ξ of helical conformation. For the first time we re-derive the partition function of zipper model by taking the limits of the Zimm–Bragg eigenvalues. The critical consideration of applicability boundaries for the single-sequence (zipper) and the long chain approximations has shown a gap in description for the range of experimentally relevant chain lengths of 5–10 persistence lengths ξ. Correction to the helicity degree expression is reported. For the exact partition function we have additionally found, that: at N/ξ ≈ 10 the transition temperature T m reaches its asymptotic behavior of infinite N; the transition interval ∆T needs about a thousand persistence lengths to saturate at its asymptotic, infinite length value. Obtained results not only contribute to the development of the Zimm–Bragg model, but are also relevant for a wide range of Biotechnologies, including the Biosensing applications.
Ključne besede: Zimm-Bragg model, helix-coil transition, zipper model
Objavljeno v RUNG: 17.06.2021; Ogledov: 1537; Prenosov: 76
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Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins
Artem Badasyan, Sh. A. Tonoyan, Matjaž Valant, Jože Grdadolnik, 2021, izvirni znanstveni članek

Opis: Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra- molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold dena- turation and thus clarifies its absence in some proteins.
Ključne besede: protein folding, cold denaturation, water, Zimm-Bragg model
Objavljeno v RUNG: 06.05.2021; Ogledov: 1614; Prenosov: 12
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Atmospheric peroxyacetyl nitrate (PAN) : a global budget and source attribution
E. V. Fischer, D. J. Jacob, R. M. Yantosca, M. P. Sulprizio, D. B. Millet, Jiandong Mao, F. Paulot, H. B. Singh, A. Roiger, Katja Džepina, 2014, izvirni znanstveni članek

Opis: Peroxyacetyl nitrate (PAN) formed in the atmospheric oxidation of non-methane volatile organic compounds (NMVOCs) is the principal tropospheric reservoir for nitrogen oxide radicals (NOx = NO + NO2). PAN enables the transport and release of NOx to the remote troposphere with major implications for the global distributions of ozone and OH, the main tropospheric oxidants. Simulation of PAN is a challenge for global models because of the dependence of PAN on vertical transport as well as complex and uncertain NMVOC sources and chemistry. Here we use an improved representation of NMVOCs in a global 3-D chemical transport model (GEOS-Chem) and show that it can simulate PAN observations from aircraft campaigns worldwide. The immediate carbonyl precursors for PAN formation include acetaldehyde (44 % of the global source), methylglyoxal (30 %), acetone (7 %), and a suite of other isoprene and terpene oxidation products (19 %). A diversity of NMVOC emissions is responsible for PAN formation globally including isoprene (37 %) and alkanes (14 %). Anthropogenic sources are dominant in the extratropical Northern Hemisphere outside the growing season. Open fires appear to play little role except at high northern latitudes in spring, although results are very sensitive to plume chemistry and plume rise. Lightning NOx is the dominant contributor to the observed PAN maximum in the free troposphere over the South Atlantic.
Ključne besede: peroxyacetyl nitrate, non-methane volatile organic compounds, global 3-D chemical transport model, GEOS-chem
Objavljeno v RUNG: 11.04.2021; Ogledov: 1783; Prenosov: 0
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Molecular and physical characteristics of aerosol at a remote free troposphere site : implications for atmospheric aging
Simeon K. Schum, Bo Zhang, Katja Džepina, Paulo Fialho, Claudio Mazzoleni, Lynn R. Mazzoleni, 2018, izvirni znanstveni članek

Opis: Aerosol properties are transformed by atmospheric processes during long-range transport and play a key role in the Earth’s radiative balance. To understand the molecular and physical characteristics of free tropospheric aerosol, we studied samples collected at the Pico Mountain Observatory in the North Atlantic. The observatory is located in the marine free troposphere at 2225m above sea level, on Pico Island in the Azores archipelago. The site is ideal for the study of long-range-transported free tropospheric aerosol with minimal local influence. Three aerosol samples with elevated organic carbon concentrations were selected for detailed analysis. FLEXPART retroplumes indicated that two of the samples were influenced by North American wildfire emissions transported in the free troposphere and one by North American outflow mainly transported within the marine boundary layer. Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry was used to determine the detailed molecular composition of the samples. Thousands of molecular formulas were assigned to each of the individual samples. On average ~60% of the molecular formulas contained only carbon, hydrogen, and oxygen atoms (CHO), ~ 30% contained nitrogen (CHNO), and ~ 10% contained sulfur (CHOS). The molecular formula compositions of the two wildfire-influenced aerosol samples transported mainly in the free troposphere had relatively low average O=C ratios (0:48 ± 0:13 and 0:45 ± 0:11) despite the 7–10 days of transport time according to FLEXPART. In contrast, the molecular composition of the North American outflow transported mainly in the boundary layer had a higher average O=C ratio (0:57 ± 0:17) with 3 days of transport time. To better understand the difference between free tropospheric transport and boundary layer transport, the meteorological conditions along the FLEXPART simulated transport pathways were extracted from the Global Forecast System analysis for the model grids. We used the extracted meteorological conditions and the observed molecular chemistry to predict the relative-humidity-dependent glass transition temperatures (Tg) of the aerosol components. Comparisons of the Tg to the ambient temperature indicated that a majority of the organic aerosol components transported in the free troposphere were more viscous and therefore less susceptible to oxidation than the organic aerosol components transported in the boundary layer. Although the number of observations is limited, the results suggest that biomass burning organic aerosol injected into the free troposphere is more persistent than organic aerosol in the boundary layer having broader implications for aerosol aging.
Ključne besede: secondary organic aerosols, brown carbon, particle dispersion model, ultrahigh-resolution FT-ICR MS, Pico Mountain Observatory
Objavljeno v RUNG: 10.04.2021; Ogledov: 1736; Prenosov: 0
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Machine learning models for government to predict COVID-19 outbreak
Rajan Gupta, Gaurav Pandey, Poonam Chaudhary, Saibal K. Pal, 2020, izvirni znanstveni članek

Opis: The COVID-19 pandemic has become a major threat to the whole world. Analysis of this disease requires major attention by the government in all countries to take necessary steps in reducing the effect of this global pandemic. In this study, outbreak of this disease has been analysed and trained for Indian region till 10th May, 2020, and testing has been done for the number of cases for the next three weeks. Machine learning models such as SEIR model and Regression model have been used for predictions based on the data collected from the official portal of the Government of India in the time period of 30th January, 2020, to 10th May, 2020. The performance of the models was evaluated using RMSLE and achieved 1.52 for SEIR model and 1.75 for the regression model. The RMSLE error rate between SEIR model and Regression model was found to be 2.01. Also, the value of R0, which is the spread of the disease, was calculated to be 2.84. Expected cases are predicted around 175K--200K in the three-week time period of test data, which is very close to the actual numbers. This study will help the government and doctors in preparing their plans for the future.
Ključne besede: COVID-19, India, spread exposed infected recovered model, regression model, machine learning, predictions, forecasting
Objavljeno v RUNG: 01.04.2021; Ogledov: 1704; Prenosov: 82
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The finite size effects and two-state paradigm of protein folding
Artem Badasyan, Matjaž Valant, Jože Grdadolnik, Vladimir N. Uversky, 2021, izvirni znanstveni članek

Opis: The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the k2 measure, defined as the ratio of van ’t Hoff and calorimetric enthalpy is related to the degeneracy of the denatured state and describes the number of cooperative units involved in the transition; additionally, it is found that the widely discussed k2=1 is just the necessary condition to classify the protein as the two-state folder. We also find that Ωc, a quantity not limited from above and growing with system size, is simply proportional to the square of the transition interval. This fact allows us to perform the classical size scaling analysis of the coil-globule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding
Ključne besede: protein folding, two-state model, size scaling, thermodynamic cooperativity
Objavljeno v RUNG: 24.02.2021; Ogledov: 1679; Prenosov: 63
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