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From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang–Landau approach
2016, original scientific article

Abstract: We use a micro-canonical Wang–Landau technique to study the equilibrium properties of a single flexible homopolymer where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To mimic the characteristics of a protein-like system, the model is then refined in two different directions. Firstly, by allowing partial overlap between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. Alternatively, we introduce additional spherical beads at specific positions in the direction normal to the backbone, to represent the steric hindrance of the side chains in real proteins. Finally, we consider also a combination of these two ingredients. In all three systems, we obtain the full phase diagram in the temperature-interaction range plane and find the presence of helicoidal structures at low temperatures in the intermediate range of interactions. The effect of the range of the square-well attraction is highlighted, and shown to play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed.
Found in: ključnih besedah
Summary of found: ...Wang-Landau approach, Monte-Carlo simulations, proteins, secondary structures...
Keywords: Wang-Landau approach, Monte-Carlo simulations, proteins, secondary structures
Published: 04.05.2016; Views: 2472; Downloads: 0
.pdf Fulltext (10,13 MB)

Distance-based configurational entropy of proteins from molecular dynamics simulations
Federico Fogolari, Alessandra Corazza, Sara Fortuna, Miguel Angel Soler, Bryan VanSchouwen, Giorgia Brancolini, Stefano Corni, Giuseppe Melacini, Gennaro Esposito, 2015, original scientific article

Abstract: Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements; the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state; backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy); the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Found in: ključnih besedah
Keywords: entropy, protein, molecular dynamics, simulations, MD
Published: 12.10.2016; Views: 2574; Downloads: 173
.pdf Fulltext (2,40 MB)

Simulations of Tidal Disruption Events Observations with the LSST
Katja Bricman, 2017, master's thesis

Abstract: The Large Synoptic Survey Telescope (LSST) will produce a multi-colour survey of 25000 square deg of the Southern sky during its 10 years of operations. It will observe over 20 billion galaxies and a similar number of stars, map the Solar System and the Milky Way, and probe dark matter and dark energy. In addition, it will discover thousands of transients every night, including new classes of objects, which have not yet been observed. Due to its large coverage of the sky it will be a perfect tool for the search of rare Tidal Disruption Events (TDEs), which occur when a star passes close by a supermassive black hole and gets disrupted by its tidal force. Afterwards the stellar debris fall back to the black hole, initially at a rate exceeding the Eddington rate, producing an outflow, which releases a flare of energy. When the fallback rate subsides below the Eddington rate, the gas accretes onto the black hole via accretion disk. The LSST simulation framework enables us to simulate observations of different types of objects with the LSST. In this work, we include TDEs in the LSST simulation framework, estimate the number of detected TDEs, and simulate their light curves using a theoretical model, which predicts a t^(-2.6) light curve decline with time in the outflow phase and a t^{-0.4} decline in the disk phase. We also take a closer look at the distribution of the detected TDEs over cosmological redshift and black hole mass.
Found in: ključnih besedah
Keywords: Astronomical observations, Large Synoptic Survey Telescope, Tidal Disruption Events, Black Holes, simulations
Published: 17.10.2017; Views: 2383; Downloads: 0
.pdf Fulltext (8,73 MB)

Performance of the Cherenkov Telescope Array
Marko Zavrtanik, Danilo Zavrtanik, Gabrijela Zaharijas, Lili Yang, Serguei Vorobiov, Samo Stanič, Gašper Kukec Mezek, Christopher Eckner, G. Maier, 2017, published scientific conference contribution

Found in: ključnih besedah
Summary of found: ...CTA, Monte Carlo simulations, gamma rays...
Keywords: CTA, Monte Carlo simulations, gamma rays
Published: 16.02.2018; Views: 1614; Downloads: 99
.pdf Fulltext (321,78 KB)

Bora wind effects on common structures in the Vipava valley
Marija Bervida, 2020, doctoral dissertation

Abstract: Strong and gusty north-east wind called Bora is common in south-west regions of Slovenia, as well as along the Adriatic coast. Its intermittent behavior, related to variable strength, frequency and duration, has brought out scientific curiosity for decades. Bora affects human life and causes problems for structures built in Bora affected areas. In Slovenia, Bora is the strongest in the Vipava valley. The motivation for this research is the need to evaluate Bora wind effects on structures, commonly found in the Vipava valley region, using a high resolution computational fluid dynamics (CFD) modeling approach. To date, there are several experimental and computational constraints for accurate representation of Bora in a CFD model, therefore, the main aim of this dissertation is to build foundations for Bora wind simulations using CFD and its method of finite volumes. The dissertation incorporates the analysis of experimental measurements of Bora wind, as well as numerical modeling studies. Vertical mean wind speed profile characteristics of Bora were analyzed based on experimental measurements at Razdrto just above the Vipava valley. The obtained results contributed to the choice of Bora mean wind profiles applied at the inflow of computational models. Guidelines regarding the choice of the associated wind profile parameters were given and a new relationship between these parameters was found. As orographic barriers to the north of the Vipava valley are known to give rise to Bora and to define the specific properties of the Bora flow, numerical modeling studies were in the first place focused on the implementation of the real-scale complex terrain into a CFD model. Simulation of wind flow over orographic barrier in Vipava valley was performed using Raynolds averaged Navier-Stokes approach, providing a first estimation of the flow field over a small hill of Zemono. As resolving the turbulence characteristics of Bora is very important for the estimation of wind loads on structures, modeling studies converged towards a more appropriate approach - Large eddy simulations (LES). A crucial step in setting up an accurate LES is the generation of appropriate inflow, which was investigated for the case of atmospheric boundary layer (ABL) flow. The synthetic method PRFG^3 for the generation of unsteady inflow was tested and adapted as a source of an ABL flow with desired turbulence flow properties. Based on its performance, in particular on adequate reproduction of target turbulence intensities and length scales, it was found that PRFG^3 method may be used to generate velocity inflow with desired turbulence properties in LES. Finally, simulations of wind flow coming from Bora direction over the Vipava valley were performed with the aim to depict the effects of underlying orography on the flow within and above the valley. Modeling results were found to be comparable with the results of lidar based remote sensing of vertical atmospheric structures within and above the valley.
Found in: ključnih besedah
Summary of found: to build foundations for Bora wind simulations using CFD and its method of finite volumes....
Keywords: Vipava valley, Bora wind, Wind profile, Orography, Atmospheric boundary layer, Computational fluid dynamics, Numerical simulations
Published: 17.06.2020; Views: 1832; Downloads: 16
.pdf Fulltext (35,12 MB)

Studying TDEs in the era of LSST
Katja Bricman, Andreja Gomboc, 2019, published scientific conference contribution abstract

Found in: ključnih besedah
Summary of found: TDE light curves. Here we present simulations of TDE observations using an end-to-end LSST...
Keywords: The observing strategy with continuous scanning and large sky coverage of the upcoming ground-based Large Synoptic Survey Telescope (LSST) will make it a perfect tool in search of rare transients, such as Tidal Disruption Events (TDEs). Bright optical flares resulting from tidal disruption of stars by their host supermassive black hole (SMBH) can provide us with important information about the mass of the SMBH involved in the disruption and thus enable the study of quiescent SMBHs, which represent a large majority of SMBHs found in centres of galaxies. These types of transients are extremely rare, with only about few tens of candidates discovered so far. It is expected that the LSST will provide a large sample of new TDE light curves. Here we present simulations of TDE observations using an end-to-end LSST simulation framework. Based on the analysis of simulated light curves we estimate the number of TDEs with good quality light curves the LSST is expected to discover in 10 years of observations. In addition, we investigate whether TDEs observed by the LSST could be used to probe the SMBH mass distribution in the universe. The participation at this conference is supported by the Action CA16104 Gravitational waves, black holes and fundamental physics (GWverse), supported by COST (European Cooperation in Science and Technology).
Published: 04.01.2021; Views: 782; Downloads: 0

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