1. Simulating Cherenkov Telescope Array observation of RX J1713.7-3946Marko Zavrtanik, Danilo Zavrtanik, Gabrijela Zaharijas, Lili Yang, Serguei Vorobiov, Samo Stanič, Gašper Kukec Mezek, Andrej Filipčič, T. Nakamori, 2015, objavljeni znanstveni prispevek na konferenci Najdeno v: ključnih besedah Ključne besede: Cherenkov Telescope Array (CTA), supernova remnants, very high-energy (VHE) gamma-ray emission, RX J1713.7–3946, Monte Carlo simulations Objavljeno: 11.03.2016; Ogledov: 4178; Prenosov: 224 Polno besedilo (190,15 KB) |
2. From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang–Landau approach2016, izvirni znanstveni članek Opis: 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. Najdeno v: ključnih besedah Povzetek najdenega: ...Wang-Landau approach, Monte-Carlo simulations, proteins, secondary structures... Ključne besede: Wang-Landau approach, Monte-Carlo simulations, proteins, secondary structures Objavljeno: 04.05.2016; Ogledov: 3423; Prenosov: 0 Polno besedilo (10,13 MB) |
3. Distance-based configurational entropy of proteins from molecular dynamics simulationsFederico Fogolari, Alessandra Corazza, Sara Fortuna, Miguel Angel Soler, Bryan VanSchouwen, Giorgia Brancolini, Stefano Corni, Giuseppe Melacini, Gennaro Esposito, 2015, izvirni znanstveni članek Opis: 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. Najdeno v: ključnih besedah Ključne besede: entropy, protein, molecular dynamics, simulations, MD Objavljeno: 12.10.2016; Ogledov: 3574; Prenosov: 215 Polno besedilo (2,40 MB) |
4. Studies towards an understanding of global array pointing for the Cherenkov Telescope ArrayMarko Zavrtanik, Danilo Zavrtanik, Gabrijela Zaharijas, Lili Yang, Serguei Vorobiov, Samo Stanič, Gašper Kukec Mezek, Andrej Filipčič, Stefan Eschbach, 2015, objavljeni znanstveni prispevek na konferenci Najdeno v: ključnih besedah Ključne besede: Cherenkov Telescope Array (CTA), CTA global array pointing, point-source location accuracy, Monte Carlo simulations Objavljeno: 26.01.2017; Ogledov: 3358; Prenosov: 240 Polno besedilo (310,22 KB) |
5. Second large-scale Monte Carlo study for the Cherenkov Telescope ArrayMarko Zavrtanik, Danilo Zavrtanik, Gabrijela Zaharijas, Lili Yang, Serguei Vorobiov, Samo Stanič, Gašper Kukec Mezek, Andrej Filipčič, T. Hassan, 2015, objavljeni znanstveni prispevek na konferenci Najdeno v: ključnih besedah Ključne besede: Cherenkov Telescope Array (CTA), CTA design optimization, Monte Carlo simulations Objavljeno: 16.02.2017; Ogledov: 3265; Prenosov: 196 Polno besedilo (341,65 KB) |
6. Simulations of Tidal Disruption Events Observations with the LSSTKatja Bricman, 2017, magistrsko delo Opis: 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. Najdeno v: ključnih besedah Ključne besede: Astronomical observations, Large Synoptic Survey Telescope, Tidal Disruption Events, Black Holes, simulations Objavljeno: 17.10.2017; Ogledov: 3627; Prenosov: 0 Polno besedilo (8,73 MB) |
7. The ARCADE Raman Lidar and atmospheric simulations for the Cherenkov Telescope ArrayMarko Zavrtanik, Danilo Zavrtanik, Gabrijela Zaharijas, Lili Yang, Serguei Vorobiov, Samo Stanič, Gašper Kukec Mezek, Christopher Eckner, L. Valore, 2017, objavljeni znanstveni prispevek na konferenci Najdeno v: ključnih besedah Ključne besede: ARCADE Raman Lidar, CTA, atmospheric simulations Objavljeno: 16.02.2018; Ogledov: 2597; Prenosov: 144 Polno besedilo (750,13 KB) |
8. Performance of the Cherenkov Telescope ArrayMarko Zavrtanik, Danilo Zavrtanik, Gabrijela Zaharijas, Lili Yang, Serguei Vorobiov, Samo Stanič, Gašper Kukec Mezek, Christopher Eckner, G. Maier, 2017, objavljeni znanstveni prispevek na konferenci Najdeno v: ključnih besedah Povzetek najdenega: ...CTA,
Monte Carlo simulations,
gamma rays... Ključne besede: CTA, Monte Carlo simulations, gamma rays Objavljeno: 16.02.2018; Ogledov: 2523; Prenosov: 132 Polno besedilo (321,78 KB) |
9. Bora wind effects on common structures in the Vipava valleyMarija Bervida, 2020, doktorska disertacija Opis: 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. Najdeno v: ključnih besedah Povzetek najdenega: ...is to build foundations for Bora wind simulations using CFD and its method of finite
volumes.... Ključne besede: Vipava valley, Bora wind, Wind profile, Orography, Atmospheric boundary layer, Computational fluid dynamics, Numerical simulations Objavljeno: 17.06.2020; Ogledov: 3931; Prenosov: 44 Polno besedilo (35,12 MB) |
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