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11.
Performance of the Cherenkov Telescope Array
G. Maier, Christopher Eckner, Gašper Kukec Mezek, Samo Stanič, Serguei Vorobiov, Lili Yang, Gabrijela Zaharijas, Danilo Zavrtanik, Marko Zavrtanik, 2017, published scientific conference contribution

Keywords: CTA, Monte Carlo simulations, gamma rays
Published in RUNG: 16.02.2018; Views: 3147; Downloads: 138
.pdf Full text (321,78 KB)

12.
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.
Keywords: Astronomical observations, Large Synoptic Survey Telescope, Tidal Disruption Events, Black Holes, simulations
Published in RUNG: 17.10.2017; Views: 4234; Downloads: 0
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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.
Keywords: entropy, protein, molecular dynamics, simulations, MD
Published in RUNG: 12.10.2016; Views: 4188; Downloads: 221
.pdf Full text (2,40 MB)

16.
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.
Keywords: Wang-Landau approach, Monte-Carlo simulations, proteins, secondary structures
Published in RUNG: 04.05.2016; Views: 4059; Downloads: 0
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