Demir K. | Kiliç N. | Dudak F.C. | Boyaci I.H. | Yaşar F.

Article | 2014 | Molecular Simulation40 ( 13 ) , pp.1015 - 1025

The conformational states of two peptide sequences that bind to staphylococcal enterotoxin B are sampled by replica exchange molecular dynamic (REMD) simulations in explicit water. REMD simulations were treated with 52 replicas in the range of 280-501 K for both peptides. The conformational ensembles of both peptides are dominated by random coil, bend and turn structures with a small amount of helical structures for each temperature. In addition, while an insignificant presence of ß-bridge structures were observed for both peptides, the ß-sheet structure was observed only for peptide 3. The results obtained from simulations at 300 K . . . are consistent with the experimental results obtained from circular dichroism spectroscopy. From the analysis of REMD results, we also calculated hydrophobic and hydrophilic solvent accessible surface areas for both peptides, and it was observed that the hydrophobic segments of the peptides tend to form bend or turn structures. Moreover, the free-energy landscapes of both peptides were obtained by principal component analysis to understand how the secondary structural properties change according to their complex space. From the free-energy analysis, we have found several minima for both peptides at decreased temperature. For these obvious minima of both peptides, it was observed that the random coil, bend and turn structures are still dominant and the helix, ß-bridge or ß-sheet structures can appear or disappear with respect to minima. On the other hand, when we compare the results of REMD with conventional MD simulations for these peptides, the configurations of peptide 3 might be trapped in energy minima during the conventional MD simulations. Hence, it can be said that the REMD simulations have provided a sufficiently high sampling efficiency. © 2013 © 2013 Taylor & Francis Daha fazlası Daha az

Garip A.K.

Article | 2019 | Molecular Simulation45 ( 13 ) , pp.1004 - 1013

In this study, the classical molecular dynamics simulations in canonical ensemble conditions (NVT) were used to investigate the dynamical properties of trimetallic Pd–Pt–Ag nanoalloy clusters with the interatomic interactions modelled by the Gupta many-body potential. The optimisations for best homotops were performed using the basin-hopping algorithm for 55 atom icosahedral PdnAg(42-n)Pt13 trimetallic clusters. We performed optimisations to search the best chemical ordering of icosahedron structure not allowing any geometric changes. The icosahedron structures which are the best homotops have a core-shell segregation. The obtained . . .icosahedral structures with best homotops were taken as the initial configurations for MD simulations. The temperature ranges were explored which the surface sites of the clusters stay thermally stable. We estimated the melting temperatures of PdnAg(42-n)Pt13 trimetallic clusters using caloric curves and Lindemann parameters. No simple correlation between alloy composition and melting temperatures was determined. The Pd35Ag7Pt13 composition has the highest melting temperature, however, the Pd21Ag21Pt13 is the most stable composition according to the relative stability investigation. The simulation results showed that the melting of all PdnAg(42-n)Pt13 clusters takes place as a whole without any surface premelting. © 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group Daha fazlası Daha az