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Use this search facility to find out more about the profile of our HPC-Europa2 visitors, the type of work they have been doing, and their project achievements.
The mechanical properties of FeCr alloys heavily rely on atomic distribution and can be affected by phenomena such as Cr precipitation. While precipitation of FeCr alloys of various Cr concentrations had been studied before, dissolution of already existing Cr precipitates in FeCr alloys, had not; this was the focus of this study. Our means of investigation was MD computer simulation using the parallel code PARCAS and a 2-band EAM potential. We set up a number of configurations of FeCr alloys containing Cr precipitates of various sizes embedded in matrices of either pure Fe or with a 15% random Cr distribution, and examined their behaviour after thermal aging at T ranging between 600-2000K. The T range was selected so that it would include the (α+α’)-α transition in the standard FeCr phase diagram.
High T results provide insight to the mechanisms that govern the dissolution: Cr precipitates dissolve by vacancy exchange, leading to a random distribution of Cr atoms in an Fe matrix, as the short-range order parameter shifts from a positive value (clustering) to zero (random atomic arrangement). Precipitates at lower T seem to be stable, in agreement with previous experimental and simulation studies that challenge the standard phase diagram’s reliability.
The objective of this study is description of turbulent flow characteristics over realistic complex terrain by means of numerical simulation. Bolund hill in Denmark, the subject of a recent full-scale measurement campaign was considered topography in this study. The flow over Bolund hill has been computed using structured finite-volume Navier-Stokes code. Turbulence was accounted using Reynolds averaged Navier-Stokes (RANS) models, as well as with hybrid of RANS models and Large Eddy Simulation (RANS/LES). The applications of results are connected with energy production (siting of wind farms), prediction of pollutant dispersion, prediction of wind loads on stuctures etc.The study leads to new insights into modeling strategies for turbulent environmental flows.
During the project specialised code have been developed for manipulation of large topography data files like the one provided by RISO laboratory for Bolund hill case. The accuracy of interpolation methods offered in comercial packages (like Golden Software "Surfer") is not satisfactory so more accurate interpolation based on Lagrangian polinomials in two dimensions is implemented. Inlet boundary condition were special point of interest during the project. Different strategies of prescribing inlet conditions and approaches to pre-simulation were studied. Different approaches to wall modeling of turbulence in the case of atmospheric flow is tested. Future research will be concentrated with comparison of results from different modeling approaches. During this phase of research experimental results from Bolund hill experiment have not been made publicly available, so validation of obtained simulation results is also planned.
Central to this project are the antimicrobial peptides (AMPs) – short amphipathic positively charged membrane proteins isolated from various lower organisms. AMPs attract ample medical interest as an alternative in overcoming the bacterial resistance to antibiotics. This is due to the fact that they do not bind to specific receptors; instead, it is believed that they defend the organism by means of selective violation of the target cell membrane integrity, leaving the host undamaged. It is considered that the AMPs disrupt the lipid component of the membranes, their cationic character facilitating their binding to the anionic bacterial cell membrane. Nonetheless, the mechanism of binding to the target and subsequent destruction is not fully understood and is peptide-dependent. Molecular dynamics (MD) simulations are a suitable approach for unveiling the mechanism of action of AMPs upon contact with the cell membrane surface. The elucidation of the mechanism of interaction of Protegrin with lipids from the cell membrane necessitates investigation of systems, which are at least an order of magnitude larger than the current models employed, making the all-atom approach inapplicable. In order to overcome this limitation, coarse-grained (CG) treatment is required. This project focuses on the development of an efficient coarse-grained (CG) model for description of the interaction of AMPs with membrane lipids allowing reliable simulation of the AMPs’ permeabilization mechanism. Other project aims include the establishment of the pore properties at a multi-scale level and the study of the poration mechanism of the Protegrin peptides.
The objectives of the project have been fully achieved. For explanation of the mechanism of interaction of Protegrin with membrane lipids, coarse-grained MD simulations of 8 peptides placed above a bilayer containing 256 DLPC were performed with the modified MARTINI force field. The system is simulated for 10 ms with 20 fs time step without restraints in NPT ensemble in periodic boundary conditions at 323 K maintained by a Berendsen thermostat. During the MD simulations Protegrin forms a toroidal pore, which corresponds well to the experimentally exposed poration mechanism based on NMR measurements. Once formed, the pore was stable and remained largely unchanged. Estimation of the pore size and other pore features important for the investigation of the pore formation as water penetration and depth of insertion of peptides is made. The changes in the lipid bilayer are discussed based on inspection of the lipid tails order parameters and bilayer thickness.