| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
- Koci, L., et al.
(författare)
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Simulation of shock-induced melting of Ni using molecular dynamics coupled to a two-temperature model
- 2006
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 74:1
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Tidskriftsartikel (refereegranskat)abstract
- Using nonequilibrium molecular dynamics (MD) simulations we study shock-induced melting in Ni with an embedded atom method (EAM). Dynamic melting is probed by the pair correlation function, and we find a melting lattice temperature of T-melt=6400 +/- 300 K for a melting pressure of P-melt=275 +/- 10 GPa. When a combined MD+TTM (two-temperature model) approach is used to include electronic heat conduction and electron-phonon coupling, P-melt and T-melt change. For a given pressure, the temperature behind the shock decreases due to electronic heat diffusion into the cold, unshocked material. This cooling of the material behind the shock slightly increases the melting pressure compared to simulations without electronic heat conduction and electron-phonon coupling. The decrease in the temperature behind the shock front is enhanced if the electron-phonon coupling is artificially made larger. We also explore the feasibility of using x-ray diffraction to detect melting.
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| 3. |
- Ruestes, C. J., et al.
(författare)
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Atomistic simulation of tantalum nanoindentation: Effects of indenter diameter, penetration velocity, and interatomic potentials on defect mechanisms and evolution
- 2014
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Ingår i: Materials Science & Engineering A: Structural Materials: Properties, Microstructure and Processing. - : Elsevier BV. - 0921-5093. ; 613, s. 390-403
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Tidskriftsartikel (refereegranskat)abstract
- Nanoindentation simulations are a helpful complement to experiments. There is a dearth of nanoindentation simulations for bcc metals, partly due to the lack of computationally efficient and reliable interatomic potentials at large strains. We carry out indentation simulations for bcc tantalum using three different interatomic potentials and present the defect mechanisms responsible for the creation and expansion of the plastic deformation zone: twins are initially formed, giving rise to shear loop expansion and the formation of sequential prismatic loops. The calculated elastic constants as function of pressure as well as stacking fault energy surfaces explain the significant differences found in the defect structures generated for the three potentials investigated in this study. The simulations enable the quantification of total dislocation length and twinning fraction. The indenter velocity is varied and, as expected, the penetration depth for the first pop-in (defect emission) event shows a strain rate sensitivity m in the range of 0.037-0.055. The effect of indenter diameter on the first pop-in is discussed. A new intrinsic length-scale model is presented based on the profile of the residual indentation and geometrically necessary dislocation theory.
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