| 1. |
|
|
| 2. |
- Otto, Thomas D., et al.
(författare)
-
A comprehensive evaluation of rodent malaria parasite genomes and gene expression
- 2014
-
Ingår i: BMC Biology. - : BioMed Central. - 1741-7007. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function.RESULTS: We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the 'Plasmodium interspersed repeat genes' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family.CONCLUSIONS: Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
|
|
| 3. |
|
|
| 4. |
- Ruestes, C. J., et al.
(författare)
-
Atomistic simulation of tantalum nanoindentation: Effects of indenter diameter, penetration velocity, and interatomic potentials on defect mechanisms and evolution
- 2014
-
Ingår i: Materials Science & Engineering A: Structural Materials: Properties, Microstructure and Processing. - : Elsevier BV. - 0921-5093. ; 613, s. 390-403
-
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.
|
|
| 5. |
- Li, Shunyi, et al.
(författare)
-
Intrinsic energy band alignment of functional oxides
- 2014
-
Ingår i: Physica Status Solidi - Rapid Research Letetrs. - : Wiley. - 1862-6254 .- 1862-6270. ; 8:6, s. 571-576
-
Tidskriftsartikel (refereegranskat)abstract
- The energy band alignment at interfaces between different materials is a key factor, which determines the function of electronic devices. While the energy band alignment of conventional semiconductors is quite well understood, systematic experimental studies on oxides are still missing. This work presents an extensive study on the intrinsic energy band alignment of a wide range of functional oxides using photoelectron spectroscopy with in-situ sample preparation. The studied materials have particular technological importance in diverse fields as solar cells, piezotronics, multiferroics, photoelectrochemistry and oxide electronics. Particular efforts have been made to verify the validity of transitivity, in order to confirm the intrinsic nature of the obtained band alignment and to understand the underlying principles. Valence band offsets up to 1.6 eV are observed. The large variation of valence band maximum energy can be explained by the different orbital contributions to the density of states in the valence band. The framework provided by this work enables the general understanding and prediction of energy band alignment at oxide interfaces, and furthermore the tailoring of energy level matching for charge transfer in functional oxides. (C) 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
|
|
| 6. |
- Sadigh, B., et al.
(författare)
-
Scalable parallel Monte Carlo algorithm for atomistic simulations of precipitation in alloys
- 2012
-
Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 85:18
-
Tidskriftsartikel (refereegranskat)abstract
- We present an extension of the semi-grand-canonical (SGC) ensemble that we refer to as the variance-constrained semi-grand-canonical (VC-SGC) ensemble. It allows for transmutation Monte Carlo simulations of multicomponent systems in multiphase regions of the phase diagram and lends itself to scalable simulations on massively parallel platforms. By combining transmutation moves with molecular dynamics steps, structural relaxations and thermal vibrations in realistic alloys can be taken into account. In this way, we construct a robust and efficient simulation technique that is ideally suited for large-scale simulations of precipitation in multicomponent systems in the presence of structural disorder. To illustrate the algorithm introduced in this work, we study the precipitation of Cu in nanocrystalline Fe.
|
|
| 7. |
- Erhart, Paul, 1978, et al.
(författare)
-
Efficacy of the DFT plus U formalism for modeling hole polarons in perovskite oxides
- 2014
-
Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 90:3, s. 035204-
-
Tidskriftsartikel (refereegranskat)abstract
- We investigate the formation of self-trapped holes (STH) in three prototypical perovskites (SrTiO3, BaTiO3, PbTiO3) using a combination of density functional theory (DFT) calculations with local potentials and hybrid functionals. First we construct a local correction potential for polaronic configurations in SrTiO3 that is applied via the DFT + U method and matches the forces from hybrid calculations. We then use the DFT + U potential to search the configuration space and locate the lowest energy STH configuration. It is demonstrated that both the DFT + U potential and the hybrid functional yield a piecewise linear dependence of the total energy on the occupation of the STH level, suggesting that self-interaction effects have been properly removed. The DFT + U model is found to be transferable to BaTiO3 and PbTiO3, and STH formation energies from DFT + U and hybrid calculations are in close agreement for all three materials. STH formation is found to be energetically favorable in SrTiO3 and BaTiO3 but not in PbTiO3, which can be rationalized by considering the alignment of the valence band edges on an absolute energy scale. In the case of PbTiO3 the strong coupling between Pb 6s and O 2p states lifts the valence band minimum (VBM) compared to SrTiO3 and BaTiO3. This reduces the separation between VBM and STH level and renders the STH configuration metastable with respect to delocalization (band hole state). We expect that the present approach can be adapted to study STH formation also in oxides with different crystal structures and chemical compositions.
|
|
| 8. |
- Erhart, Paul, 1978, et al.
(författare)
-
Quasiparticle spectra, absorption spectra, and excitonic properties of NaI and SrI2 from many-body perturbation theory
- 2014
-
Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 89:7, s. art no 075132 -
-
Tidskriftsartikel (refereegranskat)abstract
- We investigate the basic quantum-mechanical processes behind the nonproportional response of scintillators to incident radiation responsible for reduced resolution. For this purpose, we conduct a comparative first-principles study of quasiparticle spectra on the basis of the G(0)W(0) approximation as well as absorption spectra and excitonic properties by solving the Bethe-Salpeter equation for two important systems, NaI and SrI2. The former is a standard scintillator material with well-documented nonproportionality, while the latter has recently been found to exhibit a very proportional response. We predict band gaps for NaI and SrI2 of 5.5 and 5.2 eV, respectively, in good agreement with experiment. Furthermore, we obtain binding energies for the ground state excitons of 216 meV for NaI and 195 +/- 25 meV for SrI2. We analyze the degree of exciton anisotropy and spatial extent by means of a coarse-grained electron-hole pair-correlation function. Thereby, it is shown that the excitons in NaI differ strongly from those in SrI2 in terms of structure and symmetry, even if their binding energies are similar. Furthermore, we show that quite unexpectedly the spatial extents of the highly-anisotropic low-energy excitons in SrI2 in fact exceed those in NaI by a factor of two to three in terms of the full width at half maxima of the electron-hole pair-correlation function.
|
|
| 9. |
- Genenko, Y.A., et al.
(författare)
-
Potential barrier at the ferroelectric grain boundary due to asymmetric screening of depolarization fields
- 2012
-
Ingår i: Proceedings of 2012 21st IEEE Int. Symp. on Applications of Ferroelectrics held jointly with 11th IEEE European Conference on the Applications of Polar Dielectrics and IEEE PFM, ISAF/ECAPD/PFM 2012, Aveiro;9 July 2012 through 13 July 2012. - 1099-4734. - 9781467326681 ; :Article number 6297727, s. 1-4
-
Konferensbidrag (refereegranskat)abstract
- Electric depolarization fields generated by a stripe domain structure in ferroelectrics are considered within a semiconductor model. Field screening due to electronic band bending and due to presence of intrinsic defects leads to the building of asymmetric space charge regions near the grain boundary. This in turn results in the formation of a potential barrier between the grain surface and its interior.
|
|
| 10. |
- Genenko, Y.A., et al.
(författare)
-
Surface potential at a ferroelectric grain due to asymmetric screening of depolarization fields
- 2014
-
Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 115:10
-
Tidskriftsartikel (refereegranskat)abstract
- Nonlinear screening of electric depolarization fields, generated by a stripe domain structure in a ferroelectric grain of a polycrystalline material, is studied within a semiconductor model of ferroelectrics. It is shown that the maximum strength of local depolarization fields is rather determined by the electronic band gap than by the spontaneous polarization magnitude. Furthermore, field screening due to electronic band bending and due to presence of intrinsic defects leads to asymmetric space charge regions near the grain boundary, which produce an effective dipole layer at the surface of the grain. This results in the formation of a potential difference between the grain surface and its interior of the order of 1V, which can be of either sign depending on defect transition levels and concentrations. Exemplary acceptor doping of BaTiO3 is shown to allow tuning of the said surface potential in the region between 0.1 and 1.3V. (C) 2014 AIP Publishing LLC.
|
|
