| 1. |
- Elsik, Christine G., et al.
(author)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Journal article (peer-reviewed)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 2. |
- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)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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| 3. |
- Carvalho, A., et al.
(author)
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Identification of the local vibrational modes of small nitrogen clusters in dilute GaAsN
- 2007
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In: Physica. B, Condensed matter. - : Elsevier BV. - 0921-4526 .- 1873-2135. ; 401-402, s. 339-342
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Journal article (peer-reviewed)abstract
- Ultra-high-resolution infra-red local vibrational mode (IR LVM) spectroscopy measurements together with density-functional calculations have been used to identify the signatures of close substitutional nitrogen (NAs) pairs in GaAs1 - x Nx alloys with concentrations of x < 0.025. We show that the presence of sub-peaks close to the NAs absorption band can be attributed to nitrogen pairs up to fourth neighbor position. Additionally, we suggest that the nitrogen pairs which give rise to the deepest levels below the conduction band edge are the first to be removed upon annealing
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| 4. |
- Carvalho, A., et al.
(author)
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Density-functional theory study of Au, Ag and Cu defects in germanium
- 2008
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In: Materials Science in Semiconductor Processing. - : Elsevier BV. - 1369-8001 .- 1873-4081. ; 11:5, s. 340-343
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Journal article (peer-reviewed)abstract
- Gold, silver and copper defects in germanium are modeled using density functional theory. The structures and electrical properties of the substitutional metals are calculated in excellent agreement with experiment. Interstitial Au, Ag and Cu are found to be shallow donors, in disagreement with a previous assignment of Cui to a hole trap in the lower half of the gap. Substitutional-interstitial metal (Mi - Ms) pairs and metal-vacancy pairs (Ms - V) are also investigated.
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| 5. |
- Carvalho, A, et al.
(author)
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First-principles study of the diffusion mechanisms of the self-interstitial in germanium
- 2008
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In: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 20:13
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Journal article (peer-reviewed)abstract
- The self-interstitial in germanium can assume multiple configurations depending on the temperature and charge state. Here, we employ a first-principles density functional method to investigate the diffusion mechanisms of this defect. The energy barriers associated with the transformation between different structures are determined by the climbing nudged elastic band method, as a function of the charge state. The relation between the thermodynamic properties of the self-interstitial and the temperature evolution of electron radiation damage in germanium are discussed.
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| 6. |
- Carvalho, A., et al.
(author)
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Local-density-functional calculations of the vacancy-oxygen center in Ge
- 2007
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In: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 75:11
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Journal article (peer-reviewed)abstract
- We carry out a comprehensive density-functional study of the vacancy-oxygen (VO) center in germanium using large H-terminated Ge clusters. The importance of a nonlinear core correction to account for the involvement of the 3d electrons in Ge-O bonds is discussed. We calculate the electrical levels and the vibrational modes of VO0, VO-, and VO= finding close agreement with experiment. We also explore the reorientation, migration, and dissociation mechanisms of neutral and negatively charged VO and compare the calculated energy barriers with experimental data. We conclude that the defect is likely to anneal through both mechanisms.
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| 7. |
- Carvalho, A., et al.
(author)
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Oxygen defects in irradiated germanium
- 2007
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In: Journal of materials science. Materials in electronics. - : Springer Science and Business Media LLC. - 0957-4522 .- 1573-482X. ; 18:7, s. 781-786
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Journal article (peer-reviewed)abstract
- The defects present in oxygen-rich irradiated germanium have been extensively characterised from an experimental point of view. Here, we summarise recent theoretical findings obtained using the cluster method and discuss their relation with the experimental data. In order to find a microscopic interpretation of the reactions taking place in this material upon annealing up to 400°C, we performed nudged elastic band (NEB) calculations of the migration and dissociation paths of VO, as well as a modelling of other oxygen-related complexes that are expected to form in this temperature range. Energy barriers of 1.5 (1.1) eV and 1.2 (0.9) eV for the dissociation and migration of the neutral (negatively charged) VO defect are found. We compare these with the activation energies estimated from the analysis of Hall effect, deep level transient spectroscopy (DLTS) and infra-red (IR) spectroscopy annealing data reported in literature.
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| 8. |
- Carvalho, A., et al.
(author)
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Primary defects in n-type irradiated germanium : a first-principles investigation
- 2008
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In: Solid State Phenomena. - 1012-0394 .- 1662-9779. ; 131-133, s. 253-258
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Journal article (peer-reviewed)abstract
- The properties of point defects introduced by low temperature electron irradiation of germanium are investigated by first-principles modeling. Close Frenkel pairs, including the metastable fourfold coordinated defect, are modelled and their stability is discussed. It is found that damage evolution upon annealing below room temperature can be consistently explained with the formation of correlated interstitial-vacancy pairs if the charge-dependent properties of the vacancy and self-interstitial are taken into account. We propose that Frenkel pairs can trap up to two electrons and are responsible for conductivity loss in n-type Ge at low temperatures.
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| 9. |
- Carvalho, A., et al.
(author)
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Self-interstitial in germanium
- 2007
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 99:17, s. 175502-
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Journal article (peer-reviewed)abstract
- Low-temperature radiation damage in n- and p-type Ge is strikingly different, reflecting the charge-dependent properties of vacancies and self-interstitials. We find, using density functional theory, that in Ge the interstitial is bistable, preferring a split configuration when neutral and an open cage configuration when positively charged. The split configuration is inert while the cage configuration acts as a double donor. We evaluate the migration energies of the defects and show that the theory is able to explain the principal results of low-temperature electron-irradiation experiments.
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| 10. |
- Carvalho, A., et al.
(author)
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Self-interstitials and Frenkel pairs in electron-irradiated germanium
- 2007
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In: Physica. B, Condensed matter. - : Elsevier BV. - 0921-4526 .- 1873-2135. ; 401-402, s. 495-498
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Journal article (peer-reviewed)abstract
- First principles calculations were used to study the structures and electrical levels of the self-interstitial in Ge. We considered the possibility of structural changes consequent with change in charge state and show these have important implications in the mobility and electrical activity of the defect. The theoretical model is compared to the results of low temperature electron irradiation in germanium reported in the literature.
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