| 1. |
- Goss, J.P., et al.
(författare)
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First principles studies of H in diamond
- 2001
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Ingår i: Physica status solidi. A, Applied research. - 0031-8965 .- 1521-396X. ; 186:2, s. 263-8
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio methods are used to investigate hydrogen defects in diamond. For the isolated impurity, the bond-centered site is found lowest in energy and posses both donor and acceptor levels. The neutral defect possesses a single local mode with very small infrared effective charge, but the effective charge for the negative charge state is much larger. H+ is calculated to be very mobile with a low activation barrier. Hydrogen dimers are stable as H*2 defects which are also found to be almost IR-inactive. The complex between B and H is investigated and the activation energy for the reaction B-H → B - + H+ found to be in rasonable agreement with experiment. Hydrogen is strongly bound to dislocations which, together with H*2, may form part of the hydrogen accumulation layer detected in some plasma studies.
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| 2. |
- Goss, J. P., et al.
(författare)
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Theory of hydrogen in diamond
- 2002
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 65:11
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio cluster and supercell methods are used to investigate the local geometry and optical properties of hydrogen defects in diamond. For an isolated impurity, the bond-centered site is found to be lowest in energy, and to possess both donor and acceptor levels. The neutral defect possesses a single local mode with a very small infrared effective charge, but the effective charge for the negative charge state is much larger. H+ is calculated to be very mobile with a low activation barrier. Hydrogen dimers are stable as H2* defects, which are also found to be almost IR inactive. The complex between B and H is investigated and the activation energy for the reaction B-H→B-+H+ found to be around 1.8 eV in agreement with experiment. We also investigate complexes of hydrogen with phosphorus and nitrogen. The binding energy of H with P is too low to lead to a significant codoping effect. A hydrogen-related vibrational mode of the N-H defect, and its isotopic shifts, are close to the commonly observed 3107-cm-1 line, and we tentatively assign this center to the defect. Hydrogen is strongly bound to dislocations which, together with H2*, may form part of the hydrogen accumulation layer detected in some plasma studies.
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| 3. |
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| 4. |
- Ewels, C P, et al.
(författare)
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Shallow thermal donor defects in silicon
- 1996
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 77:5, s. 865-868
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Tidskriftsartikel (refereegranskat)abstract
- An ab initio local density functional cluster program, aimpro, is used to examine nitrogen related shallow thermal donor defects in silicon. We find the bonding of oxygen with interstitial nitrogen in Ni- O2i to be almost "normal," but the O atoms move slightly out of their bond centered sites causing the deep donor level of Ni to become shallow. The defect has properties consistent with those experimentally observed for shallow thermal donors. We also find that a CiH- O2i defect has very similar electronic properties, and suggest that shallow thermal donors do not have a unique composition.
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| 5. |
- Ewels, C.P., et al.
(författare)
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Vacancy- and acceptor-H complexes in InP
- 1996
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Ingår i: Semiconductor Science and Technology. - : IOP Publishing. - 0268-1242 .- 1361-6641. ; 11, s. 502-507
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Tidskriftsartikel (refereegranskat)abstract
- It has been suggested that iron in InP is compensated by a donor, related to the 2316 cm-1 local vibrational mode and previously assigned to the fully hydrogenated indium vacancy, VInH4. Using AIMPRO, an ab initio local density functional cluster code, we find that VInH4 acts as a single shallow donor. It has a triplet vibrational mode at around this value, consistent with this assignment. We also analyse the other hydrogenated vacancies VInHn, n = 1,3, and determine their structure, vibrational modes, and charge states. Substitutional group II impurities also act as acceptors in InP, but can be passivated by hydrogen. We investigate the passivation of beryllium by hydrogen and find that the hydrogen sits at a bond-centred site and is bonded to its phosphorus neighbour. Its calculated vibrational modes are in good agreement with experiment.
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| 6. |
- Ewels, Philip, et al.
(författare)
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A Complete Overhaul of the Electron Energy-Loss Spectroscopy and X-Ray Absorption Spectroscopy Database : eelsdb.eu
- 2016
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Ingår i: Microscopy and Microanalysis. - 1431-9276 .- 1435-8115. ; 22:3, s. 717-724
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Tidskriftsartikel (refereegranskat)abstract
- The electron energy-loss spectroscopy (EELS) and X-ray absorption spectroscopy (XAS) database has been completely rewritten, with an improved design, user interface, and a number of new tools. The database is accessible at https://eelsdb.eu/ and can now be used without registration. The submission process has been streamlined to encourage spectrum submissions and the new design gives greater emphasis on contributors' original work by highlighting their papers. With numerous new filters and a powerful search function, it is now simple to explore the database of several hundred EELS and XAS spectra. Interactive plots allow spectra to be overlaid, facilitating online comparison. An application-programming interface has been created, allowing external tools and software to easily access the information held within the database. In addition to the database itself, users can post and manage job adverts and read the latest news and events regarding the EELS and XAS communities. In accordance with the ongoing drive toward open access data increasingly demanded by funding bodies, the database will facilitate open access data sharing of EELS and XAS spectra.
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| 7. |
- Nystedt, B., et al.
(författare)
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Sarek : A portable workflow for whole-genome sequencing analysis of germline and somatic variants
- 2020
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.
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| 8. |
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| 9. |
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| 10. |
- Öberg, Sven, et al.
(författare)
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First stage of oxygen aggregation in silicon : the oxygen dimer
- 1998
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 81:14, s. 2930-2933
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Tidskriftsartikel (refereegranskat)abstract
- The structure and dynamic properties of the interstitial oxygen dimer in silicon are found using a combination of infrared spectroscopy and ab initio modeling. We find that the stable dimer consists of a pair of inequivalent weakly coupled interstitial oxygen atoms separated by a Si-Si bond. Two high frequency modes are decoupled in one 16O-18O combination but are strongly mixed in the other combination. A third lower lying mode involves the compression of the Si-Si bond joining the oxygen atoms and gives distinct modes in the mixed 16O-18O case.
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| 11. |
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| 12. |
- Bassett, Andrew R., et al.
(författare)
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Understanding functional miRNA-target interactions in vivo by site-specific genome engineering
- 2014
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4640-
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Tidskriftsartikel (refereegranskat)abstract
- MicroRNA (miRNA) target recognition is largely dictated by short 'seed' sequences, and single miRNAs therefore have the potential to regulate a large number of genes. Understanding the contribution of specific miRNA-target interactions to the regulation of biological processes in vivo remains challenging. Here we use transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technologies to interrogate the functional relevance of predicted miRNA response elements (MREs) to post-transcriptional silencing in zebrafish and Drosophila. We also demonstrate an effective strategy that uses CRISPR-mediated homology-directed repair with short oligonucleotide donors for the assessment of MRE activity in human cells. These methods facilitate analysis of the direct phenotypic consequences resulting from blocking specific miRNA-MRE interactions at any point during development.
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| 13. |
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| 14. |
- Krstic, Vojislav, et al.
(författare)
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Indirect magnetic coupling in light-element-doped single-walled carbon nanotubes
- 2010
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Ingår i: ACS Nano. - Washington, DC, USA : American Chemical Society. - 1936-0851 .- 1936-086X. ; 4:9, s. 5081-5086
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Tidskriftsartikel (refereegranskat)abstract
- Single-walled carbon nanotubes substitutionally doped with the light-element phosphorus are synthesized and are investigated by electrical and nuclear magnetic resonance measurements. Decreased spin lattice relaxation times compared to undoped tubes point toward enhanced spin-sensitive scattering. Temperature dependence of the zero-bias conductance shows step-like features, a signature of scattering from a very low density (few sites per nanotube) of localized spin moments at oxidized phosphorus sites, consistent with density functional calculations. This supports recent predictions that localized magnetic moments must be indirectly magnetically coupled through the nanotube conduction electrons.
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| 15. |
- Käller, Max, et al.
(författare)
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Cluster Flow : A user-friendly bioinformatics workflow tool
- 2016
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Ingår i: F1000 Research. - : Faculty of 1000 Ltd. - 2046-1402. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.
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| 16. |
- Patalano, Solenn, et al.
(författare)
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Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies
- 2015
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 112:45, s. 13970-13975
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Tidskriftsartikel (refereegranskat)abstract
- Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.
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| 17. |
- Rasmussen, F. Berg, et al.
(författare)
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The nitrogen-pair oxygen defect in silicon
- 1996
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Ingår i: Materials Science & Engineering. - : Elsevier BV. - 0921-5107 .- 1873-4944. ; 36:1-3, s. 91-95
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Tidskriftsartikel (refereegranskat)abstract
- The nitrogen-pair oxygen defect in silicon has been studied by infrared absorption spectroscopy on samples implanted with various combinations of 14N, 15N, 16O and 17O. The measurements give direct evidence for the involvement of nitrogen and oxygen in the defect and show that the impurity atoms comprising the defect are only weakly coupled. Ab initio cluster calculation on several models of the nitrogen-pair oxygen defect have been performed and are compared with experiment. Based on these investigations a model consisting of a bridging oxygen atom adjacent to the nitrogen pair is suggested
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| 18. |
- Rasmussen, F. Berg, et al.
(författare)
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The NNO defect in silicon
- 1995
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Ingår i: Proceedings of the 18th International Conference on Defects in Semiconductors. - : Trans Tech Publications Inc.. ; , s. 791-796
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Konferensbidrag (refereegranskat)abstract
- Nitrogen-oxygen complexes in silicon have been studied by infrared absorption spectroscopy on samples implanted with various combinations of O and N isotopes as well as O-rich samples doped with N during growth. Local vibrational modes at 805, 999 and 1030 cm-1 (14N, 16O) are directly shown to belong to a defect consisting of a N-pair interacting with an O interstitial. A recently proposed model of this NNO defect is further investigated by ab initio cluster calculations and found to account for the dynamical properties of the defect. A mode around 730 cm-1 predicted by the calculation is observed giving further support to the model.
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| 19. |
- Wagner, Philipp, et al.
(författare)
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Mechanical properties of nanosheets and nanotubes investigated using a new geometry independent volume definition
- 2013
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Ingår i: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 25:15, s. 155302-
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Tidskriftsartikel (refereegranskat)abstract
- Cross-sectional area and volume become difficult to define as material dimensions approach the atomic scale. This limits the transferability of macroscopic concepts such as Young's modulus. We propose a new volume definition where the enclosed nanosheet or nanotube average electron density matches that of the parent layered bulk material. We calculate the Young's moduli for various nanosheets (including graphene, BN and MoS2) and nanotubes. Further implications of this new volume definition such as a Fermi level dependent Young's modulus and out-of-plane Poisson's ratio are shown.
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| 20. |
- Öberg, Sven, et al.
(författare)
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Effect of functionalization and charging on resonance energy and radial breathing modes of metallic carbon nanotubes
- 2016
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Ingår i: Physical Review B. - 2469-9950 .- 2469-9969. ; 93:4
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Tidskriftsartikel (refereegranskat)abstract
- While changes in resonant Raman scattering measurements are commonly used to measure the effect of chemical functionalization on single-walled carbon nanotubes, the precise effects of functionalization on these spectra have yet to be clearly identified. In this density functional theory study, we explore the effects of functionalization on both the nanotube resonance energy and frequency shifts in radial breathing mode. Charge transfer effects cause a shift in the first Van Hove singularity spacings, and hence resonance excitation energy, and lead to a decrease in the radial breathing mode frequency, notably when the Fermi level decreases. By varying stochastically the effective mass of carbon atoms in the tube, we simulate the mass effect of functionalization on breathing mode frequency. Finally, full density functional calculations are performed for different nanotubes with varying functional group distribution and concentration using fluorination and hydrogenation, allowing us to determine overall effect on radial breathing mode and charge transfer. The results concur well with experiment, and we discuss the importance when using Raman spectroscopy to interpret experimental functionalization treatments
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