| 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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