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- Enkovaara, J., et al.
(författare)
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Electronic structure calculations with GPAW : a real-space implementation of the projector augmented-wave method
- 2010
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Ingår i: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 22:25, s. 253202-
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Forskningsöversikt (refereegranskat)abstract
- Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, Delta SCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.
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| 3. |
- Hakkinen, K, et al.
(författare)
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Implementation of CYP2D6 copy-number imputation panel and frequency of key pharmacogenetic variants in Finnish individuals with a psychotic disorder
- 2022
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Ingår i: The pharmacogenomics journal. - : Springer Science and Business Media LLC. - 1473-1150 .- 1470-269X. ; 22:3, s. 166-172
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate that CYP2D6 copy-number variation (CNV) can be imputed using existing imputation algorithms. Additionally, we report frequencies of key pharmacogenetic variants in individuals with a psychotic disorder from the genetically bottle-necked population of Finland. We combined GWAS chip and CYP2D6 CNV data from the Breast Cancer Pain Genetics study to construct an imputation panel (n = 902) for CYP2D6 CNV. The resulting data set was used as a CYP2D6 CNV imputation panel in 9262 non-related individuals from the SUPER-Finland study. Based on imputation of 9262 individuals we confirm the higher frequency of CYP2D6 ultrarapid metabolizers and a 22-fold enrichment of the UGT1A1 decreased function variant rs4148323 (UGT1A1*6) in Finland compared with non-Finnish Europeans. Similarly, the NUDT15 variant rs116855232 was highly enriched in Finland. We demonstrate that imputation of CYP2D6 CNV is possible and the methodology enables studying CYP2D6 in large biobanks with genome-wide data.
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| 7. |
- Hakkinen, E., et al.
(författare)
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Online measurement of highly oxygenated compounds from organic aerosol
- 2023
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 16:6, s. 1705-1721
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Tidskriftsartikel (refereegranskat)abstract
- Highly oxygenated compounds are important contributors to the formation and growth of atmospheric organic aerosol and thus have an impact on Earth's radiation balance and global climate. However, knowledge of the contribution of highly oxygenated compounds to organic aerosol and their fate after condensing into the particle phase has been limited by the lack of suitable detection techniques. Here, we present a new online method for measuring highly oxygenated compounds from organic aerosol. The method includes thermal evaporation of particles in a new inlet, the vaporization inlet for aerosols (VIA), followed by identification of the evaporated highly oxygenated compounds by a nitrate chemical ionization mass spectrometer (NO3-CIMS). The method does not require sample collection, enabling highly time-resolved measurements of particulate compounds. We evaluate the performance of the method by measuring the detection limit and performing background measurements. We estimate a detection limit of below 1 ng m(-3) for a single compound and below 1 mu g m(-3) for SOA with the sampling setup used here. These detection limits can be improved upon by optimizing the flow setup. Furthermore, we detect hundreds of particulate highly oxygenated compounds from organic aerosol generated from different precursors. Our results are consistent with previous studies showing that the volatility of organic compounds decreases with increasing m/z ratio and level of oxygenation and that organic aerosol consists of monomers and oligomeric compounds. By comparing the gas- and particle-phase compounds, we found indications of potential particle-phase reactions occurring in organic aerosol. Future work will focus both on further improving the sampling design and on better understanding the evaporation dynamics of the system, but already these initial tests show that the VIA coupled to the NO3-CIMS is a promising method for investigating the transformations and fate of the compounds after condensing into the particle phase.
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| 8. |
- Hong, J., et al.
(författare)
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Hygroscopicity, CCN and volatility properties of submicron atmospheric aerosol in a boreal forest environment during the summer of 2010
- 2014
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 14:9, s. 4733-4748
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Tidskriftsartikel (refereegranskat)abstract
- A Volatility-Hygroscopicity Tandem Differential Mobility Analyzer (VH-TDMA) was applied to study the hygroscopicity and volatility properties of submicron atmospheric aerosol particles in a boreal forest environment in Hyytiala, Finland during the summer of 2010. Aitken and accumulation mode internally mixed particles (50 nm, 75 nm and 110 nm in diameter) were investigated. Hygroscopicity was found to increase with particle size. The relative mass fraction of organics and SO42- is probably the major contributor to the fluctuation of the hygroscopicity for all particle sizes. The Cloud Condensation Nuclei Counter (CCNC)-derived hygroscopicity parameter kappa was observed to be slightly higher than kappa calculated from VH-TDMA data under sub-saturated conditions, potential reasons for this behavior are discussed shortly. Also, the size-resolved volatility properties of particles were investigated. Upon heating, more small particles evaporated compared to large particles. There was a significant amount of aerosol volume (non-volatile material) left, even at heating temperatures of 280 degrees C. Using size resolved volatility-hygroscopicity analysis, we concluded that there was always hygroscopic material remaining in the particles at different heating temperatures, even at 280 degrees C. This indicates that the observed non-volatile aerosol material did not consist solely of black carbon.
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| 10. |
- Mohammed Taha, Hiba, et al.
(författare)
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The NORMAN Suspect List Exchange (NORMAN-SLE) : facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
- 2022
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Ingår i: Environmental Sciences Europe. - : Springer. - 2190-4707 .- 2190-4715. ; 34:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/).
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