| 1. |
|
|
| 2. |
- Enkovaara, J., et al.
(författare)
-
Electronic structure calculations with GPAW : a real-space implementation of the projector augmented-wave method
- 2010
-
Ingår i: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 22:25, s. 253202-
-
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.
|
|
| 3. |
- Hakkinen, K, et al.
(författare)
-
Implementation of CYP2D6 copy-number imputation panel and frequency of key pharmacogenetic variants in Finnish individuals with a psychotic disorder
- 2022
-
Ingår i: The pharmacogenomics journal. - : Springer Science and Business Media LLC. - 1473-1150 .- 1470-269X. ; 22:3, s. 166-172
-
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.
|
|
| 4. |
|
|
| 5. |
- Bulten, W, et al.
(författare)
-
Artificial intelligence for diagnosis and Gleason grading of prostate cancer: the PANDA challenge
- 2022
-
Ingår i: Nature medicine. - : Springer Science and Business Media LLC. - 1546-170X .- 1078-8956. ; 28:21, s. 154-
-
Tidskriftsartikel (refereegranskat)abstract
- Artificial intelligence (AI) has shown promise for diagnosing prostate cancer in biopsies. However, results have been limited to individual studies, lacking validation in multinational settings. Competitions have been shown to be accelerators for medical imaging innovations, but their impact is hindered by lack of reproducibility and independent validation. With this in mind, we organized the PANDA challenge—the largest histopathology competition to date, joined by 1,290 developers—to catalyze development of reproducible AI algorithms for Gleason grading using 10,616 digitized prostate biopsies. We validated that a diverse set of submitted algorithms reached pathologist-level performance on independent cross-continental cohorts, fully blinded to the algorithm developers. On United States and European external validation sets, the algorithms achieved agreements of 0.862 (quadratically weighted κ, 95% confidence interval (CI), 0.840–0.884) and 0.868 (95% CI, 0.835–0.900) with expert uropathologists. Successful generalization across different patient populations, laboratories and reference standards, achieved by a variety of algorithmic approaches, warrants evaluating AI-based Gleason grading in prospective clinical trials.
|
|
| 6. |
- Hakkinen, S. A. K., et al.
(författare)
-
Long-term volatility measurements of submicron atmospheric aerosol in Hyytiala, Finland
- 2012
-
Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 12:22, s. 10771-10786
-
Tidskriftsartikel (refereegranskat)abstract
- The volatility of submicron atmospheric aerosol particles was investigated at a boreal forest site in Hyytiala, Finland from January 2008 to May 2010. These long-term observations allowed for studying the seasonal behavior of aerosol evaporation with a special focus on compounds that remained in the aerosol phase at 280 degrees C. The temperature-response of evaporation was also studied by heating the aerosol sample step-wise to six temperatures ranging from 80 degrees C to 280 degrees C. The mass fraction remaining after heating (MFR) was determined from the measured particle number size distributions before and after heating assuming a constant particle density (1.6 g cm(-3)). On average 19% of the total aerosol mass remained in the particulate phase at 280 degrees C. The particles evaporated less at low ambient temperatures during winter as compared with the warmer months. Black carbon (BC) fraction of aerosol mass correlated positively with the MFR at 280 degrees C, but could not explain it completely: most of the time a notable fraction of this nonvolatile residual was something other than BC. Using additional information on ambient meteorological conditions and results from an Aerodyne aerosol mass spectrometer (AMS), the chemical composition of MFR at 280 degrees C and its seasonal behavior was further examined. Correlation analysis with ambient temperature and mass fractions of polycyclic aromatic hydrocarbons (PAHs) indicated that MFR at 280 degrees C is probably affected by anthropogenic emissions. On the other hand, results from the AMS analysis suggested that there may be very low-volatile organics, possibly organonitrates, in the non-volatile (at 280 degrees C) fraction of aerosol mass.
|
|
| 7. |
- Hakkinen, S. A. K., et al.
(författare)
-
Semi-empirical parameterization of size-dependent atmospheric nanoparticle growth in continental environments
- 2013
-
Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 13:15, s. 7665-7682
-
Tidskriftsartikel (refereegranskat)abstract
- The capability to accurately yet efficiently represent atmospheric nanoparticle growth by biogenic and anthropogenic secondary organics is a challenge for current atmospheric large-scale models. It is, however, crucial to predict nanoparticle growth accurately in order to reliably estimate the atmospheric cloud condensation nuclei (CCN) concentrations. In this work we introduce a simple semi-empirical parameterization for sub-20 nm particle growth that distributes secondary organics to the nanoparticles according to their size and is therefore able to reproduce particle growth observed in the atmosphere. The parameterization includes particle growth by sulfuric acid, secondary organics from monoterpene oxidation (SORG(MT)) and an additional condensable vapor of non-monoterpene organics (background). The performance of the proposed parameterization was investigated using ambient data on particle growth rates in three diameter ranges (1.5-3 nm, 3-7 nm and 7-20 nm). The growth rate data were acquired from particle / air ion number size distribution measurements at six continental sites over Europe. The longest time series of 7 yr (2003-2009) was obtained from a boreal forest site in Hyytiala, Finland, while about one year of data (2008-2009) was used for the other stations. The extensive ambient measurements made it possible to test how well the parameterization captures the seasonal cycle observed in sub-20 nm particle growth and to determine the weighing factors for distributing the SORG(MT) for different sized particles as well as the background mass flux (concentration). Besides the monoterpene oxidation products, background organics with a concentration comparable to SORGMT, around 6x10(7) cm(-3) (consistent with an additional global SOA yield of 100 Tg yr(-1)) was needed to reproduce the observed nanoparticle growth. Simulations with global models suggest that the background could be linked to secondary biogenic organics that are formed in the presence of anthropogenic pollution.
|
|
| 8. |
- Manninen, H. E., et al.
(författare)
-
EUCAARI ion spectrometer measurements at 12 European sites - analysis of new particle formation events
- 2010
-
Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 10:16, s. 7907-7927
-
Tidskriftsartikel (refereegranskat)abstract
- We present comprehensive results on continuous atmospheric cluster and particle measurements in the size range similar to 1-42 nm within the European Integrated project on Aerosol Cloud Climate and Air Quality interactions (EUCAARI) project. We focused on characterizing the spatial and temporal variation of new particle formation events and relevant particle formation parameters across Europe. Different types of air ion and cluster mobility spectrometers were deployed at 12 field sites across Europe from March 2008 to May 2009. The measurements were conducted in a wide variety of environments, including coastal and continental locations as well as sites at different altitudes (both in the boundary layer and the free troposphere). New particle formation events were detected at all of the 12 field sites during the year-long measurement period. From the data, nucleation and growth rates of newly formed particles were determined for each environment. In a case of parallel ion and neutral cluster measurements, we could also estimate the relative contribution of ion-induced and neutral nucleation to the total particle formation. The formation rates of charged particles at 2 nm accounted for 1-30% of the corresponding total particle formation rates. As a significant new result, we found out that the total particle formation rate varied much more between the different sites than the formation rate of charged particles. This work presents, so far, the most comprehensive effort to experimentally characterize nucleation and growth of atmospheric molecular clusters and nanoparticles at ground-based observation sites on a continental scale.
|
|
| 9. |
|
|
| 10. |
- Akola, J., et al.
(författare)
-
Thiolate-Protected Au-25 Superatoms as Building Blocks: Dimers and Crystals
- 2010
-
Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:38, s. 15986-15994
-
Tidskriftsartikel (refereegranskat)abstract
- A particularly stable thiolate-protected gold nanocluster, Au-25(SR)(18), was structurally characterized from X-ray crystallography in 2008, and concomitantly its electronic and optical properties were analyzed via density functional theory. The robust geometry and a well-understood electronic structure of this cluster motivate explorations of properties of extended systems made out of Au-25(SR)(18) building blocks. As a first step in this direction, we analyze here structural, vibrational, electronic, and optical properties of the Au-25 cluster anion as it was observed in the crystalline environment and predict properties of cluster dimers, where the Au-25 units are linked together. via an aromatic dithiolate linker. We show that properties of each Au-25 unit of the dimer can be quite independently modified from the other by doping with a nonmagnetic (Pd) or magnetic (Mn) metal atom. We anticipate that material systems with interesting properties could be made from these building blocks, provided that a suitable chemistry for their controlled linking can be found.
|
|
