| 1. |
- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
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| 4. |
- Surendran, Praveen, et al.
(författare)
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Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals
- 2020
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 52:12, s. 1314-1332
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Tidskriftsartikel (refereegranskat)abstract
- Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to similar to 1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency <= 0.01) variant BP associations (P < 5 x 10(-8)), of which 32 were in new BP-associated loci and 55 were independent BP-associated single-nucleotide variants within known BP-associated regions. Average effects of rare variants (44% coding) were similar to 8 times larger than common variant effects and indicate potential candidate causal genes at new and known loci (for example, GATA5 and PLCB3). BP-associated variants (including rare and common) were enriched in regions of active chromatin in fetal tissues, potentially linking fetal development with BP regulation in later life. Multivariable Mendelian randomization suggested possible inverse effects of elevated systolic and diastolic BP on large artery stroke. Our study demonstrates the utility of rare-variant analyses for identifying candidate genes and the results highlight potential therapeutic targets.
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| 5. |
- Chatzikonstantinou, T, et al.
(författare)
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COVID-19 severity and mortality in patients with CLL: an update of the international ERIC and Campus CLL study
- 2021
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Ingår i: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 3635:312, s. 3444-3454
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Tidskriftsartikel (refereegranskat)abstract
- Patients with chronic lymphocytic leukemia (CLL) may be more susceptible to Coronavirus disease 2019 (COVID-19) due to age, disease, and treatment-related immunosuppression. We aimed to assess risk factors of outcome and elucidate the impact of CLL-directed treatments on the course of COVID-19. We conducted a retrospective, international study, collectively including 941 patients with CLL and confirmed COVID-19. Data from the beginning of the pandemic until March 16, 2021, were collected from 91 centers. The risk factors of case fatality rate (CFR), disease severity, and overall survival (OS) were investigated. OS analysis was restricted to patients with severe COVID-19 (definition: hospitalization with need of oxygen or admission into an intensive care unit). CFR in patients with severe COVID-19 was 38.4%. OS was inferior for patients in all treatment categories compared to untreated (p < 0.001). Untreated patients had a lower risk of death (HR = 0.54, 95% CI:0.41–0.72). The risk of death was higher for older patients and those suffering from cardiac failure (HR = 1.03, 95% CI:1.02–1.04; HR = 1.79, 95% CI:1.04–3.07, respectively). Age, CLL-directed treatment, and cardiac failure were significant risk factors of OS. Untreated patients had a better chance of survival than those on treatment or recently treated.
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| 6. |
- Joshi, Peter K, et al.
(författare)
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Directional dominance on stature and cognition in diverse human populations
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 523:7561, s. 459-462
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Tidskriftsartikel (refereegranskat)abstract
- Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10(-300), 2.1 × 10(-6), 2.5 × 10(-10) and 1.8 × 10(-10), respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months' less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.
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| 7. |
- Wessel, Jennifer, et al.
(författare)
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Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
- 2015
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Fasting glucose and insulin are intermediate traits for type 2 diabetes. Here we explore the role of coding variation on these traits by analysis of variants on the HumanExome BeadChip in 60,564 non-diabetic individuals and in 16,491 T2D cases and 81,877 controls. We identify a novel association of a low-frequency nonsynonymous SNV in GLP1R (A316T; rs10305492; MAF = 1.4%) with lower FG (beta = -0.09 +/- 0.01 mmol l(-1), P = 3.4 x 10(-12)), T2D risk (OR[95% CI] = 0.86[0.76-0.96], P = 0.010), early insulin secretion (beta = -0.07 +/- 0.035 pmol(insulin) mmol(glucose)(-1), P = 0.048), but higher 2-h glucose (beta = 0.16 +/- 0.05 mmol l(-1), P = 4.3 x 10(-4)). We identify a gene-based association with FG at G6PC2 (p(SKAT) = 6.8 x 10(-6)) driven by four rare protein-coding SNVs (H177Y, Y207S, R283X and S324P). We identify rs651007 (MAF = 20%) in the first intron of ABO at the putative promoter of an antisense lncRNA, associating with higher FG (beta = 0.02 +/- 0.004 mmol l(-1), P = 1.3 x 10(-8)). Our approach identifies novel coding variant associations and extends the allelic spectrum of variation underlying diabetes-related quantitative traits and T2D susceptibility.
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| 8. |
- Kraja, Aldi T., et al.
(författare)
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New Blood Pressure-Associated Loci Identified in Meta-Analyses of 475000 Individuals
- 2017
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Ingår i: Circulation. - : LIPPINCOTT WILLIAMS & WILKINS. - 1942-325X .- 1942-3268. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Background - Genome-wide association studies have recently identified >400 loci that harbor DNA sequence variants that influence blood pressure (BP). Our earlier studies identified and validated 56 single nucleotide variants (SNVs) associated with BP from meta-analyses of exome chip genotype data. An additional 100 variants yielded suggestive evidence of association.Methods and Results - Here, we augment the sample with 140886 European individuals from the UK Biobank, in whom 77 of the 100 suggestive SNVs were available for association analysis with systolic BP or diastolic BP or pulse pressure. We performed 2 meta-analyses, one in individuals of European, South Asian, African, and Hispanic descent (pan-ancestry, approximate to 475000), and the other in the subset of individuals of European descent (approximate to 423000). Twenty-one SNVs were genome-wide significant (P<5x10(-8) ) for BP, of which 4 are new BP loci: rs9678851 (missense, SLC4A1AP), rs7437940 (AFAP1), rs13303 (missense, STAB1), and rs1055144 (7p15.2). In addition, we identified a potentially independent novel BP-associated SNV, rs3416322 (missense, SYNPO2L) at a known locus, uncorrelated with the previously reported SNVs. Two SNVs are associated with expression levels of nearby genes, and SNVs at 3 loci are associated with other traits. One SNV with a minor allele frequency <0.01, (rs3025380 at DBH) was genome-wide significant.Conclusions - We report 4 novel loci associated with BP regulation, and 1 independent variant at an established BP locus. This analysis highlights several candidate genes with variation that alter protein function or gene expression for potential follow-up.
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| 9. |
- Dudarev, S. L., et al.
(författare)
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The EU programme for modelling radiation effects in fusion reactor materials : An overview of recent advances and future goals
- 2009
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Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 386, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- The EU fusion materials modelling programme was initiated in 2002 with the objective of developing a comprehensive set of computer modelling techniques and approaches, aimed at rationalising the extensive available experimental information on properties of irradiated fusion materials, developing capabilities for predicting the behaviour of materials under conditions not yet accessible to experimental tests, assessing results of tests involving high dose rates, and extrapolating these results to the fusion-relevant conditions. The programme presently gives emphasis to modelling a single class of materials, which are ferritic-martensitic EUROFER-type steels, and focuses on the investigation of key physical phenomena and interpretation of experimental observations. The objective of the programme is the development of computational capabilities for predicting changes in mechanical properties, hardening and embrittlement, as well as changes in the microstructure and phase stability of EUROFER and FeCr model alloys occurring under fusion reactor relevant irradiation conditions.
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| 10. |
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| 11. |
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| 12. |
- Koettgen, Anna, et al.
(författare)
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Genome-wide association analyses identify 18 new loci associated with serum urate concentrations
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:2, s. 145-154
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Tidskriftsartikel (refereegranskat)abstract
- Elevated serum urate concentrations can cause gout, a prevalent and painful inflammatory arthritis. By combining data from >140,000 individuals of European ancestry within the Global Urate Genetics Consortium (GUGC), we identified and replicated 28 genome-wide significant loci in association with serum urate concentrations (18 new regions in or near TRIM46, INHBB, SEMBT1, TMEM171, VEGFA, BAZ1B, PRKAG2, STC1, HNF4G, A1CF, ATXN2, UBE2Q2, IGF1R, NFAT5, MAF, HLF, ACVR1B-ACVRL1 and B3GNT4). Associations for many of the loci were of similar magnitude in individuals of non-European ancestry. We further characterized these loci for associations with gout, transcript expression and the fractional excretion of urate. Network analyses implicate the inhibins-activins signaling pathways and glucose metabolism in systemic urate control. New candidate genes for serum urate concentration highlight the importance of metabolic control of urate production and excretion, which may have implications for the treatment and prevention of gout.
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| 13. |
- Assimes, Themistocles L., et al.
(författare)
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Lack of Association Between the Trp719Arg Polymorphism in Kinesin-Like Protein-6 and Coronary Artery Disease in 19 Case-Control Studies
- 2010
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Ingår i: Journal of the American College of Cardiology. - : Elsevier BV. - 0735-1097. ; 56:19, s. 1552-1563
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Tidskriftsartikel (refereegranskat)abstract
- Objectives We sought to replicate the association between the kinesin-like protein 6 (KIF6) Trp719Arg polymorphism (rs20455), and clinical coronary artery disease (CAD). Background Recent prospective studies suggest that carriers of the 719Arg allele in KIF6 are at increased risk of clinical CAD compared with noncarriers. Methods The KIF6 Trp719Arg polymorphism (rs20455) was genotyped in 19 case-control studies of nonfatal CAD either as part of a genome-wide association study or in a formal attempt to replicate the initial positive reports. Results A total of 17,000 cases and 39,369 controls of European descent as well as a modest number of South Asians, African Americans, Hispanics, East Asians, and admixed cases and controls were successfully genotyped. None of the 19 studies demonstrated an increased risk of CAD in carriers of the 719Arg allele compared with noncarriers. Regression analyses and fixed-effects meta-analyses ruled out with high degree of confidence an increase of >= 2% in the risk of CAD among European 719Arg carriers. We also observed no increase in the risk of CAD among 719Arg carriers in the subset of Europeans with early-onset disease (younger than 50 years of age for men and younger than 60 years of age for women) compared with similarly aged controls as well as all non-European subgroups. Conclusions The KIF6 Trp719Arg polymorphism was not associated with the risk of clinical CAD in this large replication study. (J Am Coll Cardiol 2010;56:1552-63) (C) 2010 by the American College of Cardiology Foundation
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| 14. |
- Mahajan, Anubha, et al.
(författare)
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Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes
- 2018
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:4, s. 559-571
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Tidskriftsartikel (refereegranskat)abstract
- We aggregated coding variant data for 81,412 type 2 diabetes cases and 370,832 controls of diverse ancestry, identifying 40 coding variant association signals (P < 2.2 × 10−7); of these, 16 map outside known risk-associated loci. We make two important observations. First, only five of these signals are driven by low-frequency variants: even for these, effect sizes are modest (odds ratio ≤1.29). Second, when we used large-scale genome-wide association data to fine-map the associated variants in their regional context, accounting for the global enrichment of complex trait associations in coding sequence, compelling evidence for coding variant causality was obtained for only 16 signals. At 13 others, the associated coding variants clearly represent ‘false leads’ with potential to generate erroneous mechanistic inference. Coding variant associations offer a direct route to biological insight for complex diseases and identification of validated therapeutic targets; however, appropriate mechanistic inference requires careful specification of their causal contribution to disease predisposition.
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| 15. |
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| 16. |
- Malerba, L., et al.
(författare)
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Ab initio calculations and interatomic potentials for iron and iron alloys : Achievements within the Perfect Project
- 2010
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Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 406:1, s. 7-18
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Tidskriftsartikel (refereegranskat)abstract
- The objective of the FP6 Perfect Project was to develop a first example of integrated multiscale computational models, capable of describing the effects of irradiation in nuclear reactor components, namely vessel and internals. The use of ab initio techniques to study, in the most reliable way currently possible, atomic-level interactions between species and defects, and the transfer of this knowledge to interatomic potentials, of use for large scale dynamic simulations, lie at the core of this effort. The target materials of the Project were bainitic steels (vessel) and austenitic steels (internals), i.e. iron alloys. In this article, the advances made within the Project in the understanding of defect properties in Fe alloys, by means of ab initio calculations, and in the development of interatomic potentials for Fe and Fe alloys are overviewed, thereby providing a reference basis for further progress in the field. Emphasis is put in showing how the produced data have enhanced our level of understanding of microstructural processes occurring under irradiation in model alloys and steels used in existing nuclear power plants.
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| 17. |
- Surendran, Praveen, et al.
(författare)
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Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension
- 2016
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 48:10, s. 1151-1161
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Tidskriftsartikel (refereegranskat)abstract
- High blood pressure is a major risk factor for cardiovascular disease and premature death. However, there is limited knowledge on specific causal genes and pathways. To better understand the genetics of blood pressure, we genotyped 242,296 rare, low-frequency and common genetic variants in up to 192,763 individuals and used -1/4155,063 samples for independent replication. We identified 30 new blood pressure- or hypertension-associated genetic regions in the general population, including 3 rare missense variants in RBM47, COL21A1 and RRAS with larger effects (>1.5 mm Hg/allele) than common variants. Multiple rare nonsense and missense variant associations were found in A2ML1, and a low-frequency nonsense variant in ENPEP was identified. Our data extend the spectrum of allelic variation underlying blood pressure traits and hypertension, provide new insights into the pathophysiology of hypertension and indicate new targets for clinical intervention.
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| 18. |
- Victoria, M., et al.
(författare)
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Modelling irradiation effects in fusion materials
- 2007
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Ingår i: Fusion engineering and design. - : Elsevier BV. - 0920-3796 .- 1873-7196. ; 82:15-24, s. 2413-2421
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Tidskriftsartikel (refereegranskat)abstract
- We review the current status of the European fusion materials modelling programme. We describe recent findings and outline potential areas for future development. Large-scale density functional theory (DFT) calculations reveal the structure of the point defects in alpha-Fe, and highlight the crucial part played by magnetism. The calculations give accurate migration energies of point defects and the strength of their interaction with He atoms. Kinetic models based on DFT results reproduce the stages of radiation damage recovery in iron, and stages of He-desorption from pre-implanted iron. Experiments aimed at validating the models will be carried out in the future using a multi-beam ion irradiation facility chosen for its versatility and rapid feedback.
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| 19. |
- Björkas, C., et al.
(författare)
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Simulation of displacement cascades in Fe90Cr10 using a two band model potential
- 2008
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Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 372:2-3, s. 312-317
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics (MD) simulations of displacement cascades, with recoil energies up to 50 keV, have been performed in Fe90Cr10 and Fe using a recently developed two band embedded atomic model (2BM) potential that correctly describes the mixing enthalpy and the binding energy of the mixed dumbbell configurations. Comparisons between results obtained with the 2BM potential fitted to different data sets, a one band model (1BM), and another existing FeCr-potential previously used for similar calculations were done, showing differences in the vacancy clustered fraction and the Cr content in interstitials predicted by the potentials. The 2BM potential resulted in roughly the same concentration of Cr in interstitial positions as in the matrix, and the 1BM, which incorrectly predicts a positive heat of mixing, predicted even smaller concentrations. The calculated short range order parameter is around zero for the 2BM, and takes positive values within the 1BM, as expected from the mixing enthalpies.
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| 20. |
- Bonny, G., et al.
(författare)
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Numerical prediction of thermodynamic properties of iron-chromium alloys using semi-empirical cohesive models : The state of the art
- 2009
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Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 385:2, s. 268-277
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Tidskriftsartikel (refereegranskat)abstract
- In this work the capability of existing cohesive models to predict the thermodynamicproperties of Fe-Cr alloys are critically evaluated and compared. The two-band model and the concentration-dependent model, which are independently developed extensions of the embedded-atom method, are demonstrated to be equivalent and equally capable of reproducing the thermodynamic properties of Fe-Cr alloys. The existing potentials fitted with these formalisms are discussed and compared with an existing cluster expansionmodel. The phase diagram corresponding to these models is evaluated using different but complementary methods. The influence of mixing enthalpy, low-energy states and vibrational entropy on the phase diagram is examined for the different cohesive models.
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| 21. |
- Bonny, G., et al.
(författare)
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The impact of alloying elements on the precipitation stability and kinetics in iron based alloys : An atomistic study
- 2019
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Ingår i: Computational materials science. - : Elsevier. - 0927-0256 .- 1879-0801. ; 161, s. 309-320
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Tidskriftsartikel (refereegranskat)abstract
- Iron based industrial steels typically contain a large number of alloying elements, even so-called low alloyed steels. Under irradiation, these alloying elements form clusters that have a detrimental impact of the mechanical properties of the steel. The stability and formation mechanisms of such clusters are presently not fully understood. Therefore, in this work, we study the thermal stability and formation kinetics of small solute clusters in the bcc Fe matrix. We use density functional theory (DFT) to characterize the binding energy of vacancy/solute clusters containing Cr, Mn, Ni, Cu, Si and P, thereby exploring >700 different configurations. The constructed DFT data base is used to fit a cluster expansion (CE) for the vacancy-FeCrMnNiCuSiP system. In turn, the obtained CE is applied in atomistic kinetic Monte Carlo simulations to study the effect of Mn, Ni, Cr, Si and P on the precipitation formation in the FeCu alloy. We conclude that the addition of Mn and Ni delay the precipitation kinetics by an order of magnitude. The additional alloying with traces of P/Si further delays the kinetics by an additional order of magnitude. We found that Si plays an essential role in the formation of spatially mixed MnNiCuSi cluster
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| 22. |
- Castin, N., et al.
(författare)
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Advanced atomistic models for radiation damage in Fe-based alloys : Contributions and future perspectives from artificial neural networks
- 2018
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Ingår i: Computational materials science. - : Elsevier. - 0927-0256 .- 1879-0801. ; 148, s. 116-130
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Tidskriftsartikel (refereegranskat)abstract
- Machine learning, and more specifically artificial neural networks (ANN), are powerful and flexible numerical tools that can lead to significant improvements in many materials modelling techniques. This paper provides a review of the efforts made so far to describe the effects of irradiation in Fe-based and W-based alloys, in a multiscale modelling framework. ANN were successfully used as innovative parametrization tools in these models, thereby greatly enhancing their physical accuracy and capability to accomplish increasingly challenging goals. In the provided examples, the main goal of ANN is to predict how the chemical complexity of local atomic configurations, and/or specific strain fields, influence the activation energy of selected thermally-activated events. This is most often a more efficient approach with respect to previous computationally heavy methods. In a future perspective, similar schemes can be potentially used to calculate other quantities than activation energies. They can thus transfer atomic-scale properties to higher-scale simulations, providing a proper bridging across scales, and hence contributing to the achievement of accurate and reliable multiscale models.
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| 23. |
- Castin, N., et al.
(författare)
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The dominant mechanisms for the formation of solute-rich clusters in low-Cu steels under irradiation
- 2020
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Ingår i: Materials Today Energy. - : Elsevier BV. - 2468-6069. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- The formation of nano-sized, coherent, solute-rich clusters (NSRC) is known to be an important factor causing the degradation of the macroscopic properties of steels under irradiation. The mechanisms driving their formation are still debated. This work focuses on low-Cu reactor pressure vessel (RPV) steels, where solute species are generally not expected to precipitate. We rationalize the processes that take place at the nanometer scale under irradiation, relying on the latest theoretical and experimental evidence on atomic-level diffusion and transport processes. These are compiled in a new model, based on the object kinetic Monte Carlo (OKMC) technique. We evaluate the relevance of the underlying physical assumptions by applying the model to a large variety of irradiation experiments. Our model predictions are compared with new experimental data obtained with atom probe tomography and small angle neutron scattering, complemented with information from the literature. The results of this study reveal that the role of immobilized self-interstitial atoms (SIA) loops dominates the nucleation process of NSRC.
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| 24. |
- Djurabekova, F., et al.
(författare)
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Kinetics versus thermodynamics in materials modeling : The case of the di-vacancy in iron
- 2010
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Ingår i: Philosophical Magazine. - : Informa UK Limited. - 1478-6435 .- 1478-6443. ; 90:19, s. 2585-2595
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Tidskriftsartikel (refereegranskat)abstract
- Monte Carlo models are widely used for the study of microstructural and microchemical evolution of materials under irradiation. However, they often link explicitly the relevant activation energies to the energy difference between local equilibrium states. We provide a simple example (di-vacancy migration in iron) in which a rigorous activation energy calculation, by means of both empirical interatomic potentials and density functional theory methods, clearly shows that such a link is not granted, revealing a migration mechanism that a thermodynamics-linked activation energy model cannot predict. Such a mechanism is, however, fully consistent with thermodynamics. This example emphasizes the importance of basing Monte Carlo methods on models where the activation energies are rigorously calculated, rather than deduced from widespread heuristic equations.
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| 25. |
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| 26. |
- Juslin, N., et al.
(författare)
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Simulation of threshold displacement energies in FeCr
- 2007
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Ingår i: Nuclear Instruments and Methods in Physics Research Section B. - : Elsevier BV. - 0168-583X .- 1872-9584. ; 255:1, s. 75-77
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the role of chromium on threshold displacement energies in FeCr for the fusion reactor steel relevant concentration 10% Cr. We have used molecular dynamics simulations in order to determine whether the observed Cr-content dependence of macroscopic properties can be due to the defect production. We compare FeCr-alloys with pure iron and chromium, employing two different potential sets for the Fe-Cr system. We find that there are no significant differences between pure iron and FeCr with 10% Cr for the 100, 110 and 111 directions and the average threshold energy.
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| 27. |
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| 28. |
- Li, Man, et al.
(författare)
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SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function
- 2017
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Ingår i: Journal of the American Society of Nephrology: JASN. - 1533-3450. ; 28:3, s. 981-994
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L; PStage1<3.7×10-7), of which most were common and annotated as nonsynonymous variants. Gene-based analysis identified associations of functional rare variants in three genes with eGFRcrea, including a novel association with the SOS Ras/Rho guanine nucleotide exchange factor 2 gene, SOS2 (P=5.4×10-8 by sequence kernel association test). Experimental follow-up in zebrafish embryos revealed changes in glomerular gene expression and renal tubule morphology in the embryonic kidney of acp1- and sos2-knockdowns. These developmental abnormalities associated with altered blood clearance rate and heightened prevalence of edema. This study expands the number of loci associated with kidney function and identifies novel genes with potential roles in kidney formation.
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| 29. |
- Malerba, L., et al.
(författare)
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Comparison of empirical interatomic potentials for iron applied to radiation damage studies
- 2010
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Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 406:1, s. 19-38
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Tidskriftsartikel (refereegranskat)abstract
- The performance of four recent semi-empirical interatomic potentials for iron, developed or used within the FP6 Perfect Project, is evaluated by comparing them between themselves and with available experimental or, more often, density functional theory data. The quantities chosen for the comparison are of specific interest for radiation damage studies, i.e. they concern mainly properties of point-defects and their clusters, as well as dislocations. For completeness, an earlier, widely used (also within the Project) iron potential is included in the comparison exercise as well. This exercise allows conclusions to be drawn about the reliability of the available potentials, while providing a snapshot of the state-of-the-art concerning fundamental properties of iron, thereby being also useful as a kind of handbook and as a framework for the validation of future semi-empirical interatomic potentials for iron. It is found that Mendelev-type potentials are currently the best choice in order to "extend density functional theory" to larger scales and this justifies their widespread use, also for the development of iron alloy potentials. However, a fully reliable description of self-interstitial atom clusters and dislocations with interatomic potentials remains largely an elusive objective, that calls for further effort within the concerned scientific community.
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| 30. |
- Malerba, L., et al.
(författare)
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Modelling of Radiation Damage in Fe-Cr Alloys
- 2008
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Ingår i: EFFECTS OF RADIATION ON MATERIALS. - 9780803134218 ; , s. 159-176
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Konferensbidrag (refereegranskat)abstract
- High-Cr ferritic/martensitic steels are being considered as structural materials for a large number of future nuclear applications, from fusion to accelerator-driven systems and GenIV reactors. Fe-Cr alloys can be used as model materials to investigate some of the mechanisms governing their microstructure evolution under irradiation and its correlation to changes in their macroscopic properties. Focusing on these alloys, we show an example of how the integration of computer simulation and theoretical models can provide keys for the interpretation of a host of relevant experimental observations. In particular we show that proper accounting for two basic features of these alloys, namely, the existence of a fairly strong attractive interaction between self-interstitials and Cr atoms and of a mixing enthalpy that changes sign from negative to positive around 8 to 10 % Cr, is a necessary and, to a certain extent, sufficient condition to rationalize and understand their behavior under irradiation. These features have been revealed by ab initio calculations, are supported by experimental evidence, and have been adequately transferred into advanced empirical interatomic potentials, which have been and are being used for the simulation of damage production, defect behavior, and phase transformation in these alloys. The results of the simulations have been and are being used to parameterize models capable of extending the description of radiation effects to scales beyond the reach of molecular dynamics. The present paper intends to highlight the most important achievements and results of this research activity.
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| 31. |
- Malerba, L., et al.
(författare)
-
Modelling of radiation damage in Fe-Cr alloys
- 2007
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Ingår i: Journal of ASTM International. - 1546-962X. ; 4:6
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Tidskriftsartikel (refereegranskat)abstract
- High-Cr ferritic/martensitic steels are being considered as structural materials for a large number of future nuclear applications, from fusion to accelerator-driven systems and GenIV reactors. Fe-Cr alloys can be used as model materials to investigate some of the mechanisms governing their microstructure evolution under irradiation and its correlation to changes in their macroscopic properties. Focusing on these alloys, we show an example of how the integration of computer simulation and theoretical models can provide keys for the interpretation of a host of relevant experimental observations. In particular we show that proper accounting for two basic features of these alloys, namely, the existence of a fairly strong attractive interaction between self-interstitials and Cr atoms and of a mixing enthalpy that changes sign from negative to positive around 8 to 10% Cr, is a necessary and, to a certain extent, sufficient condition to rationalize and understand their behavior under irradiation. These features have been revealed by ab initio calculations, are supported by experimental evidence, and have been adequately transferred into advanced empirical interatomic potentials, which have been and are being used for the simulation of damage production, defect behavior, and phase transformation in these alloys. The results of the simulations have been and are being used to parameterize models capable of extending the description of radiation effects to scales beyond the reach of molecular dynamics. The present paper intends to highlight the most important achievements and results of this research activity.
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| 32. |
- Malerba, L., et al.
(författare)
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Molecular dynamics simulation of displacement cascades in Fe-Cr alloys
- 2004
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Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 329-33, s. 1156-1160
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Tidskriftsartikel (refereegranskat)abstract
- An embedded atom method (EAM) empirical potential recently fitted and validated for Fe-Cr systems is used to simulate displacement cascades up to 15 keV in Fe and Fe-10%Cr. The evolution of these cascades up to thermalisation of the primary damage state is followed and quantitatively analysed. Particular attention is devoted to assessing the effect of Cr atoms on the defect distribution versus pure Fe. Using the Wigner-Seitz cell criterion to identify point defects, first results show that the main effect of the presence of Cr in the system is the preferential formation of mixed Fe-Cr dumbbells and mixed interstitial clusters, with expected lower mobility than in pure Fe.
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| 33. |
- Malerba, L., et al.
(författare)
-
Multiscale modelling for fusion and fission materials : The M4F project
- 2021
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Ingår i: Nuclear Materials and Energy. - : Elsevier BV. - 2352-1791. ; 29, s. 101051-
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Tidskriftsartikel (refereegranskat)abstract
- The M4F project brings together the fusion and fission materials communities working on the prediction of radiation damage production and evolution and their effects on the mechanical behaviour of irradiated ferritic/martensitic (F/M) steels. It is a multidisciplinary project in which several different experimental and computational materials science tools are integrated to understand and model the complex phenomena associated with the formation and evolution of irradiation induced defects and their effects on the macroscopic behaviour of the target materials. In particular the project focuses on two specific aspects: (1) To develop physical understanding and predictive models of the origin and consequences of localised deformation under irradiation in F/M steels; (2) To develop good practices and possibly advance towards the definition of protocols for the use of ion irradiation as a tool to evaluate radiation effects on materials. Nineteen modelling codes across different scales are being used and developed and an experimental validation programme based on the examination of materials irradiated with neutrons and ions is being carried out. The project enters now its 4th year and is close to delivering high-quality results. This paper overviews the work performed so far within the project, highlighting its impact for fission and fusion materials science.
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| 34. |
- Nordlund, K., et al.
(författare)
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Molecular dynamics simulations of threshold displacement energies in Fe
- 2006
-
Ingår i: Nuclear Instruments and Methods in Physics Research Section B. - : Elsevier BV. - 0168-583X .- 1872-9584. ; 246:2, s. 322-332
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Tidskriftsartikel (refereegranskat)abstract
- We compare systematically the threshold displacement energy surface of 11 interatomic potentials in Fe. We discuss in detail different possible definitions of threshold displacement energies, and how they relate to different kinds of experimental threshold displacement energies. We compare the threshold results to experiments, and find that none of the 11 tested potentials agrees fully with experiments. However, all the potentials predict some qualitative features in the same way, most importantly that the threshold energy surface close to the 100 crystal direction is flat and that the largest threshold energies occur around very roughly the 123 crystal direction.
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| 35. |
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| 36. |
- Olsson, Pär, et al.
(författare)
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Two-band modeling of alpha-prime phase formation in Fe-Cr
- 2005
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 72:21
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a two-band model of Fe-Cr, fitted to properties of the ferromagnetic alloy. Fitting many-body functionals to the calculated mixing enthalpy of the alloy and the mixed interstitial binding energy in iron, our potential reproduces changes in sign of the formation energy as a function of Cr concentration. When applied in kinetic Monte Carlo simulations, the potential correctly predicts decomposition of initially random Fe-Cr alloys into the alpha-prime phase as function of Cr concentration.
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| 37. |
- Pattaro, Cristian, et al.
(författare)
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Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.
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| 38. |
- Rosendahl, J, et al.
(författare)
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Genome-wide association study identifies inversion in the CTRB1-CTRB2 locus to modify risk for alcoholic and non-alcoholic chronic pancreatitis
- 2018
-
Ingår i: Gut. - : BMJ. - 1468-3288 .- 0017-5749. ; 67:10, s. 1855-1863
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Tidskriftsartikel (refereegranskat)abstract
- Alcohol-related pancreatitis is associated with a disproportionately large number of hospitalisations among GI disorders. Despite its clinical importance, genetic susceptibility to alcoholic chronic pancreatitis (CP) is poorly characterised. To identify risk genes for alcoholic CP and to evaluate their relevance in non-alcoholic CP, we performed a genome-wide association study and functional characterisation of a new pancreatitis locus.Design1959 European alcoholic CP patients and population-based controls from the KORA, LIFE and INCIPE studies (n=4708) as well as chronic alcoholics from the GESGA consortium (n=1332) were screened with Illumina technology. For replication, three European cohorts comprising 1650 patients with non-alcoholic CP and 6695 controls originating from the same countries were used.ResultsWe replicated previously reported risk loci CLDN2-MORC4, CTRC, PRSS1-PRSS2 and SPINK1 in alcoholic CP patients. We identified CTRB1-CTRB2 (chymotrypsin B1 and B2) as a new risk locus with lead single-nucleotide polymorphism (SNP) rs8055167 (OR 1.35, 95% CI 1.23 to 1.6). We found that a 16.6 kb inversion in the CTRB1-CTRB2 locus was in linkage disequilibrium with the CP-associated SNPs and was best tagged by rs8048956. The association was replicated in three independent European non-alcoholic CP cohorts of 1650 patients and 6695 controls (OR 1.62, 95% CI 1.42 to 1.86). The inversion changes the expression ratio of the CTRB1 and CTRB2 isoforms and thereby affects protective trypsinogen degradation and ultimately pancreatitis risk.ConclusionAn inversion in the CTRB1-CTRB2 locus modifies risk for alcoholic and non-alcoholic CP indicating that common pathomechanisms are involved in these inflammatory disorders.
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| 39. |
- Terentyev, D. A., et al.
(författare)
-
Displacement cascades in Fe-Cr : A molecular dynamics study
- 2006
-
Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 349:1-2, s. 119-132
-
Tidskriftsartikel (refereegranskat)abstract
- Displacement cascades up to 50 keV have been simulated in Fe-10%Cr by molecular dynamics (MD), using an embedded-atom method (EAM) interatomic potential which satisfactorily reproduces the interaction between Cr atoms and point-defects in alpha-Fe. In particular, the potential can reproduce the strong interaction with self interstitial atoms characteristic of Fe-Cr alloys. The results, when compared to the case of pure Fe, show that the presence of Cr does not significantly influence either the ballistic phase of the cascade, or the primary damage state, in terms of number of surviving defects or clustered fraction. However, the fraction of Cr atoms in interstitial position greatly exceeds the alloy concentration, in agreement with some experimental indications, and this feature is expected to influence the long-term evolution of radiation damage in the alloy. The mechanisms leading to the accumulation of Cr in interstitial positions and the expected trapping effect on interstitial clusters are analysed and discussed.
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| 40. |
- Terentyev, D. A., et al.
(författare)
-
Self-trapped interstitial-type defects in iron
- 2008
-
Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 100:14
-
Tidskriftsartikel (refereegranskat)abstract
- Small interstitial-type defects in iron with complex structures and very low mobilities are revealed by molecular dynamics simulations. The stability of these defect clusters formed by nonparallel < 110 > dumbbells is confirmed by density functional theory calculations, and it is shown to increase with increasing temperature due to large vibrational formation entropies. This new family of defects provides an explanation for the low mobility of clusters needed to account for experimental observations of microstructure evolution under irradiation at variance with the fast migration obtained from previous atomistic simulations for conventional self-interstitial clusters.
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| 41. |
- Terentyev, D., et al.
(författare)
-
Characterization of dislocation loops and chromium-rich precipitates in ferritic iron-chromium alloys as means of void swelling suppression
- 2007
-
Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 362:2-3, s. 167-173
-
Tidskriftsartikel (refereegranskat)abstract
- We have used both ab initio and empirical potential based molecular dynamics and static calculations to parameterize a model accounting for the mobility of self-interstitial clusters and small dislocation loops in Fe-Cr alloys depending on Cr content. Particularly, we have considered the interval of 5-15% of Cr, corresponding to the typical concentration of Cr in ferritic/martensitic steels. The mobility of self-interstitial clusters and small dislocation loops was found to be strongly reduced in the presence of Cr due to attractive interaction between self-interstitials and Cr atoms, whereas Cr-rich precipitates act as repulsive obstacles. The results obtained allow the experimental trend of swelling measurements in neutron and high-energy electron irradiated Fe-Cr alloys to be interpreted and explained.
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| 42. |
- Terentyev, D., et al.
(författare)
-
Diffusion of 3D-migrating self-interstitial clusters in diluted and concentrated Fe-Cr alloys
- 2009
-
Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 386-88:C, s. 140-142
-
Tidskriftsartikel (refereegranskat)abstract
- We show, using atomic-level simulations, that the mobility of small 3D-migrating self-interstitial atom (SIA) clusters produced in displacement cascades is significantly reduced in concentrated Fe-Cr alloys (up to 15%Cr) as compared to Fe. The presence of alpha' precipitates, on the other hand, is only expected to provide scattering centers for interstitial-type defects, whose formation inside the precipitates is energetically unfavorable. The significant reduction in the mobility of 3D-migrating SIA clusters is expected to have an important impact on the microstructure evolution of high-Cr steels, depending on Cr concentration.
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| 43. |
- Terentyev, D., et al.
(författare)
-
Effect of the interatomic potential on the features of displacement cascades in alpha-Fe : A molecular dynamics study
- 2006
-
Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 351:03-jan, s. 65-77
-
Tidskriftsartikel (refereegranskat)abstract
- The primary state of damage obtained in molecular dynamics (MD) simulations of displacement cascades in alpha-Fe, particularly the fraction of point-defects in clusters, depends on the interatomic potential used to describe the atomic interactions. The differences may influence the microstructural evolution predicted in damage accumulation models which use results from MD cascade simulations as input. In this work, a number of displacement cascades of energy ranging from 5 to 40 keV have been simulated using the same procedure with four different interatomic potentials for alpha-Fe, each of them providing, among other things, varying descriptions of self-interstitial atoms (SIA) in this metal. The behaviour of the cascades at their different phases and the final surviving defect population have been studied and compared applying the same cascade analysis criteria for all potentials. The outcome is discussed trying to identify the characteristics of the potential that have the largest influence on the predicted primary state of damage.
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| 44. |
- Terentyev, D., et al.
(författare)
-
Further development of large-scale atomistic modelling techniques for Fe-Cr alloys
- 2011
-
Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 409:2, s. 167-175
-
Tidskriftsartikel (refereegranskat)abstract
- In this paper we review the current status of our efforts to model the Fe-Cr system, which is a model alloy for high-Cr ferritic-martensitic steels, using large-scale atomistic methods. The core of such methods are semi-empirical interatomic potentials. Here we discuss their performance with respect to the features that are important for an accurate description of radiation effects in Fe-Cr alloys. We describe their most recent improvements regarding macroscopic thermodynamic properties as well as microscopic point-defect properties. Furthermore we describe a new type of large-scale atomistic kinetic Monte Carlo (AKMC) approach driven by an artificial neural network (ANN) regression method to generate the local migration barrier for a defect accounting for the local chemistry around it. The results of the thermal annealing of the Fe-20Cr alloy modelled using this AKMC approach, parameterized by our newly developed potential, were found to be in very good agreement with experimental data. Furthermore the interaction of a 1/2 (1 1 1) screw dislocation with Cr precipitates as obtained from the AKMC simulations was studied using the same potential. In summary, we critically discuss our current achievements, findings and outline issues to be addressed in the near future development.
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| 45. |
- Terentyev, D., et al.
(författare)
-
On the migration and trapping of single self-interstitial atoms in dilute and concentrated Fe-Cr alloys : Atomistic study and comparison with resistivity recovery experiments
- 2008
-
Ingår i: Computational materials science. - : Elsevier BV. - 0927-0256 .- 1879-0801. ; 43:4, s. 1183-1192
-
Tidskriftsartikel (refereegranskat)abstract
- Atomistic simulations have been used to characterize the mobility of single self interstitial atoms (SIAs) in Fe-Cr alloys of different compositions. Density functional theory (DFT) results concerning the interaction energies between an SIA and Cr atoms in different configurations and relative positions have been extended to concentrated alloys by using an empirical potential (EP). This EP, fitted to a set of DFT data so as to provide a correct heat of mixing and point defect features, has been further validated. Static calculations using the EP allowed the existence of configuration traps for SIAs to be identified and their strength and concentration to be assessed. Dynamic simulations were used to estimate the diffusion coefficient of the SIA, as well as to characterize the primary damage state after low-temperature electron irradiation (1-5 MeV), in Fe-Cr alloys of different Cr content. The results correlate with available experimental data and provide a qualitative and partially also quantitative explanation for the observed differences in the resistivity recovery stages in diluted and concentrated Fe-Cr alloys of different composition.
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| 46. |
- Wallenius, Janne, 1968-, et al.
(författare)
-
Development of an EAM potential for simulation of radiation damage in Fe-Cr alloys
- 2004
-
Ingår i: Journal of Nuclear Materials. - : Elsevier BV. - 0022-3115 .- 1873-4820. ; 329-33, s. 1175-1179
-
Tidskriftsartikel (refereegranskat)abstract
- We have developed a set of EAM potentials for simulation of Fe-Cr alloys. By relaxing the requirement of reproducing the pressure-volume relation at short distances and by fitting to the thermal expansion coefficients of Fe and Cr, stability of theself-interstitial could be obtained. For Cr, properties of the paramagnetic state were applied, providing a positive Cauchy pressure. Mixed Fe-Cr pair potentials were fitted to the calculated mixing enthalpy of ferromagnetic Fe-Cr. Simulation of thermal ageing in Fe-Cr alloys using the Fe-20Cr potential exhibited pronounced Cr-precipitation for temperatures below 900 K, a feature not observed at any temperature using a potential fitted to the mixing enthalpy of Fe-5Cr.
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| 47. |
|
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| 48. |
- Wang, T, et al.
(författare)
-
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
- 2020
-
Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1, s. 4932-
-
Tidskriftsartikel (refereegranskat)abstract
- Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case–control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF < 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p < 1.25E−06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p < 3.64E−07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype–genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.
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