| 1. |
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| 2. |
- Botvinik-Nezer, Rotem, et al.
(author)
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Variability in the analysis of a single neuroimaging dataset by many teams
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 582, s. 84-88
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Journal article (peer-reviewed)abstract
- Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses(1). The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset(2-5). Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed. The results obtained by seventy different teams analysing the same functional magnetic resonance imaging dataset show substantial variation, highlighting the influence of analytical choices and the importance of sharing workflows publicly and performing multiple analyses.
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| 3. |
- Pfeiffer, D., et al.
(author)
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Genetic Imbalance Is Associated With Functional Outcome After Ischemic Stroke
- 2019
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In: Stroke. - : Ovid Technologies (Wolters Kluwer Health). - 0039-2499 .- 1524-4628. ; 50:2, s. 298-304
-
Journal article (peer-reviewed)abstract
- Background and Purpose-We sought to explore the effect of genetic imbalance on functional outcome after ischemic stroke (IS). Methods-Copy number variation was identified in high-density single-nucleotide polymorphism microarray data of IS patients from the CADISP (Cervical Artery Dissection and Ischemic Stroke Patients) and SiGN (Stroke Genetics Network)/ GISCOME (Genetics of Ischaemic Stroke Functional Outcome) networks. Genetic imbalance, defined as total number of protein-coding genes affected by copy number variations in an individual, was compared between patients with favorable (modified Rankin Scale score of 0-2) and unfavorable (modified Rankin Scale score of = 3) outcome after 3 months. Subgroup analyses were confined to patients with imbalance affecting ohnologs-a class of dose-sensitive genes, or to those with imbalance not affecting ohnologs. The association of imbalance with outcome was analyzed by logistic regression analysis, adjusted for age, sex, stroke subtype, stroke severity, and ancestry. Results-The study sample comprised 816 CADISP patients (age 44.2 +/- 10.3 years) and 2498 SiGN/GISCOME patients (age 67.7 +/- 14.2 years). Outcome was unfavorable in 122 CADISP and 889 SiGN/GISCOME patients. Multivariate logistic regression analysis revealed that increased genetic imbalance was associated with less favorable outcome in both samples (CADISP: P=0.0007; odds ratio=0.89; 95% CI, 0.82-0.95 and SiGN/GISCOME: P=0.0036; odds ratio=0.94; 95% CI, 0.91-0.98). The association was independent of age, sex, stroke severity on admission, stroke subtype, and ancestry. On subgroup analysis, imbalance affecting ohnologs was associated with outcome (CADISP: odds ratio=0.88; 95% CI, 0.80-0.95 and SiGN/GISCOME: odds ratio=0.93; 95% CI, 0.89-0.98) whereas imbalance without ohnologs lacked such an association. Conclusions-Increased genetic imbalance was associated with poorer functional outcome after IS in both study populations. Subgroup analysis revealed that this association was driven by presence of ohnologs in the respective copy number variations, suggesting a causal role of the deleterious effects of genetic imbalance.
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| 4. |
- Erhart, P., et al.
(author)
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Finite Element Analysis in Asymptomatic, Symptomatic, and Ruptured Abdominal Aortic Aneurysms : In Search of New Rupture Risk Predictors
- 2015
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In: European Journal of Vascular and Endovascular Surgery. - : Elsevier BV. - 1078-5884 .- 1532-2165. ; 49:3, s. 239-245
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Journal article (peer-reviewed)abstract
- Objectives: To compare biomechanical rupture risk parameters of asymptomatic, symptomatic and ruptured abdominal aortic aneurysms (AAA) using finite element analysis (FEA). Study design: Retrospective biomechanical single center analysis of asymptomatic, symptomatic, and ruptured AAAs. Comparison of biomechanical parameters from FEA. Materials and methods: From 2011 to 2013 computed tomography angiography (CTA) data from 30 asymptomatic, 15 symptomatic, and 15 ruptured AAAs were collected consecutively. FEA was performed according to the successive steps of AAA vessel reconstruction, segmentation and finite element computation. Biomechanical parameters Peak Wall Rupture Risk Index (PWRI), Peak Wall Stress (PWS), and Rupture Risk Equivalent Diameter (RRED) were compared among the three subgroups. Results: PWRI differentiated between asymptomatic and symptomatic AAAs (p < .0004) better than PWS (p < .1453). PWRI-dependent RRED was higher in the symptomatic subgroup compared with the asymptomatic subgroup (p < .0004). Maximum AAA external diameters were comparable between the two groups (p < .1355). Ruptured AAAs showed the highest values for external diameter, total intraluminal thrombus volume, PWS, RRED, and PWRI compared with asymptomatic and symptomatic AAAs. In contrast with symptomatic and ruptured AAAs, none of the asymptomatic patients had a PWRI value >1.0. This threshold value might identify patients at imminent risk of rupture: Conclusions: From different FEA derived parameter, PWRI distinguishes most precisely between asymptomatic and symptomatic AAAs. If elevated, this value may represent a negative prognostic factor for asymptomatic AAAs.
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| 5. |
- Juslin, N., et al.
(author)
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Analytical interatomic potential for modeling nonequilibrium processes in the W-C-H system
- 2005
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In: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 98:12
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Journal article (peer-reviewed)abstract
- A reactive interatomic potential based on an analytical bond-order scheme is developed for the ternary system W-C-H. The model combines Brenner's hydrocarbon potential with parameter sets for W-W, W-C, and W-H interactions and is adjusted to materials properties of reference structures with different local atomic coordinations including tungsten carbide, W-H molecules, as well as H dissolved in bulk W. The potential has been tested in various scenarios, such as surface, defect, and melting properties, none of which were considered in the fitting. The intended area of application is simulations of hydrogen and hydrocarbon interactions with tungsten, which have a crucial role in fusion reactor plasma-wall interactions. Furthermore, this study shows that the angular-dependent bond-order scheme can be extended to second nearest-neighbor interactions, which are relevant in body-centered-cubic metals. Moreover, it provides a possibly general route for modeling metal carbides.
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| 6. |
- Otto, Thomas D., et al.
(author)
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A comprehensive evaluation of rodent malaria parasite genomes and gene expression
- 2014
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In: BMC Biology. - : BioMed Central. - 1741-7007. ; 12
-
Journal article (peer-reviewed)abstract
- BACKGROUND: Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function.RESULTS: We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the 'Plasmodium interspersed repeat genes' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family.CONCLUSIONS: Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
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| 7. |
- Bernal, Ivan, 1984, et al.
(author)
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Exciton broadening and band renormalization due to Dexter-like intervalley coupling
- 2018
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In: 2D Materials. - : IOP Publishing. - 2053-1583. ; 5:2
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Journal article (peer-reviewed)abstract
- A remarkable property of atomically thin transition metal dichalcogenides (TMDs) is the possibility to selectively address single valleys by circularly polarized light. In the context of technological applications, it is very important to understand possible intervalley coupling mechanisms. Here, we show how the Dexter-like intervalley coupling mixes A and B states from opposite valleys leading to a significant broadening γB 1s of the B 1s exciton. The effect is much more pronounced in tungsten-based TMDs, where the coupling excitonic states are quasi-resonant. We calculate a ratio γB B 1s /γA B 1s ≈ 4.0, which is in good agreement with the experimentally measured value of 3.9 ± 0.7. In addition to the broadening effect, the Dexter-like intervalley coupling also leads to a considerable energy renormalization resulting in an increased energetic distance between A 1s and B 1s states.
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| 8. |
- Brorsson, Joakim, 1988, et al.
(author)
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Efficient Calculation of the Lattice Thermal Conductivity by Atomistic Simulations with Ab Initio Accuracy
- 2022
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In: Advanced Theory and Simulations. - : Wiley. - 2513-0390. ; 5:2
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Journal article (peer-reviewed)abstract
- High-order force constant expansions can provide accurate representations of the potential energy surface relevant to vibrational motion. They can be efficiently parametrized using quantum mechanical calculations and subsequently sampled at a fraction of the cost of the underlying reference calculations. Here, force constant expansions are combined via the hiphive package with GPU-accelerated molecular dynamics simulations via the GPUMD package to obtain an accurate, transferable, and efficient approach for sampling the dynamical properties of materials. The performance of this methodology is demonstrated by applying it both to materials with very low thermal conductivity (Ba8Ga16Ge30, SnSe) and a material with a relatively high lattice thermal conductivity (monolayer-MoS2). These cases cover both situations with weak (monolayer-MoS2, SnSe) and strong (Ba8Ga16Ge30) pho renormalization. The simulations also enable to access complementary information such as the spectral thermal conductivity, which allows to discriminate the contribution by different phonon modes while accounting for scattering to all orders. The software packages described here are made available to the scientific community as free and open-source software in order to encourage the more widespread use of these techniques as well as their evolution through continuous and collaborative development.
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| 9. |
- Djimde, Moussa, et al.
(author)
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Efficacy and safety of pyronaridine-artesunate (PYRAMAX) for the treatment of P. falciparum uncomplicated malaria in African pregnant women (PYRAPREG) : study protocol for a phase 3, non-inferiority, randomised open-label clinical trial
- 2023
-
In: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 13:10
-
Journal article (peer-reviewed)abstract
- Introduction Malaria infection during pregnancy increases the risk of low birth weight and infant mortality and should be prevented and treated. Artemisinin-based combination treatments are generally well tolerated, safe and effective; the most used being artemether-lumefantrine (AL) and dihydroartemisinin-piperaquine (DP). Pyronaridine-artesunate (PA) is a new artemisinin-based combination. The main objective of this study is to determine the efficacy and safety of PA versus AL or DP when administered to pregnant women with confirmed Plasmodium falciparum infection in the second or third trimester. The primary hypothesis is the pairwise non-inferiority of PA as compared with either AL or DP.Methods and analysis A phase 3, non-inferiority, randomised, open-label clinical trial to determine the safety and efficacy of AL, DP and PA in pregnant women with malaria in five sub-Saharan, malaria-endemic countries (Burkina Faso, Democratic Republic of the Congo, Mali, Mozambique and the Gambia). A total of 1875 pregnant women will be randomised to one of the treatment arms. Women will be actively monitored until Day 63 post-treatment, at delivery and 4–6 weeks after delivery, and infants’ health will be checked on their first birthday. The primary endpoint is the PCR-adjusted rate of adequate clinical and parasitological response at Day 42 in the per-protocol population.Ethics and dissemination This protocol has been approved by the Ethics Committee for Health Research in Burkina Faso, the National Health Ethics Committee in the Democratic Republic of Congo, the Ethics Committee of the Faculty of Medicine and Odontostomatology/Faculty of Pharmacy in Mali, the Gambia Government/MRCG Joint Ethics Committee and the National Bioethics Committee for Health in Mozambique. Written informed consent will be obtained from each individual prior to her participation in the study. The results will be published in peer-reviewed open access journals and presented at (inter)national conferences and meetings.Trial registration number PACTR202011812241529.
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| 10. |
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| 11. |
- Erhart, P., et al.
(author)
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Finite-Elemente-Analyse abdomineller Aortenaneurysmen : Aktuelle Wertigkeit als Ergänzung zur herkömmlichen Diagnostik
- 2015
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In: Gefässchirurgie. - : Springer Science and Business Media LLC. - 0948-7034 .- 1434-3932. ; 20:7, s. 503-507
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Journal article (peer-reviewed)abstract
- Finite element analysis (FEA) of abdominal aortic aneurysms (AAA) could enable a more precise patient-specific risk assessment of AAA rupture. Further clinical studies are needed to validate this model as a clinical decision-making tool. The A4clinics™ software provides a simple and detailed FEA simulation. After implementation of a FEA workstation in a high volume university vascular center, relevant studies for further model validation are expected to be carried out.
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| 12. |
- Erhart, Paul, 1978, et al.
(author)
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Formation and switching of defect dipoles in acceptor-doped lead titanate: A kinetic model based on first-principles calculations
- 2013
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In: Physical Review B. - 1098-0121. ; 88:2, s. artikel nr 024107-
-
Journal article (peer-reviewed)abstract
- The formation and field-induced switching of defect dipoles in acceptor doped lead titanate is described by a kinetic model representing an extension of the well established Arlt-Neumann model [Ferroelectrics 76, 303 (1987)]. Energy barriers for defect association and reorientation of oxygen vacancy-dopant (Cu and Fe) complexes are obtained from first-principles calculations and serve as input for kinetic coefficients of the rate equation model. The numerical solution of the model describes the time evolution of the oxygen vacancy distribution at different temperatures and dopant concentrations in the presence or absence of an alternating external field. We predict the characteristic time scale for the alignment of all defect dipoles with the spontaneous polarization of the surrounding matrix. In this state the defect dipoles act as obstacles for domain wall motion and contribute to the experimentally observed aging. Under cycling conditions the fully aligned configuration is perturbed and a dynamic equilibrium is established with defect dipoles in parallel and antiparallel orientation relative to the spontaneous polarization. This process can be related to the deaging behavior of piezoelectric ceramics.
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| 13. |
- Erhart, P, et al.
(author)
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Prediction of Rupture Sites in Abdominal Aortic Aneurysms After Finite Element Analysis
- 2016
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In: Journal of endovascular therapy : an official journal of the International Society of Endovascular Specialists. - : SAGE Publications. - 1545-1550. ; 23:1, s. 115-120
-
Journal article (peer-reviewed)abstract
- Purpose: To associate regions of highest local rupture risk from finite element analysis (FEA) to subsequent rupture sites in abdominal aortic aneurysms (AAA). Methods: This retrospective multicenter study analyzed computed tomography angiography (CTA) data from 13 asymptomatic AAA patients (mean age 76 years; 8 men) experiencing rupture at a later point in time between 2005 and 2011. All patients had CTA scans before and during the rupture event. FEA was performed to calculate peak wall stress (PWS), peak wall rupture risk (PWRR), rupture risk equivalent diameters (RRED), and the intraluminal thrombus volume (ILTV). PWS and PWRR locations in the prerupture state were compared with subsequent CTA rupture findings. Visible contrast extravasation was considered a definite (n=5) rupture sign, while a periaortic hematoma was an indefinite (n=8) sign. A statistical comparison was performed between the 13-patient asymptomatic AAA group before and during rupture and a 23-patient diameter-matched asymptomatic AAA control group that underwent elective surgery. Results: The asymptomatic AAAs before rupture showed significantly higher PWRR and RRED values compared to the matched asymptomatic AAA control group (median values 0.74 vs 0.52 and 77 vs 59 mm, respectively; p<0.0001 for both). No statistical differences could be found for PWS and ILTV. Ruptured AAAs showed the highest maximum diameters, PWRR, and RRED values. In 7 of the ruptured AAAs (2 definite and 5 indefinite rupture signs), CTA rupture sites correlated with prerupture PWRR locations. Conclusion: The location of the PWRR in unruptured AAAs predicted future rupture sites in several cases. Asymptomatic AAA patients with high PWRR and RRED values have an increased rupture risk.
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| 14. |
- Fojt, Jakub, 1996, et al.
(author)
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Dipolar coupling of nanoparticle-molecule assemblies: An efficient approach for studying strong coupling
- 2021
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In: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 154:9
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Journal article (peer-reviewed)abstract
- Strong light-matter interactions facilitate not only emerging applications in quantum and non-linear optics but also modifications of properties of materials. In particular, the latter possibility has spurred the development of advanced theoretical techniques that can accurately capture both quantum optical and quantum chemical degrees of freedom. These methods are, however, computationally very demanding, which limits their application range. Here, we demonstrate that the optical spectra of nanoparticle-molecule assemblies, including strong coupling effects, can be predicted with good accuracy using a subsystem approach, in which the response functions of different units are coupled only at the dipolar level. We demonstrate this approach by comparison with previous time-dependent density functional theory calculations for fully coupled systems of Al nanoparticles and benzene molecules. While the present study only considers few-particle systems, the approach can be readily extended to much larger systems and to include explicit optical-cavity modes.
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| 15. |
- Fojt, Jakub, 1996, et al.
(author)
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Hot-Carrier Transfer across a Nanoparticle-Molecule Junction: The Importance of Orbital Hybridization and Level Alignment
- 2022
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In: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 22:21, s. 8786-8792
-
Journal article (peer-reviewed)abstract
- While direct hot-carrier transfer can increase photocatalytic activity, it is difficult to discern experimentally and competes with several other mechanisms. To shed light on these aspects, here, we model from first-principles hot-carrier generation across the interface between plasmonic nanoparticles and a CO molecule. The hot-electron transfer probability depends nonmonotonically on the nanoparticle-molecule distance and can be effective at long distances, even before a strong chemical bond can form; hot-hole transfer on the other hand is limited to shorter distances. These observations can be explained by the energetic alignment between molecular and nanoparticle states as well as the excitation frequency. The hybridization of the molecular orbitals is the key predictor for hot-carrier transfer in these systems, emphasizing the necessity of ground state hybridization for accurate predictions. Finally, we show a nontrivial dependence of the hot-carrier distribution on the excitation energy, which could be exploited when optimizing photocatalytic systems.
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| 16. |
- Fojt, Jakub, 1996, et al.
(author)
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Tailoring Hot-Carrier Distributions of Plasmonic Nanostructures through Surface Alloying
- 2024
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In: ACS Nano. - 1936-086X .- 1936-0851. ; 18:8, s. 6398-6405
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Journal article (peer-reviewed)abstract
- Alloyed metal nanoparticles are a promising platform for plasmonically enabled hot-carrier generation, which can be used to drive photochemical reactions. Although the non-plasmonic component in these systems has been investigated for its potential to enhance catalytic activity, its capacity to affect the photochemical process favorably has been underexplored by comparison. Here, we study the impact of surface alloy species and concentration on hot-carrier generation in Ag nanoparticles. By first-principles simulations, we photoexcite the localized surface plasmon, allow it to dephase, and calculate spatially and energetically resolved hot-carrier distributions. We show that the presence of non-noble species in the topmost surface layer drastically enhances hot-hole generation at the surface at the expense of hot-hole generation in the bulk, due to the additional d-type states that are introduced to the surface. The energy of the generated holes can be tuned by choice of the alloyant, with systematic trends across the d-band block. Already low surface alloy concentrations have a large impact, with a saturation of the enhancement effect typically close to 75% of a monolayer. Hot-electron generation at the surface is hindered slightly by alloying, but here a judicious choice of the alloy composition allows one to strike a balance between hot electrons and holes. Our work underscores the promise of utilizing multicomponent nanoparticles to achieve enhanced control over plasmonic catalysis and provides guidelines for how hot-carrier distributions can be tailored by designing the electronic structure of the surface through alloying.
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| 17. |
- Hashemi, A., et al.
(author)
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Photoluminescence line shapes for color centers in silicon carbide from density functional theory calculations
- 2021
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In: Physical Review B. - 2469-9969 .- 2469-9950. ; 103:12
-
Journal article (peer-reviewed)abstract
- Silicon carbide with optically and magnetically active point defects offers unique opportunities for quantum technology applications. Since interaction with these defects commonly happens through optical excitation and deexcitation, a complete understanding of their light-matter interaction in general and optical signatures in particular is crucial. Here, we employ quantum mechanical density functional theory calculations to investigate the photoluminescence line shapes of selected, experimentally observed color centers (including single vacancies, double vacancies, and vacancy-impurity pairs) in 4H-SiC. The analysis of zero-phonon lines as well as Huang-Rhys and Debye-Waller factors is accompanied by a detailed study of the underlying lattice vibrations. We show that the defect line shapes are governed by strong coupling to bulk phonons at lower energies and localized vibrational modes at higher energies. Generally, good agreement with the available experimental data is obtained, and thus we expect our theoretical work to be beneficial for the identification of defect signatures in the photoluminescence spectra and thereby advance the research in quantum photonics and quantum information processing.
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| 18. |
- Ibragimova, Rina, et al.
(author)
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Surface Functionalization of 2D MXenes: Trends in Distribution, Composition, and Electronic Properties
- 2021
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In: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 12:9, s. 2377-2384
-
Journal article (peer-reviewed)abstract
- Using a multiscale computational scheme, we study the trends in distribution and composition of the surface functional groups -O, -OH, and -F on two-dimensional (2D) transition metal carbides and nitrides (MXenes). We consider Ti2N, Ti4N3, Nb2C, Nb4C3, Ti2C, and Ti3C2 to explore MXenes with different chemistry and different number of atomic layers. Using a combination of cluster expansion, Monte Carlo, and density functional theory methods, we study the distribution and composition of functional groups at experimentally relevant conditions. We show that mixtures of functional groups are favorable on all studied MXene surfaces. The distribution of functional groups appears to be largely independent of the type of metal, carbon, or nitrogen species and/or number of atomic layers in the MXene. We further show that some properties (e.g., the work function) strongly depend on the surface composition, while others, for example, the electric conductivity, exhibit only a weak dependence.
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| 19. |
- Imboden, Medea, et al.
(author)
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Epigenome-wide association study of lung function level and its change
- 2019
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In: European Respiratory Journal. - : European Respiratory Society. - 0903-1936 .- 1399-3003. ; 54:1
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Journal article (peer-reviewed)abstract
- Previous reports link differential DNA methylation (DNAme) to environmental exposures that are associated with lung function. Direct evidence on lung function DNAme is, however, limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults.In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, 6-15 years apart, in the same participants of three adult population-based discovery cohorts (n=2043). Associated DNAme markers (p<5×10-7) were tested in seven replication cohorts (adult: n=3327; childhood: n=420). Technical bias-adjusted residuals of a regression of the normalised absolute β-values on control probe-derived principle components were regressed on level and change of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and their ratio (FEV1/FVC) in the covariate-adjusted discovery EWAS. Inverse-variance-weighted meta-analyses were performed on results from discovery and replication samples in all participants and never-smokers.EWAS signals were enriched for smoking-related DNAme. We replicated 57 lung function DNAme markers in adult, but not childhood samples, all previously associated with smoking. Markers not previously associated with smoking failed replication. cg05575921 (AHRR (aryl hydrocarbon receptor repressor)) showed the statistically most significant association with cross-sectional lung function (FEV1/FVC: pdiscovery=3.96×10-21 and pcombined=7.22×10-50). A score combining 10 DNAme markers previously reported to mediate the effect of smoking on lung function was associated with lung function (FEV1/FVC: p=2.65×10-20).Our results reveal that lung function-associated methylation signals in adults are predominantly smoking related, and possibly of clinical utility in identifying poor lung function and accelerated decline. Larger studies with more repeat time-points are needed to identify lung function DNAme in never-smokers and in children.
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| 20. |
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| 21. |
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| 22. |
- Rossi, T. P., et al.
(author)
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Kohn-Sham Decomposition in Real-Time Time-Dependent Density-Functional Theory: An Efficient Tool for Analyzing Plasmonic Excitations
- 2017
-
In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9626 .- 1549-9618. ; 13:10, s. 4779-4790
-
Journal article (peer-reviewed)abstract
- Electronic excitations can be efficiently analyzed in terms of the underlying Kohn-Sham (KS) electron-hole transitions. While such a decomposition is readily available in the linear-response time-dependent density-functional theory (TDDFT) approaches based on the Casida equations, a comparable analysis is less commonly conducted within the real-time-propagation TDDFT (RT-TDDFT). To improve this situation, we present here an implementation of a KS decomposition tool within the local-basis-set RT-TDDFT code in the free GPAW package. Our implementation is based on postprocessing of data that is readily available during time propagation, which is important for retaining the efficiency of the underlying RT-TDDFT to large systems. After benchmarking our implementation on small benzene derivatives by explicitly reconstructing the Casida eigenvectors from RT-TDDFT, we demonstrate the performance of the method by analyzing the plasmon resonances of icosahedral silver nanoparticles up to Ag-561. The method provides a clear description of the splitting of the plasmon in small nanoparticles due to individual single-electron transitions as well as the formation of a distinct d-electron-screened plasmon resonance in larger nanoparticles.
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| 23. |
- Shang, Z., et al.
(author)
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Local vibrational modes of Si vacancy spin qubits in SiC
- 2020
-
In: Physical Review B. - 2469-9969 .- 2469-9950. ; 101:14
-
Journal article (peer-reviewed)abstract
- Silicon carbide is a very promising platform for quantum applications because of the extraordinary spin and optical properties of point defects in this technologically friendly material. These properties are strongly influenced by crystal vibrations, but the exact relationship between them and the behavior of spin qubits is not fully investigated. We uncover the local vibrational modes of the Si vacancy spin qubits in as-grown 4H-SiC. We apply microwave-assisted spectroscopy to isolate the contribution from one particular type of defects, the so-called V2 center, and observe the zero-phonon line together with seven equally separated phonon replicas. Furthermore, we present first-principles calculations of the photoluminescence line shape, which are in excellent agreement with our experimental data. To boost up the calculation accuracy and decrease the computation time, we extract the force constants using machine-learning algorithms. This allows us to identify the dominant modes in the lattice vibrations coupled to an excited electron during optical emission in the Si vacancy. A resonance phonon energy of 36 meV and a Debye-Waller factor of about 6% are obtained. We establish experimentally that the activation energy of the optically induced spin polarization is given by the local vibrational energy. Our findings give insight into the coupling of electronic states to vibrational modes in SiC spin qubits, which is essential to predict their spin, optical, mechanical, and thermal properties. The approach described can be applied to a large variety of spin defects with spectrally overlapped contributions in SiC as well as in other three-and two-dimensional materials.
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| 24. |
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| 25. |
- Thompson, J. J.P., et al.
(author)
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Phonon-Bottleneck Enhanced Exciton Emission in 2D Perovskites
- 2024
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In: Advanced Energy Materials. - 1614-6840 .- 1614-6832. ; 14:20
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Journal article (peer-reviewed)abstract
- Layered halide perovskites exhibit remarkable optoelectronic properties and technological promise, driven by strongly bound excitons. The interplay of spin-orbit and exchange coupling creates a rich excitonic landscape, determining their optical signatures and exciton dynamics. Despite the dark excitonic ground state, surprisingly efficient emission from higher-energy bright states has puzzled the scientific community, sparking debates on relaxation mechanisms. Combining low-temperature magneto-optical measurements with sophisticated many-particle theory, the origin of the bright exciton emission in perovskites is elucidated by tracking the thermalization of dark and bright excitons under a magnetic field. The unexpectedly high emission is clearly attributed to a pronounced phonon-bottleneck effect, considerably slowing down the relaxation toward the energetically lowest dark states. It is demonstrated that this bottleneck can be tuned by manipulating the bright-dark energy splitting and optical phonon energies, offering valuable insights and strategies for controlling exciton emission in layered perovskite materials that is crucial for optoelectronics applications.
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