| 11. |
- Fan, Zheyong, et al.
(författare)
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GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations
- 2022
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 157:11
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Tidskriftsartikel (refereegranskat)abstract
- We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in Fan et al. [Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package gpumd. We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach. We also detail our efficient implementation of the NEP approach in graphics processing units as well as our workflow for the construction of NEP models and demonstrate their application in large-scale atomistic simulations. By comparing to state-of-the-art MLPs, we show that the NEP approach not only achieves above-average accuracy but also is far more computationally efficient. These results demonstrate that the gpumd package is a promising tool for solving challenging problems requiring highly accurate, large-scale atomistic simulations. To enable the construction of MLPs using a minimal training set, we propose an active-learning scheme based on the latent space of a pre-trained NEP model. Finally, we introduce three separate Python packages, viz., gpyumd, calorine, and pynep, that enable the integration of gpumd into Python workflows.
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| 12. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 13. |
- Guo, Jiawei, et al.
(författare)
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Bimetallic Sulfides with Vacancy Modulation Exhibit Enhanced Electrochemical Performance
- 2024
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Ingår i: Advanced Functional Materials. - 1616-3028 .- 1616-301X. ; In Press
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Tidskriftsartikel (refereegranskat)abstract
- Transition bimetallic sulfides show significant promise for energy-related applications because of their plentiful active sites and synergistic redox activity. However, limited pore size and low-conductivity issues hinder their application. The structure of NiCo-S with rich sulfur vacancies is first predicted by density functional theory (DFT) calculations. Different sulfur vacancy concentrations are modeled by DFT calculations, and the results confirm that sulfur vacancies enhance the conductivity of the electrode material and are more beneficial for the adsorption of OH* species. It is verified by the differential charge density that the electric field formed on the surface of the electrode can lead to strong interfacial interactions by electron aggregation, which promotes electron/ion transfer kinetics. Furthermore, NiCo-S nanosheets are prepared on carbon cloth enriched with different concentrations of sulfur vacancies (denoted as NiCo-Sv-x, with x representing the concentration of sulfur vacancies) by sulfide etching NiCo-MOF and annealing under H2/Ar atmosphere. The NiCo-Sv-x electrodes obtained are applied to the cathode of supercapacitors and the anode of the oxygen evolution reaction. Through combining experimental and theoretical analysis, the effect of vacancy defect engineering on the electrochemical performance of the electrode materials is further confirmed. This work constructs transition metal sulfides with different sulfur vacancy concentrations through DFT model prediction and experimental validation, further confirming the effect of vacancy defect engineering on the electrochemical performance of electrode materials. Therefore, this modulation of sulfur vacancy concentration by vacancy defects contributes to the construction of electrode materials with excellent performance for energy applications.
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| 14. |
- He, Lei, et al.
(författare)
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Non-symmetric responses of leaf onset date to natural warming and cooling in northern ecosystems
- 2023
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Ingår i: PNAS Nexus. - 2752-6542. ; 2:9
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Tidskriftsartikel (refereegranskat)abstract
- The northern hemisphere has experienced regional cooling, especially during the global warming hiatus (1998-2012) due to ocean energy redistribution. However, the lack of studies about the natural cooling effects hampers our understanding of vegetation responses to climate change. Using 15,125 ground phenological time series at 3,620 sites since the 1950s and 31-year satellite greenness observations (1982-2012) covering the warming hiatus period, we show a stronger response of leaf onset date (LOD) to natural cooling than to warming, i.e. the delay of LOD caused by 1°C cooling is larger than the advance of LOD with 1°C warming. This might be because cooling leads to larger chilling accumulation and heating requirements for leaf onset, but this non-symmetric LOD response is partially offset by warming-related drying. Moreover, spring greening magnitude, in terms of satellite-based greenness and productivity, is more sensitive to LOD changes in the warming area than in the cooling. These results highlight the importance of considering non-symmetric responses of spring greening to warming and cooling when predicting vegetation-climate feedbacks.
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| 15. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 16. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 17. |
- Liu, Wei, et al.
(författare)
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Coherent dynamics of multi-spin V-B(-) center in hexagonal boron nitride
- 2022
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Ingår i: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Hexagonal boron nitride (hBN) has recently been demonstrated to contain optically polarized and detected electron spins that can be utilized for implementing qubits and quantum sensors in nanolayered-devices. Understanding the coherent dynamics ofmicrowave driven spins in hBN is of crucial importance for advancing these emerging new technologies. Here, we demonstrate and study the Rabi oscillation and related phenomena of a negatively charged boron vacancy (V-B(-)) spin ensemble in hBN. We report on different dynamics of the V-B(-) spins at weak and strong magnetic fields. In the former case the defect behaves like a single electron spin system, while in the latter case it behaves like a multi-spin system exhibiting multiple-frequency dynamical oscillation as beat in the Ramsey fringes. We also carry out theoretical simulations for the spin dynamics of V-B(-) and reveal that the nuclear spins can be driven via the strong electron nuclear coupling existing in V-B(-) center, which can be modulated by the magnetic field and microwave field.
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| 18. |
- Mishra, A., et al.
(författare)
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Stroke genetics informs drug discovery and risk prediction across ancestries
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 611, s. 115-123
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Tidskriftsartikel (refereegranskat)abstract
- Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry(1,2). Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis(3), and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach(4), we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry(5). Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries.
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| 19. |
- Pang, Kanglei, 1993-, et al.
(författare)
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Redirecting configuration of atomically dispersed selenium catalytic sites for efficient hydrazine oxidation
- 2024
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Ingår i: Matter. - 2590-2393 .- 2590-2385. ; 7:2, s. 655-667
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the reconstruction of surface sites is crucial for gaining insights into the true active sites and catalytic mechanisms. While extensive research has been conducted on reconstruction behaviors of atomically dispersed metallic catalytic sites, limited attention has been paid to non-metallic ones despite their potential catalytic activity comparable or even superior to their noble-metal counterpart. Herein, we report a carbonaceous, atomically dispersed non-metallic selenium catalyst that displayed exceptional catalytic activity in the hydrazine oxidation reaction (HzOR) in alkaline media, outperforming the noble-metal Pt catalysts. In situ X-ray absorption spectroscopy (XAS) and Fourier transform infrared spectroscopy revealed that the pristine SeC4 site pre-adsorbs an ∗OH ligand, followed by HzOR occurring on the other side of the OH–SeC4. Theoretical calculations proposed that the pre-adsorbed ∗OH group pulls electrons from the Se site, resulting in a more positively charged Se and a higher polarity of Se–C bonds, thereby enhancing surface reactivity toward HzO/R.
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| 20. |
- Turenne, Diego, et al.
(författare)
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Nonequilibrium sub–10 nm spin-wave soliton formation in FePt nanoparticles
- 2022
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:13
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Tidskriftsartikel (refereegranskat)abstract
- Magnetic nanoparticles such as FePt in the L10 phase are the bedrock of our current data storage technology. As the grains become smaller to keep up with technological demands, the superparamagnetic limit calls for materials with higher magnetocrystalline anisotropy. This, in turn, reduces the magnetic exchange length to just a few nanometers, enabling magnetic structures to be induced within the nanoparticles. Here, we describe the existence of spin-wave solitons, dynamic localized bound states of spin-wave excitations, in FePt nanoparticles. We show with time-resolved x-ray diffraction and micromagnetic modeling that spin-wave solitons of sub–10 nm sizes form out of the demagnetized state following femtosecond laser excitation. The measured soliton spin precession frequency of 0.1 THz positions this system as a platform to develop novel miniature devices.
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