| 1. |
- Ahlberg, Sebastian, et al.
(författare)
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Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA
- 2015
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- 30% of the DNA in E. coli bacteria is covered by proteins. Such a high degree of crowding affects the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc) in ways that are not yet fully understood. In this paper, we theoretically address the diffusion constant of a tracer particle in a one-dimensional system surrounded by impenetrable crowder particles. While the tracer particle always stays on the lattice, crowder particles may unbind to a surrounding bulk and rebind at another, or the same, location. In this scenario we determine how the long time diffusion constant D (after many unbinding events) depends on (i) the unbinding rate of crowder particles k(off), and (ii) crowder particle line density rho, from simulations (using the Gillespie algorithm) and analytical calculations. For small k(off), we find D similar to k(off)/rho(2) when crowder particles do not diffuse on the line, and D similar to root Dk(off)/rho when they are diffusing; D is the free particle diffusion constant. For large k(off), we find agreement with mean-field results which do not depend on k(off). From literature values of k(off) and D, we show that the small k(off) -limit is relevant for in vivo protein diffusion on crowded DNA. Our results apply to single-molecule tracking experiments.
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| 2. |
- Dods, Robert, 1989, et al.
(författare)
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Ultrafast structural changes within a photosynthetic reaction centre.
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 589:7841, s. 310-314
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Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.
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| 3. |
- Felsberg, Michael, 1974-, et al.
(författare)
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The Thermal Infrared Visual Object Tracking VOT-TIR2016 Challenge Results
- 2016
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Ingår i: Computer Vision – ECCV 2016 Workshops. ECCV 2016.. - Cham : SPRINGER INT PUBLISHING AG. - 9783319488813 - 9783319488806 ; , s. 824-849
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Konferensbidrag (refereegranskat)abstract
- The Thermal Infrared Visual Object Tracking challenge 2016, VOT-TIR2016, aims at comparing short-term single-object visual trackers that work on thermal infrared (TIR) sequences and do not apply pre-learned models of object appearance. VOT-TIR2016 is the second benchmark on short-term tracking in TIR sequences. Results of 24 trackers are presented. For each participating tracker, a short description is provided in the appendix. The VOT-TIR2016 challenge is similar to the 2015 challenge, the main difference is the introduction of new, more difficult sequences into the dataset. Furthermore, VOT-TIR2016 evaluation adopted the improvements regarding overlap calculation in VOT2016. Compared to VOT-TIR2015, a significant general improvement of results has been observed, which partly compensate for the more difficult sequences. The dataset, the evaluation kit, as well as the results are publicly available at the challenge website.
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| 4. |
- Frisk, Andreas, et al.
(författare)
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Magnetic and structural characterization of CoFeZr thin films grown by combinatorial sputtering
- 2019
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Ingår i: Physical Review Materials. - 2475-9953. ; 3:7
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Tidskriftsartikel (refereegranskat)abstract
- We report on a detailed investigation of structural and magnetic properties of thin CoFeZr films, produced by combinatorial cosputtering, with compositions in the ranges 30-85 at.% Co, 12-63 at.% Fe, and 4-8 at.% Zr. Extended x-ray absorption fine structure and x-ray diffraction measurements reveal that alloys with a Zr content below 5 at.% are polycrystalline with a bcc structure, while an amorphous morphology is stabilized at Zr contents above 6 at.%. All samples display a growth-induced in-plane uniaxial anisotropy, which is closely related to the Zr concentration gradients across the wafers. A model for the angular dependence of the reduced remanence, including a Gaussian distribution of easy/hard anisotropy axes, is presented and successfully used to fit the data for all samples. The magnetic moments of the polycrystalline films approximately follow the Slater-Pauling curve, and the magnetic moments of the amorphous films follow a similar trend, but with about 20 % lower values. X-ray magnetic circular dichroism measurements show, for the amorphous films, that the Co moments are virtually constant at 1.7(2)μB/atom.
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| 5. |
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| 6. |
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| 7. |
- Muscas, Giuseppe, et al.
(författare)
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Unveiling the local structure of the amorphous metal Fe(1−x)Zrx combining first-principles-based simulations and modelling of EXAFS spectra
- 2023
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Amorphous alloys exhibit useful properties such as the excellent soft magnetic behaviour of Fe-based metallic glasses. The detailed structure of amorphous Fe(1−x)Zrx with x = 0.07, 0.10, and 0.20 is in this work explored through a synergetic combination of atomistic simulations and experimental characterisation. Thin-film samples were investigated using X-ray diffraction and extended X-ray absorption fine structure (EXAFS), while the corresponding atomic structures were simulated using an efficient first-principles-based method called stochastic quenching (SQ). The simulated local atomic arrangements are investigated by constructing the radial- and angular-distribution functions, as well as by Voronoi tesselation. The radial distribution functions are then used to construct a model to fit simultaneously the experimental EXAFS data of multiple samples with different compositions, creating a simple yet accurate description of the atomic structures valid for any composition in the range x = 0.07 to 0.20, using a minimal number of free parameters. This approach significantly improves the accuracy of the fitted parameters and allows us to relate the compositional dependence of the amorphous structures with the magnetic properties. The proposed EXAFS fitting process can be generalised to other amorphous systems, contributing to the understanding of structure-property relationships and the development of amorphous alloys with tailored functional properties.
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| 8. |
- Yu, Meng, et al.
(författare)
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Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19
- 2023
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Ingår i: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Effective humoral immune responses require well-orchestrated B and T follicular helper (Tfh) cell interactions. Whether these interactions are impaired and associated with COVID-19 disease severity is unclear. Here, longitudinal blood samples across COVID-19 disease severity are analysed. We find that during acute infection SARS-CoV-2-specific circulating Tfh (cTfh) cells expand with disease severity. SARS-CoV-2-specific cTfh cell frequencies correlate with plasmablast frequencies and SARS-CoV-2 antibody titers, avidity and neutralization. Furthermore, cTfh cells but not other memory CD4 T cells, from severe patients better induce plasmablast differentiation and antibody production compared to cTfh cells from mild patients. However, virus-specific cTfh cell development is delayed in patients that display or later develop severe disease compared to those with mild disease, which correlates with delayed induction of high-avidity neutralizing antibodies. Our study suggests that impaired generation of functional virus-specific cTfh cells delays high-quality antibody production at an early stage, potentially enabling progression to severe disease. T follicular helper cells (Tfh) enhance antibody responses and can circulate or be resident in lymph nodes. Here the authors show that during acute SARS-CoV-2 infection, circulating Tfh cells correlate with antibody titres and plasmablast levels but in more severe COVID-19 cases, cTfh generation is delayed.
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