| 1. |
- Bacic, Luka, et al.
(författare)
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Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome
- 2021
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and suggest that ALC1 preferentially slides nucleosomes away from DNA breaks.
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| 2. |
- Barker, David, et al.
(författare)
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Experimental Verification of the Work Fluctuation-Dissipation Relation for Information-to-Work Conversion
- 2022
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Ingår i: Physical Review Letters. - 0031-9007. ; 128:4
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Tidskriftsartikel (refereegranskat)abstract
- We study experimentally work fluctuations in a Szilard engine that extracts work from information encoded as the occupancy of an electron level in a semiconductor quantum dot. We show that as the average work extracted per bit of information increases toward the Landauer limit Formula Presented, the work fluctuations decrease in accordance with the work fluctuation-dissipation relation. We compare the results to a protocol without measurement and feedback and show that when no information is used, the work output and fluctuations vanish simultaneously, contrasting the information-to-energy conversion case where increasing amount of work is produced with decreasing fluctuations. Our study highlights the importance of fluctuations in the design of information-to-work conversion processes.
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| 3. |
- Calabrese, Claudia, et al.
(författare)
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Genomic basis for RNA alterations in cancer
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
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Tidskriftsartikel (refereegranskat)abstract
- Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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| 4. |
- Debbarma, Rousan, et al.
(författare)
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Effects of Parity and Symmetry on the Aharonov-Bohm Phase of a Quantum Ring
- 2021
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992.
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Tidskriftsartikel (refereegranskat)abstract
- We experimentally investigate the properties of one-dimensional quantum rings that form near the surface of nanowire quantum dots. In agreement with theoretical predictions, we observe the appearance of forbidden gaps in the evolution of states in a magnetic field as the symmetry of a quantum ring is reduced. For a twofold symmetry, our experiments confirm that orbital states are grouped pairwise. Here, a π-phase shift can be introduced in the Aharonov-Bohm relation by controlling the relative orbital parity using an electric field. Studying rings with higher symmetry, we note exceptionally large orbital contributions to the effective g-factor (up to 300), which are many times higher than those previously reported. These findings show that the properties of a phase-coherent system can be significantly altered by the nanostructure symmetry and its interplay with wave function parity.
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| 5. |
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| 6. |
- Debbarma, Rousan, et al.
(författare)
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Josephson Junction π-0 Transition Induced by Orbital Hybridization in a Double Quantum Dot
- 2023
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Ingår i: Physical Review Letters. - 0031-9007. ; 131:25
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Tidskriftsartikel (refereegranskat)abstract
- In this Letter, we manipulate the phase shift of a Josephson junction using a parallel double quantum dot (QD). By employing a superconducting quantum interference device, we determine how orbital hybridization and detuning affect the current-phase relation in the Coulomb blockade regime. For weak hybridization between the QDs, we find π junction characteristics if at least one QD has an unpaired electron. Notably the critical current is higher when both QDs have an odd electron occupation. By increasing the inter-QD hybridization the critical current is reduced, until eventually a π-0 transition occurs. A similar transition appears when detuning the QD levels at finite hybridization. Based on a zero-bandwidth model, we argue that both cases of phase-shift transitions can be understood considering an increased weight of states with a double occupancy in the ground state and with the Cooper pair transport dominated by local Andreev reflection.
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| 7. |
- Dorsch, Sven, et al.
(författare)
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Gate control, g factors, and spin-orbit energy of p -type GaSb nanowire quantum dot devices
- 2021
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Ingår i: Physical Review B. - 2469-9950. ; 103:24
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Tidskriftsartikel (refereegranskat)abstract
- Proposals for quantum information applications are frequently based on the coherent manipulation of spins confined to quantum dots. For these applications, p-type III-V material systems promise a reduction of the hyperfine interaction while maintaining large g factors and strong spin-orbit interaction. In this Letter, we study bottom-gated device architectures to realize single and serial multiquantum dot systems in Schottky-contacted p-type GaSb nanowires. We find that the effect of potentials applied to gate electrodes on the nanowire is highly localized to the immediate vicinity of the gate electrode only, which prevents the formation of double quantum dots with commonly used device architectures. We further study the transport properties of a single quantum dot induced by bottom gating and find large gate-voltage dependent variations of the g∗ factors up to 8.1±0.2 as well as spin-orbit energies between 110 and 230 μeV.
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| 8. |
- Ek, M., et al.
(författare)
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Electron channelling : challenges and opportunities for compositional analysis of nanowires by TEM
- 2020
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Ingår i: Nanotechnology. - : IOP Publishing. - 0957-4484 .- 1361-6528. ; 31:36
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Tidskriftsartikel (refereegranskat)abstract
- Energy dispersive x-ray spectroscopy in a transmission electron microscope is often the first method employed to characterize the composition of nanowires. Ideally, it should be accurate and sensitive down to fractions of an atomic percent, and quantification results are often reported as such. However, one can often get substantial errors in accuracy even though the precision is high: for nanowires it is common for the quantified V/III atomic ratios to differ noticeably from 1. Here we analyse the origin of this systematic error in accuracy for quantification of the composition of III-V nanowires. By varying the electron illumination direction, we find electron channelling to be the primary cause, being responsible for errors in quantified V/III atomic ratio of 50%. Knowing the source of the systematic errors is required for applying appropriate corrections. Lastly, we show how channelling effects can provide information on the crystallographic position of dopants.
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| 9. |
- Escobar Steinvall, Simon, et al.
(författare)
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Visualizing the Mechanism Switching in High-Temperature Au-Catalyzed InAs Nanowire Growth
- 2023
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Ingår i: Crystal Growth and Design. - 1528-7483. ; 23:9, s. 6228-6232
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Tidskriftsartikel (refereegranskat)abstract
- We use environmental transmission electron microscopy to observe in situ the switch from an axial vapor-liquid-solid (VLS) growth mechanism in Au-catalyzed InAs nanowires toward a radial vapor-solid (VS) one, dominated by layers nucleating at the triple-phase line. At elevated temperatures, in addition to high V/III ratios, the affinity for In in the Au catalyst will be greater than that of In in InAs, which in turn reduces the driving force and probability for nucleation at the liquid-solid interface. Consequently, with increased temperature, the catalyst particle stops acting as a sink for incoming material and the decomposition of precursors away from the catalyst increases, making radial vapor-solid growth the dominating growth mechanism. It is further observed that the growth proceeds through multistep propagation rather than a layer-by-layer propagation under these conditions.
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| 10. |
- Gawel, Erik, et al.
(författare)
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Security of supply as a political bargaining issue : Why Germany opted against capacity markets
- 2022
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Ingår i: Energy Research & Social Science. - : Elsevier. - 2214-6296 .- 2214-6326. ; 86
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Tidskriftsartikel (refereegranskat)abstract
- The large-scale deployment of intermittent renewable energy sources for electricity generation has raised concerns regarding the future security of supply. Previous research has studied efficient reforms of electricity markets to address these concerns. In contrast, our paper aims to explain actual policy choices made to provide security of supply. For this purpose, we develop a Public Choice framework, which looks at three interacting decision variables: the timing of regulatory intervention, the decision-making process and the market design. We apply this framework to study the policy debates and decisions related to Germany’s 2016 electricity market reform. The analysis builds on the rich empirical material made available through a consultation process preceding the German parliamentary decision. The electricity market reform eventually combined measures to strengthen the energy-only market and the implementation of only limited new capacity payments through a strategic reserve. This was despite the fact that conventional electricity producers strongly lobbied for a fully-fledged capacity market by which they would have benefited from new broad-band capacity payments. Our analysis suggests that the eventual market design decision was strongly affected by the timing of regulatory intervention (existing oversupply of generation capacity) and the decision-making process (an open consultation process revealing broad opposition against capacity markets).
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