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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Behrends, Jan, et al.
(författare)
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Landau levels, Bardeen polynomials, and Fermi arcs in Weyl semimetals : Lattice-based approach to the chiral anomaly
- 2019
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 99:14
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Tidskriftsartikel (refereegranskat)abstract
- Condensed matter systems realizing Weyl fermions exhibit striking phenomenology derived from their topologically protected surface states as well as chiral anomalies induced by electromagnetic fields. More recently, inhomogeneous strain or magnetization were predicted to result in chiral electric E-5 and magnetic B-5 fields, which modify and enrich the chiral anomaly with additional terms. In this Rapid Communication, we develop a lattice-based approach to describe the chiral anomaly, which involves Landau and pseudo-Landau levels and treats all anomalous terms on equal footing, while naturally incorporating Fermi arcs. We exemplify its potential by physically interpreting the largely overlooked role of Fermi arcs in the covariant (Fermi level) contribution to the anomaly and revisiting the factor of 1/3 difference between the covariant and consistent (complete band) contributions to the E-5 . B-5 term in the anomaly. Our framework provides a versatile tool for the analysis of anomalies in realistic lattice models as well as a source of simple physical intuition for understanding strained and magnetized inhomogeneous Weyl semimetals.
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| 4. |
- Behrends, Jan, et al.
(författare)
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Nodal-line semimetals from Weyl superlattices
- 2017
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Ingår i: Physical Review B. - 2469-9950 .- 2469-9969. ; 96:24
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Tidskriftsartikel (refereegranskat)abstract
- The existence and topological classification of lower-dimensional Fermi surfaces is often tied to the crystal symmetries of the underlying lattice systems. Artificially engineered lattices, such as heterostructures and other superlattices, provide promising avenues to realize desired crystal symmetries that protect lower-dimensional Fermi surfaces, such as nodal lines. In this work, we investigate a Weyl semimetal subjected to spatially periodic onsite potential, giving rise to several phases, including a nodal-line semimetal phase. In contrast to proposals that purely focus on lattice symmetries, the emergence of the nodal line in this setup does not require small spin-orbit coupling, but rather relies on its presence. We show that the stability of the nodal line is understood from reflection symmetry and a combination of a fractional lattice translation and charge-conjugation symmetry. Depending on the choice of parameters, this model exhibits drumhead surface states that are exponentially localized at the surface, or weakly localized surface states that decay into the bulk at all energies.
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| 5. |
- Behrends, Jan, et al.
(författare)
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Strongly angle-dependent magnetoresistance in Weyl semimetals with long-range disorder
- 2017
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 96:6
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Tidskriftsartikel (refereegranskat)abstract
- The chiral anomaly in Weyl semimetals states that the left- and right-handed Weyl fermions, constituting the low energy description, are not individually conserved, resulting, for example, in a negative magnetoresistance in such materials. Recent experiments see strong indications of such an anomalous resistance response; however, with a response that at strong fields is more sharply peaked for parallel magnetic and electric fields than expected from simple theoretical considerations. Here, we uncover a mechanism, arising from the interplay between the angle-dependent Landau-level structure and long-range scalar disorder, that has the same phenomenology. In particular, we analytically show, and numerically confirm, that the internode scattering time decreases exponentially with the angle between the magnetic field and the Weyl node separation in the large field limit, while it is insensitive to this angle at weak magnetic fields. Since, in the simplest approximation, the internode scattering time is proportional to the anomaly-related conductivity, this feature may be related to the experimental observations of a sharply peaked magnetoresistance.
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| 6. |
- Behrends, Jan, et al.
(författare)
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Tenfold way and many-body zero modes in the Sachdev-Ye-Kitaev model
- 2019
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 99:19
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Tidskriftsartikel (refereegranskat)abstract
- The Sachdev-Ye-Kitaev (SYK) model, in its simplest form, describes k Majorana fermions with random all-to-all four-body interactions. We consider the SYK model in the framework of a many-body Altland-Zirnbauer classification that sees the system as belonging to one of eight (real) symmetry classes depending on the value of k mod 8. We show that, depending on the symmetry class, the system may support exact many-body zero modes with the symmetries also dictating whether these may have a nonzero contribution to Majorana fermions, i.e., single-particle weight. These zero modes appear in all but two of the symmetry classes. When present, they leave clear signatures in physical observables that go beyond the threefold (Wigner-Dyson) possibilities for level spacing statistics studied earlier. Signatures we discover include a zero-energy peak or hole in the single-particle spectral function, depending on whether symmetries allow or forbid zero modes to have single-particle weight. The zero modes are also shown to influence the many-body dynamics, where signatures include a nonzero long-time limit for the out-of-time-order correlation function. Furthermore, we show that the extension of the four-body SYK model by quadratic terms can be interpreted as realizing the remaining two complex symmetry classes; we thus demonstrate how the entire tenfold Altland-Zirnbauer classification may emerge in the SYK model.
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| 7. |
- Behrends, Jan, et al.
(författare)
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Transversal magnetotransport in Weyl semimetals : Exact numerical approach
- 2018
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Ingår i: Physical Review B. - 2469-9950 .- 2469-9969. ; 97:6
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Tidskriftsartikel (refereegranskat)abstract
- Magnetotransport experiments on Weyl semimetals are essential for investigating the intriguing topological and low-energy properties of Weyl nodes. If the transport direction is perpendicular to the applied magnetic field, experiments have shown a large positive magnetoresistance. In this work we present a theoretical scattering matrix approach to transversal magnetotransport in a Weyl node. Our numerical method confirms and goes beyond the existing perturbative analytical approach by treating disorder exactly. It is formulated in real space and is applicable to mesoscopic samples as well as in the bulk limit. In particular, we study the case of clean and strongly disordered samples.
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| 8. |
- Gorman, Jeffrey, et al.
(författare)
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Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides
- 2022
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:1, s. 368-376
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Tidskriftsartikel (refereegranskat)abstract
- Natural photosystems use protein scaffolds to control intermolecular interactions that enable exciton flow, charge generation, and long-range charge separation. In contrast, there is limited structural control in current organic electronic devices such as OLEDs and solar cells. We report here the DNA-encoded assembly of pi-conjugated perylene diimides (PDIs) with deterministic control over the number of electronically coupled molecules. The PDIs are integrated within DNA chains using phosphoramidite coupling chemistry, allowing selection of the DNA sequence to either side, and specification of intermolecular DNA hybridization. In this way, we have developed a "toolbox" for construction of any stacking sequence of these semiconducting molecules. We have discovered that we need to use a full hierarchy of interactions: DNA guides the semiconductors into specified close proximity, hydrophobic-hydrophilic differentiation drives aggregation of the semiconductor moieties, and local geometry and electrostatic interactions define intermolecular positioning. As a result, the PDIs pack to give substantial intermolecular pi wave function overlap, leading to an evolution of singlet excited states from localized excitons in the PDI monomer to excimers with wave functions delocalized over all five PDIs in the pentamer. This is accompanied by a change in the dominant triplet forming mechanism from localized spin-orbit charge transfer mediated intersystem crossing for the monomer toward a delocalized excimer process for the pentamer. Our modular DNA-based assembly reveals real opportunities for the rapid development of bespoke semiconductor architectures with molecule-by-molecule precision.
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| 9. |
- Orsborne, Sarah R.E., et al.
(författare)
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Photogeneration of Spin Quintet Triplet-Triplet Excitations in DNA-Assembled Pentacene Stacks
- 2023
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 145:9, s. 5431-5438
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Tidskriftsartikel (refereegranskat)abstract
- Singlet fission (SF), an exciton-doubling process observed in certain molecular semiconductors where two triplet excitons are generated from one singlet exciton, requires correctly tuned intermolecular coupling to allow separation of the two triplets to different molecular units. We explore this using DNA-encoded assembly of SF-capable pentacenes into discrete π-stacked constructs of defined size and geometry. Precise structural control is achieved via a combination of the DNA duplex formation between complementary single-stranded DNA and the local molecular geometry that directs the SF chromophores into a stable and predictable slip-stacked configuration, as confirmed by molecular dynamics (MD) modeling. Transient electron spin resonance spectroscopy revealed that within these DNA-assembled pentacene stacks, SF evolves via a bound triplet pair quintet state, which subsequently converts into free triplets. SF evolution via a long-lived quintet state sets specific requirements on intermolecular coupling, rendering the quintet spectrum and its zero-field-splitting parameters highly sensitive to intermolecular geometry. We have found that the experimental spectra and zero-field-splitting parameters are consistent with a slight systematic strain relative to the MD-optimized geometry. Thus, the transient electron spin resonance analysis is a powerful tool to test and refine the MD-derived structure models. DNA-encoded assembly of coupled semiconductor molecules allows controlled construction of electronically functional structures, but brings with it significant dynamic and polar disorders. Our findings here of efficient SF through quintet states demonstrate that these conditions still allow efficient and controlled semiconductor operation and point toward future opportunities for constructing functional optoelectronic systems.
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