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| 11. |
- 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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| 13. |
- Akola, J., et al.
(författare)
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Thiolate-Protected Au-25 Superatoms as Building Blocks: Dimers and Crystals
- 2010
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:38, s. 15986-15994
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Tidskriftsartikel (refereegranskat)abstract
- A particularly stable thiolate-protected gold nanocluster, Au-25(SR)(18), was structurally characterized from X-ray crystallography in 2008, and concomitantly its electronic and optical properties were analyzed via density functional theory. The robust geometry and a well-understood electronic structure of this cluster motivate explorations of properties of extended systems made out of Au-25(SR)(18) building blocks. As a first step in this direction, we analyze here structural, vibrational, electronic, and optical properties of the Au-25 cluster anion as it was observed in the crystalline environment and predict properties of cluster dimers, where the Au-25 units are linked together. via an aromatic dithiolate linker. We show that properties of each Au-25 unit of the dimer can be quite independently modified from the other by doping with a nonmagnetic (Pd) or magnetic (Mn) metal atom. We anticipate that material systems with interesting properties could be made from these building blocks, provided that a suitable chemistry for their controlled linking can be found.
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| 14. |
- Clayborne, P. A., et al.
(författare)
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Evidence of superatom electronic shells in ligand-stabilized aluminum clusters
- 2011
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 135:9
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Tidskriftsartikel (refereegranskat)abstract
- Ligand-stabilized aluminum clusters are investigated by density functional theory calculations. Analysis of Kohn-Sham molecular orbitals and projected density of states uncovers an electronic shell structure that adheres to the superatom complex model for ligand-stabilized aluminum clusters. In this current study, we explain how the superatom complex electron-counting rule is influenced by the electron-withdrawing ligand and a dopant atom in the metallic core. The results may guide the prediction of new stable ligand-stabilized (superatom) complexes, regardless of core and electronwithdrawing ligand composition.
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| 15. |
- Clayborne, P. A., et al.
(författare)
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The Al50Cp*(12) Cluster - A 138-Electron Closed Shell (L=6) Superatom
- 2011
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Ingår i: European Journal of Inorganic Chemistry. - : Wiley. - 1434-1948 .- 1099-0682. ; :17, s. 2649-2652
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Tidskriftsartikel (refereegranskat)abstract
- Metal clusters stabilized by a surface ligand shell represent an interesting intermediate state of matter between molecular metal-ligand complexes and bulk metal. Such "metalloid" clusters are characterized by the balance between metal-metal bonds in the core and metal-ligand bonds at the exterior of the cluster. In previous studies, the electronic stability for the Al50Cp*(12) cluster was not fully understood. We show here that the known cluster Al50Cp*(12) can be considered as an analogue to a giant atom ("superatom") with 138 sp electrons organized in concentric angular momentum shells up to L = 6 symmetry.
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| 16. |
- Enkovaara, J., et al.
(författare)
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Electronic structure calculations with GPAW : a real-space implementation of the projector augmented-wave method
- 2010
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Ingår i: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 22:25, s. 253202-
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Forskningsöversikt (refereegranskat)abstract
- Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, Delta SCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.
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- Kacprzak, K. A., et al.
(författare)
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Theoretical Characterization of Cyclic Thiolated Copper, Silver, and Gold Clusters
- 2010
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:32, s. 13571-13576
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Tidskriftsartikel (refereegranskat)abstract
- Density functional theory calculations are used to study structural, electronic, and vibrational properties of cyclic (MeSM)(x) clusters where MeS is methylthiolate and M is copper, silver, or gold. The clusters show a flexible bond motif where monocyclic rings, catenanes, and helix structures compete in energy. In the investigated series, the copper-sulfur bond is found to be the strongest metal-sulfur bond, followed by gold-sulfur and silver-sulfur. Analysis of the bond character reveals that Cu-S is the most polar bond, whereas Au-S is mainly of covalent type. Vibrational analysis shows characteristic metal-sulfur stretch vibrations for each noble metal.
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| 21. |
- Makkonen, Esko, et al.
(författare)
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Real-time time-dependent density functional theory implementation of electronic circular dichroism applied to nanoscale metal-organic clusters
- 2021
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 154:11
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Tidskriftsartikel (refereegranskat)abstract
- Electronic circular dichroism (ECD) is a powerful spectroscopy method for investigating chiral properties at the molecular level. ECD calculations with the commonly used linear-response time-dependent density functional theory (LR-TDDFT) framework can be prohibitively costly for large systems. To alleviate this problem, we present here an ECD implementation within the projector augmented-wave method in a real-time-propagation TDDFT framework in the open-source GPAW code. Our implementation supports both local atomic basis sets and real-space finite-difference representations of wave functions. We benchmark our implementation against an existing LR-TDDFT implementation in GPAW for small chiral molecules. We then demonstrate the efficiency of our local atomic basis set implementation for a large hybrid nanocluster and discuss the chiroptical properties of the cluster.
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