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| 3. |
- 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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- Li, Xiao-Fei, et al.
(författare)
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Half-filled energy bands induced negative differential resistance in nitrogen-doped graphene
- 2015
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 7:9, s. 4156-4162
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogen-doping brings novel properties and promising applications into graphene, but the underlying mechanism is still in debate. To determine the key factor in motivating the negative differential resistance (NDR) behaviour of nitrogen-doped graphene, the electronic structure and transport properties of an 11-dimer wide nitrogen-doped armchair graphene nanoribbon (N-AGNR) were systematically studied by first principles calculations. Both the effect of interaction between N-dopants and the effect of doping-sublattice on the NDR were examined for the first time. Taking into account the two effects, N-AGNR becomes metallic or semiconducting depending on the doping configuration, and its Fermi level varies in a large range. NDR was firmly verified not to be intrinsic for N-AGNRs. However, it is totally determined by whether nitrogen-doping induces half-filled energy bands (HFEBs) because it is HFEBs that cross the Fermi level and determine the transport properties of N-AGNR under low biases. With the bias increasing, the transmission spectrum near the Fermi level showed a flag shape, and therefore, the corresponding transport channel is totally suppressed at a certain bias, resulting in the NDR behaviour with a configuration-dependent peak-to-valley current ratio (PVCR) up to 10(4). Our findings give new insights into the microscopic mechanism of chemical doping induced NDR behaviour and will be useful in building NDR-based nanodevices in the future.
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| 5. |
- Li, Xiao-Fei, et al.
(författare)
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Unraveling the formation mechanism of graphitic nitrogen-doping in thermally treated graphene with ammonia
- 2016
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogen-doped graphene (N-graphene) has attractive properties that has been widely studied over the years. However, its possible formation process still remains unclear. Here, we propose a highly feasible formation mechanism of the graphitic-N doing in thermally treated graphene with ammonia by performing ab initio molecular dynamic simulations at experimental conditions. Results show that among the commonly native point defects in graphene, only the single vacancy 5-9 and divacancy 555-777 have the desirable electronic structures to trap N-containing groups and to mediate the subsequent dehydrogenation processes. The local structure of the defective graphene in combining with the thermodynamic and kinetic effect plays a crucial role in dominating the complex atomic rearrangement to form graphitic-N which heals the corresponding defect perfectly. The importance of the symmetry, the localized force field, the interaction of multiple trapped N-containing groups, as well as the catalytic effect of the temporarily formed bridge-N are emphasized, and the predicted doping configuration agrees well with the experimental observation. Hence, the revealed mechanism will be helpful for realizing the targeted synthesis of N-graphene with reduced defects and desired properties.
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| 6. |
- Lian, Ke-Yan, et al.
(författare)
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Big Bandgap in Highly Reduced Graphene Oxides
- 2013
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 117:12, s. 6049-6054
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Tidskriftsartikel (refereegranskat)abstract
- It is generally believed that the bandgap of the graphene oxide is proportional to the concentration of the oxygen atoms and a highly reduced graphene oxide (rGO) without vacancy defects should be gapless. We show here from first principles calculations that the bandgap can be effectively opened even in low oxidation level with the absorption of oxygen atoms either symmetrically or asymmetrically. The properly arranged absorption can induce a bandgap up to 1.19 eV for a C/O ratio of 16/1 in a symmetric system and a bandgap up to 1.58 eV for a C/O ratio of 32/3 in an asymmetric system, at generalized gradient approximation (GGA) level. The hybridization between the in-plane p(xy) orbitals of oxygen atoms and the out-of-plane p(z) frontier orbital of graphene is responsible for the opening of the bandgap. This finding sheds new light on the bandgap engineering of graphene.
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| 7. |
- Lian, Ke-Yan, et al.
(författare)
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Density-functional studies of plasmons in small metal clusters
- 2009
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 130:17
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Tidskriftsartikel (refereegranskat)abstract
- We study the formation of plasmon modes of small gold clusters by modeling the excitation spectra. The shape change of the longitudinal mode as a function of cluster size is studied using time-dependent Kohn-Sham theory and Gaussian basis sets. The presence of d electrons in gold atoms affect the plasmon formation process, resulting in a high excitation energy for transverse mode and a complicated spectra profile in general. The transverse mode can still be identified with the help of a frozen-orbital approximation.
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| 8. |
- Lian, Ke-yan, et al.
(författare)
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Stable High-Energy Density Super-Atom Clusters of Aluminum Hydride
- 2012
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Ingår i: Chinese Journal of Chemical Physics. - : AIP Publishing. - 1674-0068 .- 2327-2244. ; 25:2, s. 147-152
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Tidskriftsartikel (refereegranskat)abstract
- With the concept of super-atom, first principles calculations propose a new type of super stable cage clusters AlnH3n that are much more energetic stable than the well established clusters, AlnHn+2. In the new clusters, the aluminum core-frame acts as a super-atom with n vertexes and 2n Al-Al edges, which allow to adsorb n hydrogen atoms at the top-site and 2n at the bridge-site. Using Al12H36 as the basic unit, stable chain structures, (Al12H36)(m), have been constructed following the same connection mechanism as for (AlH3)(n) linear polymeric structures. Apart from high hydrogen percentage per molecule, calculations have shown that these new clusters possess large heat of formation values and their combustion heat is about 4.8 times of the methane, making them a promising high energy density material.
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| 10. |
- Lian, Ke-Yan, et al.
(författare)
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Tuning electronic and magnetic properties of armchair vertical bar zigzag hybrid graphene nanoribbons by the choice of supercell model of grain boundaries
- 2014
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 115:10, s. 104303-
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Tidskriftsartikel (refereegranskat)abstract
- Grain boundaries (GBs) attract much interest for its ability to tune the property of hybrid materials. Theoretically predicting the properties of hybrid graphene with GBs, even a linear GB remains challenging due to its inhomogeneous structure, which makes supercell model tough to choose in theoretic studies. For the first time, the applicability of supercells with different GBs and lattice-mismatches for describing armchair-zigzag hybrid graphene nanoribbons was validated by ab initio molecular dynamic simulations and first principles electronic structure calculations. And to what extent the electronic properties can be tuned by the strain effects resulting from the lattice-mismatch and the GBs distortion in supercells was demonstrated. This work showed that the intrinsic strain in such system plays a decisive role in determining the band structure and spin polarization properties. Hybrid graphene nanoribbon was found to be ferromagnetic in the ground state, especially for the case of using the supercell with nearly-perfect lattice match. Its high Curie temperature suggests the potential applications of this material in spintronics.
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