Polar surface engineering in ultra-thin MgO(111)/Ag(111) -- possibility of metal-insulator transition and magnetism

A recent report [Kiguchi {\it et al.}, Phys. Rev. B {\bf 68}, 115402 (2003)] that the (111) surface of 5 MgO layers grown epitaxially on Ag(111) becomes metallic to reduce the electric dipole moment raises a question of what will happen when we have fewer MgO layers. Here we have revealed, first experimentally with electron energy-loss spectroscopy, that MgO(111) remains metallic even when one-layer thick, and theoretically with the density functional theory that the metallization should depend on the nature of the substrate. We further show, with a spin-density functional calculation, that a ferromagnetic instability may be expected for thicker films.Comment: 5 pages, 7 figure

Metal-Induced Gap States at Well Defined Alkali-Halide/Metal Interfaces

In order to search for states specific to insulator/metal interfaces, we have studied epitaxially grown interfaces with element-selective near edge X-ray absorption fine structure (NEXAFS). An extra peak is observed below the bulk edge onset for LiCl films on Cu and Ag substrates. The nature of chemical bonds as probed by X-ray photoemission spectroscopy and Auger electron spectroscopy remains unchanged, so we regard this as evidence for metal-induced gap states(MIGS) formed by the proximity to a metal, rather than local bonds at the interface. The dependence on the film thickness shows that the MIGS are as thin as one monolayer. An ab initio electronic structure calculation supports the existence of the MIGS that are strongly localized at the interface.Comment: 4 pages, 5 figures, to be published in Phys. Rev. Let

Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J. Chem. Phys. ${\bf 123}$, 084108 (2005)]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant $\lambda$, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies $\Delta G$ thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda $et al$ [H. Gouda, I. D. Kuntz, D. A. Case, and P. A. Kollman, Biopolymers ${\bf 68}$, 16 (2003)], the predictive accuracy of the relative values $\Delta\Delta G$ is almost comparable to that of TI: the correlation coefficients (R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of $\sim$ -7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated.Comment: 23 pages including 6 figure

Image-potential band-gap narrowing at a metal/semiconductor interface

GW approximation is used to systematically revisit the image-potential band-gap narrowing at metal/semiconductor interfaces proposed by Inkson in the 1970's. Here we have questioned how the narrowing as calculated from quasi-particle energy spectra for the jellium/Si interface depends on $r_s$ of the jellium. The gap narrowing is found to only weakly depend on $r_s$ (i.e., narrowing $\simeq 0.3$ eV even for a large $r_s = 6)$. Hence we can turn to smaller polarizability in the semiconductor side as an important factor in looking for larger narrowing.Comment: 6 pages, 7 figure

Electronic properties of metal induced gap states at insulator/metal interfaces -- dependence on the alkali halide and the possibility of excitonic mechanism of superconductivity

Motivated from the experimental observation of metal induced gap states (MIGS) at insulator/metal interfaces by Kiguchi {\it et al.} [Phys. Rev. Lett. {\bf 90}, 196803 (2003)], we have theoretically investigated the electronic properties of MIGS at interfaces between various alkali halides and a metal represented by a jellium with the first-principles density functional method. We have found that, on top of the usual evanescent state, MIGS generally have a long tail on halogen sites with a $p_z$-like character, whose penetration depth ($\lambda$) is as large as half the lattice constant of bulk alkali halides. This implies that $\lambda$, while little dependent on the carrier density in the jellium, is dominated by the lattice constant (hence by energy gap) of the alkali halide, where $\lambda_{\rm LiF} < \lambda_{\rm LiCl} < \lambda_{\rm LiI}$. We also propose a possibility of the MIGS working favorably for the exciton-mediated superconductivity.Comment: 7 pages, 9 figure

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

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. For example, 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 versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost 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 fi eld 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. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. 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. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. 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

Metal-induced gap states in epitaxial organic-insulator/metal interfaces

We have shown, both experimentally and theoretically, that the metal-induced gap states (MIGS) can exist in epitaxially grown organic insulator/metal interfaces. The experiment is done for alkane/Cu(001) with an element-selective near edge x-ray absorption fine structure (NEXAFS), which exhibits a prepeak indicative of MIGS. An ab initio electronic structure calculation supports the existence of the MIGS. When the Cu substrate is replaced with Ni, an interface magnetism may be possible with a carrier doping