Mechanical and Electronic Properties of MoS2_2 Nanoribbons and Their Defects

We present our study on atomic, electronic, magnetic and phonon properties of one dimensional honeycomb structure of molybdenum disulfide (MoS$_2$) using first-principles plane wave method. Calculated phonon frequencies of bare armchair nanoribbon reveal the fourth acoustic branch and indicate the stability. Force constant and in-plane stiffness calculated in the harmonic elastic deformation range signify that the MoS$_2$ nanoribbons are stiff quasi one dimensional structures, but not as strong as graphene and BN nanoribbons. Bare MoS$_2$ armchair nanoribbons are nonmagnetic, direct band gap semiconductors. Bare zigzag MoS$_2$ nanoribbons become half-metallic as a result of the (2x1) reconstruction of edge atoms and are semiconductor for minority spins, but metallic for the majority spins. Their magnetic moments and spin-polarizations at the Fermi level are reduced as a result of the passivation of edge atoms by hydrogen. The functionalization of MoS$_2$ nanoribbons by adatom adsorption and vacancy defect creation are also studied. The nonmagnetic armchair nanoribbons attain net magnetic moment depending on where the foreign atoms are adsorbed and what kind of vacancy defect is created. The magnetization of zigzag nanoribbons due to the edge states is suppressed in the presence of vacancy defects.Comment: 11 pages, 5 figures, first submitted at November 23th, 200

Electronic structure of the quasi-one-dimensional organic conductor TTF-TCNQ

We study the electronic structure of the quasi-one-dimensional organic conductor TTF-TCNQ by means of density-functional band theory, Hubbard model calculations, and angle-resolved photoelectron spectroscopy (ARPES). The experimental spectra reveal significant quantitative and qualitative discrepancies to band theory. We demonstrate that the dispersive behavior as well as the temperature-dependence of the spectra can be consistently explained by the finite-energy physics of the one-dimensional Hubbard model at metallic doping. The model description can even be made quantitative, if one accounts for an enhanced hopping integral at the surface, most likely caused by a relaxation of the topmost molecular layer. Within this interpretation the ARPES data provide spectroscopic evidence for the existence of spin-charge separation on an energy scale of the conduction band width. The failure of the one-dimensional Hubbard model for the {\it low-energy} spectral behavior is attributed to interchain coupling and the additional effect of electron-phonon interaction.Comment: 18 pages, 9 figure

Extensive Variation in Chromatin States Across Humans

The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans

Correlated local distortions of the TlO layers in Tl2_2Ba2_2CuOy_{y}: An x-ray absorption study

We have used the XAFS (x-ray-absorption fine structure) technique to investigate the local structure about the Cu, Ba, and Tl atoms in orthorhombic Tl-2201 with a superconducting transition temperature T$_c$=60 K. Our results clearly show that the O(1), O(2), Cu, and Ba atoms are at their ideal sites as given by the diffraction measurements, while the Tl and O(3) atoms are more disordered than suggested by the average crystal structure. The Tl-Tl distance at 3.5 \AA{ } between the TlO layers does not change, but the Tl-Tl distance at 3.9 \AA{ } within the TlO layer is not observed and the Tl-Ba and Ba-Tl peaks are very broad. The shorter Tl-O(3) distance in the TlO layer is about 2.33 \AA, significantly shorter than the distance calculated with both the Tl and O(3) atoms at their ideal $4e$ sites ( $x=y=$0 or $\frac{1}{2}$). A model based on these results shows that the Tl atom is displaced along the directions from its ideal site by about 0.11 \AA; the displacements of neighboring Tl atoms are correlated. The O(3) atom is shifted from the $4e$ site by about 0.53 \AA{ } roughly along the directions. A comparison of the Tl L$_{III}$-edge XAFS spectra from three samples, with T$_c$=60 K, 76 K, and 89 K, shows that the O environment around the Tl atom is sensitive to T$_c$ while the Tl local displacement is insensitive to T$_c$ and the structural symmetry. These conclusions are compared with other experimental results and the implications for charge transfer and superconductivity are discussed. This paper has been submitted to Phys. Rev. B.Comment: 20 pages plus 14 ps figures, REVTEX 3.

Multiband model of high Tc superconductors

We propose an extension to other high T_{c } compounds of a model introduced earlier for YBCO. In the ''self-doped'' compounds we assume that the doping part (namely the BiO, HgO, TlO planes in BSCCO, HBCCO, TBCCO respectively) is metallic, which leads to a multiband model. This assumption is supported by band structure calculations. Taking a repulsive pairing interaction between these doping bands and the CuO_{2} bands leads to opposite signs for the order parameter on these bands and to nodes whenever the Fermi surfaces of these bands cross. We show that in BSCCO the low temperature dependence of the penetration depth is reasonably accounted for. In this case the nodes are not located near the 45^{o} direction, which makes the experimental determination of the node locations an important test for our model. The situation in HBCCO and TBCCO is rather analogous to BSCCO. We consider the indications given by NMR and find that they rather favor a metallic character for the doping bands. Finally we discuss the cases of NCCO and LSCO which are not ''self-doped'' and where our model does not give nodes.Comment: 11 pages, revtex, 1 figure

Change of Structural Behaviors of Organo-Silane Exposed Graphene Nanoflakes

[[abstract]]The electronic structures of graphene nanoflakes (GNFs) exposed to an organo-silane precursor [tetramethylsilane, TMS, Si(CH3)4] were studied using electron field emission (EFE), Raman spectroscopy, X-ray absorption near-edge structure (XANES), X-ray photoelectron spectroscopy (XPS), X-ray emission spectroscopy (XES), and first-principles calculation. The results of XANES, XPS, and Raman spectroscopy indicate that the silyl radical strong covalent bonds were formed in GNFs, which induced local structural relaxations and enhanced sp3 hybridization. Comparison of calculated electronic structure, XANES, and XES spectra of Sitreated GNFs suggests that the Si atom substitutes one 3-fold coordinated C atom in a given graphene layer and relaxes outward to form sp3 bonding with another C atom in the adjacent graphene layer. The EFE measurements show an increase in the turn-on electric field with the increase of the Si content, which suggests an enhancement of the nonmetallic sp3 bonding[[journaltype]]國外[[incitationindex]]SCI[[booktype]]紙本[[countrycodes]]US

A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays

Protein binding microarrays (PBM) are a high throughput technology used to characterize protein-DNA binding. The arrays measure a protein's affinity toward thousands of double-stranded DNA sequences at once, producing a comprehensive binding specificity catalog. We present a linear model for predicting the binding affinity of a protein toward DNA sequences based on PBM data. Our model represents the measured intensity of an individual probe as a sum of the binding affinity contributions of the probe's subsequences. These subsequences characterize a DNA binding motif and can be used to predict the intensity of protein binding against arbitrary DNA sequences. Our method was the best performer in the Dialogue for Reverse Engineering Assessments and Methods 5 (DREAM5) transcription factor/DNA motif recognition challenge. For the DREAM5 bonus challenge, we also developed an approach for the identification of transcription factors based on their PBM binding profiles. Our approach for TF identification achieved the best performance in the bonus challenge

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

<p>Abstract</p> <p>Background</p> <p>Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of <it>Drosophila melanogaster</it>.</p> <p>Results</p> <p>Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis.</p> <p>Conclusions</p> <p>Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis.</p

dPORE-miRNA: Polymorphic Regulation of MicroRNA Genes

Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed a