Current-induced energy barrier suppression for electromigration from first principles

We present an efficient method for evaluating current-induced forces in nanoscale junctions, which naturally integrates into the non-equilibrium Green's function formalism implemented within density functional theory. This allows us to perform dynamical atomic relaxation in the presence of an electric current while also evaluating the current-voltage characteristics. The central idea consists in expressing the system energy density matrix in terms of Green's functions. In order to validate our implementation we perform a series of benchmark calculations, both at zero and finite bias. Firstly we evaluate the current-induced forces acting over an Al nanowire and compare them with previously published results for fixed geometries. Then we perform structural relaxation of the same wires under bias and determine the critical voltage at which they break. We find that, while a perfectly straight wire does not break at any of the voltages considered, a zigzag wire is more fragile and snaps at 1.4 V, with the Al atoms moving against the electron flow. Finally we demonstrate the capability of our scheme to tackle the electromigration problem by studying the current-induced motion of a single Si atom covalently attached to the sidewall of a (4,4) armchair single-walled carbon nanotube. Our calculations indicate that if Si is attached along the current path, then current-induced forces can induce migration. In contrast, if the bonding site is away from the current path, then the adatom will remain stable regardless of the voltage. An analysis based on decomposing the total force into a wind and an electrostatic component, as well as on a detailed evaluation of the bond currents, shows that this remarkable electromigration phenomenon is due solely to the position-dependent wind force.Comment: 25 pages, 14 figure

The Clinical Signifcance of Expression of ERCC1 and PKCalpha in Non-small Cell Lung Cancer

Background and objective Excision repair cross-complementing 1 (Excision-Repair Cross-Complementing 1, ERCC1), an important member of the DNA repair gene family, plays a key role in nucleotide excision repair and apoptosis of tumor cells. Protein kinase C-α (Protein kinase C, PKCα), an isozyme in protein kinase C family, is an important signaling molecule in signal transduction pathways of tumors, which has been implicated in malignant transformation and proliferation. The aim of this study was to explore the clinical significance of ERCC1 and PKCα in non-small cell lung cancer (NSCLC). Methods The expression of ERCC1 and PKCα were examined by immunohistochemistry (IHC) in the specimens of 51 cases of NSCLC patients tissue and 21 cases of paracancerous tissue. The relationship between detected data and patients′ clinical parameters was analyzed by SPSS 13.0 software. Results The positive expression rate of ERCC1 and PKCα in NSCLC tissues was significantly higher than paracancerous tissues (Ρ<0.05). Expression of ERCC1 was closely related to clinical stage and N stage. The positive rate of ERCC1 was higher in III+IV or N1+N2 stage patients compared with I+II or N0 stage (Ρ=0.011, P=0.015). We also found that 5-year survival of negative group of ERCC1 was remarkably higher than that of positive group by χ2 test (Ρ<0.05). Expression of ERCC1 was positively correlative to PKCα by Spearman′s correlation analysis (r=0.425, P=0.002) in NSCLC. Conclusion The results suggest ERCC1 and PKCα might be correlated with the development of NSCLC. ERCC1 might be related to prognosis of NSCLC. There might be existed a mechanism of coordination or regulation between ERCC1 and PKCα

First-principles calculation on the transport properties of molecular wires between Au clusters under equilibrium

Based on the matrix Green's function method combined with hybrid tight-binding / density functional theory, we calculate the conductances of a series of gold-dithiol molecule-gold junctions including benzenedithiol (BDT), benzenedimethanethiol (BDMT), hexanedithiol (HDT), octanedithiol (ODT) and decanedithiol (DDT). An atomically-contacted extended molecule model is used in our calculation. As an important procedure, we determine the position of the Fermi level by the energy reference according to the results from ultraviolet photoelectron spectroscopy (UPS) experiments. After considering the experimental uncertainty in UPS measurement, the calculated results of molecular conductances near the Fermi level qualitatively agree with the experimental values measured by Tao et. al. [{\it Science} 301, 1221 (2003); {\it J. Am. Chem. Soc.} 125, 16164 (2003); {\it Nano. Lett.} 4, 267 (2004).]Comment: 12 pages,8 figure

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Effect of molecular conformations on the electronic transport in oxygen-substituted alkanethiol molecular junctions

The relationship between the molecular structure and the electronic transport properties of molecular junctions based on thiol-terminated oligoethers, which are obtained by replacing every third methylene unit in the corresponding alkanethiols with an oxygen atom, is investigated by employing the non-equilibrium Green?s function formalism combined with density functional theory. Our calculations show that the low-bias conductance depends strongly on the conformation of the oligoethers in the junction. Specifically, in the cases of trans-extended conformation, the oxygen-dominated transmission peaks are very sharp and well below the Fermi energy, EF, thus hardly affect the transmission around EF; the Au?S interface hybrid states couple with ?-bonds in the molecular backbone forming the conduction channel at EF, resulting in a conductance decay against the molecular length close to that for alkanethiols. By contrast, for junctions with oligoethers in helical conformations, some ?-type oxygen orbitals coupling with the Au?S interface hybrid states contribute to the transmission around EF. The molecule-electrode electronic coupling is also enhanced at the non-thiol side due to the specific spatial orientation introduced by the twist of the molecular backbone. This leads to a much smaller conductance decay constant. Our findings highlight the important role of the molecular conformation of oligoethers in their electronic transport properties and are also helpful for the design of molecular wires with heteroatom-substituted alkanethiols