One-electron states and interband optical absorption in single-wall carbon nanotubes

Explicit expressions for the wave functions and dispersion equation for the band p - electrons in single-wall carbon nanotubes are obtained within the method of zero-range potentials. They are then used to investigate the absorption spectrum of polarized light caused by direct interband transitions in isolated nanotubes. It is shown that, at least, under the above approximations, the circular dichroism is absent in chiral nanotubes for the light wave propagating along the tube axis. The results obtained are compared with those calculated in a similar way for a graphite plane.Comment: 16 pages, 8 figures, 1 tabl

Genome-Scale Validation of Deep-Sequencing Libraries

Chromatin immunoprecipitation followed by high-throughput (HTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximize the efficiency of library creation and quickly generate reliable preliminary data on a chromosomal scale in advance of deep sequencing. We also exploit this technique to compare enriched regions identified using microarrays with those identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizing the additional enriched regions identifiable using HTP sequencing

A life story in three parts: the use of triptychs to make sense of personal digital data

Many social media platforms support the curation of personal digital data, and, more recently, the use of that data for review and reflection. We explored the process of reflection by asking users to create a meaningful ‘triptych’ of photographs drawn from their Facebook accounts. In a first study, we asked participants to manually trawl their own accounts and select three relevant images, which we then framed and used as an interview probe. In a second study, we designed an automated triptych generation system and assessed participants’ experiences of using this system. We conducted qualitative analyses of participant interviews from both studies. Consistent with other ‘slow technology’ work, we found the act of creating a physical artefact from social media data gave that data new meaning, albeit with notable differences between manual vs automatically generated triptychs. We conclude by discussing possible improvements to the design of the automated triptych system

Bandgap Change of Carbon Nanotubes: Effect of Small Tensile and Torsional Strain

We use a simple picture based on the $\pi$ electron approximation to study the bandgap variation of carbon nanotubes with uniaxial and torsional strain. We find (i) that the magnitude of slope of bandgap versus strain has an almost universal behaviour that depends on the chiral angle, (ii) that the sign of slope depends on the value of $(n-m) \bmod 3$ and (iii) a novel change in sign of the slope of bandgap versus uniaxial strain arising from a change in the value of the quantum number corresponding to the minimum bandgap. Four orbital calculations are also presented to show that the $\pi$ orbital results are valid.Comment: Revised. Method explained in detai

Subband population in a single-wall carbon nanotube diode

We observe current rectification in a molecular diode consisting of a semiconducting single-wall carbon nanotube and an impurity. One half of the nanotube has no impurity, and it has a current-voltage (I-V) charcteristic of a typical semiconducting nanotube. The other half of the nanotube has the impurity on it, and its I-V characteristic is that of a diode. Current in the nanotube diode is carried by holes transported through the molecule's one-dimensional subbands. At 77 Kelvin we observe a step-wise increase in the current through the diode as a function of gate voltage, showing that we can control the number of occupied one-dimensional subbands through electrostatic doping.Comment: to appear in Physical Review Letters. 4 pages & 3 figure

Latent regulatory potential of human-specific repetitive elements

At least half of the human genome is derived from repetitive elements, which are often lineage specific and silenced by a variety of genetic and epigenetic mechanisms. Using a transchromosomic mouse strain that transmits an almost complete single copy of human chromosome 21 via the female germline, we show that a heterologous regulatory environment can transcriptionally activate transposon-derived human regulatory regions. In the mouse nucleus, hundreds of locations on human chromosome 21 newly associate with activating histone modifications in both somatic and germline tissues, and influence the gene expression of nearby transcripts. These regions are enriched with primate and human lineage-specific transposable elements, and their activation corresponds to changes in DNA methylation at CpG dinucleotides. This study reveals the latent regulatory potential of the repetitive human genome and illustrates the species specificity of mechanisms that control it

Rapid turnover of long noncoding RNAs and the evolution of gene expression.

A large proportion of functional sequence within mammalian genomes falls outside protein-coding exons and can be transcribed into long RNAs. However, the roles in mammalian biology of long noncoding RNA (lncRNA) are not well understood. Few lncRNAs have experimentally determined roles, with some of these being lineage-specific. Determining the extent by which transcription of lncRNA loci is retained or lost across multiple evolutionary lineages is essential if we are to understand their contribution to mammalian biology and to lineage-specific traits. Here, we experimentally investigated the conservation of lncRNA expression among closely related rodent species, allowing the evolution of DNA sequence to be uncoupled from evolution of transcript expression. We generated total RNA (RNAseq) and H3K4me3-bound (ChIPseq) DNA data, and combined both to construct catalogues of transcripts expressed in the adult liver of Mus musculus domesticus (C57BL/6J), Mus musculus castaneus, and Rattus norvegicus. We estimated the rate of transcriptional turnover of lncRNAs and investigated the effects of their lineage-specific birth or death. LncRNA transcription showed considerably greater gain and loss during rodent evolution, compared with protein-coding genes. Nucleotide substitution rates were found to mirror the in vivo transcriptional conservation of intergenic lncRNAs between rodents: only the sequences of noncoding loci with conserved transcription were constrained. Finally, we found that lineage-specific intergenic lncRNAs appear to be associated with modestly elevated expression of genomically neighbouring protein-coding genes. Our findings show that nearly half of intergenic lncRNA loci have been gained or lost since the last common ancestor of mouse and rat, and they predict that such rapid transcriptional turnover contributes to the evolution of tissue- and lineage-specific gene expression

van der Waals interaction in nanotube bundles : consequences on vibrational modes

We have developed a pair-potential approach for the evaluation of van der Waals interaction between carbon nanotubes in bundles. Starting from a continuum model, we show that the intertube modes range from $5 cm^{-1}$ to $60 cm^{-1}$. Using a non-orthogonal tight-binding approximation for describing the covalent intra-tube bonding in addition, we confirme a slight chiral dependance of the breathing mode frequency and we found that this breathing mode frequency increase by $\sim$ 10 % if the nanotube lie inside a bundle as compared to the isolated tube.Comment: 5 pages, 2 figure

Negative differential resistance in nanotube devices

Carbon nanotube junctions are predicted to exhibit negative differential resistance, with very high peak-to-valley current ratios even at room temperature. We treat both nanotube p-n junctions and undoped metal-nanotube-metal junctions, calculating quantum transport through the self-consistent potential within a tight-binding approximation. The undoped junctions in particular may be suitable for device integration.Comment: 4 pages, 4 figures, to appear in Physical Review Letter

The strain energy and Young's Moduli of single-wall Carbon nanotubules calculated from the electronic energy-band theory

The strain energies in straight and bent single-walled carbon nanotubes (SWNTs) are calculated by taking account of the total energy of all the occupied band electrons. The obtained results are in good agreement with previous theoretical studies and experimental observations. The Young's modulus and the effective wall thickness of SWNT are obtained from the bending strain energies of SWNTs with various cross-sectional radii. The repulsion potential between ions contributes the main part of the Young's modulus of SWNT. The wall thickness of SWNT comes completely from the overlap of electronic orbits, and is approximately of the extension of $\pi$ orbit of carbon atom. Both the Young's modulus and the wall thickness are independent of the radius and the helicity of SWNT, and insensitive to the fitting parameters. The results show that continuum elasticity theory can serve well to describe the mechanical properties of SWNTs.Comment: 12 pages, 2 figure