Scanning Tunneling Spectroscopy of Suspended Single-Wall Carbon Nanotubes

We have performed low-temperature STM measurements on single-wall carbon nanotubes that are freely suspended over a trench. The nanotubes were grown by CVD on a Pt substrate with predefined trenches etched into it. Atomic resolution was obtained on the freestanding portions of the nanotubes. Spatially resolved spectroscopy on the suspended portion of both metallic and semiconducting nanotubes was also achieved, showing a Coulomb-staircase behavior superimposed on the local density of states. The spacing of the Coulomb blockade peaks changed with tip position reflecting a changing tip-tube capacitance

Tracking advanced persistent threats in critical infrastructures through opinion dynamics

Advanced persistent threats pose a serious issue for modern industrial environments, due to their targeted and complex attack vectors that are difficult to detect. This is especially severe in critical infrastructures that are accelerating the integration of IT technologies. It is then essential to further develop effective monitoring and response systems that ensure the continuity of business to face the arising set of cyber-security threats. In this paper, we study the practical applicability of a novel technique based on opinion dynamics, that permits to trace the attack throughout all its stages along the network by correlating different anomalies measured over time, thereby taking the persistence of threats and the criticality of resources into consideration. The resulting information is of essential importance to monitor the overall health of the control system and cor- respondingly deploy accurate response procedures. Advanced Persistent Threat Detection Traceability Opinion Dynamics.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Gene regulatory networks in lactation: identification of global principles using bioinformatics

<p>Abstract</p> <p>Background</p> <p>The molecular events underlying mammary development during pregnancy, lactation, and involution are incompletely understood.</p> <p>Results</p> <p>Mammary gland microarray data, cellular localization data, protein-protein interactions, and literature-mined genes were integrated and analyzed using statistics, principal component analysis, gene ontology analysis, pathway analysis, and network analysis to identify global biological principles that govern molecular events during pregnancy, lactation, and involution.</p> <p>Conclusion</p> <p>Several key principles were derived: (1) nearly a third of the transcriptome fluctuates to build, run, and disassemble the lactation apparatus; (2) genes encoding the secretory machinery are transcribed prior to lactation; (3) the diversity of the endogenous portion of the milk proteome is derived from fewer than 100 transcripts; (4) while some genes are differentially transcribed near the onset of lactation, the lactation switch is primarily post-transcriptionally mediated; (5) the secretion of materials during lactation occurs not by up-regulation of novel genomic functions, but by widespread transcriptional suppression of functions such as protein degradation and cell-environment communication; (6) the involution switch is primarily transcriptionally mediated; and (7) during early involution, the transcriptional state is partially reverted to the pre-lactation state. A new hypothesis for secretory diminution is suggested – milk production gradually declines because the secretory machinery is not transcriptionally replenished. A comprehensive network of protein interactions during lactation is assembled and new regulatory gene targets are identified. Less than one fifth of the transcriptionally regulated nodes in this lactation network have been previously explored in the context of lactation. Implications for future research in mammary and cancer biology are discussed.</p

Smoke-Free Policy in Vermont Public Housing Authorities

Introduction. Millions of adults and children living in public housing face exposure to second hand smoke from adjacent apartments. These tenants are less able to escape smoke exposure by moving, and Housing Authorities are beginning to implement smoke-free policies. We assessed the status of smoke-free policy in Vermont public housing, and explored the experience of tenants and managers in Burlington who recently implemented such a policy.https://scholarworks.uvm.edu/comphp_gallery/1080/thumbnail.jp

Quantum Interference Effects in Electronic Transport through Nanotube Contacts

Quantum interference has dramatic effects on electronic transport through nanotube contacts. In optimal configuration the intertube conductance can approach that of a perfect nanotube ($4e^2/h$). The maximum conductance increases rapidly with the contact length up to 10 nm, beyond which it exhibits long wavelength oscillations. This is attributed to the resonant cavity-like interference phenomena in the contact region. For two concentric nanotubes symmetry breaking reduces the maximum intertube conductance from $4e^2/h$ to $2e^2/h$. The phenomena discussed here can serve as a foundation for building nanotube electronic circuits and high speed nanoscale electromechanical devices

Convective Term and Transversely Driven Charge-Density Waves

We derive the convective terms in the damping which determine the structure of the moving charge-density wave (CDW), and study the effect of a current flowing transverse to conducting chains on the CDW dynamics along the chains. In contrast to a recent prediction we find that the effect is orders of magnitude smaller, and that contributions from transverse currents of electron- and hole-like quasiparticles to the force exerted on the CDW along the chains act in the opposite directions. We discuss recent experimental verification of the effect and demonstrate experimentally that geometry effects might mimic the transverse current effect.Comment: RevTeX, 9 pages, 1 figure, accepted for publications in PR

Viscoelastic Depinning of Driven Systems: Mean-Field Plastic Scallops

We have investigated the mean field dynamics of an overdamped viscoelastic medium driven through quenched disorder. The model introduced incorporates coexistence of pinned and sliding degrees of freedom and can exhibit continuous elastic depinning or first order hysteretic depinning. Numerical simulations indicate mean field instabilities that correspond to macroscopic stick-slip events and lead to premature switching. The model is relevant for the dynamics of driven vortex arrays in superconductors and other extended disordered systems.Comment: 4 pages, 2 figure

Understanding the errors of SHAPE-directed RNA structure modeling

Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer extension (SHAPE) can give near-zero error rates (0-2%) in modeling the helices of RNA secondary structure. Here, we benchmark the method using six molecules for which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic di-GMP, and glycine. SHAPE-directed modeling of these highly structured RNAs gave an overall false negative rate (FNR) of 17% and a false discovery rate (FDR) of 21%, with at least one helix prediction error in five of the six cases. Extensive variations of data processing, normalization, and modeling parameters did not significantly mitigate modeling errors. Only one varation, filtering out data collected with deoxyinosine triphosphate during primer extension, gave a modest improvement (FNR = 12%, and FDR = 14%). The residual structure modeling errors are explained by the insufficient information content of these RNAs' SHAPE data, as evaluated by a nonparametric bootstrapping analysis. Beyond these benchmark cases, bootstrapping suggests a low level of confidence (<50%) in the majority of helices in a previously proposed SHAPE-directed model for the HIV-1 RNA genome. Thus, SHAPE-directed RNA modeling is not always unambiguous, and helix-by-helix confidence estimates, as described herein, may be critical for interpreting results from this powerful methodology.Comment: Biochemistry, Article ASAP (Aug. 15, 2011