Electronic signature of DNA nucleotides via transverse transport

We report theoretical studies of charge transport in single-stranded DNA in the direction perpendicular to the backbone axis. We find that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries a unique signature due to the different electronic and chemical structure of the four bases. This signature is independent of the nearest-neighbor nucleotides. Furthermore, except for the nucleotides with Guanine and Cytosine bases, we find that the difference in conductance of the nucleotides is large for most orientations of the bases with respect to the electrodes. By exploiting these differences it may be possible to sequence single-stranded DNA by scanning its length with conducting probes.Comment: 4 pages, 5 figure

Colloquium: Physical approaches to DNA sequencing and detection

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single-nucleotide level. This is in sharp contrast to current techniques and instruments that probe (through chemical elongation, electrophoresis, and optical detection) length differences and terminating bases of strands of DNA. Several physical approaches to DNA detection have the potential to deliver fast and low-cost sequencing. Central to these approaches is the concept of nanochannels or nanopores, which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. This Colloquium emphasizes the physics behind these methods and ideas, critically describes their advantages and drawbacks, and discusses future research opportunities in the field

Efficient mining of discriminative molecular fragments

Frequent pattern discovery in structured data is receiving an increasing attention in many application areas of sciences. However, the computational complexity and the large amount of data to be explored often make the sequential algorithms unsuitable. In this context high performance distributed computing becomes a very interesting and promising approach. In this paper we present a parallel formulation of the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The application is characterized by a highly irregular tree-structured computation. No estimation is available for task workloads, which show a power-law distribution in a wide range. The proposed approach allows dynamic resource aggregation and provides fault and latency tolerance. These features make the distributed application suitable for multi-domain heterogeneous environments, such as computational Grids. The distributed application has been evaluated on the well known National Cancer Institute’s HIV-screening dataset

Comment on "Characterization of the tunneling conductance across DNA bases"

In a recent article, Zikic {\it et al.} [Phys. Rev. E {\bf 74}, 011919 (2006)] present first-principles calculations of the DNA nucleotides electrical conductance. They report qualitative and quantitative differences with previous work, in particular with that of Zwolak and Di Ventra [Nano Lett. {\bf 5}, 421 (2005)] and Lagerqvist {\it et al.} [Nano Lett. {\bf 6}, 779 (2006)]. In this comment we address the alleged discrepancies and show that Zikic {\it et al.} have seriously misread and misunderstood the existing literature. In addition, we point out the deficiencies of their approach in calculating the conductance of nucleotides and the consequent erroneous conclusions they report.Comment: 3 pages, 1 figur

On the Lyapunov Matrix of Linear Delay Difference Equations in Continuous Time

The fundamental matrix and the delay Lyapunov matrix of linear delay difference equations are introduced. Some properties of the Lyapunov matrix, and the jump discontinuities of its derivative are proven, leading to its construction in the case of single delay or commensurate delays. An approximation is proposed for the non-commensurate case

Prescriptions on antiproton cross section data for precise theoretical antiproton flux predictions

After the breakthrough from the satellite-borne PAMELA detector, the flux of cosmic-ray (CR) antiprotons has been provided with unprecedented accuracy by AMS-02 on the International Space Station. Its data spans an energy range from below 1 GeV up to 400 GeV and most of the data points contain errors below the amazing level of 5%. The bulk of the antiproton flux is expected to be produced by the scatterings of CR protons and helium off interstellar hydrogen and helium atoms at rest. The modeling of these interactions, which requires the relevant production cross sections, induces an uncertainty in the determination of the antiproton source term that can even exceed the uncertainties in the CR $\bar{p}$ data itself. The aim of the present analysis is to determine the uncertainty required for $p+p\rightarrow \bar{p} + X$ cross section measurements such that the induced uncertainties on the $\bar{p}$ flux are at the same level. Our results are discussed both in the center-of-mass reference frame, suitable for collider experiments, and in the laboratory frame, as occurring in the Galaxy. We find that cross section data should be collected with accuracy better that few percent with proton beams from 10 GeV to 6 TeV and a pseudorapidity $\eta$ ranging from 2 to almost 8 or, alternatively, with $p_T$ from 0.04 to 2 GeV and $x_R$ from 0.02 to 0.7. Similar considerations hold for the $p$He production channel. The present collection of data is far from these requirements. Nevertheless, they could, in principle, be reached by fixed target experiments with beam energies in the reach of CERN accelerators.Comment: 15 pages, 13 figures, matches published versio