Covering Pairs in Directed Acyclic Graphs

The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a classical problem that provides a clear and simple mathematical formulation for several applications in different areas and that has an efficient algorithmic solution. In this paper, we study the computational complexity of two constrained variants of Minimum Path Cover motivated by the recent introduction of next-generation sequencing technologies in bioinformatics. The first problem (MinPCRP), given a DAG and a set of pairs of vertices, asks for a minimum cardinality set of paths "covering" all the vertices such that both vertices of each pair belong to the same path. For this problem, we show that, while it is NP-hard to compute if there exists a solution consisting of at most three paths, it is possible to decide in polynomial time whether a solution consisting of at most two paths exists. The second problem (MaxRPSP), given a DAG and a set of pairs of vertices, asks for a path containing the maximum number of the given pairs of vertices. We show its NP-hardness and also its W[1]-hardness when parametrized by the number of covered pairs. On the positive side, we give a fixed-parameter algorithm when the parameter is the maximum overlapping degree, a natural parameter in the bioinformatics applications of the problem

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Out-of-equilibrium singlet-triplet Kondo effect in a single C_60 quantum dot

We have used an electromigration technique to fabricate a $\rm{C_{{60}}}$ single-molecule transistor (SMT). Besides describing our electromigration procedure, we focus and present an experimental study of a single molecule quantum dot containing an even number of electrons, revealing, for two different samples, a clear out-of-equilibrium Kondo effect. Low temperature magneto-transport studies are provided, which demonstrates a Zeeman splitting of the finite bias anomaly.Comment: 6 pages, 4 figure

Biogenic Versus Anthropogenic Sources of CO in the United States

Aircraft observations of carbon monoxide (CO) from the ICARTT campaign over the eastern United States in summer 2004 (July 1–August 15), interpreted with a global 3-D model of tropospheric chemistry (GEOS-Chem), show that the national anthropogenic emission inventory from the U.S. Environmental Protection Agency (93 Tg CO y−1) is too high by 60% in summer. Our best estimate of the CO anthropogenic source for the ICARTT period is 6.4 Tg CO, including 4.6 Tg from direct emission and 1.8 Tg CO from oxidation of anthropogenic volatile organic compounds (VOCs). The biogenic CO source for the same period from the oxidation of isoprene and other biogenic VOCs is 8.3 Tg CO, and is independently constrained by ICARTT observations of formaldehyde (HCHO). Anthropogenic emissions of CO in the U.S. have decreased to the point that they are now lower than the biogenic source in summer.Earth and Planetary SciencesEngineering and Applied Science

Abnormal phenomena in a one-dimensional periodic structure containing left-handed materials

The explicit dispersion equation for a one-dimensional periodic structure with alternative layers of left-handed material (LHM) and right-handed material (RHM) is given and analyzed. Some abnormal phenomena such as spurious modes with complex frequencies, discrete modes and photon tunnelling modes are observed in the band structure. The existence of spurious modes with complex frequencies is a common problem in the calculation of the band structure for such a photonic crystal. Physical explanation and significance are given for the discrete modes (with real values of wave number) and photon tunnelling propagation modes (with imaginary wave numbers in a limited region).Comment: 10 pages, 4 figure

Quasi-local Energy for Spherically Symmetric Spacetimes

We present two complementary approaches for determining the reference for the covariant Hamiltonian boundary term quasi-local energy and test them on spherically symmetric spacetimes. On the one hand, we isometrically match the 2-surface and extremize the energy. This can be done in two ways, which we call programs I (without constraint) and II (with additional constraints). On the other hand, we match the orthonormal 4-frames of the dynamic and the reference spacetimes. Then, if we further specify the observer by requiring the reference displacement to be the timelike Killing vector of the reference, the result is the same as program I, and the energy can be positive, zero, or even negative. If, instead, we require that the Lie derivatives of the two-area along the displacement vector in both the dynamic and reference spacetimes to be the same, the result is the same as program II, and it satisfies the usual criteria: the energies are non-negative and vanish only for Minkowski (or anti-de Sitter) spacetime.Comment: 16 pages, no figure

A first principles study of sub-monolayer Ge on Si(001)

Experimental observations of heteroepitaxial growth of Ge on Si(001) show a (2xn) reconstruction for sub-monolayer coverages, with dimer rows crossed by missing-dimer trenches. We present first-principles density-functional calculations designed to elucidate the energetics and relaxed geometries associated with this reconstruction. We also address the problem of how the formation energies of reconstructions having different stoichiometries should be compared. The calculations reveal a strong dependence of the formation energy of the missing-dimer trenches on spacing n, and demonstrate that this dependence stems almost entirely from elastic relaxation. The results provide a natural explanation for the experimentally observed spacings in the region of n \~ 8.Comment: 13 pages, 4 figures, submitted to Surface Scienc

Amplitude to phase conversion of InGaAs pin photo-diodes for femtosecond lasers microwave signal generation

When a photo-diode is illuminated by a pulse train from a femtosecond laser, it generates microwaves components at the harmonics of the repetition rate within its bandwidth. The phase of these components (relative to the optical pulse train) is known to be dependent on the optical energy per pulse. We present an experimental study of this dependence in InGaAs pin photo-diodes illuminated with ultra-short pulses generated by an Erbium-doped fiber based femtosecond laser. The energy to phase dependence is measured over a large range of impinging pulse energies near and above saturation for two typical detectors, commonly used in optical frequency metrology with femtosecond laser based optical frequency combs. When scanning the optical pulse energy, the coefficient which relates phase variations to energy variations is found to alternate between positive and negative values, with many (for high harmonics of the repetition rate) vanishing points. By operating the system near one of these vanishing points, the typical amplitude noise level of commercial-core fiber-based femtosecond lasers is sufficiently low to generate state-of-the-art ultra-low phase noise microwave signals, virtually immune to amplitude to phase conversion related noise.Comment: 7 pages, 6 figures, submitted to Applied Physics

Finite temperature phase diagram of spin-1/2 bosons in two-dimensional optical lattice

We study a two-species bosonic Hubbard model on a two-dimensional square lattice by means of quantum Monte Carlo simulations and focus on finite temperature effects. We show in two different cases, ferro- and antiferromagnetic spin-spin interactions, that the phase diagram is composed of solid Mott phases, liquid phases and superfluid phases. In the antiferromagnetic case, the superfluid (SF) is polarized while the Mott insulator (MI) and normal Bose liquid (NBL) phases are not. On the other hand, in the ferromagnetic case, none of the phases is polarized. The superfluid-liquid transition is of the Berezinsky-Kosterlitz-Thouless type whereas the solid-liquid passage is a crossover.Comment: 9 pages, 13 figure