Deterministic Polynomial-Time Algorithms for Designing Short DNA Words

Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of additional constraints. This problem has applications in, e.g., DNA self-assembly and DNA arrays. Previous works include those that extended results from coding theory to obtain bounds on code and word sizes for biologically motivated constraints and those that applied heuristic local searches, genetic algorithms, and randomized algorithms. In particular, Kao, Sanghi, and Schweller (2009) developed polynomial-time randomized algorithms to construct n DNA words of length within a multiplicative constant of the smallest possible word length (e.g., 9 max{log n, k}) that satisfy various sets of constraints with high probability. In this paper, we give deterministic polynomial-time algorithms to construct DNA words based on derandomization techniques. Our algorithms can construct n DNA words of shorter length (e.g., 2.1 log n + 6.28 k) and satisfy the same sets of constraints as the words constructed by the algorithms of Kao et al. Furthermore, we extend these new algorithms to construct words that satisfy a larger set of constraints for which the algorithms of Kao et al. do not work.Comment: 27 page

LAMOST 1: A Disrupted Satellite in the Constellation Draco

Using LAMOST spectroscopic data, we find a strong signal of a comoving group of stars in the constellation of Draco. The group, observed near the apocenter of its orbit, is 2.6 kpc from the Sun with a metallicity of -0.64 dex. The system is observed as a streaming population of unknown provenance with mass of about 2.1E4 solar masses and an absolute V band magnitude of about -3.6. Its high metallicity, diffuse physical structure, and eccentric orbit may indicate that the progenitor satellite was a globular cluster rather than a dwarf galaxy or an open cluster.Comment: 6 pages, 4 Figures, 1 Table, Accepted to ApJ

Gate Tunable Dissipation and "Superconductor-Insulator" Transition in Carbon Nanotube Josephson Transistors

Dissipation is ubiquitous in quantum systems, and its interplay with fluctuations is critical to maintaining quantum coherence. We experimentally investigate the dissipation dynamics in single-walled carbon nanotubes coupled to superconductors. The voltage-current characteristics display gate-tunable hysteresis, with sizes that perfectly correlate with the normal state resistance RN, indicating the junction undergoes a periodic modulation between underdamped and overdamped regimes. Surprisingly, when a device's Fermi-level is tuned through a local conductance minimum, we observe a gate-controlled transition from superconducting-like to insulating-like states, with a "critical" R_N value of about 8-20 kohm.Comment: Figures revised to improve clarity. Accepted for publication by Physical Review Letter

Normal heat conduction in one dimensional momentum conserving lattices with asymmetric interactions

The heat conduction behavior of one dimensional momentum conserving lattice systems with asymmetric interparticle interactions is numerically investigated. It is found that with certain degree of interaction asymmetry, the heat conductivity measured in nonequilibrium stationary states converges in the thermodynamical limit, in clear contrast to the well accepted viewpoint that Fourier's law is generally violated in low dimensional momentum conserving systems. It suggests in nonequilibrium stationary states the mass gradient resulted from the asymmetric interactions may provide an additional phonon scattering mechanism other than that due to the nonlinear interactions.Comment: 4 pages, 4 figure

Salicylic acid collaborates with gene silencing to tomato defense against tomato yellow leaf curl virus (TYLCV)

Antiviral research in plants has been focused on RNA silencing (i.e. RNA interference), and several studies suggest that salicylic acid (SA)-mediated resistance is a key part of plant antiviral defense. However, the antiviral defense mechanism of SA-mediation is still unclear, and several recent studies have suggested a connection between SA-mediated defense and RNA silencing, which needs further characterization in TYLCV infection. In this study, both SA-mediated defense and the RNA silencing mechanism were observed to play an important role in the antiviral response against TYLCV. First, we found that SA application enhanced the resistance to TYLCV in tomato plants. The expression of RNA-silencing-related genes, such as SlDCL1, SlDCL2, SlDCL4, SlRDR2, SlRDR3a, SlRDR6a, SlAGO1, and SlAGO4, were significantly triggered by exogenous SA application and inoculation with TYLCV, respectively. Furthermore, silencing of SlDCL2, SlDCL4 in tomato resulted in attenuated resistance to TYLCV, and reduced the expression of defense-related genes (SlPR1 and SlPR1b) in SA-mediated defense after infection with TYLCV, particularly in SlDCL2/SlDCL4-silenced plants. Taken together, we conclude that SA collaborates with gene silencing in tomato defense against TYLCV