Silent MST approximation for tiny memory

In network distributed computing, minimum spanning tree (MST) is one of the key problems, and silent self-stabilization one of the most demanding fault-tolerance properties. For this problem and this model, a polynomial-time algorithm with $O(\log^2\!n)$ memory is known for the state model. This is memory optimal for weights in the classic $[1,\text{poly}(n)]$ range (where $n$ is the size of the network). In this paper, we go below this $O(\log^2\!n)$ memory, using approximation and parametrized complexity. More specifically, our contributions are two-fold. We introduce a second parameter~$s$, which is the space needed to encode a weight, and we design a silent polynomial-time self-stabilizing algorithm, with space $O(\log n \cdot s)$. In turn, this allows us to get an approximation algorithm for the problem, with a trade-off between the approximation ratio of the solution and the space used. For polynomial weights, this trade-off goes smoothly from memory $O(\log n)$ for an $n$-approximation, to memory $O(\log^2\!n)$ for exact solutions, with for example memory $O(\log n\log\log n)$ for a 2-approximation

The zero exemplar distance problem

Given two genomes with duplicate genes, \textsc{Zero Exemplar Distance} is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome. Blin, Fertin, Sikora, and Vialette recently proved that \textsc{Zero Exemplar Distance} for monochromosomal genomes is NP-hard even if each gene appears at most two times in each genome, thereby settling an important open question on genome rearrangement in the exemplar model. In this paper, we give a very simple alternative proof of this result. We also study the problem \textsc{Zero Exemplar Distance} for multichromosomal genomes without gene order, and prove the analogous result that it is also NP-hard even if each gene appears at most two times in each genome. For the positive direction, we show that both variants of \textsc{Zero Exemplar Distance} admit polynomial-time algorithms if each gene appears exactly once in one genome and at least once in the other genome. In addition, we present a polynomial-time algorithm for the related problem \textsc{Exemplar Longest Common Subsequence} in the special case that each mandatory symbol appears exactly once in one input sequence and at least once in the other input sequence. This answers an open question of Bonizzoni et al. We also show that \textsc{Zero Exemplar Distance} for multichromosomal genomes without gene order is fixed-parameter tractable if the parameter is the maximum number of chromosomes in each genome.Comment: Strengthened and reorganize

Neutrino-Nucleus Reactions and Muon Capture in 12C

The neutrino-nucleus cross section and the muon capture rate are discussed within a simple formalism which facilitates the nuclear structure calculations. The corresponding formulae only depend on four types of nuclear matrix elements, which are currently used in the nuclear beta decay. We have also considered the non-locality effects arising from the velocity-dependent terms in the hadronic current. We show that for both observables in 12C the higher order relativistic corrections are of the order of ~5 only, and therefore do not play a significant role. As nuclear model framework we use the projected QRPA (PQRPA) and show that the number projection plays a crucial role in removing the degeneracy between the proton-neutron two quasiparticle states at the level of the mean field. Comparison is done with both the experimental data and the previous shell model calculations. Possible consequences of the present study on the determination of the $\nu_\mu ->\nu_e$ neutrino oscillation probability are briefly addressed.Comment: 29 pages, 6 figures, Revtex4. Several changes were made to the previous manuscript, the results and final conclusions remain unalterable. It has been accepted for publication as a Regular Article in Physical Review

Voltage controlled terahertz transmission through GaN quantum wells

We report measurements of radiation transmission in the 0.220--0.325 THz frequency domain through GaN quantum wells grown on sapphire substrates at room and low temperatures. A significant enhancement of the transmitted beam intensity with the applied voltage on the devices under test is found. For a deeper understanding of the physical phenomena involved, these results are compared with a phenomenological theory of light transmission under electric bias relating the transmission enhancement to changes in the differential mobility of the two-dimensional electron gas

Isoscalar g Factors of Even-Even and Odd-Odd Nuclei

We consider T=0 states in even-even and odd-odd N=Z nuclei. The g factors that emerge are isoscalar. We find that the single j shell model gives simple expressions for these g factors which for even-even nuclei are suprisingly close to the collective values for K=0 bands. The g factors of many 2+ in even-even nuclei and 1+ and 3+ states in odd-odd nuclei have g factors close to 0.5

Hyperfine Structure Constants for Eu Isotopes: Is The Empirical Formula of HFS Anomaly Universal ?

We calculate the hyperfine structure constant for the Eu isotopes with shell model wave functions. The calculated results are compared with those predicted by the Moskowitz-Lombardi (M-L) empirical formula. It turns out that the two approaches give the very different behaviors of the hfs constants in the isotope dependence. This should be easily measured by experiment, which may lead to the universality check of the M-L formula.Comment: 18 pages, Latex, two figure

Counting, generating and sampling tree alignments

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformative, and detrimental to any probabilistic analysis.In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees $S$ and $T$. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal RNA secondary structures alignments.Comment: ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. 201

Identification of TMEM206 proteins as pore of PAORAC/ASOR acid-sensitive chloride channels

Acid-sensing ion channels have important functions in physiology and pathology, but the molecular composition of acid-activated chloride channels had remained unclear. We now used a genome-wide siRNA screen to molecularly identify the widely expressed acid-sensitive outwardly-rectifying anion channel PAORAC/ASOR. ASOR is formed by TMEM206 proteins which display two transmembrane domains (TMs) and are expressed at the plasma membrane. Ion permeation-changing mutations along the length of TM2 and at the end of TM1 suggest that these segments line ASOR's pore. While not belonging to a gene family, TMEM206 has orthologs in probably all vertebrates. Currents from evolutionarily distant orthologs share activation by protons, a feature essential for ASOR's role in acid-induced cell death. TMEM206 defines a novel class of ion channels. Its identification will help to understand its physiological roles and the diverse ways by which anion-selective pores can be formed