Automated parameters for troubled-cell indicators using outlier detection

In Vuik and Ryan (2014) we studied the use of troubled-cell indicators for discontinuity detection in nonlinear hyperbolic partial differential equations and introduced a new multiwavelet technique to detect troubled cells. We found that these methods perform well as long as a suitable, problem-dependent parameter is chosen. This parameter is used in a threshold which decides whether or not to detect an element as a troubled cell. Until now, these parameters could not be chosen automatically. The choice of the parameter has impact on the approximation: it determines the strictness of the troubled-cell indicator. An inappropriate choice of the parameter will result in detection (and limiting) of too few or too many elements. The optimal parameter is chosen such that the minimal number of troubled cells is detected and the resulting approximation is free of spurious oscillations. In this paper we will see that for each troubled-cell indicator the sudden increase or decrease of the indicator value with respect to the neighboring values is important for detection. Indication basically reduces to detecting the outliers of a vector (one dimension) or matrix (two dimensions). This is done using Tukey's boxplot approach to detect which coefficients in a vector are straying far beyond others (Tukey, 1977). We provide an algorithm that can be applied to various troubled-cell indication variables. Using this technique the problem-dependent parameter that the original indicator requires is no longer necessary as the parameter will be chosen automatically

Design of two-dimensional particle assemblies using isotropic pair interactions with an attractive well

Using ground-state and relative-entropy based inverse design strategies, isotropic interactions with an attractive well are determined to stabilize and promote as- sembly of particles into two-dimensional square, honeycomb, and kagome lattices. The design rules inferred from these results are discussed and validated in the dis- covery of interactions that favor assembly of the highly open truncated-square and truncated-hexagonal lattices.Comment: 11 pages, 5 figures and supplemental materia

Neutrinoless double-beta decay. A brief review

In this brief review we discuss the generation of Majorana neutrino masses through the see-saw mechanism, the theory of neutrinoless double-beta decay, the implications of neutrino oscillation data for the effective Majorana mass, taking into account the recent Daya Bay measurement of theta_13, and the interpretation of the results of neutrinoless double-beta decay experiments.Comment: 22 page

Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication

Replication Protein A (RPA) is a heterotrimeric protein complex that binds single-stranded DNA. In plants, multiple genes encode the three RPA subunits (RPA1, RPA2 and RPA3), including five RPA1-like genes in Arabidopsis. Phylogenetic analysis suggests two distinct groups composed of RPA1A, RPA1C, RPA1E (ACE group) and RPA1B, RPA1D (BD group). ACE-group members are transcriptionally induced by ionizing radiation, while BD-group members show higher basal transcription and are not induced by ionizing radiation. Analysis of rpa1 T-DNA insertion mutants demonstrates that although each mutant line is likely null, all mutant lines are viable and display normal vegetative growth. The rpa1c and rpa1e single mutants however display hypersensitivity to ionizing radiation, and combination of rpa1c and rpa1e results in additive hypersensitivity to a variety of DNA damaging agents. Combination of the partially sterile rpa1a with rpa1c results in complete sterility, incomplete synapsis and meiotic chromosome fragmentation, suggesting an early role for RPA1C in promoting homologous recombination. Combination of either rpa1c and/or rpa1e with atr revealed additive hypersensitivity phenotypes consistent with each functioning in unique repair pathways. In contrast, rpa1b rpa1d double mutant plants display slow growth and developmental defects under non-damaging conditions. We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division

The Carboxyl-Terminal Segment of Apolipoprotein A-V Undergoes a Lipid-Induced Conformational Change

Apolipoprotein (apo) A-V is a 343-residue, multidomain protein that plays an important role in regulation of plasma triglyceride homeostasis. Primary sequence analysis revealed a unique tetraproline sequence (Pro293-Pro296) near the carboxyl terminus of the protein. A peptide corresponding to the 48-residue segment beyond the tetraproline motif was generated from a recombinant apoA-V precursor wherein Pro295 was replaced by Met. Cyanogen bromide cleavage of the precursor protein, followed by negative affinity chromatography, yielded a purified peptide. Nondenaturing polyacrylamide gel electrophoresis verified that apoA-V(296-343) solubilizes phospholipid vesicles, forming a relatively heterogeneous population of reconstituted high-density lipoprotein with Stokes’ diameters\u3e17 nm. At the same time, apoA-V(296-343) failed to bind a spherical lipoprotein substrate in vitro. Far-UV circular dichroism spectroscopy revealed the peptide is unstructured in buffer yet adopts significant R-helical secondary structure in the presence of the lipid mimetic solvent trifluoroethanol (TFE; 50% v/v). Heteronuclear multidemensional NMR spectroscopy experiments were conducted with uniformly 15N- and 15N/13C-labeled peptide in 50% TFE. Peptide backbone assignment and secondary structure prediction using TALOSþ reveal the peptide adopts R-helix secondary structure from residues 309 to 334. In TFE, apoA-V(296-343) adopts an extended amphipathic R-helix, consistent with a role in lipoprotein binding as a component of full-length apoA-V

The role of the quantum properties of gravitational radiation in the dete ction of gravitational waves

The role that the quantum properties of a gravitational wave could play in the detection of gravitational radiation is analyzed. It is not only corroborated that in the current laser-interferometric detectors the resolution of the experimental apparatus could lie very far from the corresponding quantum threshold (thus the backreaction effect of the measuring device upon the gravitational wave is negligible), but it is also suggested that the consideration of the quantum properties of the wave could entail the definition of dispersion of the measurement outputs. This dispersion would be a function not only of the sensitivity of the measuring device, but also of the interaction time (between measuring device and gravitational radiation) and of the arm length of the corresponding laser- interferometer. It would have a minimum limit, and the introduction of the current experimental parameters insinuates that the dispersion of the existing proposals could lie very far from this minimum, which means that they would show a very large dispersion.Comment: 19 pages, Latex (use epsfig.sty

The spectrum of radial, orbital and gluonic excitations of charmonium

We present results for the charmonium spectrum from $N_f=2$ dynamical QCD simulations on $12^3\times 80$ anisotropic lattices. Using all-to-all propagators we determine the ground and excited states of S, P and D waves and hybrids. We also evaluate the disconnected (OZI suppressed) contribution to the $\eta_c$ and $J/\Psi$Comment: 6 pages, 3 figures, Presented at 24th International Symposium on Lattice Field Theory (Lattice 2006), Tucson, Arizona, 23-28 Jul 200