Model-based asymptotically optimal dispersion measure correction for pulsar timing

In order to reach the sensitivity required to detect gravitational waves, pulsar timing array experiments need to mitigate as much noise as possible in timing data. A dominant amount of noise is likely due to variations in the dispersion measure. To correct for such variations, we develop a statistical method inspired by the maximum likelihood estimator and optimal filtering. Our method consists of two major steps. First, the spectral index and amplitude of dispersion measure variations are measured via a time-domain spectral analysis. Second, the linear optimal filter is constructed based on the model parameters found in the first step, and is used to extract the dispersion measure variation waveforms. Compared to current existing methods, this method has better time resolution for the study of short timescale dispersion variations, and generally produces smaller errors in waveform estimations. This method can process irregularly sampled data without any interpolation because of its time-domain nature. Furthermore, it offers the possibility to interpolate or extrapolate the waveform estimation to regions where no data is available. Examples using simulated data sets are included for demonstration.Comment: 15 pages, 15 figures, submitted 15th Sept. 2013, accepted 2nd April 2014 by MNRAS. MNRAS, 201

Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive model

Chromatin accessibility assays are central to the genome-wide identification of gene regulatory elements associated with transcriptional regulation. However, the data have highly variable quality arising from several biological and technical factors. To surmount this problem, we developed a sequence-based machine learning method to evaluate and refine chromatin accessibility data. Our framework, gapped k-mer SVM quality check (gkmQC), provides the quality metrics for a sample based on the prediction accuracy of the trained models. We tested 886 DNase-seq samples from the ENCODE/Roadmap projects to demonstrate that gkmQC can effectively identify high-quality (HQ) samples with low conventional quality scores owing to marginal read depths. Peaks identified in HQ samples are more accurately aligned at functional regulatory elements, show greater enrichment of regulatory elements harboring functional variants, and explain greater heritability of phenotypes from their relevant tissues. Moreover, gkmQC can optimize the peak-calling threshold to identify additional peaks, especially for rare cell types in single-cell chromatin accessibility data

Renormalization Group Study of the A+B->0 Diffusion-Limited Reaction

The $A + B\to 0$ diffusion-limited reaction, with equal initial densities $a(0) = b(0) = n_0$, is studied by means of a field-theoretic renormalization group formulation of the problem. For dimension $d > 2$ an effective theory is derived, from which the density and correlation functions can be calculated. We find the density decays in time as a,b \sim C\sqrt{\D}(Dt)^{-d/4} for $d < 4$, with \D = n_0-C^\prime n_0^{d/2} + \dots, where $C$ is a universal constant, and $C^\prime$ is non-universal. The calculation is extended to the case of unequal diffusion constants $D_A \neq D_B$, resulting in a new amplitude but the same exponent. For $d \le 2$ a controlled calculation is not possible, but a heuristic argument is presented that the results above give at least the leading term in an $\epsilon = 2-d$ expansion. Finally, we address reaction zones formed in the steady-state by opposing currents of $A$ and $B$ particles, and derive scaling properties.Comment: 17 pages, REVTeX, 13 compressed figures, included with epsf. Eq. (6.12) corrected, and a moderate rewriting of the introduction. Accepted for publication in J. Stat. Phy

Anisotropic Coarsening: Grain Shapes and Nonuniversal Persistence

We solve a coarsening system with small but arbitrary anisotropic surface tension and interface mobility. The resulting size-dependent growth shapes are significantly different from equilibrium microcrystallites, and have a distribution of grain sizes different from isotropic theories. As an application of our results, we show that the persistence decay exponent depends on anisotropy and hence is nonuniversal.Comment: 4 pages (revtex), 2 eps figure

A GALEX Ultraviolet Imaging Survey of Galaxies in the Local Volume

We present results from a GALEX ultraviolet (UV) survey of a complete sample of 390 galaxies within ~11 Mpc of the Milky Way. The UV data are a key component of the composite Local Volume Legacy (LVL), an ultraviolet-to-infrared imaging program designed to provide an inventory of dust and star formation in nearby spiral and irregular galaxies. The ensemble dataset is an especially valuable resource for studying star formation in dwarf galaxies, which comprise over 80% of the sample. We describe the GALEX survey programs which obtained the data and provide a catalog of far-UV (~1500 Angstroms) and near-UV (~2200 Angstroms) integrated photometry. General UV properties of the sample are briefly discussed. We compute two measures of the global star formation efficiency, the SFR per unit HI gas mass and the SFR per unit stellar mass, to illustrate the significant differences that can arise in our understanding of dwarf galaxies when the FUV is used to measure the SFR instead of H-alpha. We find that dwarf galaxies may not be as drastically inefficient in coverting gas into stars as suggested by prior H-alpha studies. In this context, we also examine the UV properties of late-type dwarf galaxies that appear to be devoid of star formation because they were not detected in previous H-alpha narrowband observations. Nearly all such galaxies in our sample are detected in the FUV, and have FUV SFRs that fall below the limit where the H-alpha flux is robust to Poisson fluctuations in the formation of massive stars. The UV colors and star formation efficiencies of H-alpha-undetected, UV-bright dwarf irregulars appear to be relatively unremarkable with respect to those exhibited by the general population of star-forming galaxies.Comment: submitted to ApJS, revised per referee's comments; accepted Oct. 30 w/o further revision; 37 pages; figure 6 omitted due to size; figure available from http://users.obs.carnegiescience.edu/jlee/paper

Ginzburg Criterion for Coulombic Criticality

To understand the range of close-to-classical critical behavior seen in various electrolytes, generalized Debye-Hueckel theories (that yield density correlation functions) are applied to the restricted primitive model of equisized hard spheres. The results yield a Landau-Ginzburg free-energy functional for which the Ginzburg criterion can be explicitly evaluated. The predicted scale of crossover from classical to Ising character is found to be similar in magnitude to that derived for simple fluids in comparable fashion. The consequences in relation to experiments are discussed briefly.Comment: 4 pages, revtex, 2 tables (latex2.09 required due to revtex's incompatibility with latex2e tables