Homotopy Method for the Large, Sparse, Real Nonsymmetric Eigenvalue Problem

A homotopy method to compute the eigenpairs, i.e., the eigenvectors and eigenvalues, of a given real matrix A1 is presented. From the eigenpairs of some real matrix A0, the eigenpairs of A(t) ≡ (1 − t)A0 + tA1 are followed at successive "times" from t = 0 to t = 1 using continuation. At t = 1, the eigenpairs of the desired matrix A1 are found. The following phenomena are present when following the eigenpairs of a general nonsymmetric matrix: • bifurcation, • ill conditioning due to nonorthogonal eigenvectors, • jumping of eigenpaths. These can present considerable computational difficulties. Since each eigenpair can be followed independently, this algorithm is ideal for concurrent computers. The homotopy method has the potential to compete with other algorithms for computing a few eigenvalues of large, sparse matrices. It may be a useful tool for determining the stability of a solution of a PDE. Some numerical results will be presented

FeAs-based superconductivity: a case study of the effects of transition metal doping on BaFe2As2

The recently discovered FeAs-based superconductors are a new, promising set of materials for both technological as well as basic research. They offer transition temperatures as high as 55 K as well as essentially isotropic and extremely large upper, superconducting critical fields in excess of 40 T at 20 K. In addition they may well provide insight into exotic superconductivity that extends beyond just FeAs-based superconductivity, perhaps even shedding light on the still perplexing CuO-based high-Tc materials. Whereas superconductivity can be induced in the RFeAsO (R = rare earth) and AEFe2As2 (AE = Ba, Sr, Ca)) families by a number of means, transition metal doping of BaFe2As2, e.g. Ba(Fe1-xTMx)2As2, offers the easiest experimental access to a wide set of materials. In this review we present an overview and summary of the effect of TM doping (TM = Co, Ni, Cu, Pd, and Rh) on BaFe2As2. The resulting phase diagrams reveal the nature of the interaction between the structural, magnetic and superconducting phase transitions in these compounds and delineate a region of phase space that allows for the stabilization of superconductivity.Comment: edited and shortened version is accepted to AR:Condensed Matter Physic

Understanding the role of chromatin remodeling in the regulation of circadian transcription in Drosophila.

Circadian clocks enable organisms to anticipate daily changes in the environment and coordinate temporal rhythms in physiology and behavior with the 24-h day-night cycle. The robust cycling of circadian gene expression is critical for proper timekeeping, and is regulated by transcription factor binding, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Recently, it has become clear that dynamic alterations in chromatin landscape at the level of histone posttranslational modification and nucleosome density facilitate rhythms in transcription factor recruitment and RNAPII activity, and are essential for progression through activating and repressive phases of circadian transcription. Here, we discuss the characterization of the BRAHMA (BRM) chromatin-remodeling protein in Drosophila in the context of circadian clock regulation. By dissecting its catalytic vs. non-catalytic activities, we propose a model in which the non-catalytic activity of BRM functions to recruit repressive factors to limit the transcriptional output of CLOCK (CLK) during the active phase of circadian transcription, while the primary function of the ATP-dependent catalytic activity is to tune and prevent over-recruitment of negative regulators by increasing nucleosome density. Finally, we divulge ongoing efforts and investigative directions toward a deeper mechanistic understanding of transcriptional regulation of circadian gene expression at the chromatin level

The Catalytic and Non-catalytic Functions of the Brahma Chromatin-Remodeling Protein Collaborate to Fine-Tune Circadian Transcription in Drosophila.

Daily rhythms in gene expression play a critical role in the progression of circadian clocks, and are under regulation by transcription factor binding, histone modifications, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Although previous studies have shown that clock-controlled genes exhibit rhythmic chromatin modifications, less is known about the functions performed by chromatin remodelers in animal clockwork. Here we have identified the Brahma (Brm) complex as a regulator of the Drosophila clock. In Drosophila, CLOCK (CLK) is the master transcriptional activator driving cyclical gene expression by participating in an auto-inhibitory feedback loop that involves stimulating the expression of the main negative regulators, period (per) and timeless (tim). BRM functions catalytically to increase nucleosome density at the promoters of per and tim, creating an overall restrictive chromatin landscape to limit transcriptional output during the active phase of cycling gene expression. In addition, the non-catalytic function of BRM regulates the level and binding of CLK to target promoters and maintains transient RNAPII stalling at the per promoter, likely by recruiting repressive and pausing factors. By disentangling its catalytic versus non-catalytic functions at the promoters of CLK target genes, we uncovered a multi-leveled mechanism in which BRM fine-tunes circadian transcription

Application of theoretical models to active and passive remote sensing of saline ice

The random medium model is used to interpret the polarimetric active and passive measurements of saline ice. The ice layer is described as a host ice medium embedded with randomly distributed inhomogeneities, and the underlying sea water is considered as a homogeneous half-space. The scatterers in the ice layer are modeled with an ellipsoidal correlation function. The orientation of the scatterers is vertically aligned and azimuthally random. The strong permittivity fluctuation theory is employed to calculate the effective permittivity and the distorted Born approximation is used to obtain the polarimetric scattering coefficients. We also calculate the thermal emissions based on the reciprocity and energy conservation principles. The effects of the random roughness at the air-ice, and ice-water interfaces are accounted for by adding the surface scattering to the volume scattering return incoherently. The above theoretical model, which has been successfully applied to analyze the radar backscatter data of the first-year sea ice near Point Barrow, AK, is used to interpret the measurements performed in the CRRELEX program

Measurement of Cosmic-ray Muons and Muon-induced Neutrons in the Aberdeen Tunnel Underground Laboratory

We have measured the muon flux and production rate of muon-induced neutrons at a depth of 611 m water equivalent. Our apparatus comprises three layers of crossed plastic scintillator hodoscopes for tracking the incident cosmic-ray muons and 760 L of gadolinium-doped liquid scintillator for producing and detecting neutrons. The vertical muon intensity was measured to be $I_{\mu} = (5.7 \pm 0.6) \times 10^{-6}$ cm$^{-2}$s$^{-1}$sr$^{-1}$. The yield of muon-induced neutrons in the liquid scintillator was determined to be $Y_{n} = (1.19 \pm 0.08 (stat) \pm 0.21 (syst)) \times 10^{-4}$ neutrons/($\mu\cdot$g$\cdot$cm$^{-2}$). A fit to the recently measured neutron yields at different depths gave a mean muon energy dependence of $\left\langle E_{\mu} \right\rangle^{0.76 \pm 0.03}$ for liquid-scintillator targets.Comment: 14 pages, 17 figures, 3 table

Characterization of Toxoplasma gondii isolates in free-range chickens from Chile, South America

The prevalence of Toxoplasma gondii in free-ranging chickens is a good indicator of the prevalence of T. gondii oocysts in the soil because chickens feed from the ground. The prevalence of T. gondii in 85 free-range chickens (Gallus domesticus) from Chile was determined. Antibodies to T. gondii were assayed by the modified agglutination test (MAT), and found in 47 of 85 (55.3.9%) chickens with titers of 1:5 in six, 1:10 in four, 1:20 in four 1: 40 in three, 1: 80 in nine, 1: 160 in four 1:320 in nine, and 1: 640 or higher in eight. Hearts and brains of 47 chickens with titers of 1:5 or higher were pooled for each chicken and bioassayed in mice. Tissues from 16 seronegative (MAT < 1:5) chickens were pooled and fed to one T. gondii-free cat. Feces of the cat were examined for oocysts but none was found based on bioassay of fecal floats in mice. Hearts and brains from seven seronegative (<1:5) were pooled and bioassayed in mice; T. gondii was not isolated. T. gondii was isolated by bioassay in mice from 22 chickens with MAT titers of 1:20 or higher. Genotyping of these 22 isolates using polymorphisms at the loci SAG1, SAG2, SAG3, BTUB and GRA6 revealed three genotypes. Seventeen isolates had type II alleles and four isolates had type III alleles at all loci. One isolate contained the combination of type I and III alleles. This is the first report of genetic characterization of T. gondii isolates from Chile, South America