Dynamics of chromatin and transcription during transient depletion of the RSC chromatin remodeling complex

Nucleosome organization has a key role in transcriptional regulation, yet the precise mechanisms establishing nucleosome locations and their effect on transcription are unclear. Here, we use an induced degradation system to screen all yeast ATP-dependent chromatin remodelers. We characterize how rapid clearance of the remodeler affects nucleosome locations. Specifically, depletion of Sth1, the catalytic subunit of the RSC (remodel the structure of chromatin) complex, leads to rapid fill-in of nucleosome-free regions at gene promoters. These changes are reversible upon reintroduction of Sth1 and do not depend on DNA replication. RSC-dependent nucleosome positioning is pivotal in maintaining promoters of lowly expressed genes free from nucleosomes. In contrast, we observe that upon acute stress, the RSC is not necessary for the transcriptional response. Moreover, RSC-dependent nucleosome positions are tightly related to usage of specific transcription start sites. Our results suggest organizational principles that determine nucleosome positions with and without RSC and how these interact with the transcriptional process

Determination of the Baryon Density from Large Scale Galaxy Redshift Surveys

We estimate the degree to which the baryon density, $\Omega_{b}$, can be determined from the galaxy power spectrum measured from large scale galaxy redshift surveys, and in particular, the Sloan Digital Sky Survey. A high baryon density will cause wiggles to appear in the power spectrum, which should be observable at the current epoch. We assume linear theory on scales $\geq 20h^{-1}Mpc$ and do not include the effects of redshift distortions, evolution, or biasing. With an optimum estimate of $P(k)$ to $k\sim 2\pi/(20 h^{-1} Mpc)$, the $1 \sigma$ uncertainties in $\Omega_{b}$ are roughly 0.07 and 0.016 in flat and open ($\Omega_{0}=0.3$) cosmological models, respectively. This result suggests that it should be possible to test for consistency with big bang nucleosynthesis estimates of $\Omega_{b}$ if we live in an open universe.Comment: 23 Pages, 10 Postscript figure

Turbulent Magnetic Reconnection in Two Dimensions

Two-dimensional numerical simulations of the effect of background turbulence on 2D resistive magnetic reconnection are presented. For sufficiently small values of the resistivity ($\eta$) and moderate values of the turbulent power ($\epsilon$), the reconnection rate is found to have a much weaker dependence on $\eta$ than the Sweet-Parker scaling of $\eta^{1/2}$ and is even consistent with an $\eta-$independent value. For a given value of $\eta$, the dependence of the reconnection rate on the turbulent power exhibits a critical threshold in $\epsilon$ above which the reconnection rate is significantly enhanced.Comment: Accepted to MNRA

Dynamics in binary cluster crystals

As a result of the application of coarse-graining procedures to describe complex fluids, the study of systems consisting of particles interacting through bounded, repulsive pair potentials has become of increasing interest in the last years. A well known example is the so-called Generalized Exponential Model (GEM-$m$), for which the interaction between particles is described by the potential $v(r)=\epsilon\exp[-(r/\sigma)^m]$. Interactions with $m > 2$ lead to the formation of a novel phase of soft matter consisting of cluster crystals. Recent studies on the phase behavior of binary mixtures of GEM-$m$ particles have provided evidence for the formation of novel kinds of alloys, depending on the cross interactions between the two species. This work aims to study the dynamic behavior of such binary mixtures by means of extensive molecular dynamics simulations, and in particular to investigate the effect of the addition of non-clustering particles on the dynamic scenario of one-component cluster crystals. Analogies and differences with the one-component case are revealed and discussed by analyzing self- and collective dynamic correlators.Comment: 17 pages, 8 figures, submitted to JSTA

The X-ray Spectral Properties and Variability of Luminous High-Redshift Active Galactic Nuclei

We perform a detailed investigation of moderate-to-high quality X-ray spectra of ten of the most luminous active galactic nuclei (AGNs) known at z>4 (up to z~6.28). This study includes five new XMM observations and five archived X-ray observations (four by XMM and one by Chandra). We find that the X-ray power-law photon indices of our sample, composed of eight radio-quiet sources and two that are moderately radio loud, are not significantly different from those of lower redshift AGNs. The upper limits obtained on intrinsic neutral hydrogen column densities, N_H<~10^{22}-10^{23} cm^{-2}, indicate that these AGNs are not significantly absorbed. A joint fit performed on our eight radio-quiet sources, with a total of ~7000 photons, constrains the mean photon index of z>4 radio-quiet AGNs to Gamma=1.97^{+0.06}_{-0.04}, with no detectable intrinsic dispersion from source to source. We also obtain a strong constraint on the mean intrinsic column density, N_H<~3x10^{21} cm^{-2}, showing that optically selected radio-quiet AGNs at z>4 are, on average, not more absorbed than their lower-redshift counterparts. All this suggests that the X-ray production mechanism and the central environment in radio-quiet AGNs have not significantly evolved over cosmic time. The mean equivalent width of a putative neutral narrow Fe Ka line is constrained to be <~190 eV, and similarly we place constraints on the mean Compton reflection component (R<~1.2). None of the AGNs varied on short (~1 hr) timescales, but on longer timescales (months-to-years) strong variability is observed in four of the sources. In particular, the X-ray flux of the z=5.41 radio-quiet AGN SDSS 0231-0728 dropped by a factor of ~4 over a rest-frame period of 73 d. This is the most extreme X-ray variation observed in a luminous z>4 radio-quiet AGN.Comment: 10 pages (emulateapj), 5 figures. Accepted by Ap