Identification of the YfgF MASE1 domain as a modulator of bacterial responses to aspartate

Complex 3'-5'-cyclic diguanylic acid (c-di-GMP) responsive regulatory networks that are modulated by the action of multiple diguanylate cyclases (DGC; GGDEF domain proteins) and phosphodiesterases (PDE; EAL domain proteins) have evolved in many bacteria. YfgF proteins possess a membrane-anchoring domain (MASE1), a catalytically inactive GGDEF domain and a catalytically active EAL domain. Here, sustained expression of the Salmonella enterica spp. Enterica ser. Enteritidis YfgF protein is shown to mediate inhibition of the formation of the aspartate chemotactic ring on motility agar under aerobic conditions. This phenomenon was c-di-GMP-independent because it occurred in a Salmonella strain that lacked the ability to synthesize c-di-GMP and also when PDE activity was abolished by site-directed mutagenesis of the EAL domain. YfgF-mediated inhibition of aspartate chemotactic ring formation was impaired in the altered redox environment generated by exogenous p-benzoquinone. This ability of YfgF to inhibit the response to aspartate required a motif, (213)Lys-Lys-Glu(215), in the predicted cytoplasmic loop between trans-membrane regions 5 and 6 of the MASE1 domain. Thus, for the first time the function of a MASE1 domain as a redox-responsive regulator of bacterial responses to aspartate has been shown

Constraints on models for the initial collision geometry in ultra relativistic heavy ion collisions

Monte Carlo (MC) simulations are used to compute the centrality dependence of the collision zone eccentricities ($\epsilon_{2,4}$), for both spherical and deformed ground state nuclei, for different model scenarios. Sizable model dependent differences are observed. They indicate that measurements of the $2^{\text{nd}}$ and $4^{\text{th}}$ order Fourier flow coefficients $v_{2,4}$, expressed as the ratio $\frac{v_4}{(v_2)^2}$, can provide robust constraints for distinguishing between different theoretical models for the initial-state eccentricity. Such constraints could remove one of the largest impediments to a more precise determination of the specific viscosity from precision $v_{2,4}$ measurements at the Relativistic Heavy Ion Collider (RHIC).Comment: 4 pages, 3 figs - version accepted for publicatio

Dark-Halo Cusp: Asymptotic Convergence

We propose a model for how the buildup of dark halos by merging satellites produces a characteristic inner cusp, of a density profile \rho \prop r^-a with a -> a_as > 1, as seen in cosmological N-body simulations of hierarchical clustering scenarios. Dekel, Devor & Hetzroni (2003) argue that a flat core of a<1 exerts tidal compression which prevents local deposit of satellite material; the satellite sinks intact into the halo center thus causing a rapid steepening to a>1. Using merger N-body simulations, we learn that this cusp is stable under a sequence of mergers, and derive a practical tidal mass-transfer recipe in regions where the local slope of the halo profile is a>1. According to this recipe, the ratio of mean densities of halo and initial satellite within the tidal radius equals a given function psi(a), which is significantly smaller than unity (compared to being 1 according to crude resonance criteria) and is a decreasing function of a. This decrease makes the tidal mass transfer relatively more efficient at larger a, which means steepening when a is small and flattening when a is large, thus causing converges to a stable solution. Given this mass-transfer recipe, linear perturbation analysis, supported by toy simulations, shows that a sequence of cosmological mergers with homologous satellites slowly leads to a fixed-point cusp with an asymptotic slope a_as>1. The slope depends only weakly on the fluctuation power spectrum, in agreement with cosmological simulations. During a long interim period the profile has an NFW-like shape, with a cusp of 1<a<a_as. Thus, a cusp is enforced if enough compact satellite remnants make it intact into the inner halo. In order to maintain a flat core, satellites must be disrupted outside the core, possibly as a result of a modest puffing up due to baryonic feedback.Comment: 37 pages, Latex, aastex.cls, revised, ApJ, 588, in pres

The mass function

We present the mass functions for different mass estimators for a range of cosmological models. We pay particular attention to how universal the mass function is, and how it depends on the cosmology, halo identification and mass estimator chosen. We investigate quantitatively how well we can relate observed masses to theoretical mass functions.Comment: 14 pages, 12 figures, to appear in ApJ

A new method for the experimental study of topological effects in the quark-gluon plasma

A new method is presented for the quantitative measurement of charge separation about the reaction plane. A correlation function is obtained whose shape is concave when there is a net separation of positive and negative charges. Correlations not specifically associated with charge, from flow, jets and momentum conservation, do not influence the shape or magnitude of the correlation function. Detailed simulations are used to demonstrate the effectiveness of the method for the quantitative measurement of charge separation. Such measurements are a pre-requisite to the investigation of topological charge effects in the QGP as derived from the "strong $\cal{CP}$ problem".Comment: Six pages 13 figures. Submitted for publicatio

Measuring the Cosmic Equation of State with Counts of Galaxies

The classical dN/dz test allows the determination of fundamental cosmological parameters from the evolution of the cosmic volume element. This test is applied by measuring the redshift distribution of a tracer whose evolution in number density is known. In the past, ordinary galaxies have been used as such a tracer; however, in the absence of a complete theory of galaxy formation, that method is fraught with difficulties. In this paper, we propose studying instead the evolution of the apparent abundance of dark matter halos as a function of their circular velocity, observable via the linewidths or rotation speeds of visible galaxies. Upcoming redshift surveys will allow the linewidth distribution of galaxies to be determined at both z~1 and the present day. In the course of studying this test, we have devised a rapid, improved semi-analytic method for calculating the circular velocity distribution of dark halos based upon the analytic mass function of Sheth et al. (1999) and the formation time distribution of Lacey & Cole (1993). We find that if selection effects are well-controlled and minimal external constraints are applied, the planned DEEP Redshift Survey should allow the measurement of the cosmic equation-of-state parameter w to 10% (as little as 3% if Omega_m has been well-determined from other observations). This type of test has the potential also to provide a constraint on any evolution of w such as that predicted by ``tracker'' models.Comment: 4 pages plus 3 embedded figures; version approved by Ap. J. Letters. A greatly improved error analysis has been added, along with a figure showing complementarity to other cosmological test