The role of packaging sites in efficient and specific virus assembly

During the lifecycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively assemble around the viral RNA amidst diverse host RNAs is a key question in virology. In one proposed mechanism, sequence elements (packaging sites) within the genomic RNA promote rapid and efficient assembly through specific interactions with the capsid proteins. In this work we develop a coarse-grained particle-based computational model for capsid proteins and RNA which represents protein-RNA interactions arising both from non-specific electrostatics and specific packaging sites interactions. Using Brownian dynamics simulations, we explore how the efficiency and specificity of assembly depend on solution conditions (which control protein-protein and nonspecific protein-RNA interactions) as well as the strength and number of packaging sites. We identify distinct regions in parameter space in which packaging sites lead to highly specific assembly via different mechanisms, and others in which packaging sites lead to kinetic traps. We relate these computational predictions to in vitro assays for specificity in which cognate viral RNAs are compete against non-cognate RNAs for assembly by capsid proteins

Dynamics of Massive Scalar Fields in dS Space and the dS/CFT Correspondence

Global geometric properties of dS space are presented explicitly in various coordinates. A Robertson-Walker like metric is deduced, which is convenient to be used in study of dynamics in dS space. Singularities of wavefunctions of massive scalar fields at boundary are demonstrated. A bulk-boundary propagator is constructed by making use of the solutions of equations of motion. The dS/CFT correspondence and the Strominger's mass bound is shown.Comment: latex, 14 pages and 3 figure

de Sitter black hole with a conformally coupled scalar field in four dimensions

A four-dimensional black hole solution of the Einstein equations with a positive cosmological constant, coupled to a conformal scalar field, is given. There is a curvature singularity at the origin, and scalar field diverges inside the event horizon. The electrically charged solution, which has a fixed charge-to-mass ratio is also found. The quartic self-interacting coupling becomes bounded in terms of Newton's and the cosmological constants.Comment: 5 pages, no figures, CECS style, energy conditions are discussed and some references were added. To appear in Phys. Rev.

The Nearby Supernova Factory

The Nearby Supernova Factory (SNfactory) is an ambitious project to find and study in detail approximately 300 nearby Type Ia supernovae (SNe~Ia) at redshifts 0.03<z<0.08. This program will provide an exceptional data set of well-studied SNe in the nearby smooth Hubble flow that can be used as calibration for the current and future programs designed to use SNe to measure the cosmological parameters. The first key ingredient for this program is a reliable supply of Hubble-flow SNe systematically discovered in unprecedented numbers using the same techniques as those used in distant SNe searches. In 2002, 35 SNe were found using our test-bed pipeline for automated SN search and discovery. The pipeline uses images from the asteroid search conducted by the Near Earth Asteroid Tracking group at JPL. Improvements in our subtraction techniques and analysis have allowed us to increase our effective SN discovery rate to ~12 SNe/month in 2003.Comment: 7 pages, 3 figures to be published in New Astronomy Review

Phantom Accretion onto the Schwarzschild de-Sitter Black Hole

We deal with phantom energy accretion onto the Schwarzschild de-Sitter black hole. The energy flux conservation, relativistic Bernoulli equation and mass flux conservation equation are formulated to discuss the phantom accretion. We discuss the conditions for critical accretion. It is found that mass of the black hole decreases due to phantom accretion. There exist two critical points which lie in the exterior of horizons (black hole and cosmological horizons). The results for the phantom energy accretion onto the Schwarzschild black hole can be recovered by taking $\Lambda\rightarrow0$.Comment: 9 pages, no figur

Reconstructing the Cosmic Equation of State from Supernova distances

Observations of high-redshift supernovae indicate that the universe is accelerating. Here we present a {\em model-independent} method for estimating the form of the potential $V(\phi)$ of the scalar field driving this acceleration, and the associated equation of state $w_\phi$. Our method is based on a versatile analytical form for the luminosity distance $D_L$, optimized to fit observed distances to distant supernovae and differentiated to yield $V(\phi)$ and $w_\phi$. Our results favor $w_\phi\simeq -1$ at the present epoch, steadily increasing with redshift. A cosmological constant is consistent with our results.Comment: 4 pages, 5 figures, uses RevTex. Minor typo's in equations (1) and (10) correcte

Self-tuning of the cosmological constant

Here, I discuss the cosmological constant (CC) problems, in particular paying attention to the vanishing cosmological constant. There are three cosmological constant problems in particle physics. Hawking's idea of calculating the probability amplitude for our Universe is peaked at CC = 0 which I try to obtain after the initial inflationary period using a self-tuning model. I review what has been discussed on the Hawking type calculation, and present a (probably) correct way to calculate the amplitude, and show that the Kim-Kyae-Lee self-tuning model allows a finite range of parameters for the CC = 0 to have a singularly large probability, approached from the AdS side.Comment: 12 pages with 8 figure

A critical-density closed Universe in Brans-Dicke theory

In a Brans-Dicke (BD) cosmological model, the energy density associated with some scalar field decreases as \displaystyle a^{{-2}(\frac{\omega_{o}+ {\frac12}%}{\omega_{o}+1})} with the scale factor $a(t)$ of the Universe, giving a matter with an Equation of state $\displaystyle p=-{1/3}(\frac{2+\omega_{o}}{1+\omega_{o}}) \rho$. In this model, the Universe could be closed but still have a nonrelativistic-matter density corresponding to its critical value, $\Omega_{o}=1$. Different cosmological expressions, such as, luminosity distance, angular diameter, number count and ratio of the redshift tickness-angular size, are determined in terms of the redshift for this model.Comment: To appear in MNRAS, 7 pages, 5 eps figure

SUSY Dark Matter in the Universe- Theoretical Direct Detection Rates

Exotic dark matter together with the vacuum energy or cosmological constant seem to dominate in the Universe. An even higher density of such matter seems to be gravitationally trapped in the Galaxy. Thus its direct detection is central to particle physics and cosmology. Current supersymmetric models provide a natural dark matter candidate which is the lightest supersymmetric particle (LSP). Such models combined with fairly well understood physics like the quark substructure of the nucleon and the nuclear structure (form factor and/or spin response function), permit the evaluation of the event rate for LSP-nucleus elastic scattering. The thus obtained event rates are, however, very low or even undetectable. So it is imperative to exploit the modulation effect, i.e. the dependence of the event rate on the earth's annual motion. Also it is useful to consider the directional rate, i.e its dependence on the direction of the recoiling nucleus. In this paper we study such a modulation effect both in non directional and directional experiments. We calculate both the differential and the total rates using both isothermal, symmetric as well as only axially asymmetric, and non isothermal, due to caustic rings, velocity distributions. We find that in the symmetric case the modulation amplitude is small. The same is true for the case of caustic rings. The inclusion of asymmetry, with a realistic enhanced velocity dispersion in the galactocentric direction, yields an enhanced modulation effect, especially in directional experiments.Comment: 17 LATEX pages, 1 table and 6 ps figures include

GRB 050408: An Atypical Gamma-Ray Burst as a Probe of an Atypical Galactic Environment

The bright GRB 050408 was localized by HETE-II near local midnight, enabling an impressive ground-based followup effort as well as space-based followup from Swift. The Swift data from the X-Ray Telescope (XRT) and our own optical photometry and spectrum of the afterglow provide the cornerstone for our analysis. Under the traditional assumption that the visible waveband was above the peak synchrotron frequency and below the cooling frequency, the optical photometry from 0.03 to 5.03 days show an afterglow decay corresponding to an electron energy index of p_lc = 2.05 +/- 0.04, without a jet break as suggested by others. A break is seen in the X-ray data at early times (at ~12600 sec after the GRB). The spectral slope of the optical spectrum is consistent with p_lc assuming a host-galaxy extinction of A_V = 1.18 mag. The optical-NIR broadband spectrum is also consistent with p = 2.05, but prefers A_V = 0.57 mag. The X-ray afterglow shows a break at 1.26 x 10^4 sec, which may be the result of a refreshed shock. This burst stands out in that the optical and X-ray data suggest a large H I column density of N_HI ~ 10^22 cm^-2; it is very likely a damped Lyman alpha system and so the faintness of the host galaxy (M_V > -18 mag) is noteworthy. Moreover, we detect extraordinarily strong Ti II absorption lines with a column density through the GRB host that exceeds the largest values observed for the Milky Way by an order of magnitude. Furthermore, the Ti II equivalent width is in the top 1% of Mg II absorption-selected QSOs. This suggests that the large-scale environment of GRB 050408 has significantly lower Ti depletion than the Milky Way and a large velocity width (delta v > 200 km/s).Comment: ApJ submitte