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

Can the Universe escape eternal acceleration?

Recent astronomical observations of distant supernovae light-curves suggest that the expansion of the universe has recently begun to accelerate. Acceleration is created by an anti-gravitational repulsive stress, like that produced by a positive cosmological constant, or universal vacuum energy. It creates a rather bleak eschatological picture. An ever-expanding universe's future appears to be increasingly dominated by its constant vacuum energy. A universe doomed to accelerate forever will produce a state of growing uniformity and cosmic loneliness. Structures participating in the cosmological expansion will ultimately leave each others' horizons and information-processing must eventually die out. Here, we examine whether this picture is the only interpretation of the observations. We find that in many well-motivated scenarios the observed spell of vacuum domination is only a transient phenomenon. Soon after acceleration starts, the vacuum energy's anti-gravitational properties are reversed, and a matter-dominated decelerating cosmic expansion resumes. Thus, contrary to general expectations, once an accelerating universe does not mean always an accelerating universe.Comment: 6 pages, 2 figure

Cosmology with two compactification scales

We consider a (4+d)-dimensional spacetime broken up into a (4-n)-dimensional Minkowski spacetime (where n goes from 1 to 3) and a compact (n+d)-dimensional manifold. At the present time the n compactification radii are of the order of the Universe size, while the other d compactification radii are of the order of the Planck length.Comment: 16 pages, Latex2e, 7 figure

Opportunities for future supernova studies of cosmic acceleration

We investigate the potential of a future supernova dataset, as might be obtained by the proposed SNAP satellite, to discriminate among different ``dark energy'' theories that describe an accelerating Universe. We find that many such models can be distinguished with a fit to the effective pressure-to-density ratio, $w$, of this energy. More models can be distinguished when the effective slope, $dw/dz$, of a changing $w$ is also fit, but only if our knowledge of the current mass density, $\Omega_m$, is improved. We investigate the use of ``fitting functions'' to interpret luminosity distance data from supernova searches, and argue in favor of a particular preferred method, which we use in our analysis.Comment: Four pages including figures. Final published version. No significant changes from v

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

Why we need to see the dark matter to understand the dark energy

The cosmological concordance model contains two separate constituents which interact only gravitationally with themselves and everything else, the dark matter and the dark energy. In the standard dark energy models, the dark matter makes up some 20% of the total energy budget today, while the dark energy is responsible for about 75%. Here we show that these numbers are only robust for specific dark energy models and that in general we cannot measure the abundance of the dark constituents separately without making strong assumptions.Comment: 4 pages, to be published in the Journal of Physics: Conference Series as a contribution to the 2007 Europhysics Conference on High Energy Physic

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