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

Natural extension of the Generalised Uncertainty Principle

We discuss a gedanken experiment for the simultaneous measurement of the position and momentum of a particle in de Sitter spacetime. We propose an extension of the so-called generalized uncertainty principle (GUP) which implies the existence of a minimum observable momentum. The new GUP is directly connected to the nonzero cosmological constant, which becomes a necessary ingredient for a more complete picture of the quantum spacetime.Comment: 4 pages, 1 figure, v2 with added references, revised and extended as published in CQ

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

Thermodynamical description of the interacting new agegraphic dark energy

We describe the thermodynamical interpretation of the interaction between new agegraphic dark energy and dark matter in a non-flat universe. When new agegraphic dark energy and dark matter evolve separately, each of them remains in thermodynamic equilibrium. As soon as an interaction between them is taken into account, their thermodynamical interpretation changes by a stable thermal fluctuation. We obtain a relation between the interaction term of the dark components and this thermal fluctuation.Comment: 11 pages, accepted for publication in MPLA (2010

Gamma-ray burst contributions to constraining the evolution of dark energy

We explore the gamma-ray bursts' (GRBs') contributions in constraining the dark energy equation of state (EOS) at high ($1.8 < z < 7$) and at middle redshifts ($0.5 < z < 1.8$) and estimate how many GRBs are needed to get substantial constraints at high redshifts. We estimate the constraints with mock GRBs and mock type Ia supernovae (SNe Ia) for comparisons. When constraining the dark energy EOS in a certain redshift range, we allow the dark energy EOS parameter to vary only in that redshift bin and fix EOS parameters elsewhere to -1. We find that it is difficult to constrain the dark energy EOS beyond the redshifts of SNe Ia with GRBs unless some new luminosity relations for GRBs with smaller scatters are discovered. However, at middle redshifts, GRBs have comparable contributions with SNe Ia in constraining the dark energy EOS.Comment: 3 pages, 5 figures. Published in Astronomy and Astrophysics. Corrected referenc

The R_h=ct Universe Without Inflation

The horizon problem in the standard model of cosmology (LDCM) arises from the observed uniformity of the cosmic microwave background radiation, which has the same temperature everywhere (except for tiny, stochastic fluctuations), even in regions on opposite sides of the sky, which appear to lie outside of each other's causal horizon. Since no physical process propagating at or below lightspeed could have brought them into thermal equilibrium, it appears that the universe in its infancy required highly improbable initial conditions. In this paper, we examine this well-known problem by considering photon propagation through a Friedmann-Robertson-Walker (FRW) spacetime at a more fundamental level than has been attempted before, demonstrating that the horizon problem only emerges for a subset of FRW cosmologies, such as LCDM, that include an early phase of rapid deceleration. We show that the horizon problem is nonexistent for the recently introduced R_h=ct universe, obviating the principal motivation for the inclusion of inflation. We demonstrate through direct calculation that, in the R_h=ct universe, even opposite sides of the cosmos have remained causally connected to us - and to each other - from the very first moments in the universe's expansion. Therefore, within the context of the R_h=ct universe, the hypothesized inflationary epoch from t=10^{-35} seconds to 10^{-32} seconds was not needed to fix this particular "problem", though it may still provide benefits to cosmology for other reasons.Comment: 17 pages, 5 figures. arXiv Slight revisions in refereed version. Accepted for publication in Astronomy & Astrophysic

Entropic Accelerating Universe

To accommodate the observed accelerated expansion of the universe, one popular idea is to invoke a driving term in the Friedmann-Lemaitre equation of dark energy which must then comprise 70% of the present cosmological energy density. We propose an alternative interpretation which takes into account the entropy and temperature intrinsic to the horizon of the universe due to the information holographically stored there. Dark energy is thereby obviated and the acceleration is due to an entropic force naturally arising from the information storage on the horizon surface screen. We consider an additional quantitative approach inspired by surface terms in general relativity and show that this leads to the entropic accelerating universe.Comment: 14 pages, 1 figure, extended and clarifie