23,914 research outputs found
Stability-mediated epistasis constrains the evolution of an influenza protein.
John Maynard Smith compared protein evolution to the game where one word is converted into another a single letter at a time, with the constraint that all intermediates are words: WORD→WORE→GORE→GONE→GENE. In this analogy, epistasis constrains evolution, with some mutations tolerated only after the occurrence of others. To test whether epistasis similarly constrains actual protein evolution, we created all intermediates along a 39-mutation evolutionary trajectory of influenza nucleoprotein, and also introduced each mutation individually into the parent. Several mutations were deleterious to the parent despite becoming fixed during evolution without negative impact. These mutations were destabilizing, and were preceded or accompanied by stabilizing mutations that alleviated their adverse effects. The constrained mutations occurred at sites enriched in T-cell epitopes, suggesting they promote viral immune escape. Our results paint a coherent portrait of epistasis during nucleoprotein evolution, with stabilizing mutations permitting otherwise inaccessible destabilizing mutations which are sometimes of adaptive value. DOI:http://dx.doi.org/10.7554/eLife.00631.001
Probing Dark Energy Dynamics from Current and Future Cosmological Observations
We report the constraints on the dark energy equation-of-state w(z) using the
latest 'Constitution' SNe sample combined with the WMAP5 and SDSS data. Based
on the localized principal component analysis and the model selection criteria,
we find that the LCDM model is generally consistent with the current data, yet
there exists weak hint of the possible dynamics of dark energy. In particular,
a model predicting w(z)-1 at z\in[0.5,0.75),
which means that w(z) crosses -1 in the range of z\in[0.25,0.75), is mildly
favored at 95% confidence level. Given the best fit model for current data as a
fiducial model, we make future forecast from the joint data sets of JDEM,
Planck and LSST, and we find that the future surveys can reduce the error bars
on the w bins by roughly a factor of 10 for a 5-w-bin model.Comment: Accepted by PRD; minor changes from v
A Simple Three-Parameter Model Potential For Diatomic Systems: From Weakly and Strongly Bound Molecules to Metastable Molecular Ions
Based on a simplest molecular orbital theory of H, a
three-parameter model potential function is proposed to describe ground-state
diatomic systems with closed-shell and/or S-type valence-shell constituents
over a significantly wide range of internuclear distances. More than 200 weakly
and strongly bound diatomics have been studied, including neutral and
singly-charged diatomics (e.g., H, Li, LiH, Cd, Na,
and RbH), long-range bound diatomics (e.g., NaAr, CdNe, He, CaHe,
SrHe, and BaHe), metastable molecular dications (e.g., BeH, AlH,
Mg, and LiBa), and molecular trications (e.g., YHe
and ScHe).Comment: 5 pages, 4 figures, accepted by Physical Review Letter
Cosmological Dynamics of a Dirac-Born-Infeld field
We analyze the dynamics of a Dirac-Born-Infeld (DBI) field in a cosmological
set-up which includes a perfect fluid. Introducing convenient dynamical
variables, we show the evolution equations form an autonomous system when the
potential and the brane tension of the DBI field are arbitrary power-law or
exponential functions of the DBI field. In particular we find scaling solutions
can exist when powers of the field in the potential and warp-factor satisfy
specific relations. A new class of fixed-point solutions are obtained
corresponding to points which initially appear singular in the evolution
equations, but on closer inspection are actually well defined. In all cases, we
perform a phase-space analysis and obtain the late-time attractor structure of
the system. Of particular note when considering cosmological perturbations in
DBI inflation is a fixed-point solution where the Lorentz factor is a finite
large constant and the equation of state parameter of the DBI field is .
Since in this case the speed of sound becomes constant, the solution can
be thought to serve as a good background to perturb about.Comment: 24 pages, 7 figures, minor corrections, references adde
The lessons from the running of the tensor-to-scalar ratio
We derive a simple consistency relation from the running of the
tensor-to-scalar ratio. This new relation is first order in the slow-roll
approximation. While for single field models we can obtain what can be found by
using other observables, multi-field cases in general give non-trivial
contributions dependent on the geometry of the field space and the inflationary
dynamics, which can be probed observationally from this relation. The running
of the tensor-to-scalar ratio may be detected by direct laser interferometer
experiments.Comment: (v1) 7 pages, 1 figure; (v2) Discussions refined and references
added; (v3) More discussions on detectability, to appear in Physical Review
Inflation in minimal left-right symmetric model with spontaneous D-parity breaking
We present a simplest inflationary scenario in the minimal left-right
symmetric model with spontaneous D-parity breaking, which is a well motivated
particle physics model for neutrino masses. This leads us to connect the
observed anisotropies in the cosmic microwave background to the sub-eV neutrino
masses. The baryon asymmetry via the leptogenesis route is also discussed
briefly.Comment: (v1) 4 pages, 1 figure; (v2) typos corrected; (v3) title and abstract
changed, numerical estimates given, minor changes; (v4) 5 pages, relations
between the neutrino masses and the CMB fluctuations become more explicit,
miscellaneous changes, to appear in Physical Review
Improved cosmological constraints on the curvature and equation of state of dark energy
We apply the Constitution compilation of 397 supernova Ia, the baryon
acoustic oscillation measurements including the parameter, the distance
ratio and the radial data, the five-year Wilkinson microwave anisotropy probe
and the Hubble parameter data to study the geometry of the universe and the
property of dark energy by using the popular Chevallier-Polarski-Linder and
Jassal-Bagla-Padmanabhan parameterizations. We compare the simple
method of joined contour estimation and the Monte Carlo Markov chain method,
and find that it is necessary to make the marginalized analysis on the error
estimation. The probabilities of and in the
Chevallier-Polarski-Linder model are skew distributions, and the marginalized
errors are ,
, , and
. For the Jassal-Bagla-Padmanabhan model, the
marginalized errors are ,
, , and
. The equation of state parameter of dark energy
is negative in the redshift range at more than level.
The flat CDM model is consistent with the current observational data
at the level.Comment: 10 figures, 12 pages, Classical and Quantum Gravity in press; v2 to
match the pulished versio
Dynamics of a scalar field in Robertson-Walker spacetimes
We analyze the dynamics of a single scalar field in
Friedmann-Robertson-Walker universes with spatial curvature. We obtain the
fixed point solutions which are shown to be late time attractors. In
particular, we determine the corresponding scalar field potentials which
correspond to these stable solutions. The analysis is quite general and
incorporates expanding and contracting universes with both positive and
negative scalar potentials. We demonstrate that the known power law,
exponential, and de-Sitter solutions are certain limits of our general set of
solutions.Comment: 10 pages, v2:references added. Accepted for publication in PR
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