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

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 $w=-1$. Since in this case the speed of sound $c_s$ 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

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$_{2}^{+}$, 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$_{2}$, Li$_{2}$, LiH, Cd$_{2}$, Na$_{2}^{+}$, and RbH$^{-}$), long-range bound diatomics (e.g., NaAr, CdNe, He$_{2}$, CaHe, SrHe, and BaHe), metastable molecular dications (e.g., BeH$^{++}$, AlH$^{++}$, Mg$_{2}^{++}$, and LiBa$^{++}$), and molecular trications (e.g., YHe$^{+++}$ and ScHe$^{+++}$).Comment: 5 pages, 4 figures, accepted by Physical Review Letter

Millisecond Electron-Phonon Relaxation in Ultrathin Disordered Metal Films at Millikelvin Temperatures

We have measured directly the thermal conductance between electrons and phonons in ultra-thin Hf and Ti films at millikelvin temperatures. The experimental data indicate that electron-phonon coupling in these films is significantly suppressed by disorder. The electron cooling time $\tau_\epsilon$ follows the $T^{-4}$-dependence with a record-long value $\tau_\epsilon=25ms$ at $T=0.04K$. The hot-electron detectors of far-infrared radiation, fabricated from such films, are expected to have a very high sensitivity. The noise equivalent power of a detector with the area 1\mum^2 would be $(2-3)10^{-20}W/Hz^{1/2}$, which is two orders of magnitude smaller than that of the state-of-the-art bolometers.Comment: 13 pages, including 3 figure

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 $A$ 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 $\chi^2$ 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 $\Omega_k$ and $w_a$ in the Chevallier-Polarski-Linder model are skew distributions, and the marginalized $1\sigma$ errors are $\Omega_m=0.279^{+0.015}_{-0.008}$, $\Omega_k=0.005^{+0.006}_{-0.011}$, $w_0=-1.05^{+0.23}_{-0.06}$, and $w_a=0.5^{+0.3}_{-1.5}$. For the Jassal-Bagla-Padmanabhan model, the marginalized $1\sigma$ errors are $\Omega_m=0.281^{+0.015}_{-0.01}$, $\Omega_k=0.000^{+0.007}_{-0.006}$, $w_0=-0.96^{+0.25}_{-0.18}$, and $w_a=-0.6^{+1.9}_{-1.6}$. The equation of state parameter $w(z)$ of dark energy is negative in the redshift range $0\le z\le 2$ at more than $3\sigma$ level. The flat $\Lambda$CDM model is consistent with the current observational data at the $1\sigma$ 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

When is Quantum Decoherence Dynamics Classical?

A direct classical analog of quantum decoherence is introduced. Similarities and differences between decoherence dynamics examined quantum mechanically and classically are exposed via a second-order perturbative treatment and via a strong decoherence theory, showing a strong dependence on the nature of the system-environment coupling. For example, for the traditionally assumed linear coupling, the classical and quantum results are shown to be in exact agreement.Comment: 5 pages, no figures, to appear in Physical Review Letter

Cosmology in massive gravity

We argue that more cosmological solutions in massive gravity can be obtained if the metric tensor and the tensor $\Sigma_{\mu\nu}$ defined by St\"{u}ckelberg fields take the homogeneous and isotropic form. The standard cosmology with matter and radiation dominations in the past can be recovered and $\Lambda$CDM model is easily obtained. The dynamical evolution of the universe is modified at very early times.Comment: 4 pages, 1 figure,add more reference