Assessment of insert sizes and adapter content in fastq data from NexteraXT libraries

The Illumina NexteraXT transposon protocol is a cost effective way to generate paired end libraries. However the resulting insert size is highly sensitive to the concentration of DNA used, and the variation of insert sizes is often large. One consequence of this is some fragments may have an insert shorter than the length of a single read, particularly where the library is designed to produce overlapping paired end reads in order to produce longer continuous sequences. Such small insert sizes mean fewer longer reads, and also result in the presence of adapter at the end of the read. Here is presented a protocol to use publicly available tools to identify read pairs with small insert sizes and so likely to contain adapter, to check the sequence of the adapter, and remove adapter sequence from the reads. This protocol does not require a reference genome or prior knowledge of the sequence to be trimmed. Whilst the presence of fragments with small insert sizes may be a particular problem for NexteraXT libraries, the principle can be applied to any Illumina dataset in which the presence of such small inserts is suspected

Model- and calibration-independent test of cosmic acceleration

We present a calibration-independent test of the accelerated expansion of the universe using supernova type Ia data. The test is also model-independent in the sense that no assumptions about the content of the universe or about the parameterization of the deceleration parameter are made and that it does not assume any dynamical equations of motion. Yet, the test assumes the universe and the distribution of supernovae to be statistically homogeneous and isotropic. A significant reduction of systematic effects, as compared to our previous, calibration-dependent test, is achieved. Accelerated expansion is detected at significant level (4.3 sigma in the 2007 Gold sample, 7.2 sigma in the 2008 Union sample) if the universe is spatially flat. This result depends, however, crucially on supernovae with a redshift smaller than 0.1, for which the assumption of statistical isotropy and homogeneity is less well established.Comment: 13 pages, 2 figures, major change

Density mismatch in thin diblock copolymer films

Thin films of diblock copolymer subject to gravitational field are simulated by means of a cell dynamical system model. The difference in density of the two sides of the molecule and the presence of the field causes the formation of lamellar patterns with orientation parallel to the confining walls even when they are neutral. The concentration profile of those films is analyzed in the weak segregation regime and a functional form for the profile is proposed.Comment: 9 pages and 8 figures. Needs EPSF macros. Submitted to PR

Cosmological Effects of Radion Oscillations

We show that the redshift of pressureless matter density due to the expansion of the universe generically induces small oscillations in the stabilized radius of extra dimensions (the radion field). The frequency of these oscillations is proportional to the mass of the radion and can have interesting cosmological consequences. For very low radion masses $m_b$ ($m_b\sim10-100 H_0\simeq10^{-32} eV$) these low frequency oscillations lead to oscillations in the expansion rate of the universe. The occurrence of acceleration periods could naturally lead to a resolution of the coincidence problem, without need of dark energy. Even though this scenario for low radion mass is consistent with several observational tests it has difficulty to meet fifth force constraints. If viewed as an effective Brans-Dicke theory it predicts $\omega=-1+\frac{1}{D}$ ($D$ is the number of extra dimensions), while experiments on scales larger than $1mm$ imply $\omega>2500$. By deriving the generalized Newtonian potential corresponding to a massive toroidally compact radion we demonstrate that Newtonian gravity is modified only on scales smaller than $m_b^{-1}$. Thus, these constraints do not apply for $m_b>10^{-3} eV$ (high frequency oscillations) corresponding to scales less than the current experiments ($0.3mm$). Even though these high frequency oscillations can not resolve the coincidence problem they provide a natural mechanism for dark matter generation. This type of dark matter has many similarities with the axion.Comment: Accepted in Phys. Rev. D. Clarifying comments added in the text and some additional references include

Equation of State of Oscillating Brans-Dicke Scalar and Extra Dimensions

We consider a Brans-Dicke scalar field stabilized by a general power law potential with power index $n$ at a finite equilibrium value. Redshifting matter induces oscillations of the scalar field around its equilibrium due to the scalar field coupling to the trace of the energy momentum tensor. If the stabilizing potential is sufficiently steep these high frequency oscillations are consistent with observational and experimental constraints for arbitrary value of the Brans-Dicke parameter $\omega$. We study analytically and numerically the equation of state of these high frequency oscillations in terms of the parameters $\omega$ and $n$ and find the corresponding evolution of the universe scale factor. We find that the equation of state parameter can be negative and less than -1 but it is not related to the evolution of the scale factor in the usual way. Nevertheless, accelerating expansion is found for a certain parameter range. Our analysis applies also to oscillations of the size of extra dimensions (the radion field) around an equilibrium value. This duality between self-coupled Brans-Dicke and radion dynamics is applicable for $\omega= -1 + 1/D$ where D is the number of extra dimensions.Comment: 10 two-column pages, RevTex4, 8 figures. Added clarifying discussions, new references. Accepted in Phys. Rev. D (to appear

Gravitomagnetic Effects in the Propagation of Electromagnetic Waves in Variable Gravitational Fields of Arbitrary-Moving and Spinning Bodies

Propagation of light in the gravitational field of self-gravitating spinning bodies moving with arbitrary velocities is discussed. The gravitational field is assumed to be "weak" everywhere. Equations of motion of a light ray are solved in the first post-Minkowskian approximation that is linear with respect to the universal gravitational constant $G$. We do not restrict ourselves with the approximation of gravitational lens so that the solution of light geodesics is applicable for arbitrary locations of source of light and observer. This formalism is applied for studying corrections to the Shapiro time delay in binary pulsars caused by the rotation of pulsar and its companion. We also derive the correction to the light deflection angle caused by rotation of gravitating bodies in the solar system (Sun, planets) or a gravitational lens. The gravitational shift of frequency due to the combined translational and rotational motions of light-ray-deflecting bodies is analyzed as well. We give a general derivation of the formula describing the relativistic rotation of the plane of polarization of electromagnetic waves (Skrotskii effect). This formula is valid for arbitrary translational and rotational motion of gravitating bodies and greatly extends the results of previous researchers. Finally, we discuss the Skrotskii effect for gravitational waves emitted by localized sources such as a binary system. The theoretical results of this paper can be applied for studying various relativistic effects in microarcsecond space astrometry and developing corresponding algorithms for data processing in space astrometric missions such as FAME, SIM, and GAIA.Comment: 36 pages, 1 figure, submitted to Phys. Rev.

Can induced gravity isotropize Bianchi I, V, or IX Universes?

We analyze if Bianchi I, V, and IX models in the Induced Gravity (IG) theory can evolve to a Friedmann--Roberson--Walker (FRW) expansion due to the non--minimal coupling of gravity and the scalar field. The analytical results that we found for the Brans-Dicke (BD) theory are now applied to the IG theory which has $\omega \ll 1$ ($\omega$ being the square ratio of the Higgs to Planck mass) in a cosmological era in which the IG--potential is not significant. We find that the isotropization mechanism crucially depends on the value of $\omega$. Its smallness also permits inflationary solutions. For the Bianch V model inflation due to the Higgs potential takes place afterwads, and subsequently the spontaneous symmetry breaking (SSB) ends with an effective FRW evolution. The ordinary tests of successful cosmology are well satisfied.Comment: 24 pages, 5 figures, to be published in Phys. Rev. D1

Scalar Field Dark Matter

This work is a review of the last results of research on the Scalar Field Dark Matter model of the Universe at cosmological and at galactic level. We present the complete solution to the scalar field cosmological scenario in which the dark matter is modeled by a scalar field $\Phi$ with the scalar potential $V(\Phi)=V_{0}(cosh {(\lambda \sqrt{\kappa_{0}}\Phi)}-1)$ and the dark energy is modeled by a scalar field $\Psi$, endowed with the scalar potential $\tilde{V}(\Psi)= \tilde{V_{0}}(\sinh{(\alpha \sqrt{\kappa_{0}}\Psi)})^{\beta}$, which together compose the 95% of the total matter energy in the Universe. The model presents successfully deals with the up to date cosmological observations, and is a good candidate to treat the dark matter problem at the galactic level.Comment: 11 pagez, 5 figures, REVTeX. To appear in proceedings of the ``Mexican Meeting on Exact Solutions and Scalar Fields in Gravity '', in honour of Heinz Dehnen's 65th Birthday and Dietrich Kramer's 60th Birthday. Mexico D.F., Mexico, in press. More info at http://www.fis.cinvestav.mx/~siddh/PHI

Quintessence and Gravitational Waves

We investigate some aspects of quintessence models with a non-minimally coupled scalar field and in particular we show that it can behave as a component of matter with $-3 \lesssim P/\rho \lesssim 0$. We study the properties of gravitational waves in this class of models and discuss their energy spectrum and the cosmic microwave background anisotropies they induce. We also show that gravitational waves are damped by the anisotropic stress of the radiation and that their energy spectrum may help to distinguish between inverse power law potential and supergravity motivated potential. We finish by a discussion on the constraints arising from their density parameter \Omega_\GW.Comment: 21 pages, 18 figures, fianl version, accepted for publication in PR

Magnetogenesis and the dynamics of internal dimensions

The dynamical evolution of internal space-like dimensions breaks the invariance of the Maxwell's equations under Weyl rescaling of the (conformally flat) four-dimensional metric. Depending upon the number and upon the dynamics of internal dimensions large scale magnetic fields can be created. The requirements coming from magnetogenesis together with the other cosmological constraints are examined under the assumption that the internal dimensions either grow or shrink (in conformal time) prior to a radiation dominated epoch. If the internal dimensions are growing the magnitude of the generated magnetic fields can seed the galactic dynamo mechanism.Comment: 27 in RevTex style, four figure