Long-wavelength metric backreactions in slow-roll inflation

We examine the importance of second order corrections to linearized cosmological perturbation theory in an inflationary background, taken to be a spatially flat FRW spacetime. The full second order problem is solved in the sense that we evaluate the effect of the superhorizon second order corrections on the inhomogeneous and homogeneous modes of the linearized flucuations. These second order corrections enter in the form of a {\it cumulative} contribution from {\it all} of their Fourier modes. In order to quantify their physical significance we study their effective equation of state by looking at the perturbed energy density and isotropic pressure to second order. We define the energy density (isotropic pressure) in terms of the (averaged) eigenvalues associated with timelike (spacelike) eigenvectors of a total stress energy for the metric and matter fluctuations. Our work suggests that that for many parameters of slow-roll inflation, the second order contributions to these energy density and pressures may dominate over the first order effects for the case of super-Hubble evolution. These results hold in our choice of first and second order coordinate conditions however we also argue that other `reasonable` coordinate conditions do not alter the relative importance of the second order terms. We find that these second order contributions approximately take the form of a cosmological constant in this coordinate gauge, as found by others using effective methods.Comment: Submitted to Phys. Rev.

Cosmological Perturbation Theory in Slow-Roll Spacetimes

We present a gauge invariant argument that a nonlocal measure of second-order metric and matter perturbations dominate that of linear fluctuations in its effect on the gravitational field in 'slow-rolling' spacetimes.Comment: Version accepted by PRL (however, with correct non PRL format for arxiv posting). Clarified and expande

On leading order gravitational backreactions in de Sitter spacetime

Backreactions are considered in a de Sitter spacetime whose cosmological constant is generated by the potential of scalar field. The leading order gravitational effect of nonlinear matter fluctuations is analyzed and it is found that the initial value problem for the perturbed Einstein equations possesses linearization instabilities. We show that these linearization instabilities can be avoided by assuming strict de Sitter invariance of the quantum states of the linearized fluctuations. We furthermore show that quantum anomalies do not block the invariance requirement. This invariance constraint applies to the entire spectrum of states, from the vacuum to the excited states (should they exist), and is in that sense much stronger than the usual Poincare invariance requirement of the Minkowski vacuum alone. Thus to leading order in their effect on the gravitational field, the quantum states of the matter and metric fluctuations must be de Sitter invariant.Comment: 12 pages, no figures, typos corrected and some clarifying comments added, version accepted by Phys. Rev.

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.

MotivationCopy number variations (CNVs) are a major source of genomic variability and are especially significant in cancer. Until recently microarray technologies have been used to characterize CNVs in genomes. However, advances in next-generation sequencing technology offer significant opportunities to deduce copy number directly from genome sequencing data. Unfortunately cancer genomes differ from normal genomes in several aspects that make them far less amenable to copy number detection. For example, cancer genomes are often aneuploid and an admixture of diploid/non-tumor cell fractions. Also patient-derived xenograft models can be laden with mouse contamination that strongly affects accurate assignment of copy number. Hence, there is a need to develop analytical tools that can take into account cancer-specific parameters for detecting CNVs directly from genome sequencing data.ResultsWe have developed WaveCNV, a software package to identify copy number alterations by detecting breakpoints of CNVs using translation-invariant discrete wavelet transforms and assign digitized copy numbers to each event using next-generation sequencing data. We also assign alleles specifying the chromosomal ratio following duplication/loss. We verified copy number calls using both microarray (correlation coefficient 0.97) and quantitative polymerase chain reaction (correlation coefficient 0.94) and found them to be highly concordant. We demonstrate its utility in pancreatic primary and xenograft sequencing data.Availability and implementationSource code and executables are available at https://github.com/WaveCNV. The segmentation algorithm is implemented in MATLAB, and copy number assignment is implemented [email protected] informationSupplementary data are available at Bioinformatics online

Controlling interferometric properties of nanoporous anodic aluminium oxide

A study of reflective interference spectroscopy [RIfS] properties of nanoporous anodic aluminium oxide [AAO] with the aim to develop a reliable substrate for label-free optical biosensing is presented. The influence of structural parameters of AAO including pore diameters, inter-pore distance, pore length, and surface modification by deposition of Au, Ag, Cr, Pt, Ni, and TiO2 on the RIfS signal (Fabry-Perot fringe) was explored. AAO with controlled pore dimensions was prepared by electrochemical anodization of aluminium using 0.3 M oxalic acid at different voltages (30 to 70 V) and anodization times (10 to 60 min). Results show the strong influence of pore structures and surface modifications on the interference signal and indicate the importance of optimisation of AAO pore structures for RIfS sensing. The pore length/pore diameter aspect ratio of AAO was identified as a suitable parameter to tune interferometric properties of AAO. Finally, the application of AAO with optimised pore structures for sensing of a surface binding reaction of alkanethiols (mercaptoundecanoic acid) on gold surface is demonstrated

On the initial value problem for second order scalar fluctuations in Einstein static

We consider fluctuations in a perfect irrotational fluid coupled to gravity in an Einstein static universe background. We show that the homogeneous linear perturbations of the scalar and metric fluctuations in the Einstein static universe must be present if the second order constraint equations are to be integrable. I.e., the 'linearization stability' constraint forces the presence of these homogeneous modes. Since these linear homogeneous scalar modes are well known to be exponentially unstable, the tactic of neglecting these modes to create a long-lived, almost Einstein universe does not work, even if all higher order (L $>$ 1) modes are dynamically stable.Comment: 8 pages, no figures, changes made to the presentation throughout to emphasize the linear nature of the analysis and the treatment of the irrotational perfect fluid. Conclusions unchanged. Submitted to PR

Role of electrostatic interactions in amyloid beta-protein (Abeta) oligomer formation: A discrete molecular dynamics study

Pathological folding and oligomer formation of the amyloid beta-protein (Abeta) are widely perceived as central to Alzheimer's disease (AD). Experimental approaches to study Abeta self-assembly are problematic, because most relevant aggregates are quasi-stable and inhomogeneous. We apply a discrete molecular dynamics (DMD) approach combined with a four-bead protein model to study oligomer formation of the amyloid beta-protein (Abeta). We address the differences between the two most common Abeta alloforms, Abeta40 and Abeta42, which oligomerize differently in vitro. We study how the presence of electrostatic interactions (EIs) between pairs of charged amino acids affects Abeta40 and Abeta42 oligomer formation. Our results indicate that EIs promote formation of larger oligomers in both Abeta40 and Abeta42. The Abeta40 size distribution remains unimodal, whereas the Abeta42 distribution is trimodal, as observed experimentally. Abeta42 folded structure is characterized by a turn in the C-terminus that is not present in Abeta40. We show that the same C-terminal region is also responsible for the strongest intermolecular contacts in Abeta42 pentamers and larger oligomers. Our results suggest that this C-terminal region plays a key role in the formation of Abeta42 oligomers and the relative importance of this region increases in the presence of EIs. These results suggest that inhibitors targeting the C-terminal region of Abeta42 oligomers may be able to prevent oligomer formation or structurally modify the assemblies to reduce their toxicity.Comment: Accepted for publication at Biophysical Journa

Experimental study on glass and polymers: determining the optimal material for potential use in terahertz technology

The optical properties of polymers and glasses useful for terahertz applications are experimentally characterized using terahertz time-domain spectroscopy (THz-TDS). A standard system setup utilizing transmission spectroscopy is used to measure different optical properties of materials including refractive index, relative permittivity, loss tangent, absorption coefficient, and transmittance. The thermal and chemical dependencies of materials are also studied to identify the appropriate materials for given terahertz applications. The selected materials can then be utilized for applications such as in waveguides, filters, lenses, polarization preserving devices, metamaterials and metasurfaces, absorbers, and sensors in the terahertz frequency range.MD Saiful Islam, Cristiano M. B. Cordeiro, Md J. Nine, Jakeya Sultana, Alice L. S. Cruz, Alex Dinovitser … et al

A parton picture of de Sitter space during slow-roll inflation

It is well-known that expectation values in de Sitter space are afflicted by infra-red divergences. Long ago, Starobinsky proposed that infra-red effects in de Sitter space could be accommodated by evolving the long-wavelength part of the field according to the classical field equations plus a stochastic source term. I argue that--when quantum-mechanical loop corrections are taken into account--the separate-universe picture of superhorizon evolution in de Sitter space is equivalent, in a certain leading-logarithm approximation, to Starobinsky's stochastic approach. In particular, the time evolution of a box of de Sitter space can be understood in exact analogy with the DGLAP evolution of partons within a hadron, which describes a slow logarithmic evolution in the distribution of the hadron's constituent partons with the energy scale at which they are probed.Comment: 36 pages; uses iopart.cls and feynmp.sty. v2: Minor typos corrected. Matches version published in JCA

Extensive and Intimate Association of the Cytoskeleton with Forming Silica in Diatoms: Control over Patterning on the Meso- and Micro-Scale

BACKGROUND: The diatom cell wall, called the frustule, is predominantly made out of silica, in many cases with highly ordered nano- and micro-scale features. Frustules are built intracellularly inside a special compartment, the silica deposition vesicle, or SDV. Molecules such as proteins (silaffins and silacidins) and long chain polyamines have been isolated from the silica and shown to be involved in the control of the silica polymerization. However, we are still unable to explain or reproduce in vitro the complexity of structures formed by diatoms. METHODS/PRINCIPAL FINDING: In this study, using fluorescence microscopy, scanning electron microscopy, and atomic force microscopy, we were able to compare and correlate microtubules and microfilaments with silica structure formed in diversely structured diatom species. The high degree of correlation between silica structure and actin indicates that actin is a major element in the control of the silica morphogenesis at the meso and microscale. Microtubules appear to be involved in the spatial positioning on the mesoscale and strengthening of the SDV. CONCLUSIONS/SIGNIFICANCE: These results reveal the importance of top down control over positioning of and within the SDV during diatom wall formation and open a new perspective for the study of the mechanism of frustule patterning as well as for the understanding of the control of membrane dynamics by the cytoskeleton