Symbolic Tensor Calculus -- Functional and Dynamic Approach

In this paper, we briefly discuss the dynamic and functional approach to computer symbolic tensor analysis. The ccgrg package for Wolfram Language/Mathematica is used to illustrate this approach. Some examples of applications are attached

Acoustics of early universe. I. Flat versus open universe models

A simple perturbation description unique for all signs of curvature, and based on the gauge-invariant formalisms is proposed to demonstrate that: (1) The density perturbations propagate in the flat radiation-dominated universe in exactly the same way as electromagnetic or gravitational waves propagate in the epoch of the matter domination. (2) In the open universe, sounds are dispersed by curvature. The space curvature defines the minimal frequency $\omega_{\rm c}$ below which the propagation of perturbations is forbidden. Gaussian acoustic fields are considered and the curvature imprint in the perturbations spectrum is discussed.Comment: The new version extended by 2 sections. Changes in notation. Some important comments adde

"Cosmological" quasiparticle production in harmonically trapped superfluid gases

We show that a variety of cosmologically motivated effective quasiparticle space-times can be produced in harmonically trapped superfluid Bose and Fermi gases. We study the analogue of cosmological particle production in these effective space-times, induced by trapping potentials and coupling constants possessing an arbitrary time dependence. The WKB probabilities for phonon creation from the superfluid vacuum are calculated, and an experimental procedure to detect quasiparticle production by measuring density-density correlation functions is proposed.Comment: 8 pages, 1 figure; references updated, as published in Physical Review

Cosmological models with bulk viscosity in presence of adiabatic matter creation and with G, c and Lambda variables

Some properties of cosmological models with a time variable bulk viscous coefficient in presence of adiabatic mater creation and G, c, Lambda variables are investigated in the framework of flat FRW line element. We trivially find a set of solutions through Dimensional Analysis. In all the studied cases it is found that the behaviour of these constants is inversely prportional to the cosmic time.Comment: 12 pages. We have been rewriting and completing the bibliography of this paper. Submitted to General Relativity and Gravitatio

Curvature in causal BD-type inflationary cosmology

We study a closed model of the universe filled with viscous fluid and quintessence matter components in a Brans-Dicke type cosmological model. The dynamical equations imply that the universe may look like an accelerated flat Friedmann-Robertson-Walker universe at low redshift. We consider here dissipative processes which follow a causal thermodynamics. The theory is applied to viscous fluid inflation, where accepted values for the total entropy in the observable universe is obtained.Comment: 11 pages, revtex 4. For a festschrift honoring Alberto Garcia. To be publishen in Gen. Rel. Gra

The SEQC2 epigenomics quality control (EpiQC) study

BACKGROUND: Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group. RESULTS: Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. CONCLUSIONS: The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research

Experimental and computational investigations of electron dynamics in micro atmospheric pressure radio-frequency plasma jets operated in He/N2 mixtures

The electron power absorption dynamics in radio frequency driven micro atmospheric pressure capacitive plasma jets are studied based on experimental phase resolved optical emission spectroscopy and the computational particle in cell simulations with Monte Carlo treatment of collisions. The jet is operated at 13.56 MHz in He with different admixture concentrations of N2 and at several driving voltage amplitudes. We find the spatio-temporal dynamics of the light emission of the plasma at various wavelengths to be markedly different. This is understood by revealing the population dynamics of the upper levels of selected emission lines/bands based on comparisons between experimental and simulation results. The populations of these excited states are sensitive to different parts of the electron energy distribution function and to contributions from other excited states. Mode transitions of the electron power absorption dynamics from the Ω- to the Penning-mode are found to be induced by changing the N2 admixture concentration and the driving voltage amplitude. Our numerical simulations reveal details of this mode transition and provide novel insights into the operation details of the Penning-mode. The characteristic excitation/emission maximum at the time of maximum sheath voltage at each electrode is found to be based on two mechanisms: (i) a direct channel, i.e. excitation/emission caused by electrons generated by Penning ionization inside the sheaths and (ii) an indirect channel, i.e. secondary electrons emitted from the electrode due to the impact of positive ions generated by Penning ionization at the electrodes