We introduce a massively parallel novel sequencing platform that combines an open flow cell design on a circular wafer with a large surface area and mostly natural nucleotides that allow optical end-point detection without reversible terminators. This platform enables sequencing billions of reads with longer read length (~300bp) and fast runs times (<20hrs) with high base accuracy (Q30 > 85%), at a low cost of $1/Gb. We establish system performance by whole-genome sequencing of the Genome-In-A-Bottle reference samples HG001-7, demonstrating high accuracy for SNPs (99.6%) and Indels in homopolymers up to length 10 (96.4%) across the vast majority (>98%) of the defined high-confidence regions of these samples. We demonstrate scalability of the whole-genome sequencing workflow by sequencing an additional 224 selected samples from the 1000 Genomes project achieving high concordance with reference data.

We use the worldline numerics technique to study a cylindrically symmetric model of magnetic flux tubes in a dense lattice and the nonlocal Casimir forces acting between regions of magnetic flux. Within a superconductor the magnetic field is constrained within magnetic flux tubes and if the background magnetic field is on the order the quantum critical field strength, Bk = ^ = 4.4 x 1013 Gauss, the magnetic field is likely to vary rapidly on the scales where QED effects are important. In this paper, we construct a cylindrically symmetric toy model of a flux tube lattice in which the nonlocal influence of QED on neighboring flux tubes is taken into account. We compute the effective action densities using the worldline numerics technique. The numerics predict a greater effective energy density in the region of the flux tube, but a smaller energy density in the regions between the flux tubes compared to a locally constant-field approximation. We also compute the interaction energy between a flux tube and its neighbors as the lattice spacing is reduced from infinity. Because our flux tubes exhibit compact support, this energy is entirely nonlocal and predicted to be zero in local approximations such as the derivative expansion. This Casimir-Polder energy can take positive or negative values depending on the distance between the flux tubes, and it may cause the flux tubes in neutron stars to form bunches. In addition to the above results we also discuss two important subtleties of determining the statistical uncertainties within the worldline numerics technique. Firstly, the distributions generated by the worldline ensembles are highly non-Gaussian, and so the standard error in the mean is not a good measure of the statistical uncertainty. Secondly, because the same ensemble of worldlines is used to compute the Wilson loops at different values of T and xctn, the uncertainties associated with each computed value of the integrand are strongly correlated. We recommend a form of jackknife analysis which deals with both of these problems.

The density fluctuations that we observe in the universe today are thought to originate from quantum fluctuations produced during a phase of the early universe called inflation. By evolving a wavefunction describing two coupled Fourier modes of a scalar field forward through an inflationary epoch, we demonstrate that non-linear effects can result in a generation of entanglement entropy between modes with different momenta in a scalar field during the inflationary period when just one of the modes is observed. Through this mechanism, the field would experience decoherence and appear more like a classical distribution today; however the mechanism is not sufficiently efficient to explain classicality. We find that the amount of entanglement entropy generated scales roughly as a power law S ∝ λ 1.75 , where λ is the coupling coefficient of the non-linear potential term. We also investigate how the entanglement entropy scales with the duration of inflation and compare various entanglement measures from the literature with the von Neumann entropy. This demonstration explicitly follows particle creation and interactions between modes; consequently, the mechanism contributing to the generation of the von Neumann entropy can be easily seen.

We compute electromagnetic wave propagation through the magnetosphere of a magnetar. The magnetosphere is modelled as the quantum electrodynamics vacuum and a cold, strongly magnetized plasma. The background field and electromagnetic waves are treated non-perturbatively and can be arbitrarily strong. This technique is particularly useful for examining non-linear effects in propagating waves. Waves travelling through such a medium typically form shocks; on the other hand we focus on the possible existence of waves that travel without evolving. Therefore, in order to examine the non-linear effects, we make a travelling wave ansatz and numerically explore the resulting wave equations. We discover a class of solutions in a homogeneous plasma which are stabilized against forming shocks by exciting non-orthogonal components which exhibit strong non-linear behaviour. These waves may be an important part of the energy transmission processes near pulsars and magnetars.

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