aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data

Data normalization and identification of significant differential expression represent crucial steps in RNA-Seq analysis. Many available tools rely on assumptions that are often not met by real data, including the common assumption of symmetrical distribution of up- and down-regulated genes, the presence of only few differentially expressed genes and/or few outliers. Moreover, the cut-off for selecting significantly differentially expressed genes for further downstream analysis often depend on arbitrary choices

New structural approach for determining load carrying capability of filament wound composite materials

Metal lined boron and graphite composites exhibit high strength and minimum weight, making them superior to aluminum cylindrical shell structures and to steel or aluminum constructed pressure vessels. S glass filament-epoxy resin matrix with aluminum liner is suitable for cryogenic tanks

Analytical Solutions of Singular Isothermal Quadrupole Lens

Using analytical method, we study the Singular Isothermal Quadrupole (SIQ) lens system, which is the simplest lens model that can produce four images. In this case, the radial mass distribution is in accord with the profile of the Singular Isothermal Sphere (SIS) lens, and the tangential distribution is given by adding a quadrupole on the monopole component. The basic properties of the SIQ lens have been studied in this paper, including deflection potential, deflection angle, magnification, critical curve, caustic, pseudo-caustic and transition locus. Analytical solutions of the image positions and magnifications for the source on axes are derived. As have been found, naked cusps will appear when the relative intensity $k$ of quadrupole to monopole is larger than 0.6. According to the magnification invariant theory of the SIQ lens, the sum of the signed magnifications of the four images should be equal to unity \citep{dal98}. However, if a source lies in the naked cusp, the summed magnification of the left three images is smaller than the invariant 1. With this simple lens system, we study the situations that a point source infinitely approaches a cusp or a fold. The sum of magnifications of cusp image triplet is usually not equal to 0, and it is usually positive for major cusp while negative for minor cusp. Similarly, the sum of magnifications of fold image pair is usually neither equal to 0. Nevertheless, the cusp and fold relations are still equal to 0, in that the sum values are divided by infinite absolute magnifications by definition.Comment: 12 pages, 2 figures, accepted for publication in ApJ

Fast quantum information transfer with superconducting flux qubits coupled to a cavity

We present a way to realize quantum information transfer with superconducting flux qubits coupled to a cavity. Because only resonant qubit-cavity interaction and resonant qubit-pulse interaction are applied, the information transfer can be performed much faster, when compared with the previous proposals. This proposal does not require adjustment of the qubit level spacings during the operation. Moreover, neither uniformity in the device parameters nor exact placement of qubits in the cavity is needed by this proposal.Comment: 6 pages, 3 figure

Coronal magnetic fields produced by photospheric shear

The magneto-frictional method is used for computing force free fields to examine the evolution of the magnetic field of a line dipole, when there is relative shearing motion between the two polarities. It found that the energy of the sheared field can be arbitrarily large compared with the potential field. It is also found that it is possible to fit the magnetic energy, as a function of shear, by a simple functional form

Free energy and extension of a semiflexible polymer in cylindrical confining geometries

We consider a long, semiflexible polymer, with persistence length $P$ and contour length $L$, fluctuating in a narrow cylindrical channel of diameter $D$. In the regime $D\ll P\ll L$ the free energy of confinement $\Delta F$ and the length of the channel $R_\parallel$ occupied by the polymer are given by Odijk's relations $\Delta F/R_\parallel=A_\circ k_BTP^{-1/3}D^{-2/3}$ and $R_\parallel=L[1-\alpha_\circ(D/P)^{2/3}]$, where $A_\circ$ and $\alpha_\circ$ are dimensionless amplitudes. Using a simulation algorithm inspired by PERM (Pruned Enriched Rosenbluth Method), which yields results for very long polymers, we determine $A_\circ$ and $\alpha_\circ$ and the analogous amplitudes for a channel with a rectangular cross section. For a semiflexible polymer confined to the surface of a cylinder, the corresponding amplitudes are derived with an exact analytic approach. The results are relevant for interpreting experiments on biopolymers in microchannels or microfluidic devices.Comment: 15 pages without figures, 5 figure

Quantum transfer matrix method for one-dimensional disordered electronic systems

We develop a novel quantum transfer matrix method to study thermodynamic properties of one-dimensional (1D) disordered electronic systems. It is shown that the partition function can be expressed as a product of $2\times2$ local transfer matrices. We demonstrate this method by applying it to the 1D disordered Anderson model. Thermodynamic quantities of this model are calculated and discussed.Comment: 7 pages, 10 figure