Harbin: a quantitation PCR analysis tool

Objectives: To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments. Results: Harbin uses the standard curve method for relative quantitation to calculate concentration ratios (CRs). To evaluate if different datasets can be combined the Harbin quantile bootstrap test is proposed. This test is more sensitive in detecting distributional differences between data sets than the Kolmogorov–Smirnov test. The utility of the test is demonstrated in a comparison of three grapevine leafroll associated virus 3 (GLRaV-3) RT-qPCR data sets. Conclusions: The quantile-based scoring system of CRs will enable the monitoring of virus titre or gene expression over different time points and be useful in other genomic applications where the combining of data sets are required

Atomic Effective Pseudopotentials for Semiconductors

We derive an analytic connection between the screened self-consistent effective potential from density functional theory (DFT) and atomic effective pseudopotentials (AEPs). The motivation to derive AEPs is to address structures with thousands to hundred thousand atoms, as given in most nanostructures. The use of AEPs allows to bypass a self-consistent procedure and to address eigenstates around a certain region of the spectrum (e.g., around the band gap). The bulk AEP construction requires two simple DFT calculations of slightly deformed elongated cells. The ensuing AEPs are given on a fine reciprocal space grid, including the small reciprocal vector components, are free of parameters, and involve no fitting procedure. We further show how to connect the AEPs of different bulk materials, which is necessary to obtain accurate band offsets. We derive a total of 20 AEPs for III-V, II-VI and group IV semiconductors and demonstrate their accuracy and transferability by comparison to DFT calculations of strained bulk structures, quantum wells with varying thickness, and semiconductor alloys.Comment: 10 pages, 5 figures, submitted to PR

Jamming Transition In Non-Spherical Particle Systems: Pentagons Versus Disks

We investigate the jamming transition in a quasi-2D granular material composed of regular pentagons or disks subjected to quasistatic uniaxial compression. We report six major findings based on experiments with monodisperse photoelastic particles with static friction coefficient μ≈1. (1) For both pentagons and disks, the onset of rigidity occurs when the average coordination number of non-rattlers, Znr, reaches 3, and the dependence of Znr on the packing fraction ϕ changes again when Znr reaches 4. (2) Though the packing fractions ϕc1 and ϕc2 at these transitions differ from run to run, for both shapes the data from all runs with different initial configurations collapses when plotted as a function of the non-rattler fraction. (3) The averaged values of ϕc1 and ϕc2 for pentagons are around 1% smaller than those for disks. (4) Both jammed pentagons and disks show Gamma distribution of the Voronoi cell area with same parameters. (5) The jammed pentagons have similar translational order for particle centers but slightly less orientational order for contacting pairs compared to jammed disks. (6) For jammed pentagons, the angle between edges at a face-to-vertex contact point shows a uniform distribution and the size of a cluster connected by face-to-face contacts shows a power-law distribution

Jamming Transition In Non-Spherical Particle Systems: Pentagons Versus Disks

We investigate the jamming transition in a quasi-2D granular material composed of regular pentagons or disks subjected to quasistatic uniaxial compression. We report six major findings based on experiments with monodisperse photoelastic particles with static friction coefficient μ≈1. (1) For both pentagons and disks, the onset of rigidity occurs when the average coordination number of non-rattlers, Znr, reaches 3, and the dependence of Znr on the packing fraction ϕ changes again when Znr reaches 4. (2) Though the packing fractions ϕc1 and ϕc2 at these transitions differ from run to run, for both shapes the data from all runs with different initial configurations collapses when plotted as a function of the non-rattler fraction. (3) The averaged values of ϕc1 and ϕc2 for pentagons are around 1% smaller than those for disks. (4) Both jammed pentagons and disks show Gamma distribution of the Voronoi cell area with same parameters. (5) The jammed pentagons have similar translational order for particle centers but slightly less orientational order for contacting pairs compared to jammed disks. (6) For jammed pentagons, the angle between edges at a face-to-vertex contact point shows a uniform distribution and the size of a cluster connected by face-to-face contacts shows a power-law distribution

Influence of the charge carrier tunneling processes on the recombination dynamics in single lateral quantum dot molecules

We report on the charge carrier dynamics in single lateral quantum dot molecules and the effect of an applied electric field on the molecular states. Controllable electron tunneling manifests itself in a deviation from the typical excitonic decay behavior which is strongly influenced by the tuning electric field and inter-molecular Coulomb energies. A rate equation model is developed to gain more insight into the charge transfer and tunneling mechanisms. Non-resonant (phonon-mediated) electron tunneling which changes the molecular exciton character from direct to indirect, and vice versa, is found to be the dominant tunable decay mechanism of excitons besides radiative recombination.Comment: 4 pages, 4 figure