A Database for TSSs of Human MicroRNAs

MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression of mRNAs by hybridizing with their 3'-UTRs or by translational repression. They have been shown to take crucial roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, even though there is very limited knowledge about their transcriptional loci. Primary miRNAs (pri-miRs) are first transcribed from the DNA, followed by the formation of precursor miRNA (pre-miR) by endonucleases activity, which finally produces mature miRNAs. Unfortunately, the identification of the loci of pri-miRs, and the associated information about transcription start sites (TSSs) and promoters is still in progress. This information, even though limited, may be useful for further study on the regulation of miRNAs. In this paper, we provide a novel database of miRNA TSSs (miRT) that might be a valuable resource for advanced research on miRNA regulation

The probe technique far-from-equilibrium: Magnetic field symmetries of nonlinear transport

The probe technique is a simple mean to incorporate elastic and inelastic processes into quantum dynamics. Using numerical simulations, we demonstrate that this tool can be employed beyond the analytically tractable linear response regime, providing a stable solution for the probe parameters: temperature and chemical potential. Adopting four probes: dephasing, voltage, temperature, and voltage-temperature, mimicking different elastic and inelastic effects, we focus on magnetic field and gate voltage symmetries of charge current and heat current in Aharonov-Bohm interferometers, potentially far-from-equilibrium. Considering electron current, we prove analytically that in the linear response regime inelastic scattering processes do not break the Onsager symmetry. Beyond linear response, even (odd) conductance terms obey an odd (even) symmetry with the threading magnetic flux, as long as the system acquires a spatial inversion symmetry. When spatial asymmetry is introduced particle-hole symmetry assures that nonlinear conductance terms maintain certain symmetries with respect to magnetic field and gate voltage. These analytic results are supported by numerical simulations. Analogous results are obtained for the electron heat current. We also demonstrate that a double-dot Aharonov-Bohm interferometer acts as a rectifier when two conditions are met: (i) many-body effects are included, here in the form of inelastic scattering, and (ii) time reversal symmetry is broken

Quantum heat transfer in harmonic chains with self consistent reservoirs: Exact numerical simulations

We describe a numerical scheme for exactly simulating the heat current behavior in a quantum harmonic chain with self-consistent reservoirs. Numerically-exact results are compared to classical simulations and to the quantum behavior under the linear response approximation. In the classical limit or for small temperature biases our results coincide with previous calculations. At large bias and for low temperatures the quantum dynamics of the system fundamentally differs from the close-to-equilibrium behavior, revealing in particular the effect of thermal rectification for asymmetric chains. Since this effect is absent in the classical analog of our model, we conclude that in the quantum model studied here thermal rectification is a purely quantum phenomenon, rooted in the quantum statistics