Interference in interacting quantum dots with spin

We study spectral and transport properties of interacting quantum dots with spin. Two particular model systems are investigated: Lateral multilevel and two parallel quantum dots. In both cases different paths through the system can give rise to interference. We demonstrate that this strengthens the multilevel Kondo effect for which a simple two-stage mechanism is proposed. In parallel dots we show under which conditions the peak of an interference-induced orbital Kondo effect can be split.Comment: 8 pages, 8 figure

Electrical and thermoelectrical transport in Dirac fermions through a quantum dot

We investigate the conductance and thermopower of massless Dirac fermions through a quantum dot using a pseudogap Anderson model in the non-crossing approximation. When the Fermi level is at the Dirac point, the conductance has a cusp where the thermopower changes its sign. When the Fermi level is away from the Dirac point, the Kondo temperature illustrates a quantum impurity transition between an asymmetric strong coupling Kondo state and a localized moment state. The conductance shows a peak near this transition and reaches the unitary limit at low temperatures. The magnitude of the thermopower exceeds $k_B/e$, and the thermoelectric figure of merit exceeds unity.Comment: 5 pages, 4 figure

Dicke Effect in the Tunnel Current through two Double Quantum Dots

We calculate the stationary current through two double quantum dots which are interacting via a common phonon environment. Numerical and analytical solutions of a master equation in the stationary limit show that the current can be increased as well as decreased due to a dissipation mediated interaction. This effect is closely related to collective, spontaneous emission of phonons (Dicke super- and subradiance effect), and the generation of a `cross-coherence' with entanglement of charges in singlet or triplet states between the dots. Furthermore, we discuss an inelastic `current switch' mechanism by which one double dot controls the current of the other.Comment: 12 pages, 6 figures, to appear in Phys. Rev.

Three-orbital Kondo effect in single quantum dot system with plural electrons

We study the Kondo effect and related transport properties in orbitally degenerate vertical quantum dot systems with plural electrons. Applying the non-crossing approximation to the three-orbital Anderson impurity model with the finite Coulomb interaction and Hund-coupling, we investigate the magnetic-field dependence of the conductance and thermopower. We also introduce an additional orbital splitting to take account of the realistic many-body effect in the vertical quantum dot system. It is clarified how the three-orbital Kondo effect influences the transport properties via the modulation of the Kondo temperature and unitary limit of transport quantities due to the change of the symmetry in the system.Comment: 11 pages, 10 figures, accepted for publication in J. Phys. Soc. Jp

An accurate and interpretable model for siRNA efficacy prediction

BACKGROUND: The use of exogenous small interfering RNAs (siRNAs) for gene silencing has quickly become a widespread molecular tool providing a powerful means for gene functional study and new drug target identification. Although considerable progress has been made recently in understanding how the RNAi pathway mediates gene silencing, the design of potent siRNAs remains challenging. RESULTS: We propose a simple linear model combining basic features of siRNA sequences for siRNA efficacy prediction. Trained and tested on a large dataset of siRNA sequences made recently available, it performs as well as more complex state-of-the-art models in terms of potency prediction accuracy, with the advantage of being directly interpretable. The analysis of this linear model allows us to detect and quantify the effect of nucleotide preferences at particular positions, including previously known and new observations. We also detect and quantify a strong propensity of potent siRNAs to contain short asymmetric motifs in their sequence, and show that, surprisingly, these motifs alone contain at least as much relevant information for potency prediction as the nucleotide preferences for particular positions. CONCLUSION: The model proposed for prediction of siRNA potency is as accurate as a state-of-the-art nonlinear model and is easily interpretable in terms of biological features. It is freely available on the web a

Benchmark thermochemistry of the C_nH_{2n+2} alkane isomers (n=2--8) and performance of DFT and composite ab initio methods for dispersion-driven isomeric equilibria

The thermochemistry of linear and branched alkanes with up to eight carbons has been reexamined by means of W4, W3.2lite and W1h theories. `Quasi-W4' atomization energies have been obtained via isodesmic and hypohomodesmotic reactions. Our best atomization energies at 0 K (in kcal/mol) are: 1220.04 n-butane, 1497.01 n-pentane, 1774.15 n-hexane, 2051.17 n-heptane, 2328.30 n-octane, 1221.73 isobutane, 1498.27 isopentane, 1501.01 neopentane, 1775.22 isohexane, 1774.61 3-methylpentane, 1775.67 diisopropyl, 1777.27 neohexane, 2052.43 isoheptane, 2054.41 neoheptane, 2330.67 isooctane, and 2330.81 hexamethylethane. Our best estimates for $\Delta H^\circ_{f,298K}$ are: -30.00 n-butane, -34.84 n-pentane, -39.84 n-hexane, -44.74 n-heptane, -49.71 n-octane, -32.01 isobutane, -36.49 isopentane, -39.69 neopentane, -41.42 isohexane, -40.72 3-methylpentane, -42.08 diisopropyl, -43.77 neohexane, -46.43 isoheptane, -48.84 neoheptane, -53.29 isooctane, and -53.68 hexamethylethane. These are in excellent agreement (typically better than 1 kJ/mol) with the experimental heats of formation at 298 K obtained from the CCCBDB and/or NIST Chemistry WebBook databases. However, at 0 K a large discrepancy between theory and experiment (1.1 kcal/mol) is observed for only neopentane. This deviation is mainly due to the erroneous heat content function for neopentane used in calculating the 0 K CCCBDB value. The thermochemistry of these systems, especially of the larger alkanes, is an extremely difficult test for density functional methods. A posteriori corrections for dispersion are essential. Particularly for the atomization energies, the B2GP-PLYP and B2K-PLYP double-hybrids, and the PW6B95 hybrid-meta GGA clearly outperform other DFT functionals.Comment: (J. Phys. Chem. A, in press

Microarray-Based Sketches of the HERV Transcriptome Landscape

Human endogenous retroviruses (HERVs) are spread throughout the genome and their long terminal repeats (LTRs) constitute a wide collection of putative regulatory sequences. Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. Herein, we have introduced a generic method aiming to optimally characterize individual loci associated with 25-mer probes by minimizing cross-hybridization risks. We therefore set up a microarray dedicated to a collection of 5,573 HERVs that can reasonably be assigned to a unique genomic position. We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment showed that almost one third of the HERV repertoire is indeed transcribed. The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. The probeset definition within the U3 and U5 regions was used to assign a function to some LTRs (i.e. promoter or polyA) and revealed that (i) autonomous active LTRs are broadly subjected to operational determinism (ii) the cellular gene density is substantially higher in the surrounding environment of active LTRs compared to silent LTRs and (iii) the configuration of neighboring cellular genes differs between active and silent LTRs, showing an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects