A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets

Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces two new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published and newly generated data. Analyses of simulated data demonstrate that the combined method has favourable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases

Experimental Progress on Zonal Flow Physics in Toroidal Plasmas

Present status of experiments on zonal flows is overviewed. Innovative use of traditional and modern diagnostics has revealed unambiguously the existence of zonal flows, their spatio-temporal characteristics, their relationship with turbulence, and their effects on confinement. Particularly, number of observations have been accumulated on the oscillatory branch of zonal flows, dubbed geodesic acoustic modes, suggesting necessity of theories to give their proper description. In addition to these basic properties of zonal flows, several new methods have elucidated the zonal flow generation processes from turbulence. Further investigation of relationship between zonal flows and confinement is strongly encouraged as cross-device activity including low temperature toroidal and linear devices

Charge qubits and limitations of electrostatic quantum gates

We investigate the characteristics of purely electrostatic interactions with external gates in constructing full single qubit manipulations. The quantum bit is naturally encoded in the spatial wave function of the electron system. Single-electron{transistor arrays based on quantum dots or insulating interfaces typically allow for electrostatic controls where the inter-island tunneling is considered constant, e.g. determined by the thickness of an insulating layer. A representative array of 3x3 quantum dots with two mobile electrons is analyzed using a Hubbard Hamiltonian and a capacitance matrix formalism. Our study shows that it is easy to realize the first quantum gate for single qubit operations, but that a second quantum gate only comes at the cost of compromising the low-energy two-level system needed to encode the qubit. We use perturbative arguments and the Feshbach formalism to show that the compromising of the two-level system is a rather general feature for electrostatically interacting qubits and is not just related to the specific details of the system chosen. We show further that full implementation requires tunable tunneling or external magnetic fields.Comment: 7 pages, 5 figures, submitted to PR

Relativistic Beaming and Flux Variability in Active Galactic Nuclei

We discuss the impact of special relativistic effects on the observed light curves and variability duty cycles of AGNs. We model the properties of AGN light curves at radio wavelengths using a simulated shot noise process in which the occurrence of major flaring events in a relativistic jet is governed by Poisson statistics. We show that flaring sources whose radiation is highly beamed toward us are able to reach very high flux levels, but will in fact spend most of their time in relatively low flaring states due to relativistic contraction of flare time scales in the observer frame. The fact that highly beamed AGNs do not return to a steady-state quiescent level between flares implies that their weakly beamed counterparts should have highly stable flux densities that result from a superposition of many long-term, low-amplitude flares. The ``apparent'' quiescent flux levels of these weakly beamed AGNs (identified in many unified models as radio galaxies) will be significantly higher than their ''true'' quiescent (i.e., non-flaring) levels. We use Monte Carlo simulations to investigate flux variability bias in the selection statistics of flat-spectrum AGN samples. In the case of the Caltech-Jodrell Flat-spectrum survey, the predicted orientation bias towards jets seen end-on is weakened if the parent population is variable, since the highly beamed sources have a stronger tendency to be found in low flaring states. This effect is small, however, since highly beamed sources are relatively rare, and their fluxes tend to be boosted sufficiently above the survey limit such that they are selected regardless of their flaring level. We find that for larger flat-spectrum AGN surveys with fainter flux cutoffs, variability should not be an appreciable source of selection bias.Comment: Accepted for publication in the Astrophysical Journa

Non-equilibrium transport through a vertical quantum dot in the absence of spin-flip energy relaxation

We investigate non-equilibrium transport in the absence of spin-flip energy relaxation in a few-electron quantum dot artificial atom. Novel non-equilibrium tunneling processes involving high-spin states which cannot be excited from the ground state because of spin-blockade, and other processes involving more than two charge states are observed. These processes cannot be explained by orthodox Coulomb blockade theory. The absence of effective spin relaxation induces considerable fluctuation of the spin, charge, and total energy of the quantum dot. Although these features are revealed clearly by pulse excitation measurements, they are also observed in conventional dc current characteristics of quantum dots.Comment: accepted for publication in Phys. Rev.Let

Non-markovian dynamics of double quantum dot charge qubit with static bias

The dynamics of charge qubit in double quantum dot coupled to phonons is investigated theoretically. The static bias is considered. By means of the perturbation approach based on unitary transformations, the dynamical tunneling current is obtained explicitly. The biased system displays broken symmetry and a significantly larger coherence-incoherence transition critical point $\alpha _{c}$. We also analyzed the decoherence induced by piezoelectric coupling phonons in detail. The results show that reducing the coupling between system and bath make coherence frequency increase and coherence time prolong. To maintain quantum coherence, applying static bias also is a good means.Comment: 13 pages, 5 figure

A gate-defined silicon quantum dot molecule

We report electron transport measurements of a silicon double dot formed in multi-gated metal-oxide-semiconductor structures with a 15-nm-thick silicon-on-insulator layer. Tunable tunnel coupling enables us to observe an excitation spectrum in weakly coupled dots and an energy level anticrossing in strongly coupled ones. Such a quantum dot molecule with both charge and energy quantization provides the essential prerequisite for future implementation of silicon-based quantum computations.Comment: 11pages,3figure

Voltage-controlled Group Velocity of Edge Magnetoplasmon in the Quantum Hall Regime

We investigate the group velocity of edge magnetoplasmons (EMPs) in the quantum Hall regime by means of time-of-flight measurement. The EMPs are injected from an Ohmic contact by applying a voltage pulse, and detected at a quantum point contact by applying another voltage pulse to its gate. We find that the group velocity of the EMPs traveling along the edge channel defined by a metallic gate electrode strongly depends on the voltage applied to the gate. The observed variation of the velocity can be understood to reflect the degree of screening caused by the metallic gate, which damps the in-plane electric field and hence reduces the velocity. The degree of screening can be controlled by changing the distance between the gate and the edge channel with the gate voltage.Comment: 5 pages, 6 figures, to be published in Physical Review

Transient current spectroscopy of a quantum dot in the Coulomb blockade regime

Transient current spectroscopy is proposed and demonstrated in order to investigate the energy relaxation inside a quantum dot in the Coulomb blockade regime. We employ a fast pulse signal to excite an AlGaAs/GaAs quantum dot to an excited state, and analyze the non-equilibrium transient current as a function of the pulse length. The amplitude and time-constant of the transient current are sensitive to the ground and excited spin states. We find that the spin relaxation time is longer than, at least, a few microsecond.Comment: 5 pages, 3 figure