Dynamical control of electron spin coherence in a quantum dot

We investigate the performance of dynamical decoupling methods at suppressing electron spin decoherence from a low-temperature nuclear spin reservoir in a quantum dot. The controlled dynamics is studied through exact numerical simulation, with emphasis on realistic pulse delays and long-time limit. Our results show that optimal performance for this system is attained by a periodic protocol exploiting concatenated design, with control rates substantially slower than expected from the upper spectral cutoff of the bath. For a known initial electron spin state, coherence can saturate at long times, signaling the creation of a stable ``spin-locked'' decoherence-free subspace. Analytical insight on saturation is obtained for a simple echo protocol, in good agreement with numerical results.Comment: 4 pages, 4 figures with 3 of them in colo

Bootstrap tomography of high-precision pulses for quantum control

Long-time dynamical decoupling and quantum control of qubits require high-precision control pulses. Full characterization (quantum tomography) of imperfect pulses presents a bootstrap problem: tomography requires initial states of a qubit which can not be prepared without imperfect pulses. We present a protocol for pulse error analysis, specifically tailored for a wide range of the single solid-state electron spins. Using a single electron spin of a nitrogen-vacancy (NV) center in diamond, we experimentally verify the correctness of the protocol, and demonstrate its usefulness for quantum control tasks

Long-time electron spin storage via dynamical suppression of hyperfine-induced decoherence in a quantum dot

The coherence time of an electron spin decohered by the nuclear spin environment in a quantum dot can be substantially increased by subjecting the electron to suitable dynamical decoupling sequences. We analyze the performance of high-level decoupling protocols by using a combination of analytical and exact numerical methods, and by paying special attention to the regimes of large inter-pulse delays and long-time dynamics, which are outside the reach of standard average Hamiltonian theory descriptions. We demonstrate that dynamical decoupling can remain efficient far beyond its formal domain of applicability, and find that a protocol exploiting concatenated design provides best performance for this system in the relevant parameter range. In situations where the initial electron state is known, protocols able to completely freeze decoherence at long times are constructed and characterized. The impact of system and control non-idealities is also assessed, including the effect of intra-bath dipolar interaction, magnetic field bias and bath polarization, as well as systematic pulse imperfections. While small bias field and small bath polarization degrade the decoupling fidelity, enhanced performance and temporal modulation result from strong applied fields and high polarizations. Overall, we find that if the relative errors of the control parameters do not exceed 5%, decoupling protocols can still prolong the coherence time by up to two orders of magnitude.Comment: 16 pages, 10 figures, submitted to Phys. Rev.

Cosmological constraints on R-parity violation from neutrino decay

If the neutrino mass is non-zero, as hinted by several experiments, then R-parity-violating supersymmetric Yukawa couplings can drive a heavy neutrino decay into lighter states. The heavy neutrino may either decay radiatively into a lighter neutrino, or it may decay into three light neutrinos through a Z-mediated penguin. For a given mass of the decaying neutrino, we calculate its lifetime for the various modes, each mode requiring certain pairs of R-parity-violating couplings be non-zero. We then check whether the calculated lifetimes fall in zones allowed or excluded by cosmological requirements. For the latter case, we derive stringent new constraints on the corresponding products of R-parity-violating couplings for given values of the decaying neutrino mass.Comment: 13 pages, Latex, uses axodraw.sty; version to appear in Physical Review

Universal Statistical Behavior of Neural Spike Trains

We construct a model that predicts the statistical properties of spike trains generated by a sensory neuron. The model describes the combined effects of the neuron's intrinsic properties, the noise in the surrounding, and the external driving stimulus. We show that the spike trains exhibit universal statistical behavior over short times, modulated by a strongly stimulus-dependent behavior over long times. These predictions are confirmed in experiments on H1, a motion-sensitive neuron in the fly visual system.Comment: 7 pages, 4 figure

An ensemble approach to accurately detect somatic mutations using SomaticSeq

SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions and deletions. The workflow currently incorporates five state-of-the-art somatic mutation callers, and extracts over 70 individual genomic and sequencing features for each candidate site. A training set is provided to an adaptively boosted decision tree learner to create a classifier for predicting mutation statuses. We validate our results with both synthetic and real data. We report that SomaticSeq is able to achieve better overall accuracy than any individual tool incorporated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0758-2) contains supplementary material, which is available to authorized users

Nonlinearity of Mechanochemical Motions in Motor Proteins

The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are traditionally analyzed in terms of normal modes and experimental data on thermal fluctuations in such macromolecules is also usually interpreted in terms of the excitation of normal modes. We have chosen two important protein motors - myosin V and kinesin KIF1A - and performed numerical investigations of their conformational relaxation properties within the coarse-grained elastic network approximation. We have found that the linearity assumption is deficient for ligand-induced conformational motions and can even be violated for characteristic thermal fluctuations. The deficiency is particularly pronounced in KIF1A where the normal mode description fails completely in describing functional mechanochemical motions. These results indicate that important assumptions of the theory of protein dynamics may need to be reconsidered. Neither a single normal mode, nor a superposition of such modes yield an approximation of strongly nonlinear dynamics.Comment: 10 pages, 6 figure

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure

Universality, limits and predictability of gold-medal performances at the Olympic Games

Inspired by the Games held in ancient Greece, modern Olympics represent the world's largest pageant of athletic skill and competitive spirit. Performances of athletes at the Olympic Games mirror, since 1896, human potentialities in sports, and thus provide an optimal source of information for studying the evolution of sport achievements and predicting the limits that athletes can reach. Unfortunately, the models introduced so far for the description of athlete performances at the Olympics are either sophisticated or unrealistic, and more importantly, do not provide a unified theory for sport performances. Here, we address this issue by showing that relative performance improvements of medal winners at the Olympics are normally distributed, implying that the evolution of performance values can be described in good approximation as an exponential approach to an a priori unknown limiting performance value. This law holds for all specialties in athletics-including running, jumping, and throwing-and swimming. We present a self-consistent method, based on normality hypothesis testing, able to predict limiting performance values in all specialties. We further quantify the most likely years in which athletes will breach challenging performance walls in running, jumping, throwing, and swimming events, as well as the probability that new world records will be established at the next edition of the Olympic Games.Comment: 8 pages, 3 figures, 1 table. Supporting information files and data are available at filrad.homelinux.or

The integrated academic information system support for education 3.0 in higher education institution: lecturer perspective

Education 3.0 has been implemented in many higher education institutions (HEIs). Education 3.0 has been directed the institution toward better educational experience. But on the other hands, the implementation of Education 3.0 also caused some problems. Previous research has found administrative problem experienced by the lecturer. This research explores deeper from the lecturer and suggested the solution from lecturer perspective, combined with information technology capabilities owned by the HEIs. The research used a case study as the method and conducted a qualitative research with a semi-structured interview. The interview analysis has found that the increase of the administrative processes is caused by online and offline administrative activities. The online activities are from e-learning and the offline activities are from traditional learning (face-to-face). The administrative processes also involved the academic information system (AIS). Simplified all of the administrative processes are more preferred. To overcome the problems, integrating the AIS and e-learning become necessary. This research suggests transforming the existing AIS into an integrated AIS and hopes the solution can simplify the administration process