WoLF PSORT: protein localization predictor

WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction. WoLF PSORT converts protein amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functional motifs such as DNA-binding motifs. After conversion, a simple k-nearest neighbor classifier is used for prediction. Using html, the evidence for each prediction is shown in two ways: (i) a list of proteins of known localization with the most similar localization features to the query, and (ii) tables with detailed information about individual localization features. For convenience, sequence alignments of the query to similar proteins and links to UniProt and Gene Ontology are provided. Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.or

Possibility of an ultra-precise optical clock using the 61S0→63P0o6 ^1S_0 \to 6 ^3P^o_0 transition in 171,173^{171, 173}Yb atoms held in an optical lattice

We report calculations designed to assess the ultimate precision of an atomic clock based on the 578 nm $6 ^1S_0 --> 6 ^3P^o_0$ transition in Yb atoms confined in an optical lattice trap. We find that this transition has a natural linewidth less than 10 mHz in the odd Yb isotopes, caused by hyperfine coupling. The shift in this transition due to the trapping light acting through the lowest order AC polarizability is found to become zero at the magic trap wavelength of about 752 nm. The effects of Rayleigh scattering, higher-order polarizabilities, vector polarizability, and hyperfine induced electronic magnetic moments can all be held below a mHz (about a part in 10^{18}), except in the case of the hyperpolarizability larger shifts due to nearly resonant terms cannot be ruled out without an accurate measurement of the magic wavelength.Comment: 4 pages, 1 figur

Mixed States of Composite Fermions Carrying Two and Four Vortices

There now exists preliminary experimental evidence for some fractions, such as $\nu$ = 4/11 and 5/13, that do not belong to any of the sequences $\nu=n/(2pn\pm 1)$, $p$ and $n$ being integers. We propose that these states are mixed states of composite fermions of different flavors, for example, composite fermions carrying two and four vortices. We also obtain an estimate of the lowest-excitation dispersion curve as well as the transport gap; the gaps for 4/11 are smaller than those for 1/3 by approximately a factor of 50.Comment: Accepted for PRB rapid communication (scheduled to appear in Nov 15, 2000 issue

Synchronization in populations of globally coupled oscillators with inertial effects

A model for synchronization of globally coupled phase oscillators including ``inertial'' effects is analyzed. In such a model, both oscillator frequencies and phases evolve in time. Stationary solutions include incoherent (unsynchronized) and synchronized states of the oscillator population. Assuming a Lorentzian distribution of oscillator natural frequencies, $g(\Omega)$, both larger inertia or larger frequency spread stabilize the incoherent solution, thereby making harder to synchronize the population. In the limiting case $g(\Omega)=\delta(\Omega)$, the critical coupling becomes independent of inertia. A richer phenomenology is found for bimodal distributions. For instance, inertial effects may destabilize incoherence, giving rise to bifurcating synchronized standing wave states. Inertia tends to harden the bifurcation from incoherence to synchronized states: at zero inertia, this bifurcation is supercritical (soft), but it tends to become subcritical (hard) as inertia increases. Nonlinear stability is investigated in the limit of high natural frequencies.Comment: Revtex, 36 pages, submit to Phys. Rev.

Long-term trends in tropical cyclone tracks around Korea and Japan in late summer and early fall

This study investigates long-term trends in tropical cyclones (TCs) over the extratropical western North Pacific (WNP) over a period of 35 years (1982-2016). The area analyzed extended across 30-45 degrees N and 120-150 degrees E, including the regions of Korea and Japan that were seriously affected by TCs. The northward migration of TCs over the WNP to the mid-latitudes showed a sharp increase in early fall. In addition, the duration of TCs over the WNP that migrated northwards showed an increase, specifically in early to mid-September. Therefore, more recently, TC tracks have been observed to significantly extend into the mid-latitudes. The recent northward extension of TC tracks over the WNP in early fall was observed to be associated with changes in environmental conditions that were favorable for TC activities, including an increase in sea surface temperature (SST), decrease in vertical wind shear, expansion of subtropical highs, strong easterly steering winds, and an increase in relative vorticity. In contrast, northward migrations of TCs to Korea and Japan showed a decline in late August, because of the presence of unfavorable environmental conditions for TC activities. These changes in environmental conditions, such as SST and vertical wind shear, can be partially associated with the Pacific decadal oscillation

Light-cone QCD Sum Rules for the Λ\Lambda Baryon Electromagnetic Form Factors and its magnetic moment

We present the light-cone QCD sum rules up to twist 6 for the electromagnetic form factors of the $\Lambda$ baryon. To estimate the magnetic moment of the baryon, the magnetic form factor is fitted by the dipole formula. The numerical value of our estimation is $\mu_\Lambda=-(0.64\pm0.04)\mu_N$, which is in accordance with the experimental data and the existing theoretical results. We find that it is twist 4 but not the leading twist distribution amplitudes that dominate the results.Comment: 13 page, 7 figures, accepted for publication in Euro. Phys. J.

Quantum Interference in Superconducting Wire Networks and Josephson Junction Arrays: Analytical Approach based on Multiple-Loop Aharonov-Bohm Feynman Path-Integrals

We investigate analytically and numerically the mean-field superconducting-normal phase boundaries of two-dimensional superconducting wire networks and Josephson junction arrays immersed in a transverse magnetic field. The geometries we consider include square, honeycomb, triangular, and kagome' lattices. Our approach is based on an analytical study of multiple-loop Aharonov-Bohm effects: the quantum interference between different electron closed paths where each one of them encloses a net magnetic flux. Specifically, we compute exactly the sums of magnetic phase factors, i.e., the lattice path integrals, on all closed lattice paths of different lengths. A very large number, e.g., up to $10^{81}$ for the square lattice, exact lattice path integrals are obtained. Analytic results of these lattice path integrals then enable us to obtain the resistive transition temperature as a continuous function of the field. In particular, we can analyze measurable effects on the superconducting transition temperature, $T_c(B)$, as a function of the magnetic filed $B$, originating from electron trajectories over loops of various lengths. In addition to systematically deriving previously observed features, and understanding the physical origin of the dips in $T_c(B)$ as a result of multiple-loop quantum interference effects, we also find novel results. In particular, we explicitly derive the self-similarity in the phase diagram of square networks. Our approach allows us to analyze the complex structure present in the phase boundaries from the viewpoint of quantum interference effects due to the electron motion on the underlying lattices.Comment: 18 PRB-type pages, plus 8 large figure

Ultrafast photoinduced reflectivity transients in (Nd0.5Sr0.5)MnO3(Nd_{0.5}Sr_{0.5})MnO_3

The temperature dependence of ultrafast photoinduced reflectivity transients is reported in Nd$_{0.5}$Sr$_{0.5}$MnO$_{3}$ thin film. The photoinduced reflectivity shows a complex response with very different temperature dependences on different timescales. The response on the sub-ps timescale appears to be only weakly sensitive to the 270K-metal-insulator phase transition. Below $\sim 160$ K the sub-ps response displays a two component behavior indicating inhomogeneity of the film resulting from the substrate induced strain. On the other hand, the slower response on the 10-100 ps timescale is sensitive only to the metal-insulator phase transition and is in agreement with some previously published results. The difference in the temperature dependences of the responses on nanosecond and $\mu$s timescales indicates that thermal equilibrium between the different degrees of fredom is established relatively slowly - on a nanosecond timescale

Implications of Compressed Supersymmetry for Collider and Dark Matter Searches

Martin has proposed a scenario dubbed ``compressed supersymmetry'' (SUSY) where the MSSM is the effective field theory between energy scales M_{\rm weak} and M_{\rm GUT}, but with the GUT scale SU(3) gaugino mass M_3<< M_1 or M_2. As a result, squark and gluino masses are suppressed relative to slepton, chargino and neutralino masses, leading to a compressed sparticle mass spectrum, and where the dark matter relic density in the early universe may be dominantly governed by neutralino annihilation into ttbar pairs via exchange of a light top squark. We explore the dark matter and collider signals expected from compressed SUSY for two distinct model lines with differing assumptions about GUT scale gaugino mass parameters. For dark matter signals, the compressed squark spectrum leads to an enhancement in direct detection rates compared to models with unified gaugino masses. Meanwhile, neutralino halo annihilation rates to gamma rays and anti-matter are also enhanced relative to related scenarios with unified gaugino masses but, depending on the halo dark matter distribution, may yet be below the sensitivity of indirect searches underway. In the case of collider signals, we compare the rates for the potentially dominant decay modes of the stop_1 which may be expected to be produced in cascade decay chains at the LHC: \tst_1\to c\tz_1 and \tst_1\to bW\tz_1. We examine the extent to which multilepton signal rates are reduced when the two-body decay mode dominates. For the model lines that we examine here, the multi-lepton signals, though reduced, still remain observable at the LHC.Comment: 22 pages including 24 eps figure

Local realizations of contact interactions in two- and three-body problems

Mathematically rigorous theory of the two-body contact interaction in three dimension is reviewed. Local potential realizations of this proper contact interaction are given in terms of Poschl-Teller, exponential and square-well potentials. Three body calculation is carried out for the halo nucleus 11Li using adequately represented contact interaction.Comment: submitted to Phys. Rev.