Crystal structure of Schmallenberg orthobunyavirus nucleoprotein-RNA complex reveals a novel RNA sequestration mechanism

Schmallenberg virus (SBV) is a newly emerged orthobunyavirus (family Bunyaviridae) that has caused severe disease in the offspring of farm animals across Europe. Like all orthobunyaviruses, SBV contains a tripartite negative-sense RNA genome that is encapsidated by the viral nucleocapsid (N) protein in the form of a ribonucleoprotein complex (RNP). We recently reported the three-dimensional structure of SBV N that revealed a novel fold. Here we report the crystal structure of the SBV N protein in complex with a 42-nt-long RNA to 2.16 Å resolution. The complex comprises a tetramer of N that encapsidates the RNA as a cross-shape inside the protein ring structure, with each protomer bound to 11 ribonucleotides. Eight bases are bound in the positively charged cleft between the N- and C-terminal domains of N, and three bases are shielded by the extended N-terminal arm. SBV N appears to sequester RNA using a different mechanism compared with the nucleoproteins of other negative-sense RNA viruses. Furthermore, the structure suggests that RNA binding results in conformational changes of some residues in the RNA-binding cleft and the N- and C-terminal arms. Our results provide new insights into the novel mechanism of RNA encapsidation by orthobunyaviruses

Mass transport perspective on an accelerated exclusion process: Analysis of augmented current and unit-velocity phases

In an accelerated exclusion process (AEP), each particle can "hop" to its adjacent site if empty as well as "kick" the frontmost particle when joining a cluster of size $\ell \leq \ell_\text{max}$. With various choices of the interaction range, $\ell_\text{max}$, we find that the steady state of AEP can be found in a homogeneous phase with augmented currents (AC) or a segregated phase with holes moving at unit velocity (UV). Here we present a detailed study on the emergence of the novel phases, from two perspectives: the AEP and a mass transport process (MTP). In the latter picture, the system in the UV phase is composed of a condensate in coexistence with a fluid, while the transition from AC to UV can be regarded as condensation. Using Monte Carlo simulations, exact results for special cases, and analytic methods in a mean field approach (within the MTP), we focus on steady state currents and cluster sizes. Excellent agreement between data and theory is found, providing an insightful picture for understanding this model system.Comment: 13 pages, 8 figure

Intrinsic Cavity QED and Emergent Quasi-Normal Modes for Single Photon

We propose a special cavity design that is constructed by terminating a one-dimensional waveguide with a perfect mirror at one end and doping a two-level atom at the other. We show that this atom plays the intrinsic role of a semi-transparent mirror for single photon transports such that quasi-normal modes (QNM's) emerge spontaneously in the cavity system. This atomic mirror has its reflection coefficient tunable through its level spacing and its coupling to the cavity field, for which the cavity system can be regarded as a two-end resonator with a continuously tunable leakage. The overall investigation predicts the existence of quasi-bound states in the waveguide continuum. Solid state implementations based on a dc-SQUID circuit and a defected line resonator embedded in a photonic crystal are illustrated to show the experimental accessibility of the generic model.Comment: 4 pages,5 figures, Comments welcom

Low-momentum interactions with Brown-Rho-Ericson scalings and the density dependence of the nuclear symmetry energy

We have calculated the nuclear symmetry energy $E_{sym}(\rho)$ up to densities of $4 \sim 5 \rho_0$ with the effects from the Brown-Rho (BR) and Ericson scalings for the in-medium mesons included. Using the $V_{low-k}$ low-momentum interaction with and without such scalings, the equations of state (EOS) of symmetric and asymmetric nuclear matter have been calculated using a ring-diagarm formalism where the particle-particle-hole-hole ring diagrams are included to all orders. The EOS for symmetric nuclear matter and neutron matter obtained with linear BR scaling are both overly stiff compared with the empirical constraints of Danielewicz {\it et al.} \cite{daniel02}. In contrast, satisfactory results are obtained by either using the nonlinear Ericson scaling or by adding a Skyrme-type three-nucleon force (TNF) to the unscaled $V_{low-k}$ interaction. Our results for $E_{sym}(\rho)$ obtained with the nonlinear Ericson scaling are in good agreement with the empirical values of Tsang {\it et al.} \cite{tsang09} and Li {\it et al.} \cite{li05}, while those with TNF are slightly below these values. For densities below the nuclear saturation density $\rho_0$, the results of the above calculations are nearly equivalent to each other and all in satisfactory agreement with the empirical values.Comment: 7 pages, 6 figure

Bulk-fragment and tube-like structures of AuN (N=2-26)

Using the relativistic all-electron density-functional calculations on the AuN (N=2-26) in the generalized gradient approximation, combined with the guided simulated annealing, we have found that the two- to three-dimensional structural transition for AuN occurs between N=13 and 15, and the AuN (16<= N <=25) prefer also the pyramid-based bulk fragment structures in addition to the Au20. More importantly, the tubelike structures are found to be the most stable for Au24 and Au26, offering another powerful structure competitor with other isomers, e.g., amorphous, bulk fragment, and gold fullerene. The mechanism to cause these unusual AuN may be attributed to the stronger s-d hybridization and the d-d interaction enhanced by the relativistic effects.Comment: 12 pages and 3 figure

The structure of parafermion vertex operator algebras

It is proved that the parafermion vertex operator algebra associated to the irreducible highest weight module for the affine Kac-Moody algebra A_1^{(1)} of level k coincides with a certain W-algebra. In particular, a set of generators for the parafermion vertex operator algebra is determined.Comment: 12 page

Fault Tolerant Filtering and Fault Detection for Quantum Systems Driven By Fields in Single Photon States

The purpose of this paper is to solve a fault tolerant filtering and fault detection problem for a class of open quantum systems driven by a continuous-mode bosonic input field in single photon states when the systems are subject to stochastic faults. Optimal estimates of both the system observables and the fault process are simultaneously calculated and characterized by a set of coupled recursive quantum stochastic differential equations.Comment: arXiv admin note: text overlap with arXiv:1504.0678

Irreversibility for all bound entangled states

We derive a new inequality for entanglement for a mixed four-partite state. Employing this inequality, we present a one-shot lower bound for entanglement cost and prove that entanglement cost is strictly larger than zero for any entangled state. We demonstrate that irreversibility occurs in the process of formation for all non-distillable entangled states. In this way we solve a long standing problem, of how "real" is entanglement of bound entangled states. Using the new inequality we also prove impossibility of local-cloning of a known entangled state.Comment: The publication version. As noted in quant-ph/0510035, the result also implies that the mathematical definition of entangled states is equivalent to the physical definition in the sense of states preparation by LOC