44,196 research outputs found
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 Ă
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 . With various choices of the
interaction range, , 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 up to
densities of with the effects from the Brown-Rho (BR) and
Ericson scalings for the in-medium mesons included. Using the
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
interaction.
Our results for 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
, 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
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