Belief Semantics of Authorization Logic

Authorization logics have been used in the theory of computer security to reason about access control decisions. In this work, a formal belief semantics for authorization logics is given. The belief semantics is proved to subsume a standard Kripke semantics. The belief semantics yields a direct representation of principals' beliefs, without resorting to the technical machinery used in Kripke semantics. A proof system is given for the logic; that system is proved sound with respect to the belief and Kripke semantics. The soundness proof for the belief semantics, and for a variant of the Kripke semantics, is mechanized in Coq

Nexus Authorization Logic (NAL): Logical Results

Nexus Authorization Logic (NAL) [Schneider et al. 2011] is a logic for reasoning about authorization in distributed systems. A revised version of NAL is given here, including revised syntax, a revised proof theory using localized hypotheses, and a new Kripke semantics. The proof theory is proved sound with respect to the semantics, and that proof is formalized in Coq

A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation

Plus-strand RNA viruses can accumulate viral RNA degradation products during infections. Some of these decay intermediates are generated by the cytosolic 5′-to-3′ exoribonuclease Xrn1 (mammals and yeast) or Xrn4 (plants) and are formed when the enzyme stalls on substrate RNAs upon encountering inhibitory RNA structures. Many Xrn-generated RNAs correspond to 3′-terminal segments within the 3′-UTR of viral genomes and perform important functions during infections. Here we have investigated a 3′-terminal small viral RNA (svRNA) generated by Xrn during infections with Tobacco necrosis virus-D (family Tombusviridae). Our results indicate that (i) unlike known stalling RNA structures that are compact and modular, the TNV-D structure encompasses the entire 212 nt of the svRNA and is not functionally transposable, (ii) at least two tertiary interactions within the RNA structure are required for effective Xrn blocking and (iii) most of the svRNA generated in infections is derived from viral polymerase-generated subgenomic mRNA1. In vitro and in vivo analyses allowed for inferences on roles for the svRNA. Our findings provide a new and distinct addition to the growing list of Xrn-resistant viral RNAs and stalling structures found associated with different plant and animal RNA viruses.York University Librarie

Two-channel Kondo physics in odd impurity chains

We study odd-membered chains of spin-(1/2) impurities, with each end connected to its own metallic lead. For antiferromagnetic exchange coupling, universal two-channel Kondo (2CK) physics is shown to arise at low energies. Two overscreening mechanisms are found to occur depending on coupling strength, with distinct signatures in physical properties. For strong inter-impurity coupling, a residual chain spin-(1/2) moment experiences a renormalized effective coupling to the leads; while in the weak-coupling regime, Kondo coupling is mediated via incipient single-channel Kondo singlet formation. We also investigate models where the leads are tunnel-coupled to the impurity chain, permitting variable dot filling under applied gate voltages. Effective low-energy models for each regime of filling are derived, and for even-fillings where the chain ground state is a spin singlet, an orbital 2CK effect is found to be operative. Provided mirror symmetry is preserved, 2CK physics is shown to be wholly robust to variable dot filling; in particular the single-particle spectrum at the Fermi level, and hence the low-temperature zero-bias conductance, is always pinned to half-unitarity. We derive a Friedel-Luttinger sum rule and from it show that, in contrast to a Fermi liquid, the Luttinger integral is non-zero and determined solely by the `excess' dot charge as controlled by gate voltage. The relevance of the work to real quantum dot devices, where inter-lead charge-transfer processes fatal to 2CK physics are present, is also discussed. Physical arguments and numerical renormalization group techniques are used to obtain a detailed understanding of these problems.Comment: 21 pages, 19 figure

Mixed mode oscillations in a conceptual climate model

Much work has been done on relaxation oscillations and other simple oscillators in conceptual climate models. However, the oscillatory patterns in climate data are often more complicated than what can be described by such mechanisms. This paper examines complex oscillatory behavior in climate data through the lens of mixed-mode oscillations. As a case study, a conceptual climate model with governing equations for global mean temperature, atmospheric carbon, and oceanic carbon is analyzed. The nondimensionalized model is a fast/slow system with one fast variable (corresponding to ice volume) and two slow variables (corresponding to the two carbon stores). Geometric singular perturbation theory is used to demonstrate the existence of a folded node singularity. A parameter regime is found in which (singular) trajectories that pass through the folded node are returned to the singular funnel in the limiting case where $\epsilon = 0$. In this parameter regime, the model has a stable periodic orbit of type $1^s$ for some $s>0$. To our knowledge, it is the first conceptual climate model demonstrated to have the capability to produce an MMO pattern.Comment: 28 pages, 11 figure

Pursuing Parameters for Critical Density Dark Matter Models

We present an extensive comparison of models of structure formation with observations, based on linear and quasi-linear theory. We assume a critical matter density, and study both cold dark matter models and cold plus hot dark matter models. We explore a wide range of parameters, by varying the fraction of hot dark matter $\Omega_{\nu}$, the Hubble parameter $h$ and the spectral index of density perturbations $n$, and allowing for the possibility of gravitational waves from inflation influencing large-angle microwave background anisotropies. New calculations are made of the transfer functions describing the linear power spectrum, with special emphasis on improving the accuracy on short scales where there are strong constraints. For assessing early object formation, the transfer functions are explicitly evaluated at the appropriate redshift. The observations considered are the four-year {\it COBE} observations of microwave background anisotropies, peculiar velocity flows, the galaxy correlation function, and the abundances of galaxy clusters, quasars and damped Lyman alpha systems. Each observation is interpreted in terms of the power spectrum filtered by a top-hat window function. We find that there remains a viable region of parameter space for critical-density models when all the dark matter is cold, though $h$ must be less than 0.5 before any fit is found and $n$ significantly below unity is preferred. Once a hot dark matter component is invoked, a wide parameter space is acceptable, including $n\simeq 1$. The allowed region is characterized by \Omega_\nu \la 0.35 and 0.60 \la n \la 1.25, at 95 per cent confidence on at least one piece of data. There is no useful lower bound on $h$, and for curious combinations of the other parameters it is possible to fit the data with $h$ as high as 0.65.Comment: 19 pages LaTeX file (uses mn.sty). Figures *not* included due to length. We strongly recommend obtaining the full paper, either by WWW at http://star-www.maps.susx.ac.uk/papers/lsstru_papers.html (UK) or http://www.bartol.udel.edu/~bob/papers (US), or by e-mailing ARL. Final version, to appear MNRAS. Main revision is update to four-year COBE data. Miscellaneous other changes and reference updates. No significant changes to principal conclusion

The C-terminal portion of the cleaved HT motif is necessary and sufficient to mediate export of proteins from the malaria parasite into its host cell

The malaria parasite exports proteins across its plasma membrane and a surrounding parasitophorous vacuole membrane, into its host erythrocyte. Most exported proteins contain a Host Targeting motif (HT motif) that targets them for export. In the parasite secretory pathway, the HT motif is cleaved by the protease plasmepsin V, but the role of the newly generated N-terminal sequence in protein export is unclear. Using a model protein that is cleaved by an exogenous viral protease, we show that the new N-terminal sequence, normally generated by plasmepsin V cleavage, is sufficient to target a protein for export, and that cleavage by plasmepsin V is not coupled directly to the transfer of a protein to the next component in the export pathway. Mutation of the fourth and fifth positions of the HT motif, as well as amino acids further downstream, block or affect the efficiency of protein export indicating that this region is necessary for efficient export. We also show that the fifth position of the HT motif is important for plasmepsin V cleavage. Our results indicate that plasmepsin V cleavage is required to generate a new N-terminal sequence that is necessary and sufficient to mediate protein export by the malaria parasite