Quartet compatibility and the quartet graph

A collection P of leaf-labelled trees is compatible if there exists a single leaf-labelled tree that displays each of the trees in P. Despite its difficulty, determining the compatibility of P is a fundamental task in evolutionary biology. Attractive characterizations in terms of chordal graphs have been previously given for this problem as well as for the problems of (i) determining if there is a unique tree that displays each of the trees in P, that is 'P is definitive and (ii) determining if there is a tree that displays P and has the property that every other tree that displays P is a refinement of it, that is 'P identifies a leaf-labelled tree. In this paper, we describe new characterizations of each of these problems in terms of edge colourings. Furthermore, for an arbitrary leaf-labelled tree 'T, we also determine the minimum number of 'quartets' required to identify 'T, thus correcting a previously published result

Off-equilibrium dynamics of the two-dimensional Coulomb glass

The dynamics of the 2D Coulomb glass model is investigated by kinetic Monte Carlo simulation. An exponential divergence of the relaxation time signals a zero-temperature freezing transition. At low temperatures the dynamics of the system is glassy. The local charge correlations and the response to perturbations of the local potential show aging. The dynamics of formation of the Coulomb gap is slow and the density of states at the Fermi level decays in time as a power law. The relevance of these findings for recent transport experiments in Anderson-insulating films is pointed out.Comment: 7 pages, 7 figure

TIRA: An OpenAPI Extension and Toolbox for GDPR Transparency in RESTful Architectures

Transparency - the provision of information about what personal data is collected for which purposes, how long it is stored, or to which parties it is transferred - is one of the core privacy principles underlying regulations such as the GDPR. Technical approaches for implementing transparency in practice are, however, only rarely considered. In this paper, we present a novel approach for doing so in current, RESTful application architectures and in line with prevailing agile and DevOps-driven practices. For this purpose, we introduce 1) a transparency-focused extension of OpenAPI specifications that allows individual service descriptions to be enriched with transparency-related annotations in a bottom-up fashion and 2) a set of higher-order tools for aggregating respective information across multiple, interdependent services and for coherently integrating our approach into automated CI/CD-pipelines. Together, these building blocks pave the way for providing transparency information that is more specific and at the same time better reflects the actual implementation givens within complex service architectures than current, overly broad privacy statements.Comment: Accepted for publication at the 2021 International Workshop on Privacy Engineering (IWPE'21). This is a preprint manuscript (authors' own version before final copy-editing

The Eliashberg Function of Amorphous Metals

A connection is proposed between the anomalous thermal transport properties of amorphous solids and the low-frequency behavior of the Eliashberg function. By means of a model calculation we show that the size and frequency dependence of the phonon mean-free-path that has been extracted from measurements of the thermal conductivity in amorphous solids leads to a sizeable linear region in the Eliashberg function at small frequencies. Quantitative comparison with recent experiments gives very good agreement.Comment: 4pp., REVTeX, 1 uuencoded ps fig. Original posting had a corrupted raw ps fig appended. Published as PRB 51, 689 (1995

Polyply:A python suite for facilitating simulations of macromolecules and nanomaterials

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle

Electroweak corrections to γZ\gamma Z production at hadron colliders

In this paper we present the results from a calculation of the full electroweak one-loop corrections for $\gamma Z$ vector-boson pair production at hadron colliders. The cases of proton--antiproton as well as proton--proton collisions, at the Tevatron and the LHC, respectively, are considered. Results are presented for the distribution of the $\gamma Z$ invariant mass and for the transverse momentum of the final-state photon. The higher-order electroweak effects are numerically significant, in particular for probing possible anomalous gauge-boson couplings

On the structure of the energy distribution function in the hopping regime

The impact of the dispersion of the transport coefficients on the structure of the energy distribution function for charge carriers far from equilibrium has been investigated in effective-medium approximation for model densities of states. The investigations show that two regimes can be observed in energy relaxation processes. Below a characteristic temperature the structure of the energy distribution function is determined by the dispersion of the transport coefficients. Thermal energy diffusion is irrelevant in this regime. Above the characteristic temperature the structure of the energy distribution function is determined by energy diffusion. The characteristic temperature depends on the degree of disorder and increases with increasing disorder. Explicit expressions for the energy distribution function in both regimes are derived for a constant and an exponential density of states.Comment: 16 page

Model for the architecture of caveolae based on a flexible, net-like assembly of Cavin1 and Caveolin discs.

Caveolae are invaginated plasma membrane domains involved in mechanosensing, signaling, endocytosis, and membrane homeostasis. Oligomers of membrane-embedded caveolins and peripherally attached cavins form the caveolar coat whose structure has remained elusive. Here, purified Cavin1 60S complexes were analyzed structurally in solution and after liposome reconstitution by electron cryotomography. Cavin1 adopted a flexible, net-like protein mesh able to form polyhedral lattices on phosphatidylserine-containing vesicles. Mutating the two coiled-coil domains in Cavin1 revealed that they mediate distinct assembly steps during 60S complex formation. The organization of the cavin coat corresponded to a polyhedral nano-net held together by coiled-coil segments. Positive residues around the C-terminal coiled-coil domain were required for membrane binding. Purified caveolin 8S oligomers assumed disc-shaped arrangements of sizes that are consistent with the discs occupying the faces in the caveolar polyhedra. Polygonal caveolar membrane profiles were revealed in tomograms of native caveolae inside cells. We propose a model with a regular dodecahedron as structural basis for the caveolae architecture

Conformally Einstein Products and Nearly K\"ahler Manifolds

In the first part of this note we study compact Riemannian manifolds (M,g) whose Riemannian product with R is conformally Einstein. We then consider compact 6--dimensional almost Hermitian manifolds of type W_1+W_4 in the Gray--Hervella classification admitting a parallel vector field and show that (under some regularity assumption) they are obtained as mapping tori of isometries of compact Sasaki-Einstein 5-dimensional manifolds. In particular, we obtain examples of inhomogeneous locally (non-globally) conformal nearly K\"ahler compact manifolds