Anomalous aging phenomena caused by drift velocities

We demonstrate via several examples that a uniform drift velocity gives rise to anomalous aging, characterized by a specific form for the two-time correlation functions, in a variety of statistical-mechanical systems far from equilibrium. Our first example concerns the oscillatory phase observed recently in a model of competitive learning. Further examples, where the proposed theory is exact, include the voter model and the Ohta-Jasnow-Kawasaki theory for domain growth in any dimension, and a theory for the smoothing of sandpile surfaces.Comment: 7 pages, 3 figures. To appear in Europhysics Letter

Simulation of surfactant transport during the rheological relaxation of two-dimensional dry foams

We describe a numerical model to predict the rheology of two-dimensional dry foams. The model accurately describes soap film curvature, viscous friction with the walls, and includes the transport of surfactant within the films and across the vertices where films meet. It accommodates the changes in foam topology that occur when a foam flows and, in particular, accurately represents the relaxation of the foam following a topological change. The model is validated against experimental data, allowing the prediction of elastic and viscous parameters associated with different surfactant solutions

Small Energy Scale for Mixed-Valent Uranium Materials

We investigate a two-channel Anderson impurity model with a $5f^1$ magnetic and a $5f^2$ quadrupolar ground doublet, and a $5f^2$ excited triplet. Using the numerical renormalization group method, we find a crossover to a non-Fermi liquid state below a temperature $T^*$ varying as the $5f^2$ triplet-doublet splitting to the 7/2 power. To within numerical accuracy, the non-linear magnetic susceptibility and the $5f^1$ contribution to the linear susceptibility are given by universal one-parameter scaling functions. These results may explain UBe$_{13}$ as mixed valent with a small crossover scale $T^*$.Comment: 4 pages, 3 figures, REVTeX, to appear in Phys. Rev. Let

Blind Normalization of Speech From Different Channels

We show how to construct a channel-independent representation of speech that has propagated through a noisy reverberant channel. This is done by blindly rescaling the cepstral time series by a non-linear function, with the form of this scale function being determined by previously encountered cepstra from that channel. The rescaled form of the time series is an invariant property of it in the following sense: it is unaffected if the time series is transformed by any time-independent invertible distortion. Because a linear channel with stationary noise and impulse response transforms cepstra in this way, the new technique can be used to remove the channel dependence of a cepstral time series. In experiments, the method achieved greater channel-independence than cepstral mean normalization, and it was comparable to the combination of cepstral mean normalization and spectral subtraction, despite the fact that no measurements of channel noise or reverberations were required (unlike spectral subtraction).Comment: 25 pages, 7 figure

Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx

Cross-linking combined with mass spectrometry (XL-MS) provides a wealth of information about the three-dimensional (3D) structure of proteins and their interactions. We introduce MaxLynx, a novel computational proteomics workflow for XL-MS integrated into the MaxQuant environment. It is applicable to noncleavable and MS-cleavable cross-linkers. For both, we have generalized the Andromeda peptide database search engine to efficiently identify cross-linked peptides. For noncleavable peptides, we implemented a novel dipeptide Andromeda score, which is the basis for a computationally efficient N-squared search engine. Additionally, partial scores summarize the evidence for the two constituents of the dipeptide individually. A posterior error probability (PEP) based on total and partial scores is used to control false discovery rates (FDRs). For MS-cleavable cross-linkers, a score of signature peaks is combined with the conventional Andromeda score on the cleavage products. The MaxQuant 3D peak detection was improved to ensure more accurate determination of the monoisotopic peak of isotope patterns for heavy molecules, which cross-linked peptides typically are. A wide selection of filtering parameters can replace the manual filtering of identifications, which is often necessary when using other pipelines. On benchmark data sets of synthetic peptides, MaxLynx outperforms all other tested software on data for both types of cross-linkers and on a proteome-wide data set of cross-linked Drosophila melanogaster cell lysate. The workflow also supports ion mobility-enhanced MS data. MaxLynx runs on Windows and Linux, contains an interactive viewer for displaying annotated cross-linked spectra, and is freely available at https://www.maxquant.org/

Chromosome mapping: radiation hybrid data and stochastic spin models

This work approaches human chromosome mapping by developing algorithms for ordering markers associated with radiation hybrid data. Motivated by recent work of Boehnke et al. [1], we formulate the ordering problem by developing stochastic spin models to search for minimum-break marker configurations. As a particular application, the methods developed are applied to 14 human chromosome-21 markers tested by Cox et al. [2]. The methods generate configurations consistent with the best found by others. Additionally, we find that the set of low-lying configurations is described by a Markov-like ordering probability distribution. The distribution displays cluster correlations reflecting closely linked loci.Comment: 26 Pages, uuencoded LaTex, Submitted to Phys. Rev. E, [email protected], [email protected]

Large Interstellar Polarisation Survey. LIPS I: FORS2 spectropolarimetry in the Southern Hemisphere

Polarimetric studies of light transmitted through interstellar clouds may give constraints on the properties of the interstellar dust grains. Traditionally, broadband linear polarisation (BBLP) measurements have been considered an important diagnostic tool for the study of the interstellar dust, while comparatively less attention has been paid to spectropolarimetric measurements. However, spectropolarimetry may offer stronger constraints than BBLP, for example by revealing narrowband features, and by allowing us to distinguish the contribution of dust from the contribution of interstellar gas. Therefore, we have decided to carry out a Large Interstellar Polarisation Survey (LIPS) using spectropolarimetric facilities in both hemispheres. Here we present the results obtained in the Southern Hemisphere with the FORS2 instrument of the ESO Very Large Telescope. Our spectra cover the wavelength range 380--950\,nm at a spectral resolving power of about 880. We have produced a publicly available catalogue of 127 linear polarisation spectra of 101 targets. We also provide the Serkowski-curve parameters, as well as the wavelength gradient of the polarisation position angle for the interstellar polarisation along 76 different lines of sight. In agreement with previous literature, we found that the best-fit parameters of the Serkowski-curve are not independent of each other. However, the relationships that we obtained are not always consistent with what was found in previous studies.Comment: Accepted by A&A (replaced on 12 October 2017 simply to correct a Metadata error

Markov bases and subbases for bounded contingency tables

In this paper we study the computation of Markov bases for contingency tables whose cell entries have an upper bound. In general a Markov basis for unbounded contingency table under a certain model differs from a Markov basis for bounded tables. Rapallo, (2007) applied Lawrence lifting to compute a Markov basis for contingency tables whose cell entries are bounded. However, in the process, one has to compute the universal Gr\"obner basis of the ideal associated with the design matrix for a model which is, in general, larger than any reduced Gr\"obner basis. Thus, this is also infeasible in small- and medium-sized problems. In this paper we focus on bounded two-way contingency tables under independence model and show that if these bounds on cells are positive, i.e., they are not structural zeros, the set of basic moves of all $2 \times 2$ minors connects all tables with given margins. We end this paper with an open problem that if we know the given margins are positive, we want to find the necessary and sufficient condition on the set of structural zeros so that the set of basic moves of all $2 \times 2$ minors connects all incomplete contingency tables with given margins.Comment: 22 pages. It will appear in the Annals of the Institution of Statistical Mathematic