Reconstruction of thermally-symmetrized quantum autocorrelation functions from imaginary-time data

In this paper, I propose a technique for recovering quantum dynamical information from imaginary-time data via the resolution of a one-dimensional Hamburger moment problem. It is shown that the quantum autocorrelation functions are uniquely determined by and can be reconstructed from their sequence of derivatives at origin. A general class of reconstruction algorithms is then identified, according to Theorem 3. The technique is advocated as especially effective for a certain class of quantum problems in continuum space, for which only a few moments are necessary. For such problems, it is argued that the derivatives at origin can be evaluated by Monte Carlo simulations via estimators of finite variances in the limit of an infinite number of path variables. Finally, a maximum entropy inversion algorithm for the Hamburger moment problem is utilized to compute the quantum rate of reaction for a one-dimensional symmetric Eckart barrier.Comment: 15 pages, no figures, to appear in Phys. Rev.

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states

Inversion of Randomly Corrugated Surfaces Structure from Atom Scattering Data

The Sudden Approximation is applied to invert structural data on randomly corrugated surfaces from inert atom scattering intensities. Several expressions relating experimental observables to surface statistical features are derived. The results suggest that atom (and in particular He) scattering can be used profitably to study hitherto unexplored forms of complex surface disorder.Comment: 10 pages, no figures. Related papers available at http://neon.cchem.berkeley.edu/~dan

Counting flags in triangle-free digraphs

Motivated by the Caccetta-Haggkvist Conjecture, we prove that every digraph on n vertices with minimum outdegree 0.3465n contains an oriented triangle. This improves the bound of 0.3532n of Hamburger, Haxell and Kostochka. The main new tool we use in our proof is the theory of flag algebras developed recently by Razborov.Comment: 19 pages, 7 figures; this is the final version to appear in Combinatoric

Black carbon measurements in the boundary layer over western and northern Europe

Europe is a densely populated region that is a significant global source of black carbon (BC) aerosol, but there is a lack of information regarding the physical properties and spatial/vertical distribution of rBC in the region. We present the first aircraft observations of sub-micron refractory BC (rBC) aerosol concentrations and physical properties measured by a single particle soot photometer (SP2) in the lower troposphere over Europe. The observations spanned a region roughly bounded by 50° to 60° N and from 15° W to 30° E. The measurements, made between April and September 2008, showed that average rBC mass concentrations ranged from about 300 ng m−3 near urban areas to approximately 50 ng m−3 in remote continental regions, lower than previous surface-based measurements. rBC represented between 0.5 and 3% of the sub-micron aerosol mass. Black carbon mass size distributions were log-normally distributed and peaked at approximately 180 nm, but shifted to smaller diameters (~160 nm) near source regions. rBC was correlated with carbon monoxide (CO) but had different ratios to CO depending on location and air mass. Light absorption coefficients were measured by particle soot absorption photometers on two separate aircraft and showed similar geographic patterns to rBC mass measured by the SP2. We summarize the rBC and light absorption measurements as a function of longitude and air mass age and also provide profiles of rBC mass concentrations and size distribution statistics. Our results will help evaluate model-predicted regional rBC concentrations and properties and determine regional and global climate impacts from rBC due to atmospheric heating and surface dimming

Fractal Analysis of Protein Potential Energy Landscapes

The fractal properties of the total potential energy V as a function of time t are studied for a number of systems, including realistic models of proteins (PPT, BPTI and myoglobin). The fractal dimension of V(t), characterized by the exponent \gamma, is almost independent of temperature and increases with time, more slowly the larger the protein. Perhaps the most striking observation of this study is the apparent universality of the fractal dimension, which depends only weakly on the type of molecular system. We explain this behavior by assuming that fractality is caused by a self-generated dynamical noise, a consequence of intermode coupling due to anharmonicity. Global topological features of the potential energy landscape are found to have little effect on the observed fractal behavior.Comment: 17 pages, single spaced, including 12 figure

Identification of schistosome-infected snails by detecting schistosomal antigens and DNA sequences

Cercarial shedding tests do not provide species identification of the schistosomes concerned and cannot detect prepatent schistosomal infections. We have demonstrated that both immunodetection by ELISA of schistosomal antigens in snail hemolymph, and dot hybridization of snail extracts by a DNA probe representing highly repeated sequences, proved suitable for detecting infected snails during prepatency as well as patency. A group-specific monoclonal antibody was found to be suitable for detecting Schistosoma mansoni infection in Biomphalaria sp., but not for positive identification of S. haematobium in Bulinus sp. Comparative evaluation of the diagnostic qualities, and technical aspects and cost of these tests, point to the superiority of the immunodetection approach for large scale detection of snails prepatently infected with S. mansoni. This approach is potentially useful for providing extended information on schistosome-snail epidemiology that may facilitate rapid evaluation of the danger of post-control reinfection, and help make decisions on the time and place of supplementary control measures. In this context the potential usefulness of the immunodetection or DNA probing approach for facilitating catalytic model representation of schistosome-snail epidemiology warrants further evaluation. Specific identification of S. haematobium in Bulinus by either of these approaches may be possible depending on the development of suitable antibodies or DNA probes

Hopping Conductivity of a Nearly-1d Fractal: a Model for Conducting Polymers

We suggest treating a conducting network of oriented polymer chains as an anisotropic fractal whose dimensionality D=1+\epsilon is close to one. Percolation on such a fractal is studied within the real space renormalization group of Migdal and Kadanoff. We find that the threshold value and all the critical exponents are strongly nonanalytic functions of \epsilon as \epsilon tends to zero, e.g., the critical exponent of conductivity is \epsilon^{-2}\exp (-1-1/\epsilon). The distribution function for conductivity of finite samples at the percolation threshold is established. It is shown that the central body of the distribution is given by a universal scaling function and only the low-conductivity tail of distribution remains $\epsilon$-dependent. Variable range hopping conductivity in the polymer network is studied: both DC conductivity and AC conductivity in the multiple hopping regime are found to obey a quasi-1d Mott law. The present results are consistent with electrical properties of poorly conducting polymers.Comment: 27 pages, RevTeX, epsf, 5 .eps figures, to be published in Phys. Rev.

Apparent Fractality Emerging from Models of Random Distributions

The fractal properties of models of randomly placed $n$-dimensional spheres ($n$=1,2,3) are studied using standard techniques for calculating fractal dimensions in empirical data (the box counting and Minkowski-sausage techniques). Using analytical and numerical calculations it is shown that in the regime of low volume fraction occupied by the spheres, apparent fractal behavior is observed for a range of scales between physically relevant cut-offs. The width of this range, typically spanning between one and two orders of magnitude, is in very good agreement with the typical range observed in experimental measurements of fractals. The dimensions are not universal and depend on density. These observations are applicable to spatial, temporal and spectral random structures. Polydispersivity in sphere radii and impenetrability of the spheres (resulting in short range correlations) are also introduced and are found to have little effect on the scaling properties. We thus propose that apparent fractal behavior observed experimentally over a limited range may often have its origin in underlying randomness.Comment: 19 pages, 12 figures. More info available at http://www.fh.huji.ac.il/~dani

The substructure of three repetitive DNA regions of Schistosoma haematobium group species as a potential marker for species recognition and interbreeding detection

The file attached is the Published/publisher’s pdf version of the article.© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated