PubNet: a flexible system for visualizing literature derived networks

We have developed PubNet, a web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. PubNet supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, Protein Data Bank (PDB) IDs, Medical Subject Headings (MeSH) terms, and authors. This feature allows one to, for example, examine a literature derived network of genes based on functional similarity

Resonance f0(1500)f_0(1500): Is it a scalar glueball ?

The ratios of partial widths for the decay of a glueball into two pseudoscalar mesons are calculated under the assumption that the production of light quark pairs ($u\bar u,d\bar d,s\bar s$) in soft gluon-\-induced reactions goes on within universal symmetry breaking. Parameter of the violation of flavour symmetry is fixed by the central hadron production data in high energy hadron collisions and/or by the ratios of radiative decay amplitudes $J/\Psi \to \gamma\eta/\gamma\eta'$ and $J/\Psi \to \gamma \phi \phi/\gamma \omega \omega$. The ratios of coupling constants $glueball\to\pi\pi,K\bar K, \eta\eta,\eta\eta'$ which are calculated with this parameter coincide reasonably with those of $f_0(1500)$, supporting an idea about glueball nature of $f_0(1500)$.Comment: LaTex, 8 pages, 2 .eps figures in one uuencoded file, uses epsfi

Direct Detection of Warm Dark Matter in the X-ray

We point out a serendipitous link between warm dark matter (WDM) models for structure formation on the one hand and the high sensitivity energy range (1-10 keV) for x-ray photon detection on the Chandra and XMM-Newton observatories on the other. This fortuitous match may provide either a direct detection of the dark matter or exclusion of many candidates. We estimate expected x-ray fluxes from field galaxies and clusters of galaxies if the dark matter halos of these objects are composed of WDM candidate particles with rest masses in the structure formation-preferred range (~1 keV to ~20 keV) and with small radiative decay branches. Existing observations lead us to conclude that for singlet neutrinos (possessing a very small mixing with active neutrinos) to be a viable WDM candidate they must have rest masses < 5 keV in the zero lepton number production mode. Future deeper observations may detect or exclude the entire parameter range for the zero lepton number case, perhaps restricting the viability of singlet neutrino WDM models to those where singlet production is driven by a significant lepton number. The Constellation X project has the capability to detect/exclude singlet neutrino WDM for lepton number values up to 10% of the photon number. We also consider diffuse x-ray background constraints on these scenarios. These same x-ray observations additionally may constrain parameters of active neutrino and gravitino WDM candidates.Comment: 11 pages, 6 figures, replacement to match ApJ versio

Classification of protein domain movements using Dynamic Contact Graphs

A new method for the classification of domain movements in proteins is described and applied to 1822 pairs of structures from the Protein Data Bank that represent a domain movement in two-domain proteins. The method is based on changes in contacts between residues from the two domains in moving from one conformation to the other. We argue that there are five types of elemental contact changes and that these relate to five model domain movements called: ‘‘free’’, ‘‘openclosed’’, ‘‘anchored’’, ‘‘sliding-twist’’, and ‘‘see-saw.’’ A directed graph is introduced called the ‘‘Dynamic Contact Graph’’ which represents the contact changes in a domain movement. In many cases a graph, or part of a graph, provides a clear visual metaphor for the movement it represents and is a motif that can be easily recognised. The Dynamic Contact Graphs are often comprised of disconnected subgraphs indicating independent regions which may play different roles in the domain movement. The Dynamic Contact Graph for each domain movement is decomposed into elemental Dynamic Contact Graphs, those that represent elemental contact changes, allowing us to count the number of instances of each type of elemental contact change in the domain movement. This naturally leads to sixteen classes into which the 1822 domain movements are classified

Communications Biophysics

Contains reports on three research projects.United States Air Force (Contract AF19(602)-4112

First Passage Time Densities in Non-Markovian Models with Subthreshold Oscillations

Motivated by the dynamics of resonant neurons we consider a differentiable, non-Markovian random process $x(t)$ and particularly the time after which it will reach a certain level $x_b$. The probability density of this first passage time is expressed as infinite series of integrals over joint probability densities of $x$ and its velocity $\dot{x}$. Approximating higher order terms of this series through the lower order ones leads to closed expressions in the cases of vanishing and moderate correlations between subsequent crossings of $x_b$. For a linear oscillator driven by white or coloured Gaussian noise, which models a resonant neuron, we show that these approximations reproduce the complex structures of the first passage time densities characteristic for the underdamped dynamics, where Markovian approximations (giving monotonous first passage time distribution) fail

Microstructural characterization and simulation of damage for geared sheet components

The evolution of damage in geared components manufactured from steel sheets was investigated, to analyse the influence of damage caused by the sheet-bulk-metal forming. Due to the inhomogeneous and multi-axial deformation in the investigated parts, different aspects such as the location-dependent shape and size of voids are analysed by means of various microscopic methods. In particular, a method to characterize the state of damage evolution, i. e. void nucleation, growth and coalescence using scanning electron microscopy (SEM) is applied. The investigations reveal a strong dependence of the void area fraction, shape of voids and thus damage evolution on the loading mode. The microstructural analysis is complemented with FEM simulations using material models which consider the characteristics of the void evolution. © Published under licence by IOP Publishing Ltd

Investigation of the electroplastic effect using nanoindentation

A promising approach to deform metallic-intermetallic composite materials is the application of electric current pulses during the deformation process to achieve a lower yield strength and enhanced elongation to fracture. This is known as the electroplastic effect. In this work, a novel setup to study the electroplastic effect during nanoindentation on individual phases and well-defined interfaces was developed. Using a eutectic Al-Al2Cu alloy as a model material, electroplastic nanoindentation results were directly compared with macroscopic electroplastic compression tests. The results of the micro- and macroscopic investigations reveal current induced displacement shifts and stress drops, respectively, with the first displacement shift/stress drop being higher than the subsequent ones. A higher current intensity, higher loading rate and larger pulsing interval all cause increased displacement shifts. This observation, in conjunction with the fact that the first displacement shift is highest, strongly indicates that de-pinning of dislocations from obstacles dominates the mechanical response, rather than solely thermal effects