Probability Models for Degree Distributions of Protein Interaction Networks

The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional form contains important clues as to underlying evolutionary processes that have shaped the network. Generally, the functional form for the degree distribution has been determined in an ad-hoc fashion, with clear power-law like behaviour often only extending over a limited range of connectivities. Here we apply formal model selection techniques to decide which probability distribution best describes the degree distributions of protein interaction networks. Contrary to previous studies this well defined approach suggests that the degree distribution of many molecular networks is often better described by distributions other than the popular power-law distribution. This, in turn, suggests that simple, if elegant, models may not necessarily help in the quantitative understanding of complex biological processes.

Conducting Polymer Ink

Disclosed are conductive polymer inks and methods for forming the inks. The disclosed inks include a dispersion of conductive core/shell nanoparticles. The core/shell nanoparticles include a polymeric core and a shell formed of a conducting polymer. The inks can include a dispersion of the core/shell nanoparticles in a liquid carrier, such as an alcohol. The disclosed inks can be formulated to high viscosities and can be utilized in high-speed printing processes including rotogravure and flexographic printing processes. Products encompassed by the disclosure include polymer devices such as sensors, OFETs, RFID tags, printed circuit board, electrochromic devices, non-volatile memory devices, photovoltaics, and the like

Channel diffusion of sodium in a silicate glass

We use classical molecular dynamics simulations to study the dynamics of sodium atoms in amorphous Na$_2$O-4SiO$_2$. We find that the sodium trajectories form a well connected network of pockets and channels. Inside these channels the motion of the atoms is not cooperative but rather given by independent thermally activated hops of individual atoms between the pockets. By determining the probability that an atom returns to a given starting site, we show that such events are not important for the dynamics of this system.Comment: 10 pages of Latex, 5 figures, one figure added, text expande

Electronic structure and light-induced conductivity in a transparent refractory oxide

Combined first-principles and experimental investigations reveal the underlying mechanism responsible for a drastic change of the conductivity (by 10 orders of magnitude) following hydrogen annealing and UV-irradiation in a transparent oxide, 12CaO.7Al2O3, found by Hayashi et al. The charge transport associated with photo-excitation of an electron from H, occurs by electron hopping. We identify the atoms participating in the hops, determine the exact paths for the carrier migration, estimate the temperature behavior of the hopping transport and predict a way to enhance the conductivity by specific doping.Comment: 4 pages including 4 figure

The False Widow\textit{False Widow} Link Between Neutron Star X-ray Binaries and Spider Pulsars

The discovery of transitional millisecond pulsars (tMSPs) provided conclusive proof that neutron star (NS) low-mass X-ray binaries (LMXBs) comprise part of the evolutionary pathway towards binary millisecond pulsars (MSPs). Redback and black widow `spider' pulsars are a sub-category of binary MSPs that `devour' their companions through ablation - the process through which material is lifted from the stellar surface by a pulsar wind. In addition to reducing the companion star's mass, ablation introduces observable characteristics like extended, energy-dependent and asymmetric eclipse profiles in systems observed at a sufficiently high inclination. Here, we present a detailed study and comparison of the X-ray eclipses of two NS LMXBs; $\textit{Swift}$ J1858.6$-$0814 and EXO 0748$-$676. Some of the X-ray eclipse characteristics observed in these two LMXBs are similar to the radio eclipse characteristics of eclipsing redback and black widow pulsars, suggesting that they may also host ablated companion stars. X-ray irradiation or a pulsar wind could drive the ablation. We conduct orbital phase-resolved spectroscopy for both LMXBs to map the column density, ionization and covering fraction of the material outflow. From this, we infer the presence of highly ionized and clumpy ablated material around the companion star in both systems. We term LMXBs undergoing ablation, $\textit{false widows}$, and speculate that they may be the progenitors of redback pulsars under the assumption that ablation begins in the LMXB stage. Therefore, the false widows could provide a link between LMXBs and spider pulsars. The detection of radio pulsations during non-accreting states can support this hypothesis.Comment: 21 pages, 15 figures. Accepted for publication in MNRAS. The full version of Table 1 is available as online supplementary material from the MNRAS websit

Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network

BACKGROUND It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems. RESULTS Using Boolean network models as an exemplar, we present a new technique to identify subsystems, based on their dynamical properties. The main part of the method depends only on the stable dynamics (attractors) of the system, thus requiring no prior knowledge of the underlying network. However, knowledge of the logical relationships between the network components can be used to describe how each subsystem is regulated. To demonstrate its applicability to genetic regulatory systems, we apply the method to a model of the Drosophila segment polarity network, providing a detailed breakdown of the system. CONCLUSION We have designed a technique for decomposing any set of discrete-state, discrete-time attractors into subsystems. Having a suitable mathematical model also allows us to describe how each subsystem is regulated and how robust each subsystem is against perturbations. However, since the subsystems are found directly from the attractors, a mathematical model or underlying network topology is not necessarily required to identify them, potentially allowing the method to be applied directly to experimental expression data

Origin of non-exponential relaxation in a crystalline ionic conductor: a multi-dimensional 109Ag NMR study

The origin of the non-exponential relaxation of silver ions in the crystalline ion conductor Ag7P3S11 is analyzed by comparing appropriate two-time and three-time 109Ag NMR correlation functions. The non-exponentiality is due to a rate distribution, i.e., dynamic heterogeneities, rather than to an intrinsic non-exponentiality. Thus, the data give no evidence for the relevance of correlated back-and-forth jumps on the timescale of the silver relaxation.Comment: 4 pages, 3 figure

Polypyrrole-Fe2O3 nanohybrid materials for electrochemical storage

We report on the synthesis and electrochemical characterization of nanohybrid polypyrrole (PPy) (PPy/Fe2O3) materials for electrochemical storage applications. We have shown that the incorporation of nanoparticles inside the PPy notably increases the charge storage capability in comparison to the “pure” conducting polymer. Incorporation of large anions, i.e., paratoluenesulfonate, allows a further improvement in the capacity. These charge storage modifications have been attributed to the morphology of the composite in which the particle sizes and the specific surface area are modified with the incorporation of nanoparticles. High capacity and stability have been obtained in PC/NEt4BF4 (at 20 mV/s), i.e., 47 mAh/g, with only a 3% charge loss after one thousand cyles. The kinetics of charge–discharge is also improved by the hybrid nanocomposite morphology modifications, which increase the rate of insertion–expulsion of counter anions in the bulk of the film. A room temperature ionic liquid such as imidazolium trifluoromethanesulfonimide seems to be a promising electrolyte because it further increases the capacity up to 53 mAh/g with a high stability during charge–discharge processes