Hot electrons in low-dimensional phonon systems

A simple bulk model of electron-phonon coupling in metals has been surprisingly successful in explaining experiments on metal films that actually involve surface- or other low-dimensional phonons. However, by an exact application of this standard model to a semi-infinite substrate with a free surface, making use of the actual vibrational modes of the substrate, we show that such agreement is fortuitous, and that the model actually predicts a low-temperature crossover from the familiar T^5 temperature dependence to a stronger T^6 log T scaling. Comparison with existing experiments suggests a widespread breakdown of the standard model of electron-phonon thermalization in metals

Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

BackgroundProtein-protein interaction networks are commonly sampled using yeast two hybrid approaches. However, whether topological information reaped from these experimentally-measured sub-networks can be extrapolated to complete protein-protein interaction networks is unclear.ResultsBy analyzing various experimental protein-protein interaction datasets, we found that they are not random samples of the parent networks. Based on the experimental bait-prey behaviors, our computer simulations show that these non-random sampling features may affect the topological information. We tested the hypothesis that a core sub-network exists within the experimentally sampled network that better maintains the topological characteristics of the parent protein-protein interaction network. We developed a method to filter the experimentally sampled network to result in a core sub-network that more accurately reflects the topology of the parent network. These findings have fundamental implications for large-scale protein interaction studies and for our understanding of the behavior of cellular networks.ConclusionThe topological information from experimental measured networks network as is may not be the correct source for topological information about the parent protein-protein interaction network. We define a core sub-network that more accurately reflects the topology of the parent network

Phylogenetic networks: A tool to display character conflict and demographic history

Evolutionary trees have the assumption that evolution and phylogeny can be represented in a strictly bifurcating manner. Firmly speaking, from one ancestral taxon, two descendant taxa emerge. Nevertheless, hybridization, recombination and horizontal gene transfer is in conflict with this straightforward concept. In such cases, evolutionary lines do not only separate from each other, but have the possibility of melting again and are called reticulations. Consequently, networks can represent evolutionary events more realistically than phylogenetic trees. Networks can display alternative topologies and co-existence of ancestors and descendants, which are otherwise not obvious when a comparison is done on several single trees or a consensus tree. Therefore, networks have the ability to visualize the conflicting information in a given data set. Moreover, the distribution, frequencies and arrangement of haplotypes in populations can reveal the phylogenetic histories of the taxa, regarding predictions from the coalescent theory. This review aims to: (1) give a brief comparison between phylogenetic trees and networks, (2) provide the overall concept of the coalescent theory, (3) clarify how phylogenetic networks can be used to display conflict data and evaluate phylogenetic histories, and (4) offer a useful starting point and guide for sequence analysis, with the aim to discover population dynamics.Key words: Phylogenetic networks, reticulation, coalescent theory, population history, character conflict

Minimizing the Average Delay at Intersections via Presignals and Speed Control

© 2018 Mina Ghanbarikarekani et al. Urban intersections have been well recognized as bottlenecks of urban transport systems. It is thus important to propose and implement strategies for increasing the efficiency of public and private transportation systems as a whole. In order to achieve this goal, an additional signal could be set up near the intersection to give priority to buses through stopping vehicles in advance of the main intersection as a presignal. It has been increasingly popular in urban cities. While presignals indeed reduce the average delay per traveler, they cause extra stops of private vehicles, which might compromise the overall efficiency, safety, and sustainability. This paper aims to propose a model to improve presignals by reducing the vehicles' number of stops behind the presignals. By applying the method, vehicles would be able to adjust their speed based on traffic conditions as well as buses' speed and approach. Numerical analyses have been conducted to determine the conditions required for implementing this method

On the Integrability, B\"Acklund Transformation and Symmetry Aspects of a Generalized Fisher Type Nonlinear Reaction-Diffusion Equation

The dynamics of nonlinear reaction-diffusion systems is dominated by the onset of patterns and Fisher equation is considered to be a prototype of such diffusive equations. Here we investigate the integrability properties of a generalized Fisher equation in both (1+1) and (2+1) dimensions. A Painlev\'e singularity structure analysis singles out a special case ($m=2$) as integrable. More interestingly, a B\"acklund transformation is shown to give rise to a linearizing transformation for the integrable case. A Lie symmetry analysis again separates out the same $m=2$ case as the integrable one and hence we report several physically interesting solutions via similarity reductions. Thus we give a group theoretical interpretation for the system under study. Explicit and numerical solutions for specific cases of nonintegrable systems are also given. In particular, the system is found to exhibit different types of travelling wave solutions and patterns, static structures and localized structures. Besides the Lie symmetry analysis, nonclassical and generalized conditional symmetry analysis are also carried out.Comment: 30 pages, 10 figures, to appear in Int. J. Bifur. Chaos (2004

Timing Features of the Accretion--driven Millisecond X-Ray Pulsar XTE J1807--294 in 2003 March Outburst

In order to probe the activity of the inner disk flow and its effect on the neutron star surface emissions, we carried out the timing analysis of the Rossi X-Ray Timing Explorer (RXTE) observations of the millisecond X-ray pulsar XTE J1807--294, focusing on its correlated behaviors in X-ray intensities, hardness ratios, pulse profiles and power density spectra. The source was observed to have a serial of broad "puny" flares on a timescale of hours to days on the top of a decaying outburst in March 2003. In the flares, the spectra are softened and the pulse profiles become more sinusoidal. The frequency of kilohertz quasi-periodic oscillation (kHz QPO) is found to be positively related to the X-ray count rate in the flares. These features observed in the flares could be due to the accreting flow inhomogeneities. It is noticed that the fractional pulse amplitude increases with the flare intensities in a range of $\sim 2$, comparable to those observed in the thermonuclear bursts of the millisecond X-ray pulsar XTE J1814--338, whereas it remains at about 6.5% in the normal state. Such a significant variation of the pulse profile in the "puny" flares may reflect the changes of physical parameters in the inner disk accretion region. Furthermore, we noticed an overall positive correlation between the kHz QPO frequency and the fractional pulse amplitude, which could be the first evidence representing that the neutron-star surface emission properties are very sensitive to the disk flow inhomogeneities. This effect should be cautiously considered in the burst oscillation studies.Comment: Accepted by ApJ, 23 pages, 7 figures, 3 table

Discovery of new quasi-periodic oscillations in the X-ray transient source V~0332+53

We report the discovery of a new quasi-period oscillation (QPO) at 0.22 Hz, centered on the source spin frequency of the high mass X-ray binary system V~0332+53 when the source was observed during its November 2004/March 2005 outburst by {\em RXTE}. Besides this new QPO, we also detected the known 0.05 Hz QPO. Both the 0.22 and 0.05 Hz QPOs stand out clearly at a mid-flux level of the outburst within January 15--19 2005, and later at an even lower flux level as the width of 0.22 Hz QPO drops. No evolution of the centroid frequency with the flux is seen in either QPO. The rms value below 10 keV is around 4--6% for both QPOs and decreases at higher energies. We discuss our results in the context of current QPO models.Comment: 5 figures, 12 pages. AASTex preprint style. (In 2005, ApJ Let., 629, L33

The Dynamics of Sustained Reentry in a Loop Model with Discrete Gap Junction Resistance

Dynamics of reentry are studied in a one dimensional loop of model cardiac cells with discrete intercellular gap junction resistance ($R$). Each cell is represented by a continuous cable with ionic current given by a modified Beeler-Reuter formulation. For $R$ below a limiting value, propagation is found to change from period-1 to quasi-periodic ($QP$) at a critical loop length ($L_{crit}$) that decreases with $R$. Quasi-periodic reentry exists from $L_{crit}$ to a minimum length ($L_{min}$) that is also shortening with $R$. The decrease of $L_{crit}(R)$ is not a simple scaling, but the bifurcation can still be predicted from the slope of the restitution curve giving the duration of the action potential as a function of the diastolic interval. However, the shape of the restitution curve changes with $R$.Comment: 6 pages, 7 figure