Bubble statistics and positioning in superhelically stressed DNA

We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our results are obtained from transfer-matrix solutions of the Zimm-Bragg model for unconstrained DNA and of a self-consistent linearization of the Benham model for superhelical DNA. The numerical efficiency of our method allows for the analysis of entire genomes and of random sequences of corresponding length ($10^6-10^9$ base pairs). We show that, at physiological conditions, opening in superhelical DNA is strongly cooperative with average bubble sizes of $10^2-10^3$ base pairs (bp), and orders of magnitude higher than in unconstrained DNA. In heterogeneous sequences, the average degree of base-pair opening is self-averaging, while bubble localization and statistics are dominated by sequence disorder. Compared to random sequences with identical GC-content, genomic DNA has a significantly increased probability to open large bubbles under superhelical stress. These bubbles are frequently located directly upstream of transcription start sites.Comment: to be appeared in Physical Review

Large-Scale Structure Shocks at Low and High Redshifts

Cosmological simulations show that, at the present time, a substantial fraction of the gas in the intergalactic medium (IGM) has been shock-heated to T>10^5 K. Here we develop an analytic model to describe the fraction of shocked, moderately overdense gas in the IGM. The model is an extension of the Press & Schechter (1974) description for the mass function of halos: we assume that large-scale structure shocks occur at a fixed overdensity during nonlinear collapse. This in turn allows us to compute the fraction of gas at a given redshift that has been shock-heated to a specified temperature. We show that, if strong shocks occur at turnaround, our model provides a reasonable description of the temperature distribution seen in cosmological simulations at z~0, although it does overestimate the importance of weak shocks. We then apply our model to shocks at high redshifts. We show that, before reionization, the thermal energy of the IGM is dominated by large-scale structure shocks (rather than virialized objects). These shocks can have a variety of effects, including stripping ~10% of the gas from dark matter minihalos, accelerating cosmic rays, and creating a diffuse radiation background from inverse Compton and cooling radiation. This radiation background develops before the first stars form and could have measurable effects on molecular hydrogen formation and the spin temperature of the 21 cm transition of neutral hydrogen. Finally, we show that shock-heating will also be directly detectable by redshifted 21 cm measurements of the neutral IGM in the young universe.Comment: 12 pages, 8 figures, submitted to Ap

Characterising epithelial tissues using persistent entropy

In this paper, we apply persistent entropy, a novel topological statistic, for characterization of images of epithelial tissues. We have found out that persistent entropy is able to summarize topological and geometric information encoded by \alpha-complexes and persistent homology. After using some statistical tests, we can guarantee the existence of significant differences in the studied tissues.Comment: 12 pages, 7 figures, 4 table

Theoretical modeling and numerical simulation of seismic motions at seafloor

This paper proposes a modelling and simulation method of seafloor seismic motions on offshore sites, which are composed of the base rock, the porous soil layers and the seawater layer, based on the fundamental hydrodynamics equations and one-dimensional wave propagation theory. The base rock motions are assumed to consist of P- and S-waves and are modelled by the seismological model in southwest of Western Australia (SWWA). The transfer functions of the offshore site are calculated by incorporating the derived dynamic-stiffness matrix of seawater layer into the total stiffness matrix. The effect of water saturation on the P-wave velocity and Poisson’s ratio of subsea soil layers are also considered in the model. Both onshore and seafloor seismic motions are stochastically simulated. The comparison results show that the seafloor vertical motions are significantly suppressed near the P-wave resonant frequencies of the upper seawater layer, which makes their intensities much lower than the onshore vertical motions. Owing to their compliance with the characteristics of available seafloor earthquake recordings, the proposed method can be used to simulate seafloor motions for offshore structural seismic analyses

Seismic fragility analysis of reinforced concrete bridges with chloride induced corrosion subjected to spatially varying ground motion

This paper studies the time-dependent seismic fragility of reinforced concrete bridges with chloride induced corrosion under spatially varying ground motions. The time-varying characteristic of the chloride corrosion current density and the uncertainties related to the structural, material and corrosion parameters are both considered in the probabilistic finite element modeling of the example RC bridge at different time steps during its life-cycle. Spatially varying ground motions at different bridge supports are stochastically simulated and used as inputs in the fragility analysis. Seismic fragility curves of the corroded RC bridge at different time steps are generated using the probabilistic seismic demand analysis (PSDA) method. Numerical results indicate that both chloride induced corrosion and ground motion spatial variations have a significant effect on the bridge structural seismic fragility. As compared to the intact bridge, the mean peak ground accelerations (PGAs) of the fragility curves of the RC bridge decrease by approximately 40% after 90 years since the initiation of corrosion. Moreover, the effect of ground motion spatial variations changes along with the process of chloride induced corrosion owing to the structural stiffness degradation. Neglecting seismic ground motion spatial variations may not lead to an accurate estimation of the lifetime seismic fragility of RC bridges with chloride induced corrosion

Temperature dependence of interlayer coupling in perpendicular magnetic tunnel junctions with GdOx barriers

Perpendicular magnetic tunnel junctions with GdOX tunneling barriers have shown a unique voltage controllable interlayer magnetic coupling effect. Here we investigate the quality of the GdOX barrier and the coupling mechanism in these junctions by examining the temperature dependence of the tunneling magnetoresistance and the interlayer coupling from room temperature down to 11 K. The barrier is shown to be of good quality with the spin independent conductance only contributing a small portion, 14%, to the total room temperature conductance, similar to AlOX and MgO barriers. The interlayer coupling, however, shows an anomalously strong temperature dependence including sign changes below 80 K. This non-trivial temperature dependence is not described by previous models of interlayer coupling and may be due to the large induced magnetic moment of the Gd ions in the barrier.Comment: 14 pages, 4 figure

Robustness and Enhancement of Neural Synchronization by Activity-Dependent Coupling

We study the synchronization of two model neurons coupled through a synapse having an activity-dependent strength. Our synapse follows the rules of Spike-Timing Dependent Plasticity (STDP). We show that this plasticity of the coupling between neurons produces enlarged frequency locking zones and results in synchronization that is more rapid and much more robust against noise than classical synchronization arising from connections with constant strength. We also present a simple discrete map model that demonstrates the generality of the phenomenon.Comment: 4 pages, accepted for publication in PR

Why does a metal-superconductor junction have a resistance?

This is a tutorial article based on a lecture delivered in June 1999 at the NATO Advanced Study Institute in Ankara. The phenomenon of Andreev reflection is introduced as the electronic analogue of optical phase-conjugation. In the optical problem, a disordered medium backed by a phase-conjugating mirror can become completely transparent. Yet, a disordered metal connected to a superconductor has the same resistance as in the normal state. The resolution of this paradox teaches us a fundamental difference between phase conjugation of light and electrons.Comment: 12 pages, 5 postscript figures [v2: all figures inline

X-ray Emission of Baryonic Gas in the Universe: Luminosity-Temperature Relationship and Soft-Band Background

We study the X-ray emission of baryon fluid in the universe using the WIGEON cosmological hydrodynamic simulations. It has been revealed that cosmic baryon fluid in the nonlinear regime behaves like Burgers turbulence, i.e. the fluid field consists of shocks. Like turbulence in incompressible fluid, the Burgers turbulence plays an important role in converting the kinetic energy of the fluid to thermal energy and heats the gas. We show that the simulation sample of the $\Lambda$CDM model without adding extra heating sources can fit well the observed distributions of X-ray luminosity versus temperature ($L_{\rm x}$ vs. $T$) of galaxy groups and is also consistent with the distributions of X-ray luminosity versus velocity dispersion ($L_{\rm x}$ vs. $\sigma$). Because the baryonic gas is multiphase, the $L_{\rm x}-T$ and $L_{\rm x}-\sigma$ distributions are significantly scattered. If we describe the relationships by power laws $L_{\rm x}\propto T^{\alpha_{LT}}$ and $L_{\rm x}\propto \sigma^{\alpha_{LV}}$, we find $\alpha_{LT}>2.5$ and $\alpha_{LV}>2.1$. The X-ray background in the soft $0.5-2$ keV band emitted by the baryonic gas in the temperature range $10^5<T<10^7$ K has also been calculated. We show that of the total background, (1) no more than 2% comes from the region with temperature less than $10^{6.5}$ K, and (2) no more than 7% is from the region of dark matter with mass density $\rho_{\rm dm}<50 \bar{\rho}_{\rm dm}$. The region of $\rho_{\rm dm}>50\bar{\rho}_{\rm dm}$ is generally clustered and discretely distributed. Therefore, almost all of the soft X-ray background comes from clustered sources, and the contribution from truly diffuse gas is probably negligible. This point agrees with current X-ray observations.Comment: 32 pages including 14 figures and 2 tables. Final version for publication in Ap