17,129 research outputs found
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 ( base pairs). We show that, at physiological
conditions, opening in superhelical DNA is strongly cooperative with average
bubble sizes of 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
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
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
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
Equilibrium Properties of Temporally Asymmetric Hebbian Plasticity
A theory of temporally asymmetric Hebb (TAH) rules which depress or
potentiate synapses depending upon whether the postsynaptic cell fires before
or after the presynaptic one is presented. Using the Fokker-Planck formalism,
we show that the equilibrium synaptic distribution induced by such rules is
highly sensitive to the manner in which bounds on the allowed range of synaptic
values are imposed. In a biologically plausible multiplicative model, we find
that the synapses in asynchronous networks reach a distribution that is
invariant to the firing rates of either the pre- or post-synaptic cells. When
these cells are temporally correlated, the synaptic strength varies smoothly
with the degree and phase of synchrony between the cells.Comment: 3 figures, minor corrections of equations and tex
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
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