13,177 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
Effect of tartaric acid and phosphoric acid on the water resistance of magnesium oxychloride (MOC) cement
Magnesium oxychloride (MOC) cement is featured with high early strength, low thermal conductivity and low density, but is not widely applied in construction engineering due to its poor water resistance capability. This research has studied the effect of phosphoric acid and tartaric acid additions on the water resistance of MOC cement pastes, in which also reports the effects on setting time, hydration reactions, compressive strength, phase composition, thermal stability and microstructure. 1 wt% of phosphoric acid and tartaric acid additions can improve the water resistance and reduce thermal stability of MOC cement pastes, which is associated with formation of gel-like 5Mg(OH) 2 ·MgCl 2 ·8H 2 O. Moreover, these additions reduce the compressive strength and prolong the setting time of MOC cement pastes, as well as increase the total porosity, the volume fraction of gel pores (100 nm), however, decrease the volume fraction of small capillary pores (10–100 nm) of MOC cement pastes. These effects are caused by both additives but are most pronounced for MOC cement pastes containing phosphoric acid. In addition, 2Mg(OH) 2 ·MgCl 2 ·2H 2 O is a transitional phase in the formative stage of 5Mg(OH) 2 ·MgCl 2 ·8H 2 O in MOC cement
Event-driven simulations of a plastic, spiking neural network
We consider a fully-connected network of leaky integrate-and-fire neurons
with spike-timing-dependent plasticity. The plasticity is controlled by a
parameter representing the expected weight of a synapse between neurons that
are firing randomly with the same mean frequency. For low values of the
plasticity parameter, the activities of the system are dominated by noise,
while large values of the plasticity parameter lead to self-sustaining activity
in the network. We perform event-driven simulations on finite-size networks
with up to 128 neurons to find the stationary synaptic weight conformations for
different values of the plasticity parameter. In both the low and high activity
regimes, the synaptic weights are narrowly distributed around the plasticity
parameter value consistent with the predictions of mean-field theory. However,
the distribution broadens in the transition region between the two regimes,
representing emergent network structures. Using a pseudophysical approach for
visualization, we show that the emergent structures are of "path" or "hub"
type, observed at different values of the plasticity parameter in the
transition region.Comment: 9 pages, 6 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
Inheritance and identification of SCAR marker linked to bacterial wilt-resistance in eggplant
In the present work, the combinations (F1) were crossed between highly resistant and susceptible to bacterial wilt eggplant parents and its F2, BC1 segregation population plants were inoculated with race1 of Ralstonia solanacearum in greenhouse. In this paper, we reported that the inheritance of bacterial wilt resistance in eggplant was controlled by a single dominant gene showing Mendelian inheritance model. In addition, a 762 bp molecular marker linked to a bacterial wilt-resistant gene of eggplant was screenedby the bulked segregant analysis (BSA) method and sequence characterized amplified region (SCAR) marker linked to bacterial wilt-resistance gene was also obtained. The genetic distance between this marker and the resistance gene is 3.33 c
Generalised Kundt waves and their physical interpretation
We present the complete family of space-times with a non-expanding,
shear-free, twist-free, geodesic principal null congruence (Kundt waves) that
are of algebraic type III and for which the cosmological constant ()
is non-zero. The possible presence of an aligned pure radiation field is also
assumed. These space-times generalise the known vacuum solutions of type N with
arbitrary and type III with . It is shown that there
are two, one and three distinct classes of solutions when is
respectively zero, positive and negative. The wave surfaces are plane,
spherical or hyperboloidal in Minkowski, de Sitter or anti-de Sitter
backgrounds respectively, and the structure of the family of wave surfaces in
the background space-time is described. The weak singularities which occur in
these space-times are interpreted in terms of envelopes of the wave surfaces.Comment: 16 pages including 2 figures. To appear in Classical and Quantum Gra
Relating a reified adaptive network’s emerging behaviour based on hebbian learning to its reified network structure
Neuronal synchrony: peculiarity and generality
Synchronization in neuronal systems is a new and intriguing application of dynamical systems theory. Why are neuronal systems different as a subject for synchronization? (1) Neurons in themselves are multidimensional nonlinear systems that are able to exhibit a wide variety of different activity patterns. Their “dynamical repertoire” includes regular or chaotic spiking, regular or chaotic bursting, multistability, and complex transient regimes. (2) Usually, neuronal oscillations are the result of the cooperative activity of many synaptically connected neurons (a neuronal circuit). Thus, it is necessary to consider synchronization between different neuronal circuits as well. (3) The synapses that implement the coupling between neurons are also dynamical elements and their intrinsic dynamics influences the process of synchronization or entrainment significantly. In this review we will focus on four new problems: (i) the synchronization in minimal neuronal networks with plastic synapses (synchronization with activity dependent coupling), (ii) synchronization of bursts that are generated by a group of nonsymmetrically coupled inhibitory neurons (heteroclinic synchronization), (iii) the coordination of activities of two coupled neuronal networks (partial synchronization of small composite structures), and (iv) coarse grained synchronization in larger systems (synchronization on a mesoscopic scale
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