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

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 ($\Lambda_c$) 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 $\Lambda_c$ and type III with $\Lambda_c=0$. It is shown that there are two, one and three distinct classes of solutions when $\Lambda_c$ 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

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