Extreme bendability of DNA double helix due to bending asymmetry

Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model which is in excellent agreement with recent experimental data.Comment: 8 pages, 9 figure

Meso-scale modelling of compressive fracture in concrete with irregularly shaped aggregates

This paper presents a meso-scale modelling framework to investigate the fracture process in concrete subjected to uniaxial and biaxial compression accounting for its mesostructural characteristics. 3D mesostructure of concrete consisting of coarse aggregates, mortar and interfacial transition zone between them was developed using an in-house code based on the Voronoi tessellation and splining method, which enables to generate the realistic-look aggregates with controllable structural features such as content, location, size and shape. Based on the generated 3D mesostructure, the concrete damage plasticity approach was employed to simulate the compressive fracture behaviour of concrete in terms of crack morphology and stress-strain response against the shape parameters of aggregate. Results indicate that the shape of aggregate has a negligible effect on compressive strength of concrete, which is highly associated with the random location and size distribution of aggregate. The aggregate irregularity has a significant influence on crack initiation and growth of concrete

Geometric approach to nonlinear coherent states using the Higgs model for harmonic oscillator

In this paper, we investigate the relation between the curvature of the physical space and the deformation function of the deformed oscillator algebra using non-linear coherent states approach. For this purpose, we study two-dimensional harmonic oscillators on the flat surface and on a sphere by applying the Higgs modell. With the use of their algebras, we show that the two-dimensional oscillator algebra on a surface can be considered as a deformed one-dimensional oscillator algebra where the effect of the curvature of the surface is appeared as a deformation function. We also show that the curvature of the physical space plays the role of deformation parameter. Then we construct the associated coherent states on the flat surface and on a sphere and compare their quantum statistical properties, including quadrature squeezing and antibunching effect.Comment: 12 pages, 7 figs. To be appeared in J. Phys.

Nano TiO2 as an efficient and reusable heterogeneous catalyst for the synthesis of 5-substituted 1H-tetrazoles

Nano TiO2 is an effective heterogeneous catalyst for the [2+3] cycloaddition of sodium azide with nitriles to afford 5-substituted 1H-tetrazoles in good yields. This method has the advantages of high yields, simple methodology and easy work-up. The catalyst is recovered and reused for several cycles with consistent activity. Keywords: 5-substituted 1H-tetrazole, [2+3] cycloaddition, nano TiO2, heterogeneous catalys