Sharif Digital Repository

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the... 

In this paper, we demonstrate the applicability of the perturbation methods to different elastic models of DNA molecule. Two different kinds of perturbation methods are presented to find a first approximation for the force-extension characteristic of DNA in the anisotropic wormlike chain model, and the persistence length of DNA in the asymmetric elastic rod model. In both cases we show that it is meaningful to use the perturbation theory, and a first-order calculation is enough to find the result with an acceptable accuracy  

A nonlocal harmonic elastic rod model is proposed to describe the elastic behavior of short DNA molecules. We show that the nonlocal interactions contribute to effective bending energy of the molecule and affect its apparent persistence length. It is also shown that the anomalous behavior which has been observed in all-atom molecular dynamic simulations [A. K. Mazur, Biophys. J. 134, 4507 (2006)] can be a consequence of both nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA  

In this paper, we try to explain the origin of the anomalous elastic behavior of nanometersized DNA molecules, which has been observed in all-atom molecular dynamic simulations [A.K. Mazur, Biophys. J. 2006]. It is shown that this anomalous behavior is a consequence of nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA. A nonlocal harmonic elastic rod model is proposed, which can successfully describe the elastic behavior of short DNA molecules  

In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure of the DNA molecule. We will show that the model can explain the high flexibility of DNA at small length scales, as well as kink formation at high deformation limit. © 2009 The American Physical Society  

We present a perturbation theory to find the response of an anisotropic DNA to the external tension. It is shown that the anisotropy has a nonzero but small contribution to the force-extension curve of the DNA. Thus an anisotropic DNA behaves like an isotropic one with an effective bending constant equal to the harmonic average of its soft and hard bending constants. © 2008 American Institute of Physics  

By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA  

Experimental data of the DNA cyclization (J-factor) at short length scales 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. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule... 

Cubic plus association (CPA) equations of state (EoSs) have found great interest in describing thermodynamic properties of associating fluids. In CPA EoSs, the association contribution proposed by Wertheim is added to cubic EoSs such as Soave–Redlich–Kwong (SRK) and Peng–Robinson (PR). In different developments of CPA EoSs, adjusting the pure component properties such as critical temperature and critical pressure in addition to the association parameters is proposed in some works in the literature. In this work, the PR EoS has been extended to water, phenol, and a number of alcohols (methanol up to dodecanol) by addition of the Wertheim association contribution. In contrast to other CPA... 

Cubic plus association (CPA) equations of state (EoSs) have found great interest in describing thermodynamic properties of associating fluids. In CPA EoSs, the association contribution proposed by Wertheim is added to cubic EoSs such as Soave–Redlich–Kwong (SRK) and Peng–Robinson (PR). In different developments of CPA EoSs, adjusting the pure component properties such as critical temperature and critical pressure in addition to the association parameters is proposed in some works in the literature. In this work, the PR EoS has been extended to water, phenol, and a number of alcohols (methanol up to dodecanol) by addition of the Wertheim association contribution. In contrast to other CPA... 

In this paper, we consider the network coding in networks with broadcast channels (called hypernetworks) as the first step for applying network coding to wireless networks. We first prove a Max-Flow Min-Cut theorem for such networks. While we propose an algorithm to achieve this bound, we will introduce new definitions and provide sufficient tools to extend many of the theorems stated for flows in wireline networks to the case of hypernetworks. As an example, we will extend the Max-Flow Min-Cut condition for feasibility of the point-to-point connection in wireline networks to the case of hypernetworks. Then, we will extend the algebraic approach of Koetter and Medard in [3] to the... 

In this paper, we consider the network coding in networks with broadcast channels (called hypernetworks) as the first step for applying network coding to wireless networks. We first prove a Max-Flow Min-Cut theorem for such networks. While we propose an algorithm to achieve this bound, we will introduce new definitions and provide sufficient tools to extend many of the theorems stated for flows in wireline networks to the case of hypernetworks. As an example, we will extend the Max-Flow Min-Cut condition for feasibility of the point-to-point connection in wireline networks to the case of hypernetworks. Then, we will extend the algebraic approach of Koetter and Medard in [3] to the... 

Using analytical approach and Monte Carlo (MC) simulations, we study the elastic behavior of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than three-dimensional (3D) conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in two dimensions, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the transient curvature increasing with a... 

Naturalness in Text-to-Speech (TTS) systems is very important in achieving high quality waveform. The naturalness of the waveform is highly correlated to phonetic coverage and prosodic features such as loudness, duration and pitch. This paper addresses the implementation of a prosodic TTS for Azeri. The TTS system to which the prosodic information is added, is a concatenative synthesizer based on diphones. For adding prosody and increasing naturalness, we have obtained a primary pitch curve for each word, based on the location of the stressed syllable. Also using sentence type effects, the final pitch contour has been modified. As far as we know, the output speech that is produced with this... 

It has been realized that the raft (mat) foundations are capable of bearing very large loads when they are assisted with a pile group. The contribution of both raft and piles to carry the surcharge loads is taken into account, considering the stiffness and strength of involved elements in the system, i.e. piles, raft and surrounding soil. The piles are usually required not to ensure the overall stability of the foundation but to act as settlement reducers. There is an alternative design in which, the piles are nonconnected from the raft to reduce the settlement, which are then known to be "settlement reducer non-connected piles" to increase the system stiffness. In this paper, two and three...