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#### Confinement dynamics of a semiflexible chain inside nano-spheres

, Article Journal of Chemical Physics ; Volume 139, Issue 4 , 2013 ; 00219606 (ISSN) ; Heidari, M ; Eslami Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
2013

Abstract

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...

#### Application of perturbation theory to elastic models of DNA

, Article Proceedings of the 13th Regional Conference on Mathematical Physics, Antalya, Turkey ; October , 2013 , Pages 241-253 ; 9789814417525 (ISBN) ; Ejtehadi, M. R ; Sharif University of Technology
2013

Abstract

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

#### Contribution of nonlocal interactions to DNA elasticity

, Article Journal of Chemical Physics ; Volume 134, Issue 12 , 2011 ; 00219606 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
2011

Abstract

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

#### Nonlocal interactions in DNA molecules at nano-scale

, Article Scientia Iranica ; Volume 17, Issue 1 F , 2010 , Pages 23-26 ; 10263098 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
2010

Abstract

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

#### Asymmetric elastic rod model for DNA

, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 80, Issue 1 , 2009 ; 15393755 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
2009

Abstract

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

#### Stretching an anisotropic DNA

, Article Journal of Chemical Physics ; Volume 128, Issue 12 , 2008 ; 00219606 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
2008

Abstract

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

#### Definition of the persistence length in the coarse-grained models of DNA elasticity

, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 86, Issue 5 , November , 2012 ; 15393755 (ISSN) ; Eslami Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
2012

Abstract

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

#### Extreme bendability of DNA double helix due to bending asymmetry

, Article Journal of Chemical Physics ; Volume 143, Issue 10 , 2015 ; 00219606 (ISSN) ; Eslami Mossallam, B ; Naderi, S ; Ejtehadi, M. R ; Sharif University of Technology
American Institute of Physics Inc
2015

Abstract

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...

#### Development of a novel Peng–Robinson plus association equation of state for industrially important associating compounds

, Article Neural Computing and Applications ; Nov , 2015 , Pages 1-9 ; 09410643 (ISSN) ; Khadem Hamedani, B ; Sharif University of Technology
Springer-Verlag London Ltd
2015

Abstract

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...

#### Development of a novel Peng–Robinson plus association equation of state for industrially important associating compounds

, Article Neural Computing and Applications ; Volume 31, Issue 7 , 2019 , Pages 2107-2115 ; 09410643 (ISSN) ; Khadem Hamedani, B ; Sharif University of Technology
Springer London
2019

Abstract

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...

#### Wireless multicasting using network coding

, Article 2006 1st Workshop on Operator-Assisted (Wireless-Mesh) Community Networks, OpComm 2006, Berlin, 18 September 2006 through 19 September 2006 ; 2006 ; 1424406927 (ISBN); 9781424406920 (ISBN) ; Khalaj, B. H ; Sharif University of Technology
2006

Abstract

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...

#### Capacity of network coding for wireless multicasting

, Article IEEE Wireless and Microwave Technology Conference, WAMICON 2006, Clearwater Beach, FL, 4 December 2006 through 5 December 2006 ; 2006 ; 1424408482 (ISBN); 9781424408481 (ISBN) ; Khalaj, B. H ; Sharif University of Technology
2006

Abstract

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...

#### Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 94, Issue 6 , 2016 ; 15393755 (ISSN) ; Eslami Mossallam, B ; Ranjbar, H. F ; Ejtehadi, M. R ; Sharif University of Technology
American Physical Society
2016

Abstract

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...

#### Prosody generation in TTS system for Azeri

, Article IEEE/ASME International Conference on Advanced Intelligent Mechatronics, AIM, 6 July 2010 through 9 July 2010, Montreal, QC ; 2010 , Pages 1335-1338 ; 9781424480319 (ISBN) ; Zahir Azami, B ; Eslami, M ; Sharif University of Technology
2010

Abstract

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...

#### Study on optimized piled-raft foundations (PRF) performance with connected and non-connected piles- three case histories

, Article International Journal of Civil Engineering ; Volume 10, Issue 2 , 2012 , Pages 100-111 ; 17350522 (ISSN) ; Veiskarami, M ; Eslami, M. M ; Sharif University of Technology
2012

Abstract

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...

#### Evaluation of Electromagnetic Forces on three-phase Core-Type Power Transformer Windings during Inrush Current by FEM

, M.Sc. Thesis Sharif University of Technology ; Vakilian, Mehdi (Supervisor)
Abstract

Inrush Current is a form of over-current that occurs during energization of a transformer. For power transformers, the magnitude of the first peak of inrush current is initially several times the rated load current but slowly decreases until it finally reaches the normal exciting current value. This process typically takes several minutes. Time-variant axial and radial electromagnetic forces under inrush current and short-circuit current are calculated (by finite element method; FEM), and compared. An analytic method is presented for computation of inrush current in transformer. The simulation results obtained by this proposed method are compared with the measured values. A compact...

#### Joint Segmentation and Motion Estimation of Cardiac Cine MR Image Sequences

, Ph.D. Dissertation Sharif University of Technology ; Jahed, Mehran (Supervisor)
Abstract

In this study a variational framework for joint segmentation and motion estimation is provided for inspecting heart in Cine MRI sequences. In the first work, a functional including Mumford-Shah segmentation and optical flow based dense motion estimation is proposed. However, the motion estimation technique is replaced with warping estimation in the second work to reach in more regular and smooth motion field based on tracking of cardiac boundaries. Both of these functionals are then approximated by using the phase-field method to make them suitable for extracting Euler-Lagrange equations. Numerical solution to the optimization problem, when the time and image spaces are discretized by finite...

#### Contract Modifications for Controlling Unnecessary Work Scope Changes in Public Construction Projects in Iran

, M.Sc. Thesis Sharif University of Technology ; Eslami, Hossein (Supervisor)
Abstract

Variation in value and initial cost of construction contracts in many cases lead to considerably increasing the finalized price. These increases are sometimes so big enough that the 25 percent of limitation which could be added to contracts couldn't make them to be finalized and exploitable, so the necessity of a new contract sometimes up to 100 percent or even up to 200 percent of initial cost for completing the same project is inevitable. Although in some specific and rare cases we couldn't avoidance from these changes, but observing the growth of these changes in public construction projects of Iran increase the requirement of special attention in order to find the main causes, prevention...

#### Integrity Analysis in the Time-Delay Systems

, M.Sc. Thesis Sharif University of Technology ; Nobakhti, Amin (Supervisor)
Abstract

Integrity of closed-loop systems with integral action control is characterized by using a series of successively more difficult to obtain conditions: Integral Stabilizable (IS), Integral Controllable (IC), Integral Controllable with Integrity (ICI), and Decentralized Integral Controllability (DIC). The IS condition requires that for a Linear Time-Invariant (LTI) finitedimensional (FD) plant, G(s), one finds a stabilizing decentralized controller with integral action. For G(s) to be IC, in addition to being IS, one should be able to reduce the gain of

all control loops by the same factor from a finite value to (but not including) zero without introducing instabilities. ICI requires that...

all control loops by the same factor from a finite value to (but not including) zero without introducing instabilities. ICI requires that...

#### Designing and Implementing a Morphological Analyzer for Persian Language

, M.Sc. Thesis Sharif University of Technology ; Eslami, Moharram (Supervisor)
Abstract

In this thesis, the theoretical foundation, the way of implementation and the uses of Pars Morph, a Persian morphological analyzer is introduced. Pars Morph is a rule-based Persian morphological analysis system, which analyzes the internal structure of word in Persian and determines the grammatical category and function of the word parts. Pars Morph being in link with a lexicon covering about 45000 lexemes and based on morphological rules in Persian can analyze the structure of complex lexemes and their possible inflected forms and even out-of-lexicon words.

Accuracy rate of the first version of Pars Morph is about 95% which could be enhanced to 100% by applying the regulations on...

Accuracy rate of the first version of Pars Morph is about 95% which could be enhanced to 100% by applying the regulations on...