Search for: elastic-rod
M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza
DNA cyclization mechanism, has an important role in many biological processes such as gene regulation, DNA replication and recombination. In addition there are DNA-loops in Bacteria an around the Histones in Chromosomes in scale of 5-100 nm. We need to a appropriate model to study about bending and loop formationin in this important molecule which is able to describe elasticity properties of DNA.One of the most successful models, to describe the physical behaviour of a long DNA molecule, is the elastic rod model. In this model, DNA is considered as a ixable rod that its bending energy is isotropic. Asymmetric elastic rod model is another model to describe elasticity properties 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
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
Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 80, Issue 1 , 2009 ; 15393755 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
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
Monte Carlo Simulation of Asymmetric Elastic Rod Model and Calculation of
Sharif University of Technology
Ejtehadi, Mohammad Reza
Probability of Loop Formation
Sharply bent DNA plays an important role in many biological processes such as gene regulation, DNA replication and recombination. DNA cyclization experiments are well suited to study of sharply bent DNA, because they are sensitive to strongly bent conformations. Results of these experiments show that short length DNA molecules are more flexible than predicted by elastic rod model. Therefore, based on these experiments, the elastic rod model is not a suitable model for explaining elastic behavior of DNA at small lengths, although it can explain DNA elasticity at large length scales. Recently, it has been shown that a new model called asymmetric elastic rod model can explain high flexibility...
Article Scientia Iranica ; Volume 17, Issue 1 F , 2010 , Pages 23-26 ; 10263098 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
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
Article Journal of Chemical Physics ; Volume 134, Issue 12 , 2011 ; 00219606 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
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
3D dynamic modeling of powder forming processes via a simple and efficient node-to-surface contact algorithm, Article Applied Mathematical Modelling ; Volume 37, Issue 1-2 , 2013 , Pages 443-462 ; 0307904X (ISSN) ; Biabanaki, S. O. R ; Parvaneh, S. M ; Sharif University of Technology
In this paper, a simple and efficient contact algorithm is presented for the evaluation of density distribution in three-dimensional dynamic modeling of powder compaction processes. The contact node-to-surface algorithm is employed to impose the contact constraints in large deformation frictional contact, and the contact frictional slip is modified by the Coulomb friction law to simulate the frictional behavior between the rigid punch and the work-piece. The 3D nonlinear contact friction algorithm is employed together with a double-surface cap plasticity model within the framework of large finite element deformation in order to predict the non-uniform relative density distribution during the...