Search for: dna-molecules
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
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
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
Article 2019 IEEE International Symposium on Information Theory, ISIT 2019, 7 July 2019 through 12 July 2019 ; Volume 2019-July , 2019 , Pages 171-175 ; 21578095 (ISSN); 9781538692912 (ISBN) ; Maddah Ali, M. A ; Abolfazl Motahari, S ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc 2019
Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we introduce the problem of private DNA sequencing, where the goal is to keep the DNA sequence private to the sequencer. We propose an architecture, where the task of reading fragments of DNA and the task of DNA assembly are separated, the former is done at the sequencer(s), and the later is completed at a local trusted data collector. To satisfy the privacy constraint at the sequencer and reconstruction condition at the data collector, we create an...
Design, Simulation and Fabrication of Integrated Centrifugal Microfluidic Platform for Separation and Lysis of Circulating Tumor Cells, M.Sc. Thesis Sharif University of Technology ; Shamloo, Amir ; Firoozbakhsh, Keykhosrow
Cancer diagnosis area has recently been in the limelight of the medical research and there exist an unremitting focus on the devices & technologies which enable cancer detection in its victims. Lately a genius diagnostic method based on isolation and entrapment of circulating tumor cells has been developed which pave the path for cancer identification. These circulating cells which are detached from the primary tumor are carried out through body by means of circulation system. They play key role in phenomenon called metastasis. Separating these rare cells from multifarious background blood cells, assessing their quantity can supply valuable information on the stage of disease as well as its...
Ph.D. Dissertation Sharif University of Technology ; Parsafar, Gholam Abbas
In this thesis, the molecular dynamics simulation is used to investigate the melting transition of B-DNA molecule, via of configurational entropy, the fraction of broken hydrogen bonds (f-curve) and hydrogen bonding energy.We have performed molecular dynamics simulation on Drew-Dickerson oligomer with sequence of (CGCGAATTGCGC) at different temperatures, within the range of 280-400 K with the 20 K intervals. The simulation was done in two different mediums (pure water and 1 M NaCl), to see influences of water and salt in stabilizing the DNA molecule. At each temperature, configurational entropy is calculated by the Schlitter’s formula, using the Cartesian coordinate of all atoms. So, in each...
Design, Simulation and Construction of a Rapid Gene Amplification Microfluidic Device Using Polymerase Chain Reaction (PCR) Method, M.Sc. Thesis Sharif University of Technology ; Shamloo, Amir
Polymerase chain reaction method is a conventional method for obtaining multiple copies of a specified segment in the DNA molecule and to amplify the DNA molecule itself. Therefore, this method has been of paramount importance in different fields of research and has been applied for different applications. PCR requires thermal cycling, or repeated temperature changes between two or three discrete temperatures to amplify specific nucleic acid target sequences. To achieve such thermal cycling, conventional bench-top thermal cyclers generally use a metal heating block powered by Peltier elements or benefit from forced convection heat transfer. Although efforts have been made in order to reduce...
Study, Optimization and Construction of a Microfluidic Gene Amplification Device by Using Thin Film Layer Method, M.Sc. Thesis Sharif University of Technology ; Vosoughi, Manouchehr ; Alemzadeh, Iran ; Shamloo, Amir
Polymerase Chain Reaction (PCR) is a process in which a special piece of a gene is amplified millions of times over a short period. This method has been of paramount importance in different fields of research and has been applied for different applications. PCR requires thermal cycling, or repeated temperature changes between two or three discrete temperatures to amplify specific nucleic acid target sequences. To achieve such thermal cycling, conventional bench-top thermal cyclers generally use a metal heating block powered by Peltier elements or benefit from forced convection heat transfer. Due to the fact that these methods are time consuming, it seems that design and fabrication of a fast...
M.Sc. Thesis Sharif University of Technology ; Akbari, Mahmood ; Fotowat-Ahmady, Ali
This paper presents a scalable and ultrasensitive magnetic biosensing scheme based on on-chip LC resonance frequency-shifting. The sensor transducer gain is demonstrated as being location-dependent on the sensing surface and proportional to the local polarization magnetic field strength |B|2 generated by the sensing inductor. To improve the gain uniformity, a periodic coil is proposed as a substitution for the standard process coil. As an implementation example, the circuit is designed in a 65nm CMOS process. The spatially uniform sensor gain of the array is verified by COMSOL simulations. Overall, the presented sensor demonstrates an improvement in the uniformity of the inductor’s magnetic...
M.Sc. Thesis Sharif University of Technology ; Hossein Khalaj, Babak
the purpose of this research is to construct the facial image of a person from corresponding DNA. In this problem, we have a set of DNAs and facial images and we want to find the relation between the DNA and the features of facial images.using this relation we can find the facial Image of a person using the DNA. for this purpose we should first extract the features of faces that have the most variation among the population. by studying the feature extraction methods in this field, we borrow the deep neural network method that is used in face recognition fields.we found significant relations between DNA and extracted features from this network. finally using this relation we can predict the...
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 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