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    An ultrasensitive label free human papilloma virus DNA biosensor using gold nanotubes based on nanoporous polycarbonate in electrical alignment

    , Article Analytica Chimica Acta ; Volume 1048 , 2019 , Pages 31-41 ; 00032670 (ISSN) Shariati, M ; Ghorbani, M ; Sasanpour, P ; Karimizefreh, A ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    An impedimetric human papilloma virus (HPV) DNA biosensor based on gold nanotubes (AuNTs) in label free detection was materialized. The AuNTs decorated nanoporous polycarbonate (AuNTs-PC) template as biosensor electrode was fabricated by electrodeposition method. The single strand DNA (ss-DNA) probe was covalently immobilized onto the AuNTs-PC electrode. The hybridization of target sequences with the ss-DNA probe was observed by the electrochemical impedance spectroscopy (EIS). The biosensor showed high selectivity and could differentiate between the complementary, mismatch and non-complementary DNA sequences. The EIS measurements were matched to Randle's equivalent circuit. The... 

    Analysis of impedance stabilization of natural and metallic DNA molecules

    , Article 2012 19th Iranian Conference of Biomedical Engineering, ICBME 2012 ; 2012 , Pages 139-142 ; 9781467331302 (ISBN) Mohajeri, R ; Khakestar, A. S ; Hejazi, M. S ; Fardmanesh, M ; Sharif University of Technology
    2012
    Abstract
    In this work, we used λ-DNA to produce metallic DNA samples and we investigated the stabilization time of their impedances. This is in order to show that the DNA molecules can possibly be utilized as a frame for assembling the nanocircuits and as an electronic element as well, in nanoelectric devices. It has been shown that metallic DNA has lower stabilization time than natural DNA. As expected, it is shown that making the bundled DNA oriented, impacts their impedance stabilization. In order to find the characteristic impedance of the DNA molecules under direct current, we designed and made patterned electrodes to make electrical connections between the DNAs and the used current source. The... 

    Speeding up DNA sequence alignment by optical correlator

    , Article Optics and Laser Technology ; Volume 108 , 2018 , Pages 124-135 ; 00303992 (ISSN) Mozafari, F ; Babashah, H ; Koohi, S ; Kavehvash, Z ; Sharif University of Technology
    Elsevier Ltd  2018
    Abstract
    In electronic computers, extensive amount of computations required for searching biological sequences in big databases leads to vast amount of energy consumption for electrical processing and cooling. On the other hand, optical processing is much faster than electrical counterpart, due to its parallel processing capability, at a fraction of energy consumption level and cost. In this regard, this paper proposes a correlation-based optical algorithm using metamaterial, taking advantages of optical parallel processing, to efficiently locate the edits as a means of DNA sequence comparison. Specifically, the proposed algorithm partitions the read DNA sequence into multiple overlapping intervals,... 

    Nonlocal interactions in DNA molecules at nano-scale

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

    Designing a polymerase chain reaction device working with radiation and convection heat transfer

    , Article 2017 International Conference on Nanomaterials and Biomaterials, ICNB 2017, 11 December 2017 through 13 December 2017 ; Volume 350, Issue 1 , 2018 ; 17578981 (ISSN) Madadelahi, M ; Kalan, K ; Shamloo, A ; Sharif University of Technology
    Institute of Physics Publishing  2018
    Abstract
    Gene proliferation is vital for infectious and genetic diseases diagnosis from a blood sample, even before birth. In addition, DNA sequencing, genetic finger-print analyzing, and genetic mutation detecting can be mentioned as other procedures requiring gene reproduction. Polymerase chain reaction, briefly known as PCR, is a convenient and effective way to accomplish this task; where the DNA containing sample faces three temperature phases alternatively. These phases are known as denaturation, annealing, and elongation/extension which in this study -regarding the type of the primers and the target DNA sequence- are set to occur at 95, 58, and 72 degrees of Celsius. In this study, a PCR device... 

    The field effect transistor DNA biosensor based on ITO nanowires in label-free hepatitis B virus detecting compatible with CMOS technology

    , Article Biosensors and Bioelectronics ; Volume 105 , 15 May , 2018 , Pages 58-64 ; 09565663 (ISSN) Shariati, M ; Sharif University of Technology
    Elsevier Ltd  2018
    Abstract
    In this paper the field-effect transistor DNA biosensor for detecting hepatitis B virus (HBV) based on indium tin oxide nanowires (ITO NWs) in label free approach has been fabricated. Because of ITO nanowires intensive conductance and functional modified surface, the probe immobilization and target hybridization were increased strongly. The high resolution transmission electron microscopy (HRTEM) measurement showed that ITO nanowires were crystalline and less than 50 nm in diameter. The single-stranded hepatitis B virus DNA (SS-DNA) was immobilized as probe on the Au-modified nanowires. The DNA targets were measured in a linear concentration range from 1fM to 10 µM. The detection limit of... 

    Simulation of DNA electrophoresis through microstructures

    , Article Electrophoresis ; Volume 28, Issue 3 , 2007 , Pages 301-308 ; 01730835 (ISSN) Maleki Jirsaraei, N ; Sarbolouki, M. N ; Rouhani, S ; Sharif University of Technology
    2007
    Abstract
    The dependence of the mobility of DNA molecules through an hexagonal array of micropillars on their length and the applied electric field was investigated and it was found that mobility is a nonmonotonic function of their length. Results also revealed that the size dependence of the DNA mobility depends on the applied electric field and there is a crossover around E ≈ 25 V/cm for the mobility of λ-DNA and T4-DNA. These observations are explained in terms of the diffusion process inside the structure affected by the solvent and are modeled using the Langevin and its corresponding Fokker-Planck equations. The phenomenon is generalized under three regimes in a phase diagram relating the... 

    Two new methods for DNA splice site prediction based on neuro-fuzzy network and clustering

    , Article Neural Computing and Applications ; Volume 23, Issue SUPPL1 , 2013 , Pages 407-414 ; 09410643 (ISSN) Moghimi, F ; Manzuri Shalmani, M. T ; Khaki Sedigh, A ; Kia, M ; Sharif University of Technology
    2013
    Abstract
    Nowadays, genetic disorders, like cancer and birth defects, are a great threat to human life. Since the first noticing of these types of diseases, many efforts have been made and researches performed in order to recognize them and find a cure for them. These disorders affect genes and they appear as abnormal traits in a genetic organism. In order to recognize abnormal genes, we need to predict splice sites in a DNA signal; then, we can process the genetic codes between two continuous splice sites and analyze the trait that it represents. In addition to abnormal genes and their consequent disorders, we can also identify other normal human traits like physical and mental features. So the... 

    Genome-Wide Association Studies: Information Theoretic Limits of Reliable Learning

    , Article 2018 IEEE International Symposium on Information Theory, ISIT 2018, 17 June 2018 through 22 June 2018 ; Volume 2018-June , 2018 , Pages 2231-2235 ; 21578095 (ISSN); 9781538647806 (ISBN) Tahmasebi, B ; Maddah Ali, M. A ; Motahari, A. S ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2018
    Abstract
    In the problems of Genome-Wide Association Study (GWAS), the objective is to associate subsequences of individual's genomes to the observable characteristics called phenotypes. The genome containing the biological information of an individual can be represented by a sequence of length G. Many observable characteristics of the individuals can be related to a subsequence of a given length L, called causal subsequence. The environmental affects make the relation between the causal subsequence and the observable characteristics a stochastic function. Our objective in this paper is to detect the causal subsequence of a specific phenotype using a dataset of N individuals and their observed... 

    Information theory of mixed population genome-wide association studies

    , Article 2018 IEEE Information Theory Workshop, ITW 2018, 25 November 2018 through 29 November 2018 ; 2019 ; 9781538635995 (ISBN) Tahmasebi, B ; Maddah Ali, M. A ; Motahari, S. A ; Sun Yat-Sen University ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2019
    Abstract
    Genome-Wide Association Study (GWAS) addresses the problem of associating subsequences of individuals' genomes to the observable characteristics called phenotypes. In a genome of length G, it is observed that each characteristic is only related to a specific subsequence of it with length L, called the causal subsequence. The objective is to recover the causal subsequence, using a dataset of N individuals' genomes and their observed characteristics. Recently, the problem has been investigated from an information theoretic point of view in [1]. It has been shown that there is a threshold effect for reliable learning of the causal subsequence at Gh ( N L/G ) by characterizing the capacity of... 

    Stretching an anisotropic DNA

    , Article Journal of Chemical Physics ; Volume 128, Issue 12 , 2008 ; 00219606 (ISSN) Eslami Mossallam, B ; 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  

    Contribution of nonlocal interactions to DNA elasticity

    , Article Journal of Chemical Physics ; Volume 134, Issue 12 , 2011 ; 00219606 (ISSN) Eslami Mossallam, B ; 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  

    Meta-aligner: long-read alignment based on genome statistics

    , Article BMC Bioinformatics ; Volume 18, Issue 1 , 2017 ; 14712105 (ISSN) Nashta Ali, D ; Aliyari, A ; Ahmadian Moghadam, A ; Edrisi, M. A ; Motahari, S. A ; Khalaj, B. H ; Sharif University of Technology
    Abstract
    Background: Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners. Results: We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates... 

    Self-assembly of tryptophan-capped gold nanoparticles onto DNA network template

    , Article Journal of Dispersion Science and Technology ; Volume 30, Issue 2 , 2009 , Pages 254-258 ; 01932691 (ISSN) Sheikholeslami, Z ; Vosoughi, M ; Alemsadeh, I ; Sharif University of Technology
    2009
    Abstract
    In this study, a simple route to the formation of DNA-gold complex has been reported, using immobilized DNA as a template. The nanoporous gold films have been prepared by the electrostatic self assembly of gold nanoparticles capped with tryptophan. Tryptophan would improve surface properties of gold nanoparticles for strongly attaching to DNA. Fourier transform infrared spectroscopy confirmed that gold nanoparticles have been capped by tryptophan. Also measured zeta potential shows that there are positive charges on the surface of gold nanoparticles. Investigations by atomic force microscopy substantially confirm that tryptophan-capped gold nanoparticles can be bonded to DNA template... 

    Fabrication of metal nanowires based on self assembly of tryptophan-capped gold nanoparticle onto DNA network template

    , Article International Journal of Nanotechnology ; Volume 6, Issue 10-11 , 2009 , Pages 1041-1049 ; 14757435 (ISSN) Sheikholeslami, Z ; Vossoughi, M ; Alemzadeh, I ; Sharif University of Technology
    2009
    Abstract
    In this study, synthesis of conductive metal nanowires by using aligned and immobilised DNA strand on solid substrate is reported. The nanoporous gold film was prepared by electrostatic self assembly of gold nanoparticles capped with tryptophan. Tryptophan would improve surface properties of gold nanoparticles for strongly attaching to DNA. Fourier transform infrared (FTIR) spectroscopy confirmed that gold nanoparticles have been capped by tryptophan. Also measured zeta potential shows that there are positive charges on the surface of gold nanoparticles. Investigations by AFM observati on substantially confirm that tryptophan-capped gold nanoparticles can be bonded to DNA template... 

    OptCAM: An ultra-fast all-optical architecture for DNA variant discovery

    , Article Journal of Biophotonics ; Volume 13, Issue 1 , August , 2020 Maleki, E ; Koohi, S ; Kavehvash, Z ; Mashaghi, A ; Sharif University of Technology
    Wiley-VCH Verlag  2020
    Abstract
    Nowadays, the accelerated expansion of genetic data challenges speed of current DNA sequence alignment algorithms due to their electrical implementations. Essential needs of an efficient and accurate method for DNA variant discovery demand new approaches for parallel processing in real time. Fortunately, photonics, as an emerging technology in data computing, proposes optical correlation as a fast similarity measurement algorithm; while complexity of existing local alignment algorithms severely limits their applicability. Hence, in this paper, employing optical correlation for global alignment, we present an optical processing approach for local DNA sequence alignment to benefit both... 

    Investigation of a protein complex network

    , Article European Physical Journal B ; Volume 41, Issue 1 , 2004 , Pages 113-121 ; 14346028 (ISSN) Mashaghi, A. R ; Ramezanpour, A ; Karimipour, V ; Sharif University of Technology
    2004
    Abstract
    The budding yeast Saccharomyces cerevisiae is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual interactions between proteins) has been analyzed. In this paper we study the structure of the yeast protein complex network in which weighted edges between complexes represent the number of shared proteins. It is found that the network of protein complexes is a small world network with scale free behavior for many of its distributions. However we find that there are no strong correlations between the weights and degrees of neighboring complexes. To reveal... 

    Simulation of mixed electroosmotic/pressure-driven flows by utilizing dissipative particle dynamics

    , Article Microfluidics and Nanofluidics ; Vol. 17, issue. 1 , July , 2014 , pp. 199-215 ; ISSN: 16134982 Mehboudi, A ; Noruzitabar, M ; Mehboudi, M ; Sharif University of Technology
    Abstract
    In this paper, we present an extension of dissipative particle dynamics method in order to study the mixed electroosmotic/pressure-driven micro- or nano-flows. This method is based on the Poisson-Boltzmann equation and has a great potential to resolve the electric double layer (EDL). Hence, apart from studying the bulk flow, it also provides a strong capability in order to resolve the complex phenomena occur inside the EDL. We utilize the proposed method to study the pure electroosmotic and also the mixed electroosmotic/pressure-driven flow through the straight micro-/nano-channels. The obtained results are in good agreement with the available analytical solutions. Furthermore, we study 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) Eslami-Mossallam, B ; 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  

    DNA-decorated graphene nanomesh for detection of chemical vapors

    , Article Applied Physics Letters ; Volume 103, Issue 18 , 2013 ; 00036951 (ISSN) Esfandiar, A ; Kybert, N. J ; Dattoli, E. N ; Hee Han, G ; Lerner, M. B ; Akhavan, O ; Irajizad, A ; Charlie Johnson, A. T ; Sharif University of Technology
    2013
    Abstract
    The promise of graphene for use as a vapor sensor motivated exploration of the vapor responses of graphene nanomesh (GNM) functionalized with single stranded DNA. Devices detected different vapor types, including carboxylic acids, aldehydes, organophosphates, and explosives. As-fabricated GNM field effect transistors (FETs) had larger vapor responses than standard graphene FETs due to the effect of oxidized edges and lattice defects. DNA-GNM devices discriminated between homologous species with detection limits of a few parts per million, with fast response and recovery. Responses varied significantly when the base sequence of the DNA was changed, making the sensor class an intriguing...