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    Monte Carlo Simulation of Asymmetric Elastic Rod Model and Calculation of
    Probability of Loop Formation

    , M.Sc. Thesis Sharif University of Technology Naderi, Mohammad Saber (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Abstract
    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... 

    A Thesis Submitted in Partial Fulfillment of the Requirement for the Degree of Master of Science in Electrical Engineering

    , M.Sc. Thesis Sharif University of Technology Mohammadi, Mahsa (Author) ; Jahed, Mehran (Supervisor) ; Motahhari, Abolfazl (Co-Advisor)
    Abstract
    Dnase I Hypersensitive Sites (DHSs) are known as comprehensive markers of DNA regulatory elements. The main function of regulatory elements is repressing or enhancing transcription of genes. Hence, the recruitment of the data is prevalent in many studies of genome. One of the applications of this data is to utilize it to predict active regulatory regions (Transcription Factor Binding Sites).There are different means to do this, divided in three major groups: first, the methods only use the number of DNase-seq reads that surround a candidate binding site. While robust, these methods do not reflect the shape of the signal. A second strategy uses a variety of approaches to model and identify... 

    Effects of Graphene Nanopores and Temperature on DNA Sequencing Using Molecular Dynamics

    , M.Sc. Thesis Sharif University of Technology Majdi, Amin (Author) ; Meghdari, Ali (Supervisor) ; Khoshnood, Atefeh (Co-Advisor)
    Abstract
    Distinguishing the structure of DNA is of outmost importance in the medicine and agriculture industry nowadays. Various methods have been suggested so far; however, high costs, incorrect results, and time-taking process are among main defects of them. Scientists try to find new ways for recognizing DNA structure and system in order to overcome such problems. One of these new methods is absorbing and passing DNA through Nano-pores in an electrolyte solution under the influence of an electrical field. The basis of this method is the ionized currents which occur due to the passing of DNA through Nano-pores. Because each DNA base pairs can form a barrier corresponding to a unique measured value,... 

    Coarse Grained Molecular Dynamics Simulation of DNA Nanomechanics

    , Ph.D. Dissertation Sharif University of Technology Fathizadeh, Arman (Author) ; Ejtehadi, Mohammad Reza (Supervisor) ; Khoei, Amir Reza (Co-Advisor)
    Abstract
    DNA is the most important biological molecule which contains all the genetic information of living organisms. The mechanical behavior of this molecule has a significant role on its functions. In this study, we introduce a model to for DNA nanomechanics. This model is called rigid base-pair chain in which every base pair is considered as a rigid object. The base-pairs only interact with their nearest neighbors via a harmonic potential. We have used this model to study the nanomechanical behavior of the DNA such as its bending, twisting, and stretching elasticity. Also the model was successful to predict the structure of DNA minicircles with extra amount of twist. After that we used the model... 

    Evaluation of Base Calling Methods in Next Generation Sequencing

    , M.Sc. Thesis Sharif University of Technology Gharibi, Hadi (Author) ; Hossein Khalaj, Babak (Supervisor) ; Motahhari, Abolfazl (Supervisor)
    Abstract
    In the mid twentieth century by discovering the existence of genetic strands and understanding their role in diseases and phenotypes of species, research initiated to decipher their content. Sequencing of the first human genome at early twenty-first century paved the way to study and even cure complex human deseases having genetic origin. Next Generation Sequencing (NGS) Technologies have significantly reduced the expenses and the timing complexity of DNA Sequencing and this has an improving trend. In this thesis, we evaluate Base Calling methods, a critical step in analyzing next generation sequencing information and deals with massive sequencing data. Base Calling tries to optimally detect... 

    Production and Purification of Recombinant Amylin Peptide and Investigating the Effects of Synthetic and Natural Products on Amyloid Fibril Formation

    , M.Sc. Thesis Sharif University of Technology Sherizadeh, Saied (Author) ; KAalhor, Hamid Reza (Supervisor) ; Matloubi Moghaddam, Firouz (Co-Advisor)
    Abstract
    What determines the function of a protein, after its synthesis by the ribosome, is its unique three dimensional structure. The unique structure of protein is achieved through process of folding which is detrimental to protein function. Although this unique structure is stable in a variety of situations, the protein may undergo conformational change, due to slight changes in physiological conditions, affecting the protein structure and function. In certain conditions, the conformational change brings about misfolding of the protein leading to protein aggregation. The protein aggregation can also result in amyloid formation in which a soluble protein is converted to fibrils with specific... 

    All-Atom Molecular Dynamics Simulation of DNA in Nanoscale

    , M.Sc. Thesis Sharif University of Technology Rezaei, Meisam (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Abstract
    Molecule of DNA is one of the most important biomolecule in cell which contains genetic information to supply the required proteins for body. Evidence shows prefered binding sequence for proteins exist to interact with proteins which this preference is determined not only by specefic chemical interactions between DNA and protein, but also specific suitable geometrical arrangements of DNA have important role to inding DNA oligomer and protein, such as winding DNA around histon to creating nucleosome is related to curvature and deformability of DNA. Thus knowing elastic behaviour and properties of DNA helps us to approach the answer of such questions. Despite the recent dvancement in labratory... 

    Synthesis of Graphene Nanosheets for Application in Biosensors

    , M.Sc. Thesis Sharif University of Technology Rahighi Yazdi, Reza (Author) ; Akhavan, Omid (Supervisor)
    Abstract
    Graphene, the newborn nanomaterial whose unique properties has extensively drawnattention of many scientists in the recent years, is an ideal candidate for sensing applications due to its exclusive properties like extremely high specific surface area, excellent electrical conductivity, andcapability of being easily functionalized. In this research, after reviewing the attempts already performed on detection of DNA, in order to detect the four bases of DNA (G, A, T, and C) via electrochemical approach, graphene nanosheets were synthesized by the popular Hummer’s method and were deposited on a graphite rod by electrophoretic deposition with a vertical preferred orientation. To eliminate the... 

    Stability Analysis of Hybrid Nanotubes Based on the Nonlocal Continuum Theories

    , M.Sc. Thesis Sharif University of Technology Rafati Heravi, Jacob (Author) ; Asghari, Mohsen (Supervisor)
    Abstract
    Strong van der Waals (vdW) potential fields of carbon nanotubes (CNTs) makes them capable to encapsulate some nanostructures inside their hollow space, which leads to the construction of new hybrid nanostructures under specific conditions. Carbon nano-peapods, carbon nanowires and the hybrid of DNA and CNT are the main categories of hybrid nanostructures of CNT. Characteristics of hybrid nanotubes are unique and different from those of CNT. In nanostructures, the lattice spacing between individual atoms is considerable with respect to the structural dimensions. Also, the range of internal characteristic length is relatively close to external ones. So that utilizing the classical continuum...