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    DNA Classification Using Optical Processing based on Alignment-free Methods

    , M.Sc. Thesis Sharif University of Technology Kalhor, Reza (Author) ; Koohi, Somayyeh (Supervisor)
    In this research, an optical processing method for DNA classification is presented in order to overcome the problems in the previous methods. With improving in the operational capacity of the sequencing process, which has increased the number of genomes, comparing sequences with a complete database of genomes is a serious challenge to computational methods. Most current classification programs suffer from either slow classification speeds, large memory requirements, or both. To achieve high speed and accuracy at the same time, we suggest using optical processing methods. The performance of electronic processing-based computing, especially in the case of large data processing, is usually... 

    Design and Analysis of DNA Sequencing Methods

    , Ph.D. Dissertation Sharif University of Technology Nashtaali, Damoun (Author) ; Hossein Khalaj, Babak (Supervisor) ; Abolfazl, Motahhari (Co-Advisor)
    A DNA sequence is the information source of living kinds. Information of this sequence is at its constructing bases which has four different kinds. Sequencing DNA is necessary to resolve this information. At 1977, Sanger reported the first sequence of a DNA string. Recently, a human DNA string can be sequenced with 1000 in ~2 hours. Knowing DNA sequence helps to find function of each organism, predict and cure diseases (especially in cancer). Next Generation Sequencing (NGS) methods are based on shot-gun sequencing which fragmentize DNA strings and sequence each fragment. After sequencing, processing information of DNA is performed by the processing machine in two different types: alignment... 

    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)
    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... 

    Modeling Two-Dimensional Face from DNA Using the Face Embedding Approach in Deep Learning

    , M.Sc. Thesis Sharif University of Technology Mirzaei, Mohammad Amin (Author) ; Hossein Khalaj, Babak (Supervisor)
    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... 

    Design, Simulation and Fabrication of Integrated Centrifugal Microfluidic Platform for Separation and Lysis of Circulating Tumor Cells

    , M.Sc. Thesis Sharif University of Technology Momeni, Maede (Author) ; Shamloo, Amir (Supervisor) ; Firoozbakhsh, Keykhosrow (Supervisor)
    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... 

    Design and Implementation of DNA Pattern Recognition Algorithm Utilizing Optical Coding Method

    , M.Sc. Thesis Sharif University of Technology Maleki, Ehsan (Author) ; Koohi, Somayyeh (Supervisor) ; Kavehvash, Zahra (Supervisor)
    In this research, two novel optical methods have been proposed for DNA local sequence alignment. The proposed methods benefit from algorithms and methods in computer field and ability of parallelism in optical wave to achieve a low-cost process and propose an easy understanding output in DNA local sequence alignment procedure. The first method is built upon moiré matching technique which is extended by proposed HAPPOC scheme using amplitude, phase, and polarization of optical wave. For analyzing the extended moiré output, a novel 3D Artificial Neural Network is designed and developed by optical structure. The second structure, as named HAWPOD method, is based on DV-Curve method. The HAWPOD... 

    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)
    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... 

    Design and Simulation of CMOS Based Magnetic Sensor for Biosensing Applications

    , M.Sc. Thesis Sharif University of Technology Mafi, Alireza (Author) ; Akbari, Mahmood (Supervisor) ; Fotowat-Ahmady, Ali (Supervisor)
    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... 

    Calculation of Quantum Transition Probabilities between Codons and Concept of Biological Information

    , Ph.D. Dissertation Sharif University of Technology Ghasemi, Fatemeh (Author) ; Shafiee, Afshin (Supervisor)
    It has been about a century since the introduction of the theory of quantum mechanics. This theory is a branch of physics that describes the behavior of nature in very small scales and microscopic systems . Since no quantum system is entirely isolated from its surroundings , it is necessary to study their interactions with the environment to understand them accurately. The theory of open quantum systems provides the theoretical and conceptual framework needed to consider these interactions. Then using the appropriate quantum operations , the evolution of the combined system can be investigated. Moreover , considering the environmental effects, some quantum features such as dissipation... 

    Design and Fabrication of a Centrifugal Microfluidic System to DNA Extraction

    , M.Sc. Thesis Sharif University of Technology Fathi Ganje Lou, Ali (Author) ; Farhadi, Fathollah (Supervisor) ; Saadatmand, Maryam (Supervisor) ; Parsa Yeganeh, Laleh (Co-Supervisor)
    Deoxyribonucleic acid (DNA) extraction, as one of the most important steps in modern molecular diagnostics, is the process by which DNA is separated from intracellular materials like proteins, membranes, and other materials contained in the cell. Microfluidic technology enables sophisticated, time-consuming and costly experiments with minimal use of raw materials, time and cost and acceptable accuracy. The predominant advantages of centrifugal microfluidic systems are utilizing centrifugal force to generate propulsion without the need for a pump, and eliminating the need for experts to run the system. Various fluidic operations such as valving, mixing, metering, heating, and sample... 

    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)
    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... 

    Cancer Detection Classification by cfDNA Methylation

    , M.Sc. Thesis Sharif University of Technology Ezzati, Saeedeh (Author) ; Sharifi Zarchi, Ali (Supervisor)
    Traditional techniques use invasive histology techniques to diagnose cancer. Cancer tissue is sampled directly in this method, which is very painful for the patient. In recent years, scientists have discovered that the cell world is released into the blood plasma after cell death, obtaining useful cancer information. Since methylation changes in cancer cells are very significant and the death rate of cancer cells is high, the methylation of each tissue is different from the other. Furthermore, they were diagnosing the type of cancer.On the other hand, due to the different patterns in methylated DNA with normal DNA and the use of bisulfite treatment technique to detect the degree of... 

    Exact Simulation of Varian Clinac 2100C/D with Use of Phase Space file and Representation of Appropriate Source Model for Clinical Applications

    , Ph.D. Dissertation Sharif University of Technology Ezzati, Ahadollah (Author) ; Sohrabpour, Mostafa (Supervisor) ; Rabi Mahdavi, Saeed (Co-Advisor)
    MC Simulation is considered to be one of the most accurate methods for transport of radiation in various media. Computational speed is the limiting factor to apply the MC method in clinical settings. One of the methods to increase the speed in MC simulations is the use of phase space file (PSF). PSF is generated by transporting the particles through the linear accelerator head. The characteristics of these particles crossing a reference plane are stored in the PSF file. The PSF can be used in subsequent simulations as a radiation source. The use of PSF is effective but has a drawback of having latent variance. Latent variance is a problem inherent in using phase space files. Latent variance... 

    Design of a Microfluidic Digital Droplet PCR

    , M.Sc. Thesis Sharif University of Technology Abedini, Ali (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Polymerase chain reaction, abbreviated as PCR, is a method of amplifying the number of copies of a desired DNA sequence through special protocols. The rapid advance of microfluidic devices and the emerging concept of digital microfluidics has resulted into the development of digital droplet PCR (ddPCR) systems with their significant uses in the detection of rare mutations, cancer diagnosis, and surveillance. A large number of micron-sized droplets are required to perform ddPCR. in this study, To investigate the gradient of confinements induced droplet self-breakup mechanism, we carried out the computational fluid dynamics (CFD) simulations for the two-phase flow using a commercial software... 

    , Ph.D. Dissertation Sharif University of Technology Saberi, Reyhanesadat (Author) ; Shahrokhian, Saeed (Supervisor)
    In the first part, preparation of different kinds of polypyrrole/carbon composites and their application for drug analysis are described. In the first work, A very sensitive electrochemical sensor constructed from a glassy carbon electrode modified with a layer-by-layer MWCNT/doped overoxidized polypyrrole (oppy/MWCNT /GCE) was used for the determination of acetaminophen (AC) in the presence of codeine and ascorbic acid (AA). In comparison to the bare glassy carbon electrode, a considerable shift in the peak potential together with an increase in the peak current was observed for AC on the surface of oppy/MWCNT/GCE, which can be related to the enlarged microscopic surface area of the... 

    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)
    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... 

    Design and Development of Electrochemical DNA Nanobiosensors for Identification and Determination of Important Biomarkers

    , Ph.D. Dissertation Sharif University of Technology Salimian, Razieh (Author) ; Shahrokhian, Saeed (Supervisor) ; Kalhor, Hamid Reza (Co-Supervisor)
    The main purpose of this Ph.D. Thesis is to develop DNA-based biosensors using Label-free approaches applying simple, inexpensive and fast electrochemical techniques to measure the biological markers of cancer.In the first part, a simple protocol for detection of specific-sequence DNA is introduced. In this method carbon nanotube is used as a hybridization indicator. This label-free system provides the advantage of eliminating additional labeling procedure. As the signal enhances in the presence of MWCNT and decreases in the presence of target, the fabricated sensor is known as a signal-off device. The oxidation signal of Fe(CN)63-/4- is followed as an analytical signal to detect target... 

    Equilibrium States of Nano scaled DNA-loops in Different Elastic Models

    , M.Sc. Thesis Sharif University of Technology Salari, Hossein (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    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.... 

    A Study in Genome Editing with Clustered Regularly Interspaced Short Palindromic Repeats

    , M.Sc. Thesis Sharif University of Technology Rostami, Mohammad (Author) ; Sharifi Tabar, Mohsen (Supervisor) ; Rabiee, Hamid Reza (Co-Supervisor) ; Rohban, Mohammad Hossein (Co-Supervisor)
    Clustered Regularly Interspaced Short Palindromic Repeats, or in short, CRISPR is a relatively new technology that enables geneticists and medical researchers to edit parts of the genome by removing, adding, or altering parts of the DNA. Initially found in the genomes of prokaryotic organisms such as bacteria and archaea, this technology can cure many illnesses such as blindness and cancer. A significant issue for a practical application of CRISPR systems is accurately predicting the single guide RNA (sgRNA) on-target efficacy and off-target sensitivity. While some methods classify these designs, most algorithms are on separate data with different genes and cells. The lack of... 

    Synthesis of Graphene Nanosheets for Application in Biosensors

    , M.Sc. Thesis Sharif University of Technology Rahighi Yazdi, Reza (Author) ; Akhavan, Omid (Supervisor)
    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...