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    Designing and Fabrication of Microfluidic Biosensor by DNA-Directed Immobilization

    , Ph.D. Dissertation Sharif University of Technology Esmaeili, Elaheh (Author) ; Vossoughi, Manouchehr (Supervisor) ; Soleimani, Masoud (Supervisor) ; Shamloo, Amir (Supervisor)
    The present study is aimed at the development of a novel approach based on the magnetically improvement of DNA-directed immobilization to prepare a highly efficient sensor for prostate diagnosis. The novelty of this work is in the use of antibody conjugated magnetic nanoparticles via DDI. DNA-modified magnetic nanoparticles are added in solution to capture DNA-conjugated, fluorescently-labeled immunocomplexes formed in solution free of steric constraints. The DDI-based nanoconstructs are then concentrated and immobilized using a magnetic field. Compared to a process in which the immunocomplex directly forms on the sensing surface, the proposed approach provides higher mass transfer and lower... 

    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... 

    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... 

    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... 

    Analysis of DNA Methylation in Single-cell Resolution Using Algorithmic Methods and Deep Neural Networks

    , M.Sc. Thesis Sharif University of Technology Rasti Ghamsari, Ozra (Author) ; Sharifi Zarchi, Ali (Supervisor)
    DNA methylation in one of the most important epigenetic variations, which causes significant variations in gene expressions of mammalians. Our current knowledge about DNA methylation is based on measurments from samples of bulk data which cause ambiguity in intracellular differences and analysis of rare cell samples. For this reason, the ability to measure DNA methylation in single-cells has the potential to play an important role in understanding many biological processes including embryonic developement, disease progression including cancer, aging, chromosome instability, X chromosome inactivation, cell differentiation and genes regulation. Recent technological advances have enabled... 

    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 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... 

    Design and Fabrication of Microfluidic System for Cell Lysis and DNA Purification

    , M.Sc. Thesis Sharif University of Technology Jalilvand, Elahe (Author) ; Shamloo, Amir (Supervisor) ; Hosseini, Vahid (Supervisor)
    Nowadays, intracellular studies have been widely developed in biological applications. Intracellular analysis requires direct experiments on cells such as cell separation, purification, lysis and DNA extraction. The process of cell lysis and the resulting DNA purification is a crucial step in diagnostic processes. Since, the basis of many genetic studies is the information existed in double-stranded DNA structures.In this project, a microfluidic system is presented which performs integrated chemical cell lysis and DNA extraction. The cell used in this study is L-929. In order to increase cell lysis, the serpentine micromixer in combination with internal and external barriers at the beginning... 

    Multi- and Single-cellular Encapsulation within Microchannels for Effective Cell Lysis and DNA Extraction and Purification

    , M.Sc. Thesis Sharif University of Technology Hassani Gangaraj, Mojtaba (Author) ; Shamloo, Amir (Supervisor)
    In this study a droplet-based microfluidic system is desighned and fabricated to effectiverly lyse MCF7 cells and extract and purify their DNAs. The main purpose of this study is to transfer all the steps from macro scale to a microfluidic system containing a fluidic chip. This system is a semi automatic system and every part of the lysis and purification process is performed in one step. The first step is to encapsulate single cells and multi cells inside the droplets. By controlling the concentration of the cell solution, the number of encapsulated cells inside the droplet is efficiently and easily controlled and the cells were encapsulated as single cells and as multi cells inside the... 

    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... 

    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, Simulation and Construction of a Rapid Gene Amplification Microfluidic Device Using Polymerase Chain Reaction (PCR) Method

    , M.Sc. Thesis Sharif University of Technology Amadeh, Ali (Author) ; Shamloo, Amir (Supervisor)
    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... 

    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)
    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... 

    Design and Fabrication of Centrifugal Microfluidic Disc for Cell Lysis and DNA Extraction

    , M.Sc. Thesis Sharif University of Technology Jalalian, Pourya (Author) ; Saadatmand, Maryam (Supervisor) ; Garshasbi, Masoud (Co-Supervisor)
    Centrifugal microfluidic systems due to their unique properties, including the ease of sample transfer, high controllability, the need for samples and reagents in a small volume scale, the possibility of embedding a complete laboratory and modeling a variety of processes on a disk, they have great potential to be used in the field of point of care diagnosis. Such devices can perform several different processes simultaneously and continuously by using inertial and pneumatic forces as well as a complex network of microchannels. The purpose of this research is to design and build a centrifugal microfluidic disc for lysing amniotic stem cells, followed by DNA extraction, in order to detect fetal... 

    Study, Optimization and Construction of a Microfluidic Gene Amplification Device by Using Thin Film Layer Method

    , M.Sc. Thesis Sharif University of Technology Eslami, Sara Sadat (Author) ; Vosoughi, Manouchehr (Supervisor) ; Alemzadeh, Iran (Co-Supervisor) ; Shamloo, Amir (Co-Supervisor)
    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... 

    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... 

    Design and Fabrication of a Centrifugal Microfluidic System to Cell Lysis

    , M.Sc. Thesis Sharif University of Technology Khorrami Jahromi, Arash (Author) ; Saadatmand, Maryam (Supervisor) ; Eghbal, Manouchehr (Supervisor) ; Parsa Yeganeh, Laleh (Co-Supervisor)
    Cell lysis, as the first procedure of cell pretreatment, is a process that breaks cell membranes open thereby facilitating access to intracellular substances, such as DNA, proteins, and other components for further analysis to diagnose and treat diseases at early stages. Currently, there are several methods for cell lysis at macroscales. However, the time-consuming and expensive procedures as well as the large scal of the system are the main disadvantages of the systems. Recently, microfluidic systems have attracted considerable attention due to advantages associated with automation, integration and miniaturization of biomedical test protocols. Centrifugal microfluidics (Lab-on-a-Disc) is a... 

    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... 

    Design & Analysis of a DNA String Matching System Based on Optical Parallel Processing

    , M.Sc. Thesis Sharif University of Technology Babashah, Hossein (Author) ; Kavehvash, Zahra (Supervisor) ; Koohi, Somaie (Co-Advisor) ; Khavasi, Amin (Co-Advisor)
    In recent years, the biological evolution of molecular detection capabilities based on gene analysis has provided a reliable performance in the diagnosis of a disease before a symptom emerges. Human gene storage requires a large amount of computer memory (about 1.5 GB for each DNA) and the search for a specific pattern within it with electronic computers is time and power consuming. Optical computing uses light parallel processing capabilities to find the pattern in a digital field, which can be used to process large volumes of data in short time and low power consumption, while electronic computers process data in series with high power dissipation. According to the Optalysys report, the... 

    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...