Sharif Digital Repository

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... 

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... 

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... 

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... 

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... 

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 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... 

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... 

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... 

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... 

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... 

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... 

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... 

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... 

New biological discussions in quantum mechanics that has grown considerably in the past decade. Meanwhile, considering some of interesting problems in biology and chemistry, the use of quantum approach superposition principle and tunneling effect explain some of the phenomena of life more than several. Nowadays, regarding quantum description, provided to explain how we recognize different odors, what the mechanism photosynthesis is, and how bind navigation occurs. Furthermore, the new field of quantum biology sheds light in underestanding the issue of heritance and genetics inforamtion. In this thesis, after reviewing some interesting topics of quantum biology, the data transfer from... 

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.... 

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... 

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... 

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... 

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...