Sharif Digital Repository

Axon is an important part of the neuronal cells and axonal microtubules are bundles in axons.In axons, microtubules are coated with microtubule-associated protein tau, a natively unfolded filamentous protein in the central nervous system. These proteins are responsible for cross-linking axonal microtubule bundles. Through complimentary dimerization with other tau proteins, bridges are formed between nearby microtubules creating bundles. Formation of bundles of microtubules causes their transverse reinforcement and has been shown to enhance their ability to bear compressive loads. Though microtubules are conventionally regarded as bearing compressive loads, in certain circumstances such as in... 

Separating cells from a mixed sample is a required task in biotechnology and modern medicine, for example to isolate CTC’s that are of interest for doing therapy and diagnosing or doing research. A minute percentage of target cells must be separated from a large amount of unwanted cells. These target cells like CTC’s could be as rare as 1 target cell per millions of unwanted background cells. Hence Microfluidic cell sorting schemes based upon fluorescent labelling, electrophoresis, dielectrophoresis and magnetophoresis have been devised. Microfluidic magnetically-activated cell sorting (MACS) does not need any optical instrument or current source and electrode. By using an electromagnet or... 

Nowadays, separation and filtration of particles has many industrial applications in biology and medicine. In this thesis, passive microfluidics are designed and simulated which are able to separate and filter particles. Although particles aer generally expected to follow laminar flow streamlines in the absence of external forces, inertial forxes van cause particles to migrate across mictochannels in an accurate and predictable manner. The effect of these forces is invedtigated, and by using previous research, a model is developed to predict these forces. First design is a microchannel with Archimedean spiral which utilizes both inertial forces and Dean flow to separate particles in the... 

All the biological diagnostic devices that are introduced to the consumers, must meet WHO criteria. Some of these criteria include being affordable, sensitive and deliverable to the user. In the last twenty years, there have been lots of efforts to use microfluidic devices for biological assay. Due to their expensive price and requirement of complex equipment for their fabrication, polymer-based microfluidic devices have not been able to be used in developing countries. It is to be hoped that introduction of paper for fabrication of microfluidic devices could make microfluidic devices meet WHO criteria. μPADs are divided into well-based and channel-based devices. In the present work, both... 

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... 

Articular cartilage has limited repair capability following traumatic injuries and current methods of treatment remain inefficient. Reconstructing cartilage provides a new way for cartilage repair and natural polymers are often used as scaffold because of their biocompatibility and biofunctionality. The goal of cartilage tissue engineering is to design a scaffold with proper pore structure and similar mechanical properties to the native tissue. In this study Porous scaffolds prepared from silk fibroin, chitosan and gelatin blends with varying ratio of silk fibroin and gelatin by freeze drying method were characterized for physicochemical, mechanical and biological properties. Among the... 

Many experimental and theoretical studies have suggested that zinc binding to Aβ could promote amyloid-β aggregation and reactive oxygen species (ROS) production induced by AD disease. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. In present study molecular docking and molecular dynamics (MD) simulations were used to evaluate the efficacy of two new bifunctional peptide drug, composed of two different domains: C-terminal hydrophobic region of Aβ and Zn2+ chelator region. To evaluate the multifunctionality of the ligands, a comprehensive set of MD simulations up... 

Prediction of the hydrophobicity of molecules using graph neural networks is one of the advanced methods for analyzing the physicochemical properties of molecules. In this method, the molecular graph structure and its features are used as inputs to neural networks to provide predictions about the hydrophobicity of molecules. This method is currently applied in the pharmaceutical industry, green chemistry, and other research fields. By using this approach, molecules with strong hydrophobic properties can be identified and used in the development of new drugs. Generally, graph neural networks are highly suitable for predicting the properties of molecules and other various applications in the... 

Cell migration plays a key role in many biological processes including metastasis, wound healing, inflammatory response, body immune response and formation of new blood vessels. The migration of cells in response to the gradient of concentration gradient is regarded as chemotaxis. In the present study, the group chemotaxis of endothelial cells is simulated in response to gradient concentration of biochemical species using a developed cell migration model. At the first step, the numerical simulation of fluid flow and concentration transport of biochemical species is performed using a developed FVM code. At the second part, a model is developed to mimic the group migration of endothelial... 

In many microfluidic devices, focusing particles into a narrow stream is usually an essential step prior to counting, detecting, and sorting them. By installation of microfluidic laboratory functions on a rotating disk, new devices called Lab-on-a-disks, which have plenty of advantages in comparison to ordinary Lab-on-a-chips, shape. In this study, to the best of our knowledge for the first time, a Lab-on-a-disk device is designed and fabricated in order to focus particles prior to detecting them by a conventional CD-ROM as a strong optical system. Hydrophoresis method, using slanted obstacles to induce transverse pressure gradients, is utilized to focus particles. In this regard, the... 

The application of computational fluid dynamics (CFD) has been growing rapidly in biomedical engineering. The altered hemodynamics inside the blood vessels plays a key role in the development of the arterial disease called atherosclerosis, which is the major cause of human death worldwide. Atherosclerosis is often treated with the stenting procedure to restore the normal blood flow. A stent is a tubular, flexible structure, usually made of metals, which is driven and expanded in the blocked arteries. The presence of non-biological device in the artery causes inflammation or re-growth of atherosclerotic lesions in the treated vessels. Several factors including the design of stents and type of... 

Lateral Flow Immunoassay kits are one of the most important instrument in laboratories and houses for diagnosing diseases, hormones, food toxins and etc. fast, exactly and by low cost. Since one of the most expensive parts in the mentioned kits, is using antibodies in their construction, an attempt has been made in this project for descending usage of antibody and consequently final cost of these sensors besides keeping desired and necessary sensitivity of these diagnostic kits. For this purpose, first of all with the help of simulating flow’s behavior in Lattice-Boltzmann method, provisions has been made to predicting flow’s movement behavior in Nitrocellulose membrane, Based on its results... 

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... 

In this study, the performance of an existing Savonius turbine has been improved through designing a curved curtain, the curtain has been placed in front of the rotor. To do so, the main purpose is to increase the net static torque of wind rotor via a newly designed curtain. A new guide vane is designed to prevent negative torque produced by convex surface of wind rotor and increasing wind velocity which is impacted concave side of wind turbine rotor blade. The numerical modeling of flow field is verified by experimental result for wind rotor without straightener. The numerical code verification accomplished at three different angle of rotation which the biggest difference between... 

Obstruction of Left Anterior Descending artery (LAD) due to thrombosis or atherosclerotic plaques is the leading cause of death world–wide. Targeted delivery of drugs through micro- Nano-particles holds noteworthy promise which can make clot busting or the restenosis treatment with minimal toxicity possible. In this work, Fluid-Structure Interaction (FSI) simulations of blood flow through a patient-specific reconstructed geometry of LAD artery have been conducted using a non-Newtonian hematocrit (HCT) dependent model for blood. Based on physiological facts, 25, 45 and 65 percentages of HCT were assumed as acceptable representations of anemic, healthy and diabetic blood conditions,... 

Nerve damage is one of the factors affecting the quality of life of patients. The nervous system does not have the ability to repair large injuries, and autologous transplantation, which is the standard treatment method for nerve injuries, is faced with a shortage of donors and a decrease in the function of the donor site. Tissue engineering hydrogels, due to their similarity to the natural tissue of the stomatal body, are a hope for the repair of nerve tissue. In this research, an injectable, minimally invasive and temperature-sensitive hydrogel based on chitosan-etaglycerophosphate-sodium hydrogen carbonate salt or trisodium phosphate salt containing aligned nanofibers made of gelatin and... 

Fuel cell is a power generator like internal combustion engines, but the first point is that internal combustion engines produce mechanical power while fuel cells produce electrical power. Secondly, internal combustion engines use hydrocarbon derivatives such as gas as fuel and their exhaust fumes are toxic gaseous, but fuel cells use hydrogen as fuel and their exhaust are only water in either vapor or liquid form. One of the most important issues in fuel cells is optimum design of micro channels of bipolar plates which is different regarding the type and application of fuel cells. Optimum designing of micro channels on bipolar plates plays a key role in fluid mass transport through micro... 

As the first barrier in front of external damages, skin is prone to the largest number of damages applied to one’s body. Acute wounds are considerably prevalent world-widely, imposing very high costs to governments. The purpose of the current project, is to propose a novel skin scaffold capable of growth factor delivery for enhancing the wound healing process in acute wounds. Such a scaffold should be able to decrease the required time for healing process, also to improve the quality of the regenerated skin compared to available commercial products. Furthermore, it should be highly biocompatible, biodegradable, and non-toxic. In this project, to manufacture the artificial skin scaffold, a... 

In this study, in the base case using a modeling system WRF=CAMx Distribution concentration of all pollutants from mobile sources in an episode of 60 days (November and December 2015) is calculated in Tehran. In this context, the emissions inventory related to mobile sources outputs the code in Fortran and WRF meteorological model to model air quality prepared and then using the CAMx, Tehran’s air quality is simulated. In order to verification in this case, the results of pollutant concentration NO2, CO, PM2٫5, with concentrations of air pollution monitoring stations compared. Given that in this study the concentration of pollutants from mobile sources is modeled, predicted by the model,... 

In this project a centrifugal, microfluidic platform to the end of separation and studying circulating tumor cells is designed, modelled and analyzed. Circulating tumor cells (CTCs) are specific types of cancer cells which leave the original tumor and enter the blood stream. For the separation of CTCs, a novel anti-body separation technic has been used which targets the specific MCF7 CTCs using their corresponding Ep-CAM antibody. First the Ep-CAM antibody is coated on magnetic nanoparticles through a chemical bonding process. Afterwards the CTCs are exposed to their antibodies, through which they will bind together and form CTCs with magnetic characteristics. Finally through exerting an...