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    Computational Modeling of Axonal Microtubule and Study the Effect of Cytoplasm on It under the Tension

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

    Design and Manufacturing of an Assay System by Lateral Flow Method and Optimize the Model by Lattice-Boltzmann Numerical Solution

    , M.Sc. Thesis Sharif University of Technology Gholami Poshtehani, Abbas (Author) ; Shamloo, Amir (Supervisor)
    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... 

    Designing, Computational Modeling and Fabrication of a Magnetic Centrifugal Microfluidic to Separate Circulating Tumor Cells from Blood Sample

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

    Development of a Paper-based Microfluidic Device for Biological Assay

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

    Design and Manufacture of an Engineered Scaffold in Order to Repair Tissue Exposed to Mechanical Force, for Tissue Engineering Application

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

    Numerical Modeling of Endothelial Cell’s Groups Migration in a Microfluidics Device

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

    Design of the Coronary Stent Device to Improve Fluid Flow in Coagulated Vascular Regions

    , M.Sc. Thesis Sharif University of Technology Haghayegh Jahromi, Mohammad (Author) ; Shamloo, Amir (Supervisor)
    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... 

    Numerical Study of Margination and Adhesion of Micro- and Nano-particles in Coronary Circulation

    , M.Sc. Thesis Sharif University of Technology Forouzandehmehr, Mohammad Amin (Author) ; Shamloo, Amir (Supervisor)
    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,... 

    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... 

    Design and Simulation of a Passive Microfluidic Device for Particle Separation

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

    Investigation of Amyloid-Beta Inhibition using Multifunctional Peptide Drugs Associated with Metal Ions

    , Ph.D. Dissertation Sharif University of Technology Asadbegi, Mohsen (Author) ; Shamloo, Amir (Supervisor)
    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... 

    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... 

    Particle Focusing on a Lab on a Disk System

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

    Design of Injectable Hydrogel Scaffold based on Smart Polymer in Tissue Engineering

    , M.Sc. Thesis Sharif University of Technology Mozhdehbakhsh Mofrad, Yasaman (Author) ; Shamloo, Amir (Supervisor)
    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... 

    Rapid Determination of Histamine by an Enzyme-based Microfluidic Biosensor

    , M.Sc. Thesis Sharif University of Technology Moradi, Mohammad Reza (Author) ; Vossoughi, Manouchehr (Supervisor) ; Shamloo, Amir (Supervisor)
    Design, simulation, optimization and manufacturing of an enzyme-based microfluidic biosensor has been carried out during this research to measure histamine concentration in a sample. The designed biosensor is composed of a micro-bioreactor to degrade histamine and yield hydrogen peroxide, and a chemical reactor to measure the amount of hydrogen peroxide, using chemiluminescence methods. The geometry of the bioreactor and chemical reactor is developed through comparison and optimization of several different geometries. In theory, the designed sensor can determine histamine concentration in a range of 10M to 1mM under one minute, with a maximum error of 5%. Designed biosensor is built using... 

    Determination of Traffic Generated Particle Distribution using Air Pollution Dispersion Models and Investigating Effectiveness of Mitigating Solutions: Case study, City of Tehran

    , M.Sc. Thesis Sharif University of Technology Saeedi, Milad (Author) ; Shamloo, Amir (Supervisor) ; Hosseini, Vahid (Co-Advisor)
    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,... 

    Fabrication of a Multi-Layered Scaffold to Be Used in Dermal Wound Healing

    , M.Sc. Thesis Sharif University of Technology Kamali, Ali (Author) ; Shamloo, Amir (Supervisor) ; Asghari, Mohsen (Co-Advisor)
    Wound healing by engineered scaffolds is a new step in bio-technology and medical studies in recent years. The goal of the current study is to propose a novel structure for a tissue-engineered scaffold to be used in wound healing. Influenced from the multi-layered structure of natural human skin, the fabricated scaffold consists of two layers to maximize similarity with natural skin. This product is comprised of an electrospun layer made of polycaprolactone and polyvinyl alcohol and a hydrogel layer made of chitosan and gelatin. In order to form a porous medium in the hydrogel layer, freeze-gelation was used instead of freeze drying. The evaluation of fabricated scaffolds was performed by... 

    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... 

    Molecular Dynamics Simulation of Actin: An Investigation into the Mechanical Properties

    , M.Sc. Thesis Sharif University of Technology Mehrafrooz, Behzad (Author) ; Shamloo, Amir (Supervisor) ; Firoozbakhsh, Keikhosrow (Supervisor)
    Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. Actin plays a crucial role in cell motility, adhesion, morphology and intracellular transport. Its biologically active form is the filament (F-actin), which is assembled from monomeric G-actin. In this thesis, the mechanical properties and characteristics of both G- and F-actin are studied using molecular dynamics simulations. In general, this thesis can be categorized into two individual parts: First, steered molecular dynamics simulation was performed to assess tension of monomeric G-actin molecule, and stress-strain curves were... 

    Development of an Optimized Skin Scaffold Capable of Growth Factor Release for Acute Skin Wound Healing

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