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    Predicting the Brain Injury Effects on Physical Arrangement of White Matter Neuronal Tracts using a Finite Element Head Model based on Tractography

    , Ph.D. Dissertation Sharif University of Technology Yousefsani, Abdolmajid (Author) ; Farahmand, Farzam (Supervisor) ; Shamloo, Amir (Co-Supervisor) ; Oghabian, Mohammad Ali (Co-Supervisor)
    Abstract
    Diffuse tensor imaging or tractography is a useful method for tracking the axonal tracts pathways within the brain white matter by monitoring the movements of water molecules along the axons. The higher the level of the tissue anisotropy, the more accurate the pathways can be estimated. But in the swelling regions around an edematous tumor, the excess of watery fluid disrupts the directional movement of water molecules, and consequently, the diffuse tensor imaging is unable to track the pathways. This impairment should be resolved by predicting the axontal tracts arrangement in the blind regions of the images using the numerical modeling. To this end, a finite element model of the human... 

    Investigation and Characterization of Circulating tumor Cells (CTCs) by the Microfluidics Systems

    , M.Sc. Thesis Sharif University of Technology Yari, Alireza (Author) ; Vossoughi, Manoucher (Supervisor) ; Alemzadeh, Iran (Supervisor) ; Shamloo, Amir (Supervisor)
    Abstract
    Cancer is the second leading cause of death among humans as one of the major human concerns. More than 500,000 people die of cancer each year in the United States alone. Cancer mortality is mainly due to cancer metastasis. Metastasis is the escape of cancer cells from a primary tumor, the circulation of cells in the circulatory system (CTSs), the penetration of/from vessel wall, and the formation of a secondary tumor. It is still not clear how the cells survive in the circulatory system, along with the mechanical pressures and stresses that exist in the body's capillary channals. In this study, a microcirculation model for circulating cells with barriers was designed and constructed by the... 

    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)
    Abstract
    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... 

    Numerical Modeling of Blood Coagulation in Stenosis

    , M.Sc. Thesis Sharif University of Technology Kord, Ali (Author) ; Taghizadeh Manzari, Mehrdad (Supervisor) ; Shamloo, Amir (Co-Advisor)
    Abstract
    Trombosis formation in blood flow is a complex biochemical and very important process for body health which impedes blood loss by creating obstacles in the path of injured wall vessels. Although this phenomenon plays a very significant role in healthy body function, unfortunately it has been observed that it could cause diseases or even stroke. The reason is that thrombosis formation in blood and its detachment from the vessel wall can result in block body capillaries and lead a catastrophic event for the body. One of the factors which motivates blood for forming unnatural thrombosis is the vessel stenosis. It would ange in normal blood flow path and cause thrombosis formation as time is... 

    Design and Simulation of a Passive Microfluidic Device for Particle Separation

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

    Fabrication and Enhancement of an Antibacterial Chitosancoated Allantoin-Loaded Skin Wound Dressing for Clinic Use

    , M.Sc. Thesis Sharif University of Technology Haki Zahi Margouk, Mohamamd (Author) ; Shamloo, Amir (Supervisor) ; Akbari, Javad (Supervisor)
    Abstract
    Skin as the largest organ of the body is constructed of three distinctive layers referred to as epidermis, dermis, and hypodermis. Epidermis is the outermost layer of the skin and acts as body’s first barrier against infectious agents and contains mostly sweat glands. Dermis is the mid-layer of the skin which makes up to 70% of the skin and plays a significant role in maintaining body’s metabolism and is home to a huge part of skin’s vascular network, nerve cells and hair follicles. Hypodermis on other hand, is the deepest layer of the skin and mainly acts as a bonding layer between upper skin layers and the soft tissue underneath. Although skin is proved to have a profound ability to... 

    Design, Simulation and Fabrication of a Centrifugal Microfluidic Device for Circulating Tumor Cells Separation

    , M.Sc. Thesis Sharif University of Technology Naghdloo, Amin (Author) ; Shamloo, Amir (Supervisor) ; Nouri Borujerdi, Ali (Supervisor)
    Abstract
    In this project, two centrifugal microfluidic platforms with the goal of separation and genetical study of circulating tumor cells have been designed, simulated and fabricated. Circulating tumor cells are the ones that are detached from the cancer tumors, entered the blood and disseminated the danger of cancer through other parts of the body. Both passive and active methods of separation are investigated in this study. The passive method is based on the inertial effects of the fluid and the active method is based on the magnetophoretic force exerted from an external magnetic field. In order to use the active method, the magnetic nanoparticles are attached to the breast cancer cells by the... 

    Simulation of Paramecium Swimming in an Environment with a Chemical Gradient

    , M.Sc. Thesis Sharif University of Technology Nematollahi Sarvestani, Ali (Author) ; Ahmadian, Mohammad Taghi (Supervisor) ; Shamloo, Amir (Supervisor)
    Abstract
    In the recent decade, researchers in the field of minimally invasive medicine have come up to the idea of utilizing micro organisms as smart micro robots. The advantage with this idea is the fact that problems such as energy supply and maneuvering are resolved for these sorts of micro swimmers. In this current work, a new numerical method for investigation of micro swimming is developed which is computationally efficient in characterizing locomotion of micro swimmers and using a finite element method software, locomotion of Paramecium has been investigated inside and outside a capillary tube. According to simulation results, it is possible to design a controlling system which is capable of... 

    Design, Simulation, and Fabrication of a Hybrid Inertial and Magnetophoretic Microfluidic Device for Target Cell Separation from Blood

    , Ph.D. Dissertation Sharif University of Technology Nasiri, Rohollah (Author) ; Shamloo, Amir (Supervisor) ; Akbari, Javad (Supervisor)
    Abstract
    Circulating tumor cells (CTCs) isolation from a blood sample has an important value in cancer research and its treatment. Microfluidics provides a great potential for target cell separation from biological samples by using different physical principles. Among the microfluidic cell separation methods, the inertial microfluidic devices are advantageous in handling samples for point-of-care diagnostics due to their simple structure, fast, label-free and low-cost characteristics. In this thesis, first, we designed and investigated the application of a symmetric serpentine inertial microfluidic device for the separation of CTCs from whole blood. For this purpose, numerical modeling was performed... 

    Modeling and Vibration Analysis of Laminated Composite Beam with Magneto-Rheological Fluid Segments

    , Ph.D. Dissertation Sharif University of Technology Naji, Jalil (Author) ; Behzad, Mehdi (Supervisor) ; Zabihollah, Abolghasem (Supervisor) ; Shamloo, Amir (Co-Advisor)
    Abstract
    Magnetorheological (MR) materials show variations in their rheological properties when subjected to varying magnetic fields. They have quick time response, in the order of milliseconds, and thus are potentially applicable to structures and devices when a tunable system response is required. When integrated with a structural system, they can produce higher variations in the dynamic response of the structure. In this thesis, vibration behavior of laminated-composite beam with MR Fluid is investigated.In most studies, shear strain across the thickness of MR layer has been considered as a constant value which does not precisely describe the actual shear strain field. Shear modulus of MR layer in... 

    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)
    Abstract
    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... 

    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)
    Abstract
    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)
    Abstract
    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... 

    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)
    Abstract
    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... 

    Jahn-Teller Effect in Diamond Vacancy Under Stress

    , M.Sc. Thesis Sharif University of Technology monfared, Mohammad (Author) ; Vesaghi, M. A (Supervisor) ; Babamoradi, M (Co-Advisor)
    Abstract
    Electron states of diamond vacancy under stress were studied theoretically. The generalized Hubbard model is used to calculate the electrons energy levels. The results shows that the degeneracy of some levels (T, with triple space degeneracy) reduced to levels with lower degeneracy (E, with double space degeneracy and A, without degeneracy). Besides this spiting of degeneracy the energy of all states changed and therefore the transition energy between these states changed too. Jahn-Teller effect was observed  

    Fabrication of Biodegradable Micro/Nano Beads for the Pharmaceutical Applications

    , M.Sc. Thesis Sharif University of Technology Mashhadian, Ali (Author) ; Shamloo, Amir (Supervisor) ; Asghari, Mohsen (Supervisor)
    Abstract
    Polymeric microspheres which can load biomolecules, proteins and growth factors play an important role in tissue engineering and drug delivery systems. The size of the microspheres and encapsulation efficiency exert a considerable impact on the usability of them. In this study double emulsion method is used for fabrication of microspheres. Effect of different parameters namely the speed of homogenization, time of homogenization, the amount of polymer in oil phase, the surfactant concentration in different phases on the size and surface morphology of the microspheres are investigated. Moreover, a release test for BSA loaded microspheres is conducted. Results indicate that by increasing the... 

    Device on a Chip, in Order to Control and Separation of Circulating Tumor Cells

    , M.Sc. Thesis Sharif University of Technology Masoudi, Mohammad Mahdi (Author) ; Shamloo, Amir (Supervisor) ; Khodaygan, Saeed (Supervisor)
    Abstract
    The process of separating cells from a laboratory sample, is a crucial step in biotechnology and medical science. Cells separation is important for various reasons, including the identification and treatment of diseases, as an example, separation of Circulating Tumor Cells (CTCs) from patient blood sample. CTCs are cells that shed from a tumor and diffuse into blood vessels. These cells are the starters of metastasis, the process in which cancer spreads in body, and are main reason of deaths caused by cancer. Extremely low percentages of target cells in the blood, clarify the importance of highly accurate and sensitive separation. Currently, conventional separation methods are of macro-order... 

    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)
    Abstract
    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... 

    Design and Fabrication of a Microfluidic Device to Study the Growth of Breast Cancer Cell

    , M.Sc. Thesis Sharif University of Technology Mohammad Hashemi, Hanieh (Author) ; Vosughi, Manuchehr (Supervisor) ; Shamloo, Amir (Supervisor) ; Naserifar, Naser (Supervisor)
    Abstract
    for decades Cancer has been one of the major causes of death universally. Though extensive efforts in developing new anticancer therapies, they face failures in clinical trials and curing the sick owing to time consuming and expensive preclinical models with poor predictions of drug responses in human. To address this challenge it is crucial to develop preclinical models mimicking the main aspects of a tumor that can provide effective prediction of therapeutic responses. Tumor on chip technology has appeared as a promising approach for providing effective cancer models and reliable preclinical predictions. In this project, collagen was first extracted as the main constituent of the tumor... 

    Fabrication of Artificial skin with Electrospun of Nanofiber made of PCL and PVA

    , M.Sc. Thesis Sharif University of Technology Mohseni, Mina (Author) ; Shamloo, Amir (Supervisor) ; Naghdabadi, Reza (Co-Advisor) ; Vosooghi, Manoochehr (Co-Advisor) ; Firoozbakhsh, Keikhosro (Co-Advisor)
    Abstract
    The main goal of this project is to fabricate the scaffolds including Polycaprolactone and Polyvinyle alcohol nanofibers in order to use as artificial skin. For this purpose, electrospinning parameters have been optimized for various injection rates and the scaffolds containing different percent of PCL and PVA have been made. By investigating the cell growth on these scaffolds, the one made up PVA/PCL (30% ) has been introduced as the best scaffold. To improve biological properties of chosen scaffold, a layer of collagen was coated. The angiogenesis capacity has been improved by adding Heparin to PVA nanofibers. Based on assay of heparin release, it was shown that Heparin is released within...