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    Three Dimensional Fluid-structure Interaction Analysis of Air Flow and Inhaled Particle Transport in Human Pulmonary Alveoli

    , Ph.D. Dissertation Sharif University of Technology Monjezi, Mojdeh (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    The prediction of deposition efficiency of submicron particles in the pulmonary alveoli has received special attention due to its importance for drug delivery systems, and for assessing air pollutants health risks. In this work, the pulmonary alveoli of a healthy human are idealized by a three dimensional honeycomb like configuration and a fluid-structure interaction analysis is performed to study the normal cyclic breathing hydrodynamics. A viscoelastic model is used for the mechanical behavior of alveolar wall tissue. In contrast to previous works in which the inlet flow rate is predefined, in this model a negative pressure is imposed on the outside surface of the alveolus which causes air... 

    Modeling of Oxygen Transport and Exchange in an Acinus

    , M.Sc. Thesis Sharif University of Technology Mortazavi Ashkzari, Mohammad Sadegh (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    An acinus is defined as the complex of airways supplied by one first order respiratory or transitional bronchiole. In this part, the replenishment of oxygen at the alveolar surface occurs by a combination of convective air flow with diffusion of oxygen in the air. So for studying gas exchange in the lung, modeling gas species transport and exchange in an acinus is important. Due to lacking direct measurements of the distribution of oxygen (or carbon dioxide) concentration in the acinus, several mathematical models have been developed and studied by numerical simulations. But in none of them the influence of breathing pattern and the role of blood flow in restricting the gas exchange rate have... 

    Simulation of Urine Concentrating Mechanism in Rat Kidney Inner Medulla

    , M.Sc. Thesis Sharif University of Technology Sanatkhani, Soroush (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Physicians use charts that are prepared by experiments on animals or humans to prescribe drug dosage for patients. This method requires much more time by the Ministry of Health to approve new drugs to be used in health-care centers. Furthermore،we have no sight on how a specific drug is going to be diffuse in our body. In order to predict the distribution of a drug or any minerals in the kidney we need to model it. The first step would be modeling the important species that influence the urine concentrating mechanism. Due to the complications in modeling that mechanism especially in the inner medulla zone، we hadn’t solid information regarding that area. It is about half a century that... 

    Developing a Roadmap for Whole Lung Modeling and Some of the Required Software

    , Ph.D. Dissertation Sharif University of Technology Sani Josheqani, Mahdi (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    In this work, a new methodology for modeling the whole lung using porous media is presented. Dealing with the details of the proposed method establishes the need for some tools. Proposed method combines data extraction from lung images to identify large airways, porosity and porous region boundaries. Combining some sequential images, change in properties with time could be obtained. To obtain behavior of this porous media with respect to flow, a method based on the classification of bifurcations and gas exchange areas and pore scale modeling of these classes is proposed. All these require a specifically designed numerical tool. Development of this tool is the subject of the next parts of... 

    Numerical Simulation of the Effect of Ultrasound and Bubble Dynamic for the Application of Gas Embolotherapy Technique

    , M.Sc. Thesis Sharif University of Technology Salajeghe, Roozbeh (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Gas embolotherapy is a therapeutic method which is a suitable replacement for traditional embolotherapy techniques. This method is especially applicable for vascularized tumors which cannot be treated using other tumor treatments. In Gas embolotherapy technique, droplets made of Perfluorocarbon, whose evaporation temperature is below body temperature are injected into blood stream. The size of this droplets is chosen so that they can freely circulate in human vasculature and finally reach the specified target. At the target point, an ultrasound transducer is focused which causes the droplets to evaporate and turn into bubbles. During the evaporation process, bubbles expand volumetrically to... 

    Modeling, Simulation and Characterization of Blood Treatment and Filtration Process in Home Hemodialysis Machines

    , M.Sc. Thesis Sharif University of Technology Masoumi, Arezou (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Dialysis which is an imperfect but most common treatment option for renal failure is divided into two main types:"peritoneal dialysis" and "hemodialysis". Peritoneal dialysis uses a fluid that is placed into the patient's stomach cavity through a special plastic tube to remove excess waste products and fluid from the body.Hemodialysis uses a special type of filter to remove excess waste products and water from the body and is divided to two groups :Clinical and Home.During hemodialysis, blood passes from the patient's body through a filter in the dialysis machine. In this Study first the basic aspect of renal failure and principle of dialysis process are described.Then information about... 

    Air Flow and Respiratory Gas Exchange Simulation in Acinar Region of Human Lung

    , M.Sc. Thesis Sharif University of Technology Eslami Saray, Mohammad Ali (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    The main function of respiratory system is to exchange gasses between air and blood. However selection of the suitable geometry and solution of the fluid flow precede all other phenomena in the lung, including particle deposition and gas exchange. The most complicated phenomena take place at the terminal generations of the lung which is known as acinar region. Due to small dimensions and inability to use experimental measurements, numerical simulations are adequate methods in this region. In the first part of this thesis a method is proposed to reduce the computational space and make it possible to model all acinar region, simultaneously. Results show that the characteristic of streamlines... 

    Simulation of the Blood Flow in a Stenotic Left Coronary Bifurcation to Study the Effects on the Endothelial Cells

    , M.Sc. Thesis Sharif University of Technology Jahromi, Reza (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Morphology and alignment of endothelial cells (ECs) have great influence on plaque formation. These alignments are based on the cyclic strains and wall shear stress (WSS) on the arterial wall. In the present study, cyclic strains and WSS are investigated to predict the secondary plaque locations downstream of the primary stenosis. Therefore, left coronary artery (LCA) with its branches to left anterior descending (LAD) and left circumflex (LCX) are 3D located on a virtual sphere to consider the cardiac motion. Stenoses are placed at the beginning of the bifurcation with varying degrees from 40% to 70% based on diameter reduction. Healthy coronary is also constructed to compare with those of... 

    Modeling of Deposition of Low Density Lipoprotein (LDL) in Carotid Artery

    , M.Sc. Thesis Sharif University of Technology Mirbagheri, Amir (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Atherosclerosis is one of the most important and common causes of death in the world. Atherosclerosis typically affects medium and large arteries in the body and it leads to plaque formation in arterial wall. The first stage of plaque formation has been related to accumulation of low density lipoproteins in arterial wall.
    The purpose of this research is presenting a four-layer model to describe the LDL transport in the arterial wall. The endothelium, intima, internal elastic lamina (IEL) and media are all treated as macroscopically homogeneous porous media and the volume-averaged porous media equations are employed to model various layers. The physiological parameters within the various... 

    Electroosmotic Flow in Microchannels

    , M.Sc. Thesis Sharif University of Technology Lesani, Mostafa (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    The present study examines both Direct Current (DC) and Alternating Current (AC) electroosmotic flows in a parallel plate microchannel. The method consists of a central finite difference scheme for spatial terms and a forward difference scheme for the temporal term. Asymmetric boundary conditions are assumed for Poison-Boltzmann equation used to determine the electric double layer (EDL) potential distribution. The potential distribution is then used to evaluate the velocity distribution for both DC and AC electroosmotic flows. The velocity distributions are obtained by applying slip boundary conditions on the walls to account for probable hydrophobicity of the surfaces. After determining the... 

    An Investigation to the Effect of Heterogeneity of Surface’s Potential on Mass Transport and Surface Reaction Kinetics in Microreactors

    , M.Sc. Thesis Sharif University of Technology Abodllahzadeh, Mojtaba (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Nowadays, technology has facilitate the miniaturization of laboratory systems, medical and drug delivery tools. As a result, researchers are interested to miniaturize these tools. The extensive research in this field led to invention of lab-on-a-chips, which with the size of a few µm to a few mm, can do multiple tasks in human body. One of most important components of these devices, is microreactor. A wide range of measurements and reactions in microreactors, need to bind with the receptors at the surface of the cylindrical microchannels. For this purpose, this study, investigates the effects of surface heterogeneity on microreactors performance. In this Thesis, the governing equations were... 

    Design, Fabrication and Testing of an Integrated Microfluidic Platform for Water Quality Testing

    , M.Sc. Thesis Sharif University of Technology Mortazavi, Mohammad Ali (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Nowadays environmental issues are of great importance and one of the most paramount issues is the quality of water, because clean water is vital to our existence. Besides different methods for water purification, water quality testing is a useful and needful tool. Traditional methods for determination of water quality parameters are mainly expensive, time consuming and require highly trained staff. In this study, we have described a centrifugal microfluidic platform (Lab- on – a- CD) for simultaneous determination of different physical and chemical parameters including Nitrite, Free Chlorine and pH. All of the processes from sample injection to detection are integrated on this low-cost and... 

    Design, Simulation and Fabrication of Human Pulmonary Alveolus Model on a Microchip

    , Ph.D. Dissertation Sharif University of Technology Moghadas, Hajar (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Microfluidic systems create great development in diseases and drug delivery in various organs of the body. In this study, human pulmonary alveolar cell performance was evaluated from the perspective of the cell culture using a microfluidic system. For this purpose, numerical simulations of the microchip channels flow field are very important to select appropriate models. So in the first step, the flow field and particle deposition were simulated. Then an optimal model was selected based on key parameters such as cell feeding, shear stress exerted on the cell, particles distribution and also the limitations and possibilities for constructing. The numerical results show that the shear stress,... 

    Simulation of Surface Chemical Reactions in Bosch Process for a Polymer Film and Investigation of Etching Quality

    , M.Sc. Thesis Sharif University of Technology Montazeri Shahtoori, Abdolsamad (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Deep reactive ion etching is one of the most used techniques for manufacturing micro-structures. The most popular silicon DRIE technique is Bosch process. Ability to manufacture high aspect ratio features made Bosch process the main technique for developing micro-electromechanical devices. Dry etching is a combination of physical and chemical processes. The chemical processes play a very important role due to their speed of material removing and also due to their high selectivity. Also chemical processes are responsible for development of passive resist layer on the surface. On the other hand, if not controlled properly it can reduce anisotropy, resulting in a low quality etch. In this... 

    Design, Numerical Simulationand and Experimental Study of a Batch-type Stirred Bioreactor

    , M.Sc. Thesis Sharif University of Technology Pavir, Fereydoon (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    The stirred tank is one of the oldest device that widely used in different industrial. a special kind of stirred tank that clled bioreactor refer to any device which supplies required biological, biochemical and biomechanical engineered product. Since the aim of bioreactor is produce of desired biological product, it is essential to accurate monitoring internal and external transfer of nutrient, heat transfer, fluid velocity, Strain stress and medium PH. good design and application of bioreactor depend on product, organism, conditions for produce desired product and scale of produce. also cost of capital and function cost are important in bioreactor design. one of the most important... 

    nvestigation of the Effects of Evaporation, Inlet Momentum, and Spacer on the Transport and Deposition of Pharmaceutical Particles Delivered by a Metered Dose Inhaler (MDI) in Human Upper Airways

    , M.Sc. Thesis Sharif University of Technology Noormandipoor, Mojtaba (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    In this study the transport and deposition of pharmaceutical particles delivered by a commercial metered dose inhaler (MDI) is investigated in a combination of human upper airways, inhaler, and spacer. The emphasis of the present work is on the effects of evaporation of ethanol from particles, inlet momentum of particles, and use of spacer on their transport and deposition phenomena. The pharmaceutical particles are typically delivered with high initial momentum to human upper airways. It is believed that this initial momentum is responsible for increased undesirable deposition of particles in upper airways, especially in case of particles larger than 1 micrometer in diameter. In the present... 

    Design of a Microfluidic Digital Droplet PCR

    , M.Sc. Thesis Sharif University of Technology Abedini, Ali (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    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 and Numerical Simulation of a Micro-chip for Separating CTCs from Peripheral Blood

    , M.Sc. Thesis Sharif University of Technology Niknam, Hamid Reza (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    According to studies, cancer is the second leading cause of death in the world and millions of people die from this disease every year. Early diagnosis is one of the most important factors in controlling and treating the disease. The ability of circulating tumor cells to diagnose and monitor the disease has led many researchers to focus on studying and researching these cells in recent years. However, due to the fact that the concentration of this type of cells in the blood is very low, their isolation is associated with challenges. Various methods isolate CTCs based on physical, biological and other differences in characteristics. In this study, we investigate performance of a microfluidic... 

    Three-dimensional Simulation of Circulating Tumor Cells Magnetic Isolation Using a Viscoelastic-based Ferrofluid Solution

    , M.Sc. Thesis Sharif University of Technology Mostafavi, Ali (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Nowadays cancer is the second major cause of death in the world after cardiovascular diseases and scientists and researchers are making considerable efforts to fight it. Detection and isolation of circulating tumor cells in the blood is of paramount importance as it can be further used to measure the disease severity as well as efficacy of chemical drugs. Magnetophoresis has attracted researchers because of its simplicity, high effectiveness and non-invasiveness. Microfluidic systems have a high potential for implementing conventional biological methods in a microscale for detection, separation and incubation of CTCs, and they also lead to reduction in costs and required samples. Prior to... 

    Design and Simulation of a Spiral Based Microfluidic Device for Separation of Circulating Tumor Cells Using Tunable Nature of Viscoelastic Fluid

    , M.Sc. Thesis Sharif University of Technology Nouri, Mohammad Moein (Author) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Nowadays, cancer, which has been mentioned as the disease of the century, is the second leading cause of death throughout the world, and its incidence is constantly increasing. Isolation of circulating tumor cells is one of the most critical steps in diagnosing and controlling cancer progression. Due to the rarity of cancer cells compared to other cells in the blood sample, the isolation process requires optimal and high-precision devices. With the advent of inertial microfluidics, the ability to control the particles movement, the processing of blood samples as quickly and accurately as possible, and the viability of cells with a high percentage, introduced microfluidic systems as a...