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    Numerical Simulation and Manufacture of a Proton Exchange Membrane Fuel Cell to Examine Mass and Charge Transport through Micro Porous Layers

    , M.Sc. Thesis Sharif University of Technology Asadzade, Mostafa (Author) ; Shamloo, Amir (Supervisor) ; Noori, Ali (Supervisor)
    Abstract
    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... 

    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... 

    Design, Simulation and Construction of a Microfluidic Device for the Purpose of Target Cells Separation and DNA Extraction

    , M.Sc. Thesis Sharif University of Technology Amani, Ali (Author) ; Shamloo, Amir (Supervisor) ; Nouri Borujerdi, Ali (Supervisor)
    Abstract
    Today, microfluidic experiments have found wide applications in medical sciences, engineering, and chemistry. Because of their small size, microfluidic devices help us to be able to use very little amount of sample for the experiments and also easily control and observe the under-experiment fluid. One of the most important applications of these devices is the separation of cancer cells in blood for counting their number and DNA genetic studies. In the current project we have tried to do the separation of cancer cells from other cells by designing an inertia microchannel. For this purpose, in the first step a geometry for the channel is designed with analyzing the induced forces on the cells.... 

    Design and Fabrication of an Integrated Lab-on-a-chip System for DNA Extraction from Cells and Gene Amplification

    , M.Sc. Thesis Sharif University of Technology Topa Heidari, Mohammad Mahdi (Author) ; Shamloo, Amir (Supervisor) ; Nouri Borujerdi, Ali (Supervisor)
    Abstract
    In this study, an integrated lab-on-a-chip (LOC) system was designed and developed to perform various processes, including cell separation, cell lysis, DNA extraction, and amplification, in an automated and unified manner. The system was designed to operate with fully disposable components, eliminating the risk of cross-contamination. The design includes five distinct microfluidic chips, each dedicated to a specific function. For cell separation, the inertial method was employed, which operates without the need for a micromixer and delivers high accuracy. Simulations demonstrated a recovery rate of 100% and a purity of 96.8%, while experimental results showed a recovery rate of 88.8% and a... 

    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... 

    Neuronal cell navigation within a microfluidic device

    , Article Middle East Conference on Biomedical Engineering, MECBME ; 17-20 February , 2014 , pp. 261-264 Shamloo, A ; Sharif University of Technology
    2014
    Abstract
    In this study, the polarization and navigation of neuronal cells was studied in response to quantified gradients of nerve growth factor (NGF). To accomplish this, a microfluidic device was designed and fabricated to generate stable concentration gradients of biomolecules in a cell culture chamber within a 3D microenvironment. Numerical simulation was implemented to optimize the device geometry for generating a uniform concentration gradient of NGF which was found to remain stable for multiple hours. Neural Stem/ Progenitor Cell (NSCs) migration and differentiation was studied within this microfluidic device in response to NGF concentration and within a 3D environment of collagen matrix.... 

    Cell-cell interactions mediate cytoskeleton organization and collective endothelial cell chemotaxis

    , Article Cytoskeleton ; Vol. 71, issue. 9 , 2014 , p. 501-512 Shamloo, A ; Sharif University of Technology
    2014
    Abstract
    This study investigates the role of cell-cell and cell-ligand interactions in cytoskeleton organization of endothelial cells (ECs) and their directional migration within a microfluidic device. The migration of ECs in response to a biochemical factor was studied. Mathematical analysis of the cell migration pathways and cellular cytoskeleton revealed that directional migration, migration persistence length, migration speed, and cytoskeletal stress fiber alignment can be mediated by the level of cell contacts as well as the presence or absence of a biochemical polarizing factor. It was shown that in the presence of a biochemical polarizing factor, higher cell density and more frequent cell... 

    Parallel in-vitro and in-vivo techniques for optimizing cellular microenvironments by implementing biochemical, biomechanical and electromagnetic stimulations

    , Article Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS ; 2012 , Pages 1397-1400 ; 1557170X (ISSN) ; 9781424441198 (ISBN) Shamloo, A ; Heibatollahi, M ; Ghafar Zadeh, E
    2012
    Abstract
    Development of novel engineering techniques that can promote new clinical treatments requires implementing multidisciplinary in-vitro and in-vivo approaches. In this study, we have implemented microfluidic devices and in-vivorat model to study the mechanism of neural stem cell migration and differentiation.These studies can result in the treatment of damages to the neuronal system. In this research, we have shown that by applying appropriate ranges of biochemical and biomechanical factors as well as by exposing the cells to electromagnetic fields, it is possible to improve viability, proliferation, directional migration and differentiation of neural stem cells. The results of this study can... 

    A microfluidic device for 2D to 3D and 3D to 3D cell navigation

    , Article Journal of Micromechanics and Microengineering ; Volume 26, Issue 1 , November , 2015 ; 09601317 (ISSN) Shamloo, A ; Amirifar, L ; Sharif University of Technology
    Institute of Physics Publishing  2015
    Abstract
    Microfluidic devices have received wide attention and shown great potential in the field of tissue engineering and regenerative medicine. Investigating cell response to various stimulations is much more accurate and comprehensive with the aid of microfluidic devices. In this study, we introduced a microfluidic device by which the matrix density as a mechanical property and the concentration profile of a biochemical factor as a chemical property could be altered. Our microfluidic device has a cell tank and a cell culture chamber to mimic both 2D to 3D and 3D to 3D migration of three types of cells. Fluid shear stress is negligible on the cells and a stable concentration gradient can be... 

    Investigation of the adhesive characteristics of polymer-protein systems through molecular dynamics simulation and their relation to cell adhesion and proliferation

    , Article Integrative Biology (United Kingdom) ; Volume 8, Issue 12 , 2016 , Pages 1276-1295 ; 17579694 (ISSN) Shamloo, A ; Sarmadi, M ; Sharif University of Technology
    Royal Society of Chemistry  2016
    Abstract
    Protein adhesion is a prevalent, however, intricate phenomenon that occurs immediately after exposure of a biomaterial to the biological system. A study on the adhesive characteristics of biomaterial-protein systems has encountered serious hurdles as experimental methods cannot properly capture the initial stages of protein adhesion, taking place within nano/picoseconds. This propels research studies toward utilizing computational approaches to gain an understanding of the interactions between different proteins and biomaterial surfaces. Herein, we use molecular dynamics (MD) modeling, as the computational framework, to study the adhesive characteristics of different biomaterial-protein... 

    Inertial particle focusing in serpentine channels on a centrifugal platform

    , Article Physics of Fluids ; Volume 30, Issue 1 , 2018 ; 10706631 (ISSN) Shamloo, A ; Mashhadian, A ; Sharif University of Technology
    American Institute of Physics Inc  2018
    Abstract
    Inertial particle focusing as a powerful passive method is widely used in diagnostic test devices. It is common to use a curved channel in this approach to achieve particle focusing through balancing of the secondary flow drag force and the inertial lift force. Here, we present a focusing device on a disk based on the interaction of secondary flow drag force, inertial lift force, and centrifugal forces to focus particles. By choosing a channel whose cross section has a low aspect ratio, the mixing effect of the secondary flow becomes negligible. To calculate inertial lift force, which is exerted on the particle from the fluid, the interaction between the fluid and particle is investigated... 

    Personalised deposition maps for micro- and nanoparticles targeting an atherosclerotic plaque: attributions to the receptor-mediated adsorption on the inflamed endothelial cells

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 18, Issue 3 , 2019 , Pages 813-828 ; 16177959 (ISSN) Shamloo, A ; Forouzandehmehr, M ; Sharif University of Technology
    Springer Verlag  2019
    Abstract
    Endothelial inflammation as a prominent precursor to atherosclerosis elicits a distinct pathological surface expression of particular vascular proteins. To exhibit a site-specific behaviour, micro- and nanoparticles, as carriers of therapeutics or imaging agents, can distinguish and use these proteins as targeted docking sites. Here, a computational patient-specific model capturing the exclusive luminal qualities has been developed to study the transport and adsorption of particles decorated with proper antibodies over an atherosclerotic plaque located in the LAD artery of the patient. Particles, in nano- and micron sizes, have been decorated with Sialyl Lewisx (sLex), P-selectin aptamer... 

    Numerical analysis of a dielectrophoresis field-flow fractionation device for the separation of multiple cell types

    , Article Journal of Separation Science ; Volume 40, Issue 20 , 2017 , Pages 4067-4075 ; 16159306 (ISSN) Shamloo, A ; Kamali, A ; Sharif University of Technology
    2017
    Abstract
    In this study, a dielectrophoresis field-flow fractionation device was analyzed using a numerical simulation method and the behaviors of a set of different cells were investigated. By reducing the alternating current frequency of the electrodes from the value used in the original setup configuration and increasing the number of exit channels, total discrimination in cell trajectories and subsequent separation of four cell types were achieved. Cells were differentiated based on their size and dielectric response that are represented in their real part of Clausius–Mossotti factor at different frequencies. A number of novel designs were also proposed based on the original setup configuration.... 

    Design and simulation of a microfluidic device for acoustic cell separation

    , Article Ultrasonics ; Volume 84 , March , 2018 , Pages 234-243 ; 0041624X (ISSN) Shamloo, A ; Boodaghi, M ; Sharif University of Technology
    Elsevier B.V  2018
    Abstract
    Experimental acoustic cell separation methods have been widely used to perform separation for different types of blood cells. However, numerical simulation of acoustic cell separation has not gained enough attention and needs further investigation since by using numerical methods, it is possible to optimize different parameters involved in the design of an acoustic device and calculate particle trajectories in a simple and low cost manner before spending time and effort for fabricating these devices. In this study, we present a comprehensive finite element-based simulation of acoustic separation of platelets, red blood cells and white blood cells, using standing surface acoustic waves... 

    Nanomechanics of actin filament: a molecular dynamics simulation

    , Article Cytoskeleton ; Volume 75, Issue 3 , March , 2018 , Pages 118-130 ; 19493584 (ISSN) Shamloo, A ; Mehrafrooz, B ; Sharif University of Technology
    John Wiley and Sons Inc  2018
    Abstract
    Actin is known as the most abundant essentially protein in eukaryotic cells. Actin plays a crucial role in many cellular processes involving mechanical forces such as cell motility, adhesion, muscle contraction, and intracellular transport. However, little is known about the mechanical properties of this protein when subjected to mechanical forces in cellular processes. In this article, a series of large-scale molecular dynamics simulations are carried out to elucidate nanomechanical behavior such as elastic and viscoelastic properties of a single actin filament. Here, we used two individual methods namely, all-atoms and coarse-grained molecular dynamics, to evaluate elastic properties of a... 

    Investigation of a Novel Microfluidic Device for Label-Free Ferrohydrodynamic Cell Separation on a Rotating Disk

    , Article IEEE Transactions on Biomedical Engineering ; Volume 67, Issue 2 , 2020 , Pages 372-378 Shamloo, A ; Besanjideh, M ; Sharif University of Technology
    IEEE Computer Society  2020
    Abstract
    Negative magnetophoresis is a novel and attractive method for continuous microparticle sorting inside a magnetic medium. In this method, diamagnetic particles are sorted based on their sizes using magnetic buoyancy force and without any labeling process. Although this method provides some attractive features, such as low-cost fabrication and ease of operation, there are some obstacles that adversely affect its performance, especially for biological applications. Most types of magnetic media, such as ferrofluids, are not biocompatible, and the time-consuming process of sample preparation can be threatening to the viability of the cells within the sample. Furthermore, in this method, both the... 

    Cyclic Behavior Modeling of Magnesium Alloy (AZ91) Under Thermo-Mechanical and Low Cycle Fatigue Loadings

    , M.Sc. Thesis Sharif University of Technology Shamloo, Ali (Author) ; Farrahi, Gholamhossein (Supervisor)
    Abstract
    Magnesium alloys have been used in the production of light weight components in automobile industries (for example: the ladder frame and the valve cover) due to a good combination of low density (1740 kg/m3), the tensile strength (160-365 MPa) and the elastic modulus (45 GPa). For the design and the optimization of these components under various loadings and different conditions, it is necessary to determine fatigue properties of the material by using thermo-mechanical and low cycle fatigue tests at different temperatures. In thermo-mechanical fatigue tests, the temperature varies in a specific range with the mechanical strain. The goal of this research is to investigate low cycle fatigue... 

    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)
    Abstract
    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... 

    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... 

    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...