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    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... 

    Plaque structure affects mechanical stress distribution within blood vessels

    , Article Proceedings of the IASTED International Conference on Biomedical Engineering, BioMed 2014 ; 2014 , pp. 239-243 Mohseni, M ; Mehboudi, N ; Abdollahi, M ; Shamloo, A ; Naghdabadi, R ; Sharif University of Technology
    2014
    Abstract
    The main goal of this study is to investigate the effects of plaque structure on its stress distribution. Rupture of plaque causes cerebrovascular diseases which lead to high mortality rates all over the world. Computers are powerful tools to understand the mechanism of plaque rupture. In this study, 3D fluid structure interaction simulation is constructed in ABAQUS 6.13 to clarify the relation between stress distribution of plaque and its structure. A model of common carotid artery with distributed stenosis was chosen for the simulation. To investigate the effects of plaque structure on stress distribution, thickness of fibrous cap and lipid core size were varied in the stenosis.... 

    Dual improvement of DNA-directed antibody immobilization utilizing magnetic fishing and a polyamine coated surface

    , Article RSC Advances ; Volume 6, Issue 112 , 2016 , Pages 111210-111216 ; 20462069 (ISSN) Esmaeili, E ; Soleimani, M ; Shamloo, A ; Mahmoudifard, M ; Vossoughi, M ; Sharif University of Technology
    Royal Society of Chemistry  2016
    Abstract
    The present study is aimed at the development of a novel approach based on the magnetic improvement of DNA-directed antibody immobilization to prepare a highly efficient sensing platform. Magnetic nanoparticle substrates with high surface area capture the dual DNA-conjugated antibodies in a solution. This allows overcoming the typical mass transport limitation of the surface-based antibody immobilization. Antibody-magnetic nanoparticle conjugation is based on a robust hybridization between a DNA tether (attached to the antibody) and its complementary sequence (immobilized on the nanoparticle). Conventional antibody immobilization for the detection of proteins is often insignificant for the... 

    A comparative study of collagen matrix density effect on endothelial sprout formation using experimental and computational approaches

    , Article Annals of Biomedical Engineering ; Volume 44, Issue 4 , 2016 , Pages 929-941 ; 00906964 (ISSN) Shamloo, A ; Mohammadaliha, N ; Heilshorn, S. C ; Bauer, A. L ; Sharif University of Technology
    2016
    Abstract
    A thorough understanding of determining factors in angiogenesis is a necessary step to control the development of new blood vessels. Extracellular matrix density is known to have a significant influence on cellular behaviors and consequently can regulate vessel formation. The utilization of experimental platforms in combination with numerical models can be a powerful method to explore the mechanisms of new capillary sprout formation. In this study, using an integrative method, the interplay between the matrix density and angiogenesis was investigated. Owing the fact that the extracellular matrix density is a global parameter that can affect other parameters such as pore size, stiffness,... 

    Molecular dynamics simulation of the dissociation mechanism of P-selectin from PSGL-1

    , Article Journal of Theoretical and Computational Chemistry ; Volume 16, Issue 4 , 2017 ; 02196336 (ISSN) Hassani Ardekani, H ; Niroomand Oscuii, H ; Nikbin, E ; Shamloo, A ; Sharif University of Technology
    World Scientific Publishing Co. Pte Ltd  2017
    Abstract
    Interactions between P-selectin, expressed on activated endothelium, and its counterpart P-selectin glycoprotein ligand-1 (PSGL-1), expressed on leukocytes, play a pivotal role in adhesive events that recruit circulating leukocytes toward inflamed or injured tissues. Atomistic understanding of the association and dissociation of these bonds under blood flow is necessary to define the underlying mechanism. In this study, steered molecular dynamics (SMD) simulations were applied to investigate the conformational changes of P-LE/SGP-3 construct (an effective binding unit of the P-selectin/PSGL-1 complex) under stretching with constant velocity. In the present simulations, a self-built force... 

    Melt electrowriting of PLA, PCL, and composite PLA/PCL scaffolds for tissue engineering application

    , Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) Shahverdi, M ; Seifi, S ; Akbari, A ; Mohammadi, K ; Shamloo, A ; Movahhedy, M. R ; Sharif University of Technology
    Nature Research  2022
    Abstract
    Fabrication of well-ordered and bio-mimetic scaffolds is one of the most important research lines in tissue engineering. Different techniques have been utilized to achieve this goal, however, each method has its own disadvantages. Recently, melt electrowriting (MEW) as a technique for fabrication of well-organized scaffolds has attracted the researchers’ attention due to simultaneous use of principles of additive manufacturing and electrohydrodynamic phenomena. In previous research studies, polycaprolactone (PCL) has been mostly used in MEW process. PCL is a biocompatible polymer with characteristics that make it easy to fabricate well-arranged structures using MEW device. However, 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... 

    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... 

    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... 

    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... 

    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... 

    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... 

    Development of a Paper-based Microfluidic Device for Biological Assay

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

    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... 

    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)
    Abstract
    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... 

    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...