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    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... 

    Parametric study of droplet formation and characteristics within microfluidic devices - A case study

    , Article International Journal of Applied Mechanics ; Volume 12, Issue 7 , 2020 Salehi, S. S ; Shamloo, A ; Kazemzadeh Hannani, S ; Sharif University of Technology
    World Scientific  2020
    Abstract
    Droplet-based microfluidics technologies hold great attention in a wide range of applications, including chemical analysis, drug screening, and food industries. This work aimed to describe the effects of different physical properties of the two immiscible phases on droplet formation in a flow-focusing microfluidic device and determining proper flow rates to form a droplet within the desired size range. A numerical model was developed to solve the governing equations of two-phase flow and the results were validated with previous experimental results. The results demonstrate different types of droplet formation regimes from dripping to jetting and different production rates of droplets as a... 

    3D Bioprinting of oxygenated cell-laden gelatin methacryloyl constructs

    , Article Advanced Healthcare Materials ; Volume 9, Issue 15 , 2020 Erdem, A ; Darabi, M. A ; Nasiri, R ; Sangabathuni, S ; Ertas, Y. N ; Alem, H ; Hosseini, V ; Shamloo, A ; Nasr, A. S ; Ahadian, S ; Dokmeci, M. R ; Khademhosseini, A ; Ashammakhi, N ; Sharif University of Technology
    Wiley-VCH Verlag  2020
    Abstract
    Cell survival during the early stages of transplantation and before new blood vessels formation is a major challenge in translational applications of 3D bioprinted tissues. Supplementing oxygen (O2) to transplanted cells via an O2 generating source such as calcium peroxide (CPO) is an attractive approach to ensure cell viability. Calcium peroxide also produces calcium hydroxide that reduces the viscosity of bioinks, which is a limiting factor for bioprinting. Therefore, adapting this solution into 3D bioprinting is of significant importance. In this study, a gelatin methacryloyl (GelMA) bioink that is optimized in terms of pH and viscosity is developed. The improved rheological properties... 

    Microfluidic-based approaches in targeted cell/particle separation based on physical properties: fundamentals and applications

    , Article Small ; Volume 16, Issue 29 , 2020 Nasiri, R ; Shamloo, A ; Ahadian, S ; Amirifar, L ; Akbari, J ; Goudie, M. J ; Lee, K ; Ashammakhi, N ; Dokmeci, M. R ; Di Carlo, D ; Khademhosseini, A ; Sharif University of Technology
    Wiley-VCH Verlag  2020
    Abstract
    Cell separation is a key step in many biomedical research areas including biotechnology, cancer research, regenerative medicine, and drug discovery. While conventional cell sorting approaches have led to high-efficiency sorting by exploiting the cell's specific properties, microfluidics has shown great promise in cell separation by exploiting different physical principles and using different properties of the cells. In particular, label-free cell separation techniques are highly recommended to minimize cell damage and avoid costly and labor-intensive steps of labeling molecular signatures of cells. In general, microfluidic-based cell sorting approaches can separate cells using “intrinsic”... 

    In-situ crosslinking of electrospun gelatin-carbodiimide nanofibers: fabrication, characterization, and modeling of solution parameters

    , Article Chemical Engineering Communications ; 2020 Hajiabbas, M ; Alemzadeh, I ; Vossoughi, M ; Shamloo, A ; Sharif University of Technology
    Taylor and Francis Ltd  2020
    Abstract
    This work has focused on in-situ crosslinking of gelatin (G) to produce electrospun scaffold with improved fiber morphology retention and mechanical properties. As per this approach, we prepared G nanofibers through mixing G, 1-ethyl-3-(3 dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) in the new solvent system. Response surface methodology (RSM) was employed to study the influence of solution parameters on fiber diameter. The morphological structure was examined, and the appropriate level of setting to obtain smooth fibers with a favorable diameter was reported. Results revealed using EDC/NHS for in-situ crosslinking improves the mechanical properties... 

    Drug delivery and adhesion of magnetic nanoparticles coated nanoliposomes and microbubbles to atherosclerotic plaques under magnetic and ultrasound fields

    , Article Engineering Applications of Computational Fluid Mechanics ; Volume 15, Issue 1 , 2021 , Pages 1703-1725 ; 19942060 (ISSN) Alishiri, M ; Ebrahimi, S ; Shamloo, A ; Boroumand, A ; Mofrad, M. R. K ; Sharif University of Technology
    Taylor and Francis Ltd  2021
    Abstract
    The use of external fields such as magnet and ultrasound to enhance the targeted drug delivery (TDD) by nano-microcarriers could be a potential method. In this research, the drug delivery of magnetic nanoparticles (NPs) coated nanoliposomes and microbubbles (MBs) to the atherosclerosis plaque was investigated under magnetic and ultrasound fields in terms of their adhesion to the plaque through ligand–receptor binding. The Halbach arrangement enhanced the surface density of nanoliposomes and MBs adhered to the plaque by ∼ (Formula presented.) and ∼ (Formula presented.), respectively. A focused transducer at the power of (Formula presented.) led to better drug delivery performance and caused ∼... 

    Drug delivery and adhesion of magnetic nanoparticles coated nanoliposomes and microbubbles to atherosclerotic plaques under magnetic and ultrasound fields

    , Article Engineering Applications of Computational Fluid Mechanics ; Volume 15, Issue 1 , 2021 , Pages 1703-1725 ; 19942060 (ISSN) Alishiri, M ; Ebrahimi, S ; Shamloo, A ; Boroumand, A ; Mofrad, M. R. K ; Sharif University of Technology
    Taylor and Francis Ltd  2021
    Abstract
    The use of external fields such as magnet and ultrasound to enhance the targeted drug delivery (TDD) by nano-microcarriers could be a potential method. In this research, the drug delivery of magnetic nanoparticles (NPs) coated nanoliposomes and microbubbles (MBs) to the atherosclerosis plaque was investigated under magnetic and ultrasound fields in terms of their adhesion to the plaque through ligand–receptor binding. The Halbach arrangement enhanced the surface density of nanoliposomes and MBs adhered to the plaque by ∼ (Formula presented.) and ∼ (Formula presented.), respectively. A focused transducer at the power of (Formula presented.) led to better drug delivery performance and caused ∼... 

    In-situ crosslinking of electrospun gelatin-carbodiimide nanofibers: fabrication, characterization, and modeling of solution parameters

    , Article Chemical Engineering Communications ; Volume 208, Issue 7 , 2021 , Pages 976-992 ; 00986445 (ISSN) Hajiabbas, M ; Alemzadeh, I ; Vossoughi, M ; Shamloo, A ; Sharif University of Technology
    Taylor and Francis Ltd  2021
    Abstract
    This work has focused on in-situ crosslinking of gelatin (G) to produce electrospun scaffold with improved fiber morphology retention and mechanical properties. As per this approach, we prepared G nanofibers through mixing G, 1-ethyl-3-(3 dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) in the new solvent system. Response surface methodology (RSM) was employed to study the influence of solution parameters on fiber diameter. The morphological structure was examined, and the appropriate level of setting to obtain smooth fibers with a favorable diameter was reported. Results revealed using EDC/NHS for in-situ crosslinking improves the mechanical properties... 

    High throughput blood plasma separation using a passive PMMA microfluidic device

    , Article Microsystem Technologies ; 2015 ; 09467076 (ISSN) Shamsi, A ; Shamloo, A ; Mohammadaliha, N ; Hajghassem, H ; Mehrabadi, J. F ; Bazzaz, M ; Sharif University of Technology
    Springer Verlag  2015
    Abstract
    Since plasma is rich in many biomarkers used in clinical diagnostic experiments, microscale blood plasma separation is a primitive step in most of microfluidic analytical chips. In this paper, a passive microfluidic device for on-chip blood plasma separation based on Zweifach–Fung effect and plasma skimming was designed and fabricated by hot embossing of microchannels on a PMMA substrate and thermal bonding process. Human blood was diluted in various times and injected into the device. The main novelty of the proposed microfluidic device is the design of diffuser-shaped daughter channels. Our results demonstrated that this design exerted a considerable positive influence on the separation... 

    Steered molecular dynamic simulation approaches for computing the blood brain barrier (BBB) diffusion coefficient

    , Article IFMBE Proceedings ; Volume 51 , 2015 , Pages 1699-1703 ; 16800737 (ISSN) ; 9783319193878 (ISBN) Pedram, M. Z ; Shamloo, A ; Alasti, A ; Zadeh, E. G ; Jaffray D. A ; Sharif University of Technology
    Springer Verlag  2015
    Abstract
    In the recent years a great attention of research deals with different physical and biological aspects of the BBB structure, a robust shield that separates the blood and brain, a recent research held by the authors of this paper has focused on figuring out computing the diffusion coefficient of endothelial cell membrane. In this study, the major efforts have been concentrated on calculating a standardized measure for the amount of permeability and diffusion of this barrier. As a result, this work is dedicated to molecular dynamics (MD) simulation of calculating the interaction force between nano-particle and BBB membrane. data is recorded by using steered molecular dynamics simulation and... 

    Superparamagnetic nanoparticles for epilepsy detection

    , Article World Congress on Medical Physics and Biomedical Engineering, 2015, 7 June 2015 through 12 June 2015 ; Volume 51 , June , 2015 , Pages 1237-1240 ; 16800737 (ISSN) ; 9783319193878 (ISBN) Pedram, M. Z ; Shamloo, A ; Alasty, A ; Ghafar Zadeh, E ; Jaffray D. A ; Sharif University of Technology
    Springer Verlag  2015
    Abstract
    Epilepsy is the most common neurological disorder that is known with uncontrolled seizure. Around 30% of patients with epilepsy resist to all forms of medical treatments and therefore, the removal of epileptic brain tissue is the only solution to get these patients free from chronical seizures. The precise detection of an epileptic zone is key to its treatment. In this paper, we propose a method of epilepsy detection using brain magnetic field. The possibility of superparamagnetic nanoparticle (SPMN) as sensors for the detection of the epileptic area inside the brain is investigated. The aggregation of nanoparticles in the weak magnetic field of epileptic brain is modeled using potential... 

    High throughput blood plasma separation using a passive PMMA microfluidic device

    , Article Microsystem Technologies ; Volume 22, Issue 10 , 2016 , Pages 2447-2454 ; 09467076 (ISSN) Shamsi, A ; Shamloo, A ; Mohammadaliha, N ; Hajghassem, H ; Fallah Mehrabadi, J ; Bazzaz, M ; Sharif University of Technology
    Springer Verlag  2016
    Abstract
    Since plasma is rich in many biomarkers used in clinical diagnostic experiments, microscale blood plasma separation is a primitive step in most of microfluidic analytical chips. In this paper, a passive microfluidic device for on-chip blood plasma separation based on Zweifach–Fung effect and plasma skimming was designed and fabricated by hot embossing of microchannels on a PMMA substrate and thermal bonding process. Human blood was diluted in various times and injected into the device. The main novelty of the proposed microfluidic device is the design of diffuser-shaped daughter channels. Our results demonstrated that this design exerted a considerable positive influence on the separation... 

    Margination and adhesion of micro- and nanoparticles in the coronary circulation: A step towards optimised drug carrier design

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 17, Issue 1 , 2018 , Pages 205-221 ; 16177959 (ISSN) Forouzandehmehr, M ; Shamloo, A ; Sharif University of Technology
    Springer Verlag  2018
    Abstract
    Obstruction of left anterior descending artery (LAD) due to the thrombosis or atherosclerotic plaques is the leading cause of death worldwide. Targeted delivery of drugs through micro- and nanoparticles is a very promising approach for developing new strategies in clot-busting or treating restenosis. In this work, we modelled the blood flow characteristics in a patient-specific reconstructed LAD artery by the fluid–solid interaction method and based on physiological boundary conditions. Next, we provided a Lagrangian description of micro- and nanoparticles dynamics in the blood flow considering their Brownian motion and the particle–particle interactions. Our results state that the number of... 

    Modeling, simulation, and employing dilution–dialysis microfluidic chip (DDMC) for heightening proteins refolding efficiency

    , Article Bioprocess and Biosystems Engineering ; Volume 41, Issue 5 , 2018 , Pages 707-714 ; 16157591 (ISSN) Kashanian, F ; Masoudi, M. M ; Shamloo, A ; Habibi Rezaei, M ; Moosavi Movahedi, A. A ; Sharif University of Technology
    Springer Verlag  2018
    Abstract
    Miniaturized systems based on the principles of microfluidics are widely used in various fields, such as biochemical and biomedical applications. Systematic design processes are demanded the proper use of these microfluidic devices based on mathematical simulations. Aggregated proteins (e.g., inclusion bodies) in solution with chaotropic agents (such as urea) at high concentration in combination with reducing agents are denatured. Refolding methods to achieve the native proteins from inclusion bodies of recombinant protein relying on denaturant dilution or dialysis approaches for suppressing protein aggregation is very important in the industrial field. In this paper, a modeling approach is... 

    Recent advances in the design and applications of amyloid-β peptide aggregation inhibitors for Alzheimer’s disease therapy

    , Article Biophysical Reviews ; Volume 11, Issue 6 , 2019 , Pages 901-925 ; 18672450 (ISSN) Jokar, S ; Khazaei, S ; Behnammanesh, H ; Shamloo, A ; Erfani, M ; Beiki, D ; Bavi, O ; Sharif University of Technology
    Springer  2019
    Abstract
    Alzheimer’s disease (AD) is an irreversible neurological disorder that progresses gradually and can cause severe cognitive and behavioral impairments. This disease is currently considered a social and economic incurable issue due to its complicated and multifactorial characteristics. Despite decades of extensive research, we still lack definitive AD diagnostic and effective therapeutic tools. Consequently, one of the most challenging subjects in modern medicine is the need for the development of new strategies for the treatment of AD. A large body of evidence indicates that amyloid-β (Aβ) peptide fibrillation plays a key role in the onset and progression of AD. Recent studies have reported... 

    Microfluidic technologies to engineer mesenchymal stem cell aggregates—applications and benefits

    , Article Biophysical Reviews ; Volume 12, Issue 1 , 2020 , Pages 123-133 Salehi, S. S ; Shamloo, A ; Kazemzadeh Hannani, S. K ; Sharif University of Technology
    Springer  2020
    Abstract
    Three-dimensional cell culture and the forming multicellular aggregates are superior over traditional monolayer approaches due to better mimicking of in vivo conditions and hence functions of a tissue. A considerable amount of attention has been devoted to devising efficient methods for the rapid formation of uniform-sized multicellular aggregates. Microfluidic technology describes a platform of techniques comprising microchannels to manipulate the small number of reagents with unique properties and capabilities suitable for biological studies. The focus of this review is to highlight recent studies of using microfluidics, especially droplet-based types for the formation, culture, and... 

    Nonlinear mechanics of soft composites: hyperelastic characterization of white matter tissue components

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 19, Issue 3 , 2020 , Pages 1143-1153 Yousefsani, S. A ; Shamloo, A ; Farahmand, F ; Sharif University of Technology
    Springer  2020
    Abstract
    This paper presents a bi-directional closed-form analytical solution, in the framework of nonlinear soft composites mechanics, for top-down hyperelastic characterization of brain white matter tissue components, based on the directional homogenized responses of the tissue in the axial and transverse directions. The white matter is considered as a transversely isotropic neo-Hookean composite made of unidirectional distribution of axonal fibers within the extracellular matrix. First, two homogenization formulations are derived for the homogenized axial and transverse shear moduli of the tissue, based on definition of the strain energy density function. Next, the rule of mixtures and... 

    Fluid-structure interaction simulation of blood flow and cerebral aneurysm: effect of partly blocked vessel

    , Article Journal of Vascular Research ; Volume 56, Issue 6 , 2019 , Pages 296-307 ; 10181172 (ISSN) Saeedi, M ; Shamloo, A ; Mohammadi, A ; Sharif University of Technology
    S. Karger AG  2019
    Abstract
    In this study, using fluid-structure interaction (FSI), 3-dimensional blood flow in an aneurysm in the circle of Willis-which is located in the middle cerebral artery (MCA)-has been simulated. The purpose of this study is to evaluate the effect of a partly blocked vessel on an aneurysm. To achieve this purpose, two cases have been investigated using the FSI method: in the first case, an ideal geometry of aneurysm in the MCA has been simulated; in the second case, modeling is performed for an ideal geometry of the aneurysm in the MCA with a partly blocked vessel. All boundary conditions, properties and modeling methods were considered the same for both cases. The only difference between the... 

    A computational model for estimation of mechanical parameters in chemotactic endothelial cells

    , Article Scientia Iranica ; Volume 23, Issue 1 , 2016 , Pages 260-267 ; 10263098 (ISSN) Kiyoumarsioskouei, A ; Shamloo, A ; Azimi, S ; Abeddoust, M ; Saidi, M.S ; Sharif University of Technology
    Sharif University of Technology 
    Abstract
    A cell migration numerical simulation is presented to mimic the motility of endothelial cells subjected to the concentration gradients of a Forebrain embryoniccortical neuron Conditioned Medium (CM). This factor was previously shflown to induce the directional chemotaxis of endothelial cells with an over-expressed G protein coupled receptor 124 (GPR 124). A cell simulator program incorporates basic elements of the cell cytoskeleton, including membrane, nucleus and cytoskeleton. The developed 2D cell model is capable of responding to concentration gradients of biochemical factors by changing the cytoskeleton arrangement. Random walk force, cell drag force and cell inertial effects are also... 

    Modeling Paramecium swimming in a capillary tube

    , Article Scientia Iranica ; Volume 23, Issue 2 , 2016 , Pages 658-667 ; 10263098 (ISSN) Sarvestani, A. N ; Shamloo, A ; Ahmadian, M. T ; Sharif University of Technology
    Sharif University of Technology 
    Abstract
    In certain types of biomimetic surgery systems, micro robots inspired by Paramecium are designed to swim in a capillary tube for gaining access to internal organs with minimal invasion. Gaining insight into the mechanics of Paramecium swimming in a capillary tube is vital for optimizing the design of such systems. There are two approaches to modeling the physics of micro swimming. In the envelope approach, which is widely accepted by researchers, Paramecium is approximated as a sphere, self-propelled by tangential and normal surface distortions. However, not only is this approach incapable of considering the specific geometry of Paramecium, but it also neglects short range hydrodynamic...