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Modeling comparison of graphene nanoribbon field effect transistors with single vacancy defect
, Article Superlattices and Microstructures ; Volume 97 , 2016 , Pages 28-45 ; 07496036 (ISSN) ; Faez, R ; Shamloo, H ; Sharif University of Technology
Academic Press
2016
Abstract
In this paper, some important circuit parameters of a monolayer armchair graphene nanoribbon (GNR) field effect transistor (GNRFET) in different structures are studied. Also, these structures are Ideal with no defect, 1SVGNRFET with one single vacancy defect, and 3SVsGNRFET with three SV defects. Moreover, the circuit parameters are extracted based on Semi Classical Top of Barrier Modeling (SCTOBM) method. The I-V characteristics simulations of Ideal GNRFET, 1SVGNRFET and 3SVsGNRFET are used for comparing with SCTOBM method. These simulations are solved with Poisson-Schrodinger equation self-consistently by using Non- Equilibrium Green Function (NEGF) and in the real space approach. The...
Improving ION / IOFF and sub-threshold swing in graphene nanoribbon field-effect transistors using single vacancy defects
, Article Superlattices and Microstructures ; Volume 86 , October , 2015 , Pages 483-492 ; 07496036 (ISSN) ; Faez, R ; Shamloo, H ; Sharif University of Technology
Academic Press
2015
Abstract
Graphene nanoribbon field effect transistors are promising devices for beyond-CMOS nanoelectronics. Graphene is a semiconductor material with zero bandgap and its bandgap must be changed. One of the opening bandgap methods is using graphene nanoribbons. By applying a defect, there is more increase on band gap of monolayer armchair graphene nanoribbon field effect transistor. So, by applying more than one defect, we can reach to much more increase in bandgap of graphene nanoribbon field effect transistors (GNRFET). In this paper, double-gated monolayer armchair graphene nanoribbon field effect transistors (GNRFET) with one single vacancy (1SV) defect (so-called 1SVGNRFET)are simulated and...
An integrative method to increase the reliability of conventional double emulsion method
, Article Analytica Chimica Acta ; Volume 1197 , 2022 ; 00032670 (ISSN) ; Afjoul, H ; Shamloo, A ; Sharif University of Technology
Elsevier B.V
2022
Abstract
Polymeric microspheres which can load biomolecules, cells and active agents play an important role in tissue engineering and drug delivery systems. The conventional double emulsion method has been frequently used to fabricate polymeric microspheres. However, this method has two major shortcomings: the complicated fabrication process which makes it difficult to predict the characteristics of the final microspheres while the size distribution of the microspheres has a wide range. In this study, we eliminate the shortcomings of the conventional double emulsion method and increase its performance without decreasing its high production rate. This can make the proposed modified method a promising...
A viscoelastic model for axonal microtubule rupture
, Article Journal of Biomechanics ; Volume 48, Issue 7 , 2015 , Pages 1241-1247 ; 00219290 (ISSN) ; Manuchehrfar, F ; Rafii Tabar, H ; Sharif University of Technology
Elsevier Ltd
2015
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 during...
Integrating hydrodynamic and acoustic cell separation in a hybrid microfluidic device: a numerical analysis
, Article Acta Mechanica ; Volume 233, Issue 5 , 2022 , Pages 1881-1894 ; 00015970 (ISSN) ; Dizani, M ; Shamloo, A ; Sharif University of Technology
Springer
2022
Abstract
Cell separation microfluidic devices have evolved into a multitude of biomedical and clinical research. Nonetheless, many critical issues remain in the way of achieving an excellent separation of target cells from a heterogeneous sample. Parallel to the abundant experimental studies related to the hybrid microfluidic methods, it is easy to perceive the lack of numerical investigations in order to optimize the separation process and its accuracy. In this study, for the first time to the best of our knowledge, a hybrid system by integrating acoustophoresis and pinched-flow fractionation (PFF) is proposed to achieve a viable system for a wide-range, precise separation. Employing the ultrasound...
Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach
, Article Journal of Magnetism and Magnetic Materials ; Volume 410 , 2016 , Pages 187-197 ; 03048853 (ISSN) ; Pedram, M. Z ; Heidari, H ; Alasty, A ; Sharif University of Technology
Elsevier
2016
Abstract
Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling...
Neuronal cell navigation within a microfluidic device
, Article Middle East Conference on Biomedical Engineering, MECBME ; 17-20 February , 2014 , pp. 261-264 ; 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 ; 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...
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) ; 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...
A plasmonic gold nanofilm-based microfluidic chip for rapid and inexpensive droplet-based photonic PCR
, Article Scientific Reports ; Volume 11, Issue 1 , December , 2021 ; 20452322 (ISSN) ; Bagheri, M ; Shamloo, A ; Kazemipour Ashkezari, A. H ; Sharif University of Technology
Nature Research
2021
Abstract
Polymerase chain reaction (PCR) is a powerful tool for nucleic acid amplification and quantification. However, long thermocycling time is a major limitation of the commercial PCR devices in the point-of-care (POC). Herein, we have developed a rapid droplet-based photonic PCR (dpPCR) system, including a gold (Au) nanofilm-based microfluidic chip and a plasmonic photothermal cycler. The chip is fabricated by adding mineral oil to uncured polydimethylsiloxane (PDMS) to suppress droplet evaporation in PDMS microfluidic chips during PCR thermocycling. A PDMS to gold bonding technique using a double-sided adhesive tape is applied to enhance the bonding strength between the oil-added PDMS and the...
Green synthesis of silica nanoparticles from olive residue and investigation of their anticancer potential
, Article Nanomedicine ; Volume 16, Issue 18 , 2021 , Pages 1581-1593 ; 17435889 (ISSN) ; Afjoul, H ; Shamloo, A ; Maleki, A ; Afjoul, N ; Sharif University of Technology
Future Medicine Ltd
2021
Abstract
Graphical abstract
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) ; 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...
Modeling of an ultrasound system in targeted drug delivery to abdominal aortic aneurysm: a patient-specificin silico study based on ligand-receptor binding
, Article IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control ; Volume 69, Issue 3 , 2022 , Pages 967-974 ; 08853010 (ISSN) ; Boroumand, A ; Ebrahimi, S ; Kalantarnia, F ; Maleki, S ; Moradi, H ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2022
Abstract
Targeted drug delivery methods have shown a significant impact on enhancing drug delivery efficiency and reducing drug side effects. While various stimuli have been used to promote the drug delivery process, applying ultrasound (US) waves to control drug particles through the human body, noninvasively, has drawn the scientist's attention. However, microcarriers delivery reaches the aneurysmal artery by US waves that exert volumetric forces on blood, and drug carriers, which can therefore affect blood flow patterns and movement pathways of drug carriers, have not yet been studied. In this study, we developed a 3-D patient-specific model of abdominal aortic aneurysm (AAA) to evaluate the...
Cyclic Behavior Modeling of Magnesium Alloy (AZ91) Under Thermo-Mechanical and Low Cycle Fatigue Loadings
, M.Sc. Thesis Sharif University of Technology ; 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 ; 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 ; 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) ; 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 ; 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) ; 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 ; 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...