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Mechanical behavior Analysis of Cancerous Cells in the Micropipette Aspiration Using Finite Element Simulations
, M.Sc. Thesis Sharif University of Technology ; Naghdabadi, Reza (Supervisor) ; Bavi, Omid (Co-Supervisor)
Abstract
Diseases such as cancer lead to extensive conversion in the biological structure of cells. These conversions can overshadow cell function. The dynamics of a cell directly depends on how it interacts with other cells and the extracellular environment. Most of these interactions are associated with the occurrence of mechanical phenomena and are due to forces that the cell has experienced. Cell mechanics manifests itself in the Mechanotransduction, the ability of a cell to sense and respond to external forces. Cancer alters the mechanical properties of the components of the cytoskeleton. Understanding the biomechanical behavior of cells and cytoskeleton can play an important role in early...
Biophysical implications of lipid bilayer rheometry for mechanosensitive channels
, Article Proceedings of the National Academy of Sciences of the United States of America ; Vol. 111, Issue. 38 , 2014 , Pages 13864-13869 ; Nakayama, Y ; Bavi, O ; Cox, C. D ; Qin, Q. H ; Martinac, B ; Sharif University of Technology
2014
Abstract
The lipid bilayer plays a crucial role in gating of mechanosensitive (MS) channels. Hence it is imperative to elucidate the rheological properties of lipid membranes. Herein we introduce a framework to characterize the mechanical properties of lipid bilayers by combining micropipette aspiration (MA) with theoretical modeling. Our results reveal that excised liposome patch fluorometry is superior to traditional cell-attached MA for measuring the intrinsic mechanical properties of lipid bilayers. The computational results also indicate that unlike the uniform bilayer tension estimated by Laplace's law, bilayer tension is not uniform across the membrane patch area. Instead, the highest tension...
Geometrical optimization of the overlap in mixed adhesive lap joints
, Article Journal of Adhesion ; Volume 89, Issue 12 , 2013 , Pages 948-972 ; 00218464 (ISSN) ; Bavi, N ; Shishesaz, M ; Sharif University of Technology
2013
Abstract
The aim of this research is to optimize the geometry of the overlap in mixed adhesive single-and double-lap joints using a modified version of Bees and Genetic Algorithms (BA and GA). Accounting for adherends Poisson's ratio in the deduced equilibrium equations, the proposed shear lag model gives a more accurate approximation of joint failure load in comparison with Volkersen's solution. The objective functions used in this work are used separately to maximize the load bearing capacity f and the specific strength (f/w) of the joint. This procedure is applied to optimize aeronautical adhesively bonded assemblies, while taking manufacturing constraints into account. The employed constraints...
The effect of local bending on gating of MscL using a representative volume element and finite element simulation
, Article Channels ; Vol. 8, issue. 4 , 2014 , p. 344-349 ; Vossoughi, M ; Naghdabadi, R ; Jamali, Y ; Sharif University of Technology
2014
Abstract
Many physiological processes such as cell division, endocytosis and exocytosis cause severe local curvature of the cell membrane. Local curvature has been shown experimentally to modulate numerous mechanosensitive (MS) ion channels. In order to quantify the effects of local curvature we introduced a coarse grain representative volume element for the bacterial mechanosensitive ion channel of large conductance (MscL) using continuum elasticity. Our model is designed to be consistent with the channel conformation in the closed and open states to capture its major continuum rheological behavior in response to the local membrane curvature. Herein we show that change in the local curvature of the...
The combined effect of hydrophobic mismatch and bilayer local bending on the regulation of mechanosensitive ion channels
, Article PLoS ONE ; Volume 11, Issue 3 , 2016 ; 19326203 (ISSN) ; Vossoughi, M ; Naghdabadi, R ; Jamali, Y ; Sharif University of Technology
Public Library of Science
2016
Abstract
The hydrophobic mismatch between the lipid bilayer and integral membrane proteins has well-defined effect on mechanosensitive (MS) ion channels. Also, membrane local bending is suggested to modulate MS channel activity. Although a number of studies have already shown the significance of each individual factor, the combined effect of these physical factors on MS channel activity have not been investigated. Here using finite element simulation, we study the combined effect of hydrophobic mismatch and local bending on the archetypal mechanosensitive channel MscL. First we show how the local curvature direction impacts on MS channel modulation. In the case of MscL, we show inward (cytoplasmic)...
Inorganic nanomaterials for chemo/photothermal therapy: a promising horizon on effective cancer treatment
, Article Biophysical Reviews ; Volume 11, Issue 3 , 2019 , Pages 335-352 ; 18672450 (ISSN) ; Zamani, M ; Golizadeh, M ; Bavi, O ; Sharif University of Technology
Springer Verlag
2019
Abstract
During the last few decades, nanotechnology has established many essential applications in the biomedical field and in particular for cancer therapy. Not only can nanodelivery systems address the shortcomings of conventional chemotherapy such as limited stability, non-specific biodistribution and targeting, poor water solubility, low therapeutic indices, and severe toxic side effects, but some of them can also provide simultaneous combination of therapies and diagnostics. Among the various therapies, the combination of chemo- and photothermal therapy (CT-PTT) has demonstrated synergistic therapeutic efficacies with minimal side effects in several preclinical studies. In this regard,...
Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study
, Article Journal of the Mechanical Behavior of Biomedical Materials ; Volume 117 , 2021 ; 17516161 (ISSN) ; Jamali, Y ; Tajkhorshid, E ; Bavi, O ; Pishkenari, H. N ; Sharif University of Technology
Elsevier Ltd
2021
Abstract
In addition to its biological importance, DPhPC lipid bilayers are widely used in droplet bilayers, study of integral membrane proteins, drug delivery systems as well as patch-clamp electrophysiology of ion channels, yet their mechanical properties are not fully measured. Herein, we examined the effect of the ether linkage on the mechanical properties of ester- and ether-DPhPC lipid bilayers using all-atom molecular dynamics simulation. The values of area per lipid, thickness, intrinsic lateral pressure profile, order parameter, and elasticity moduli were estimated using various computational frameworks and were compared with available experimental values. Overall, a good agreement was...
Investigation of Activation Mechanism of Mechanosensitive Nano Ion Channels
, Ph.D. Dissertation Sharif University of Technology ; Vosoughi, Manochehr (Supervisor) ; Jamali, Yusef (Supervisor) ; Naghdabadi, Reza (Supervisor)
Abstract
Mechanosensitive (MS) channels are ubiquitous molecular force sensors that respond to a number of different mechanical stimuli including tensile, compressive and shear stress. One of the main mechanisms to functionally study these channels is the patch clamp technique. Here we use continuum mechanics to probe the question of how curvature, in a standard patch clamp experiment, at different length scales (global and local) affects a model MS channel. Firstly, to increase the accuracy of the Laplace’s equation in tension estimation in a patch membrane and to be able to more precisely describe the transient phenomena happening during patch clamping, we propose a modified Laplace’s equation. In...
The role of mscl amphipathic n terminus indicates a blueprint for bilayer-mediated gating of mechanosensitive channels
, Article Nature Communications ; Volume 7 , 2016 ; 20411723 (ISSN) ; Cortes, D. M ; Cox, C. D ; Rohde, P. R ; Liu, W ; Deitmer, J. W ; Bavi, O ; Strop, P ; Hill, A. P ; Rees, D ; Corry, B ; Perozo, E ; Martinac, B ; Sharif University of Technology
Nature Publishing Group
2016
Abstract
The bacterial mechanosensitive channel MscL gates in response to membrane tension as a result of mechanical force transmitted directly to the channel from the lipid bilayer. MscL represents an excellent model system to study the basic biophysical principles of mechanosensory transduction. However, understanding of the essential structural components that transduce bilayer tension into channel gating remains incomplete. Here using multiple experimental and computational approaches, we demonstrate that the amphipathic N-terminal helix of MscL acts as a crucial structural element during tension-induced gating, both stabilizing the closed state and coupling the channel to the membrane. We...
Synthesize of Graphene Nanoribbons with a Non-Zero Energy Band Gap for Inactivation of Alive Cells Using Infrared Irradiation
, M.Sc. Thesis Sharif University of Technology ; Akhavan, Omid (Supervisor)
Abstract
Graphene is a one layer atom thickness and zero energy gap so for using it in nano electronic and transistors baised on graphene it's energy gap should be opened.one of the methods for opening graphene band gap is creating nano scale boundaries or synthesize graphene nanoribbons. One of the new methods for graphene nanoribbon synthesize is longitudinal opening of carbon nanotube. In this thesis graphene nanoribbons synthesize with this method and analyze with AFM and Raman spectroscopy. Carbon nanotubes also have energy gap and IR absorption recently they used for living cell destruction. In this thesis we synthesize graphene nanoribbons and analyzing their optical absorption and use it for...
Fabrication of Graphene/TiO2 Nanowalls as Visible Lights Photocatalysts
, M.Sc. Thesis Sharif University of Technology ; Akhavan, Omid (Supervisor)
Abstract
TiO2 is known as a photocatalyst in near UV-Visible light region with better efficiency compared to other semiconductor photocatalysts. Many attempts have been done to increase the efficiency of this photocatalyst. also, application of 2D carbon nanostructures namely graphene for increasing the photocatalytic activity of TiO2 has shown positive results.
In this research, we first synthesized Graphene Oxide (GO) suspension by exfolation of graphite oxide suspension. then we fabricated TiO2 thin films on glass substrates by so-called sol-gel method. finally we fabricate Graphene Oxide/TiO2 nanowalls composite films as a photocatalyst in visible light. X-ray photoelectron spectroscopy...
In this research, we first synthesized Graphene Oxide (GO) suspension by exfolation of graphite oxide suspension. then we fabricated TiO2 thin films on glass substrates by so-called sol-gel method. finally we fabricate Graphene Oxide/TiO2 nanowalls composite films as a photocatalyst in visible light. X-ray photoelectron spectroscopy...
Fabrication of Graphene-WO3 Nanocomposites as Photocatalyst in the Visible Light Region
, M.Sc. Thesis Sharif University of Technology ; Akhavan, Omid (Supervisor)
Abstract
WO3 is known as a photocatalyst in the visible light region, but with lower efficiency compared to more interesting semiconductor photocatalysts such as TiO2 and ZnO. Many attempts have been done to increase the efficiency of this photocatalyst by incorporating metal and metal oxide nanoparticles or recently carbon nanotubes.On the other hand, application of graphene, as an unrolled carbon nanotube, for increasing the photocatalytic activity of TiO2 and ZnO has shown positive results. Furthermore, it was reported that such semiconductor photocatalysts (and very recently WO3) can photocatalytically reduce the chemically exfoliated graphene oxide sheets under UV-vis irradiation.
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Synthesis of Graphene Nanosheets for Stem Cells Applications
, M.Sc. Thesis Sharif University of Technology ; Akhavan, Omid (Supervisor)
Abstract
Graphene nanogrids fabricated by graphene nanoribbons obtained through oxidative unzipping of multi-walled carbon nanotubes, used as two-dimensional selective templates for accelerated differentiation of human mesenchymal stem cells (hMSCs), isolated from umbilical cord blood, into osteogenic lineage. The biocompatible and hydrophilic graphene nanogrids showed high actin cytoskeleton proliferations that coinciding with patterns of the nanogrids. The amounts of proliferations found are slightly better than proliferation on hydrophilic graphene oxide (GO) sheets, and significantly higher than non-uniform proliferations on hydrophobic reduced graphene oxide (rGO) sheets and polydimethylsiloxane...
Identifying the risks of Iranian Knowledge BasedFirms Using Fault Tree Analysis (FTA)
, M.Sc. Thesis Sharif University of Technology ; Fattahi, Omid (Supervisor)
Abstract
Knowledge Based Firms are considered to be important for the economic development of a country in regards to both employment growth and innovative activity. The latter is believed to contribute significantly to the increase in productivity and therefore the competitiveness of Iran’s economy. This study contributes to the above literature by investigating the factors that are believed to treat the growth of such firms in Iran. The purpose of this study is to identify functional risks of vital signs monitors via Fault Tree Analysis (FTA) method to use as a guide for manufacturers to identify and control hazards. Therefore, 30 knowledge based firms were selected as sample. Then, based on a...
Synthesis of Graphene from Waste by Chemical Exfoliation and Study of It’s Physical Characteristics
, M.Sc. Thesis Sharif University of Technology ; Akhavan, Omid (Supervisor)
Abstract
One atom thick layer of pure carbon in bonded and hexagonal lattice is named graphene. graphene has unique mechanical, optical, thermal and electrical properties and because of these properties has grabbed attention. graphene has been made from high pure graphite by different methods such as CVD(chemical vapor deposition) , chemical exfoliation , micromechanical cleavage and colloidal suspension. through these methods, green methods for synthesis of graphene, using eco-friendly reductants during synthesis of graphene instead of hydrazine and recently using waste(not graphite) are attractive for synthesis of graphene. Following this idea , a group has produced graphene from wastes such as...
The Use of Hydrogen Rich Water for Synthesis of Hydrogenized Graphene and Investigation of Its Properties
, M.Sc. Thesis Sharif University of Technology ; Akhavan, Omid (Supervisor)
Abstract
Graphene is a two dimensional lattice which is created from carbon atoms. Having special feature, it has such various medical usage, for example in diagnosing and treating cancer. Adding a particular factor to graphene could improve their efficiency. In comparis on with graphene itself, graphene oxide and reduced graphene oxide are much more successful in diagnosing and treating than others because of their higher hygroscopic. Recent studies state that hydrogenized combinations including hydrogenized graphene show desired results. Due to its higher hygroscopic and the possibility of adherence to the cells, hydrogenized graphene could be very effective in diagnosing and treating the sarcomas....
A Meta Heuristic Approach for Design of a Network System in Mass Customization
, M.Sc. Thesis Sharif University of Technology ; Fattahi, Omid (Supervisor)
Abstract
This study discusses about mass customization and optimization of supply network in which both goal considering to set the flow of raw material and final product to satisfy the customer demand. The mass customization is more important concept in this study, so that this goal is placed to the first objective. In this research, the model which contained both goal is presented. The model focus on mass customization and try to satisfy various products demand, which constitute 3 kind of speed demands. Each product can satisfy in 3 way: fast, normal, slow.In the first model the new approach present in which the speed affects all of supplying, manufacturing and distributing system. The system try...
Synthesis of Graphene Oxide and Study of its Fluorescence Properties
, M.Sc. Thesis Sharif University of Technology ; Akhavan, Omid (Supervisor)
Abstract
Graphene oxide is a single sheet of Carbon atoms which has been arranged on a two-dimensional honeycomb lattice. Functional groups such as epoxy, carboxyl and carbonyl are located on basal plane and at the edges of graphene oxide and they localize electrons on the surface of graphene oxide and open band gap in its band structure. Pure graphene has zero band gap, so existence of fluorescence properties is unlikely; but graphene oxide has fluorescence properties due to band gap in its band structure. Fluorescence properties of graphene have been used in live cell imaging and drug delivery, so study and increasing of fluorescence properties is significantly important. The purpose of this...
A Novel Reliability Model for Information Technology Web services
, M.Sc. Thesis Sharif University of Technology ; Fatahi Valilai, Omid (Supervisor)
Abstract
The Internet is often used for communication-based applications such as online banking, stock trading, and shopping where service interruption is unacceptable. Thus, analysis of the impact of the failures of hardware, software, and related services’ performance quality of the service provided to users is of importance to designers and managers in these functions. In this study, we developed a strategy to the design of a dynamic combination of file servers with the aim of providing reliability and SLA. At first, we examine the reasons for the violation of service level in file host services and datacenters, and then we introduce the criteria to measure the violation of service level on the...
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) ; 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...