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    Fluids Flow Simulation in the Cell Influenced the Focal Adhesions

    , Ph.D. Dissertation Sharif University of Technology Nikmaneshi, Mohammad Reza (Author) ; Firoozabadi, Bahar (Supervisor) ; saidi, Mohammad said (Co-Advisor)
    Abstract
    In the present thesis, intracellular fluid flows have investigated for study cell motions. It is due to firmly relation between the cell motion and these flows. Generally, the cell firstly adheres to a surface, then, moves forward with the effects of the internal fluid flows. In this study, the cell structure is invided to two general parts; the front part of the cell and the cell body. The front part of the cell plays a essential roles in the cell motion, however, the cell body is considered as a extra cargo that is carried by the front of the cell. Therefor, in the present modellings, the front part is only considered. Here, using four different models for the front part of the cell, many... 

    A misbehavior‐tolerant multipath routing protocol for wireless Ad hoc networks [electronic resource]

    , Article International Journal of Research in Wireless Systems (IJRWS) ; Vol. 2, Issue 9, pp. , Sep. 2013 Sedghi, H. (Haniyeh) ; Pakravan, Mohammad Reza ; Aref, Mohammad Reza ; Sharif University of Technology
    Abstract
    Secure routing is a major key to service maintenance in ad hoc networks. Ad hoc nature exposes the network to several types of node misbehavior or attacks. As a result of the resource limitations in such networks nodes may have a tendency to behave selfishly. Selfish behavior can have drastic impacts on network performance. We have proposed a Misbehavior-Tolerant Multipath Routing protocol (MTMR) which detects and punishes all types of misbehavior such as selfish behavior, wormhole, sinkhole and grey-hole attacks. The protocol utilizes a proactive approach to enforce cooperation. In addition, it uses a novel data redirection method to mitigate the impact of node misbehavior on network... 

    Multi-scale Simulation of Tumor Microenvironment

    , M.Sc. Thesis Sharif University of Technology Nikmaneshi, Mohammad Reza (Author) ; Firoozabadi, Bahar (Supervisor) ; Mozafari, Ali Asghar (Co-Supervisor)
    Abstract
    Search for effective methods for treating cancer requires a deep understanding of the tumor microenvironment and its role in cancerous tumor growth and progression. Mathematical modeling methods, which have fewer limitations than experimental methods for examining the microcirculation of cancer in detail, are suggested to answer many questions about the behavior and dynamics of cancerous tumors. In the present study, a multi-scale mathematical model of the three-dimensional tumor microenvironment, including molecular, cellular, and tissue scales, is presented. In this model, important aspects of tumor microenvironmental dynamics including tumor growth, angiogenesis, cancer metabolism, and... 

    Investigation of cancer response to chemotherapy: a hybrid multi-scale mathematical and computational model of the tumor microenvironment

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 21, Issue 4 , 2022 , Pages 1233-1249 ; 16177959 (ISSN) Nikmaneshi, M. R ; Firoozabadi, B ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2022
    Abstract
    Tumor microenvironment (TME) is a multi-scale biological environment that can control tumor dynamics with many biomechanical and biochemical factors. Investigating the physiology of TME with a heterogeneous structure and abnormal functions not only can achieve a deeper understanding of tumor behavior but also can help develop more efficient anti-cancer strategies. In this work, we develop a hybrid multi-scale mathematical model of TME to simulate the progression of a three-dimensional tumor and elucidate its response to different chemotherapy approaches. The chemotherapy approaches include multiple low dose (MLD) of anti-cancer drug, maximum tolerated dose (MTD) of anti-cancer drug,... 

    Analysis and Improvement of Intrusion Detection Methods in Data Network Routers

    , M.Sc. Thesis Sharif University of Technology Jamshidi, Mohammad Ali (Author) ; Aref, Mohammad Reza (Supervisor) ; Pakravan, Mohammad Reza (Co-Advisor)
    Abstract
    High-quality online services demand reliable and fast packet delivery at the network layer. However, clear evidence documents the existence of compromised routers in the ISP and enterprise networks, threatening network availability and reliability. A compromised router can stealthily drop, modify, inject, or delay packets in the forwarding path to launch Denial-of-Service, surveillance, man-in-the-middle attacks, etc. So researches tried to create intrusion detection methods to identify adversarial routers and switches. To this end, data-plane fault localization (FL) aims to identify faulty links and is an effective means of achieving high network availability. FL protocols use... 

    Topological Defects in Confined Nematics by Planar Anchoring

    , M.Sc. Thesis Sharif University of Technology Seyed Nejad, Reza (Author) ; Ejtehadi, Mohammad Reza (Supervisor) ; Mozaffari, Mohammad Reza (Supervisor)
    Abstract
    Confining nematic liquid crystal between two curved boundary conditions while the nematic molecules have a degenerate planar anchoring leads to complex and beautiful textures of molecular disparagement(defect) in the bulk and on the surfaces. Such the liquid crystal shells are made with double-emulsion techniques in microfluidic devices have provided applications for micro-scale colloidal linkers.In this work, we have numerically minimized the elastic energy in one-constant approximation in present of Fournier’s degenerate surface potential with finite element method. The nematic shell is confined between two spherical surfaces that we have studied the final energies and their related... 

    Solving Symmetric Nonlinear Equations System Using BFGS Trust Region Quadratic Method

    , M.Sc. Thesis Sharif University of Technology Salimi, Samira (Author) ; Razvan, Mohammad Reza (Supervisor) ; Peyghami, Mohammad Reza (Supervisor)

    Effect of the Geometry of Colloidal Particles on Nematic Liquid Crystals

    , Ph.D. Dissertation Sharif University of Technology Hashemi, Masoumeh (Author) ; Ejtehadi, Mohammad Reza (Supervisor) ; Mozaffari, Mohammad Reza (Co-Advisor)
    Abstract
    A liquid crystal is a state of matter composed of highly anisotropic building blocks. When liquid crystals are exposed to surfaces with given shapes and anchoring conditions, the orientation of their molecules gets spatially disordered and topological defects may form in the system. The interplay between liquid crystals and the geometry and topology of the colloidal particles has motivated extensive recent studies.In this thesis, we present the numerical modeling results for two faceted colloidal particles in a thermotropic nematic liquid crystal. To obtain the equilibrium nematic field with a finiteelement method, we numerically minimize the free energy of the system that based on the... 

    Design and Implementation of 2.5 Gbps Circuit Switching Fabric

    , M.Sc. Thesis Sharif University of Technology Jahani, Sohrab (Author) ; Pakravan, Mohammad Reza (Supervisor) ; Movahhedy, Mohammad Reza (Supervisor)
    Abstract
    Providing high bandwidth network infrastructures for ever increasing need of data transport is of great importance. The underling infrastructure for many communication services such as GSM/3G/4G mobile networks and Internet services is Synchronous Digital Hierarchy (SDH) optical transport systems. SDH are standardized protocols that multiplex multiple lower rate digital bit streams, such as E1 and Ethernet, and transfer them synchronously over optical fiber using lasers or LEDs. In addition to high data transfer rates, flexible network management and protection mechanisms have great importance, hence are part of SDH standards. In order to obtain flexible network architecture and protected... 

    Preserving Privacy in Smart Grid

    , M.Sc. Thesis Sharif University of Technology Vahedi, Erfaneh (Author) ; Aref, Mohammad Reza (Supervisor) ; Pakravan, Mohammad Reza (Co-Advisor)
    Abstract
    Development of Smart Grid and deployment of smart meters in large scale has raised a lot of concerns regarding customers’ privacy. Consequently, several schemes have been proposed to overcome the above mentioned issue. These schemes mainly rely on data aggregation as a method of protecting users’ privacy from the grid operators. However, the main problem with most of these schemes is the fact that they require a large amount of processing power at the meter side. This, together with the fact that smart meters don’t usually have a powerful processor, can cause the unavailability of smart meter data at the required time for operators of the grid, and at the same time disables smart meters from... 

    Improvement of Routing Security in Ad Hoc Networks Against Several Attacks

    , M.Sc. Thesis Sharif University of Technology Sedghi, Hanie (Author) ; Aref, Mohammad Reza (Supervisor) ; Pakravan, Mohammad Reza (Supervisor)
    Abstract
    Secure routing is a major key to service maintenance in wireless ad hoc networks. Ad hoc nature exposes the network to several types of node misbehavior or attacks. Wormhole attack is one of the most severe active attacks to mobile ad hoc networks. Noting the resource limitations in such networks, nodes may have a tendency to behave selfishly. Selfish behavior can have drastic impacts on network performance. We have proposed a Misbehavior-Tolerant Multipath Routing protocol (MTMR) which detects and punishes all types of misbehavior such as selfish behavior, wormhole, sinkhole and grey-hole attacks. The protocol utilizes a proactive approach to enforce cooperation. In addition, it uses a... 

    Chemo-mechanistic multi-scale model of a three-dimensional tumor microenvironment to quantify the chemotherapy response of cancer

    , Article Biotechnology and Bioengineering ; Volume 118, Issue 10 , 2021 , Pages 3871-3887 ; 00063592 (ISSN) Nikmaneshi, M. R ; Firoozabadi, B ; Mozafari, A ; Sharif University of Technology
    John Wiley and Sons Inc  2021
    Abstract
    Exploring efficient chemotherapy would benefit from a deeper understanding of the tumor microenvironment (TME) and its role in tumor progression. As in vivo experimental methods are unable to isolate or control individual factors of the TME, and in vitro models often cannot include all the contributing factors, some questions are best addressed with mathematical models of systems biology. In this study, we establish a multi-scale mathematical model of the TME to simulate three-dimensional tumor growth and angiogenesis and then implement the model for an array of chemotherapy approaches to elucidate the effect of TME conditions and drug scheduling on controlling tumor progression. The... 

    Solving Nonlinear Systems of Mixed Iqualities and Inequalities Via Trust Region Quadratic Methods

    , M.Sc. Thesis Sharif University of Technology Ghasemi, Shojaeddin (Author) ; Razvan, Mohammad Reza (Supervisor) ; Payghami, Mohammad Reza (Supervisor)

    Jamming Resilient Algorithms for Rendezvous in Cognitive Radio Networks

    , M.Sc. Thesis Sharif University of Technology Rezaei, Roohollah (Author) ; Aref, Mohammad Reza (Supervisor) ; Pakravan, Mohammad Reza (Co-Advisor)
    Abstract
    Dynamic spectrum access with the aid of cognitive radio (CR) technology is a viable solution to spectrum scarcity. There are many military and emergency applications that require the use of cognitive radio ad-hoc networks (CRAHNs). In these net- works, nodes must first find each other in a wide spectrum and then exchange their desired data. The process of finding each other in a multichannel environment is a challenging task and is usually known as rendezvous. Since rendezvous is the first step in communication, disrupting will disable the nodes from establishing proper communication sessions. That results in a drastic degrade in the performance of the network. Therefore, it is important to... 

    Numerical Study of Spray Impingement to Solid Wall

    , M.Sc. Thesis Sharif University of Technology Abbasi Chenari, Fatemeh (Author) ; Morad, Mohammad Reza (Supervisor) ; Jahannama, Mohammad Reza (Co-Supervisor)
    Abstract
    Spray-wall impingement is one of the phenomenon that associated in different subject such as spray cooling, combustion chamber and gas turbine. With the impingement of spray to the wall, liquid film begins to form. Wall film characteristics is still an important subject to study. Due to the various stages of liquid film formation from injection of spray till spray-wall impingement, the investigation of this phenomenon is far more complicated. This paper is meant to provide detailed data on spray-wall impingement and wall film formation physics with the help of computational analysis of OpenFOAM . A Lagrangian-Eulerian method based on discrete phase model (DPM) was employed to model... 

    Assessing and Improving Algorithms to Control the Propagation of Light through Scattering Media

    , M.Sc. Thesis Sharif University of Technology Fayyaz, Zahra (Author) ; Rahimitabar, Mohammad Reza (Supervisor) ; Nasiriavanaki, Mohammad Reza (Supervisor)
    Abstract
    Light propagation through turbid media, such as biological tissues, experience scattering due to inhomogeneous distribution of refractive indices of their microscopic structure. Scattering and diffusion of light not only limit many optical imaging techniques, but are also big challenges for telecommunication, spectroscopy, and other optical techniques. Recently many new imaging methods are developed that work in strongly scattering media such as optical coherence tomography, diffusion tomography, and laser speckle velocimetry. In this thesis, we have studied how wavefront shaping techniques can tackle the problem of scattering. By spatially shaping the wavefront of the incident beam, using... 

    Continuum model of actin-myosin flow

    , Article 2013 20th Iranian Conference on Biomedical Engineering, ICBME 2013 ; December , 2013 , Pages 98-102 Nikmaneshi, M. R ; Firoozabadi, B ; Saidi, M. S ; Sharif University of Technology
    IEEE Computer Society  2013
    Abstract
    The front part of a cell is divided to two regions called lamellum and lamellipodium (lamellipodial). This part plays an essential role for cell migration. Indeed, there are many protein filaments called actin in lamellum and lamellipodium, which induce the cell motion with polymerization in the leading edge of the cell. The actin filaments adhere to the extracellular matrix (ECM) by means of focal adhesions and they have contact by myosin motor proteins. The myosin motor proteins cause actin retrograde and anterograde flow exerted contractile stress on them. The focal adhesions exert frictional stress on the actin filaments. In this work, we developed a two-dimensional continuum model of... 

    Two-phase acto-cytosolic fluid flow in a moving keratocyte: a 2d continuum model

    , Article Bulletin of Mathematical Biology ; Volume 77, Issue 9 , September , 2015 , Pages 1813-1832 ; 00928240 (ISSN) Nikmaneshi, M. R ; Firoozabadi, B ; Saidi, M. S ; Sharif University of Technology
    Springer New York LLC  2015
    Abstract
    The F-actin network and cytosol in the lamellipodia of crawling cells flow in a centripetal pattern and spout-like form, respectively. We have numerically studied this two-phase flow in the realistic geometry of a moving keratocyte. Cytosol has been treated as a low viscosity Newtonian fluid flowing through the high viscosity porous medium of F-actin network. Other involved phenomena including myosin activity, adhesion friction, and interphase interaction are also discussed to provide an overall view of this problem. Adopting a two-phase coupled model by myosin concentration, we have found new accurate perspectives of acto-cytosolic flow and pressure fields, myosin distribution, as well as... 

    Fully-coupled mathematical modeling of actomyosin-cytosolic two-phase flow in a highly deformable moving Keratocyte cell

    , Article Journal of Biomechanics ; 2017 ; 00219290 (ISSN) Nikmaneshi, M. R ; Firoozabadi, B ; Saidi, M. S ; Sharif University of Technology
    Elsevier Ltd  2017
    Abstract
    Interaction between intracellular dynamics and extracellular matrix (ECM) generally occurred into very thin fragment of moving cell, namely lamellipodia, enables all movable cells to crawl on ECM. In fast-moving cells such as fish Keratocytes, Lamellipodia including most cell area finds a fan-like shape during migration, with a variety of aspect ratio function of fish type. In this work, our purpose is to present a novel and more complete two-dimensional continuum mathematical model of actomyosin-cytosolic two-phase flow of a self-deforming Keratocyte with circular spreaded to steady fan-like shape. In the new approach, in addition to the two-phase flow of the F-actin and cytosol, the... 

    Fully-coupled mathematical modeling of actomyosin-cytosolic two-phase flow in a highly deformable moving Keratocyte cell

    , Article Journal of Biomechanics ; Volume 67 , January , 2018 , Pages 37-45 ; 00219290 (ISSN) Nikmaneshi, M. R ; Firoozabadi, B ; Saidi, M. S ; Sharif University of Technology
    Elsevier Ltd  2018
    Abstract
    Interaction between intracellular dynamics and extracellular matrix (ECM) generally occurred into very thin fragment of moving cell, namely lamellipodia, enables all movable cells to crawl on ECM. In fast-moving cells such as fish Keratocytes, Lamellipodia including most cell area finds a fan-like shape during migration, with a variety of aspect ratio function of fish type. In this work, our purpose is to present a novel and more complete two-dimensional continuum mathematical model of actomyosin-cytosolic two-phase flow of a self-deforming Keratocyte with circular spreaded to steady fan-like shape. In the new approach, in addition to the two-phase flow of the F-actin and cytosol, the...