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azimzadeh-irani--maryam
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Elucidating the Roles of Interlukin I Receptor Type II (lL-1Rll) in the Regulation of Human Immune System, Atomistic Molecular Dynamics Simulation
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor) ; Azimzadeh Irani, Maryam (Co-Supervisor)
Abstract
IL-1 family of cytokines plays a critical role in the regulation of immune response.These cytokines transfer the signals to the target cells through binding to the IL-1 receptors.Interleukin 1 Receptor Type II (IL-1RII) is the decoy receptor of the IL-1 cytokines. IL-1RII is homologous to the signaling Interleukin 1 Receptor Type I (IL1RI) in its extracellular region and can bind to the same cytokines with higher affinity and the same accessory protein. It down-regulates the signaling and suppresses the downstream pathways due to the lack of the intracellular Toll-Interleukin Receptor (TIR) domain. IL-1RII is decorated by carbohydrate units in-vivo. Dynamics and ligand binding of receptors...
GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation
, Article Glycobiology ; Volume 29, Issue 11 , 2019 , Pages 803-812 ; 14602423 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
NLM (Medline)
2019
Abstract
IL-1RI is the signaling receptor for the IL-1 family of cytokines that are involved in establishment of the innate and acquired immune systems. Glycosylated extracellular (EC) domain of the IL-1RI binds to agonist such as IL-1β or antagonist ligands and the accessory protein to form the functional signaling complex. Dynamics and ligand binding of the IL-1RI is influenced by presence of the glycosaminoglycans (GAGs) of the EC matrix. Here a combination of molecular dockings and molecular dynamics simulations of the unglycosylated, partially N-glycosylated and fully N-glycosylated IL-1RI EC domain in the apo, GAG-bound and IL-1β-bound states were carried out to explain the co-occurring...
Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response
, Article Journal of Biomolecular Structure and Dynamics ; 2020 ; Ejtehadi, M. R ; Sharif University of Technology
Taylor and Francis Ltd
2020
Abstract
Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic...
Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response
, Article Journal of Biomolecular Structure and Dynamics ; Volume 40, Issue 6 , 2022 , Pages 2575-2585 ; 07391102 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic...
A Practical Examination of the Antibacterial and Absorption Effect of Bioceramic Apatite-Coated TiO2 as a Modified Nanophotocatalyst
, M.Sc. Thesis Sharif University of Technology ; Gholami, Mohammad Reza (Supervisor) ; Haghighi, Saeed (Co-Advisor)
Abstract
Ag / AgCl /TiO2 , 2 Ap / Ag / AgCl /TiO , 2 AgI /TiO and 2 Ap / AgI /TiO were prepared by the deposition-precipitation method on 2TiO (P25) nanoparticles and their photocatalyctic activities have been investigated under visible light and dark environments. Cationic surfactant plus 2 PVPI (topical solution and dry powder) as an iodine ion source and nonionic surfactant plus KI as an iodide ion source were used to prepar 2 AgI /TiO . In less than 30 minutes, 2 AgI /TiO which has been resulted from combination of cationic surfactant and 2 PVPI showed high efficiency on Escherichia coli under visible light when small quantities of it is used . However, AgCl sample prepared with cationic...
An Efficient Architecture for A Simplified Dalvik Processor
, M.Sc. Thesis Sharif University of Technology ; Goudarzi, Maziar (Supervisor)
Abstract
Google Inc. states that, 400 million Android-powered devices have been activated and used by people until 2012. This rapid growth of Android operating system in mobile phones and other electronic devices makes it very important to improve the efficiency of this Operating System. Dalvik is the underlying virtual machine (VM) in Android that executes Android-based applications, and hence, its performance directly affects Android-powered devices. De-virtualization is a technique to improve performance of VMs. In this method, VM’s instructions (bytecode) are natively and directly executed by hardware. In addition, de-virtualization technique eliminates the software interpretation/translation...
Performance analysis of android underlying virtual machine in mobile phones
, Article IEEE International Conference on Consumer Electronics - Berlin, ICCE-Berlin ; 2012 , Pages 292-295 ; 21666814 (ISSN) ; 9781467315470 (ISBN) ; Sameki, M ; Goudarzi, M ; Sharif University of Technology
2012
Abstract
In recent years, Android is widely used in cell phones. Dalvik is the virtual machine which is embedded inside the Android operating system, and executes the Android-based applications. Thus, improving efficiency of the Dalvik virtual machine plays an important role in optimizing performance of android-based mobile phones. In this paper, we present a comprehensive analysis of the Dalvik bytecodes and their frequency of use in common Android applications and use the results to determine the most frequently used bytecodes in Dalvik virtual machine to identify best targets for improvement. Our analysis showed that over 82% of total execution time of our Android benchmarks is spent by only 5...
Preparation and Investigation of Electrochemical Sensors for Determination of Pharmaceutical and Biological Compunds Based on Glassy Carbon Electrode Modified with Polypyrrole/Carbon Nanotube Composite
, M.Sc. Thesis Sharif University of Technology ; Shahrokhian, Saeed (Supervisor)
Abstract
In the recent years, conductive polymers are widely used in the design and construction of chemical and biological sensors.The polypyrrole due to features such as good thermal and chemical stability, ease of synthesis and better conductivity than other conductive polymers, atracts much attention. In order to modification of electrode surface,adhesiveand thin polymer films can be electropolymerized in the presence of organic or inorganic dopants on the surface of metal or carbon surfaces in aqueous or organic solutions. On the other hand carbon nanotubes by owing unique properties such as chemical stability and high electrical conductivity are good choice for electrod surface modification....
3d Design of a Microfluidic Chip for Anticancer Drugs Screening
, M.Sc. Thesis Sharif University of Technology ; Mashayekhan, Shohreh (Supervisor) ; Saadatmand, Maryam (Supervisor)
Abstract
Nowadays, advanced and inexpensive pre-clinical methods for investigating the effects of anti-cancer drugs are expanding. One of the latest three-dimensional laboratory modeling for evaluating the effects of drugs is the use of tumor-on-chip technology, which actually models the physiological system of the body through three-dimensional scaffolds, multicellular cultures, and shaped vascular systems. In this study, three-dimensional culture of cancer cells was performed in the form of spheroids. A chip of U-shaped microstructures with and without gaps was used to trap cells and form cancer spheroids. We simulated the simultaneous effect of drug and oxygen concentration distribution inside the...
Efficient high harmonic generation of bromine molecule by controlling the carrier-envelope phase and polarization of driving laser pulse
, Article Chemical Physics Letters ; Volume 719 , 2019 , Pages 27-33 ; 00092614 (ISSN) ; Monfared, M ; Sharif University of Technology
Elsevier B.V
2019
Abstract
The generation of ultrashort attosecond pulse requires both an enhanced high harmonic generation and the spectral-phase control. In the present work, an efficient method is theoretically investigated for extending HHG cutoff energy in Br2 molecule using TDDFT. The effects of molecular orientation and carrier-envelope phase of the laser on the high harmonic spectrum are analyzed. As a result, by the fine modulations of the laser field, the harmonic plateau is enlarged and the position of structure-induced interference minimum shifts. We also provide a physical picture on the intensity dependence of the spectral minima in the harmonic spectra
Numerical Simulation of 2D Compressible Cavitation Flow Using Compact Finite-Difference Method
, M.Sc. Thesis Sharif University of Technology ; Hejranfar, Kazem (Supervisor)
Abstract
In the present study, the numerical simulation of 2D inviscid compressible cavitation flow is performed by using the compact finite-difference method. The problem formulation is based on the multiphase compressible Euler equations with the assumption of the homogeneous equilibrium model and the system of baseline differential equations is comprised of the continuity, momentum and energy equations for the vapor-liquid mixture. To complete the system of governing equations, the ideal gas relation is used for the vapor phase and the Tait relation is applied for the liquid phase, and therefore, the compressibility effects are considered for both the vapor and liquid phases. To analyze the flow...
2D and 3D simulation of bubble columns using CFD methods
, Article CHISA 2006 - 17th International Congress of Chemical and Process Engineering, Prague, 27 August 2006 through 31 August 2006 ; 2006 ; 8086059456 (ISBN); 9788086059457 (ISBN) ; Bozorgmehri, R ; Sharif University of Technology
2006
Abstract
This article presents the results of 2D and 3D simulations of a bubble column reactor at steady state conditions and low gas flow rates. The simulations have been done based on a two-fluid model with a k - ε model used for turbulence modeling. The experimental data have been obtained by differential pressure transducer. For analyzing of hydrodynamic parameters such as hold up and velocity profiles of phases, a system consists of water tank and air aerated from bottom is set up. The simulations have been done based on two different approaches which are mixture and eulerian approaches. Despite the fact that these approaches lead to similar results, the convergence and stability of eulerian...
Model Checking of Stochastic Activity Networks
, M.Sc. Thesis Sharif University of Technology ; Movaghar, Ali (Supervisor)
Abstract
Modeling and performance evaluation of the real time distributed systems is a significant problem. Stochastic activity network is one of the high level models used for this purpose. This network is an extension of generalized stochastic Petri net which is more powerful and flexible than other Petri net extensions. Checking the satisfiability of properties such as performance, dependability and user's expected properties is considerable in these models. Thus, using the approaches and generating modeling and model checking tools with the mentioned purpose is attractive. A model checker automatically checks the correctness of the system behaviors as properties against the model by getting the...
Fabrication of Thick Scaffold with Microfluidic Channels by Bioprinter
, M.Sc. Thesis Sharif University of Technology ; Saadatmand, Maryam (Supervisor)
Abstract
Cardiovascular diseases are among the leading causes of death worldwide. For instance, in 2015, almost 31% of the world’s mortality rate was due to these causes. One of these diseases is cardiac coronary vessels’ occlusion which leads to the insufficient blood supply to the heart tissue and cardiomyocytes death after Myocardial Infarction (MI). After MI, a hierarchy of events in the heart tissue changes heart muscle and forms cardiac fibrosis. This fibrotic tissue does not have the native one’s properties and function, so it will cause cardiac arrest and patient death. Therefore, it is obvious that vascular network plays a crucial role in the heart function. The importance of cardiac...
Robust Estimation and Control of a Planet Lander
, M.Sc. Thesis Sharif University of Technology ; Kiani, Maryam (Supervisor)
Abstract
This study has focused on the important problem of landing on a planet as an important current and future space mission. In this regard, dynamics modeling and integrated state estimation and control problems have been investigated in different views. To this aim, first a novel concurrent representation for translational and rotational kinematics has been developed based on the extension of modified Rodrigues parameters to dual space. This parameter set, called dual modified Rodrigues parameters (DMRP), is then utilized to establish an integrated roto-translational dynamic. The proposed DMRP-based kinematics and dynamics have been verified via comparison to traditional methods of...
Optimal Control of Unknown Interconnected Systems via Distributed Learning
, M.Sc. Thesis Sharif University of Technology ; Babazadeh, Maryam (Supervisor)
Abstract
This thesis addresses the problem of optimal distributed control of unknown interconnected systems. In order to deal with this problem, a data-driven learning framework for finding the optimal centralized and the suboptimal distributed controllers has been developed via convex optimization.First of all, the linear quadratic regulation (LQR) problem is formulated into a nonconvex optimization problem. Using Lagrangian duality theories, a semidefinite program is then developed that requires information about the system dynamics. It is shown that the optimal solution to this problem is independent of the initial conditions and represents the Q-function, an important concept in reinforcement...
Utilizing Gaussian Processes to Learn Dynamics of Unknown Torques Acting on a Spacecraft
, M.Sc. Thesis Sharif University of Technology ; Kiani, Maryam (Supervisor)
Abstract
Accurate and fast attitude estimation of a rigid body plays an essential role in the performance of a vehicle’s control system, especially aerospace vehicles. Ample works have been done to increase the accuracy and speed of the attitude estimation process, but all have been developed according to a model-based approach. This approach assumes that the torques acting on the body have a known dynamical model that is used for the attitude estimation. The purpose of the present research is to estimate the attitude via a model-free approach, i. e. dynamics of the torques acting on the body are no longer assumed to be known, and its learning is the next step. Thus, the problem formulation of this...
Stabilization and Pole-Placement by Structurally-Constrained Controllers: A Graph-Theoretic Approach
, M.Sc. Thesis Sharif University of Technology ; Babazadeh, Maryam (Supervisor)
Abstract
This thesis presents a new approach to design structural output feedback controllers with stabilization and pole-placement at desired points on the S plane. It is assumed that the linear time-invariant system has no fixed mode corresponding to the specified control structure, outside the desired region of the closed-loop poles, such that the structural controller design problem is theoretically feasible. To this end, the structural output controller design problem is first transformed into a structurally equivalent problem based on the solution of a set of discrete linear programs. Then, by using the resultant structure, a new method is proposed for designing static and dynamic control loops...
Fabrication the Hydrogel Microfibers Using Bioprinter with Application in Cardiovascular Model
, M.Sc. Thesis Sharif University of Technology ; Saadatmand, Maryam (Supervisor)
Abstract
Cardiovascular disease (CVD) currently remains a considerable challenge for clinical treatments. CVDs account for N17.5 million deaths per year and will predictably increase to 23.6 million by 2030. The main purpose is to create human model systems to study the effect of disease mutations or drug treatment on the heart. In addition, engineered cardiac tissues are considered promising candidates to be transplanted to improve the function of diseased hearts. For engineered active tissues/organs, 3D bioprinting can fabricate complex tissue architecture with a spatiotemporal distribution of bioactive substances (cells, growth factors, and others) to better guide tissue regeneration. However,...
Design of Microfluidic Chip for 3D Cell Culture
, M.Sc. Thesis Sharif University of Technology ; Saadatmand, Maryam (Supervisor)
Abstract
Understanding biological systems requires extensive knowledge of individual parameters, and to study the processes of cell differentiation and cell behavior, a suitable environment must be created with the physiological conditions of the human body. For this purpose, with the knowledge of microfluidics, a microenvironment can be provided to study the behavior of cells on a small scale. The use of bone tissue model microfluidic chips is an alternative and new method in which it is possible to study the behavior of cells to differentiate into bone and to examine the toxicity of drugs, which in itself can help in the effective and successful treatment of these cases show. Therefore, in this...