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    Context-Specific Reconstruction and Gap-Filling of Metabolic Networks by Sparse Reconciliation of Data Inconsistencies

    , M.Sc. Thesis Sharif University of Technology Fathi, Ali (Author) ; Tefagh, Mojtaba (Supervisor)
    With the increasingly collected biological data, appropriate usage of this data is of great importance for understanding and predicting biological systems and has been the aim of experiments and data collections. A famous category of biological data is known as “omics” which refers to transcriptomics, proteomics, metabolomics, and fluxomics, from different cells or tissues in various media and conditions. This set of data is regularly used for tasks such as studying cells and organisms, understanding cell states, cancer prediction, etc. and is of great importance in Systems Biology.In this thesis, we concentrate on studying cells or organisms using such data, where during that process, we... 

    Multi-agent based Blockchain Simulation Framework

    , M.Sc. Thesis Sharif University of Technology Alimirzaei, Fatemeh (Author) ; Tefagh, Mojtaba (Supervisor)
    A multi-agent system is a system consisting of several intelligent agents. In fact, a multi-agent system is a system that includes a large number of agents that communicate with each other through message transmission in a network structure. Multi-agent systems can solve problems that are difficult or impossible for a single agent or an integrated system to solve. Blockchain is an example of these multi-agent systems that has many use cases in different fields for example cryptocurrencies . A blockchain is a growing ledger consisting of records called blocks. In this thesis, we want to provide tools for the simulation of this multi-agent system so that we can model the issues surrounding... 

    A Library For Developing Optimization Algorithms In Metabolic Network Analysis

    , M.Sc. Thesis Sharif University of Technology Ghadimi Deylami, Iman (Author) ; Tefagh, Mojtaba (Supervisor)
    In systems biology, one of the most important biological systems that is analyzed and investigated is the metabolic network. A metabolic network is a complete set of metabolic and physical processes that determine the physiological and biochemical characteristics of a cell. These networks encompass metabolic chemical reactions, metabolic pathways, and regulatory interactions that govern these reactions. Therefore, metabolic networks at the genome scale are immensely large, making even efficient algorithms time-consuming for their analysis. To address this issue, reducing metabolic networks is crucial, as it significantly decreases the execution time of algorithms and enhances computational... 

    Analysis and Investigation of Miner Extractable Value in Constant Product Market Makers with Random Ordering

    , M.Sc. Thesis Sharif University of Technology Jadidi Amir Hossein (Author) ; Maddah Ali, Mohammad Ali (Supervisor) ; Tefagh, Mojtaba (Supervisor)
    Blockchain technology presents a decentralized management structure designed to cater to various needs, such as decentralization and the elimination of single points of failure. With the evolution of blockchain technology, smart contracts have emerged as a remarkable platform for facilitating financial activities in a decentralized manner. Among the different types of smart contracts, decentralized exchanges stand out by their absence of a central authority overseeing user transactions. This lack of a central oversight exposes users of such exchanges to potential attacks from malicious entities. A key challenge faced by these exchanges is the concept of Miner Extractable Value. Miner... 

    Introducing a framework to create telephony speech databases from direct ones

    , Article 14th International Conference on Systems Signals and Image Processing, IWSSIP 2007 and 6th EURASIP Conference Focused on Speech and Image Processing, Multimedia Communications and Services, EC-SIPMCS 2007, Maribor, 27 June 2007 through 30 June 2007 ; November , 2007 , Pages 327-330 ; 9789612480295 (ISBN) Momtazi, S ; Sameti, H ; Vaisipour, S ; Tefagh, M ; Sharif University of Technology
    A Comprehensive speech database is one of the important tools for developing speech recognition systems; these tools are necessary for telephony recognition, too. Although adequate databases for direct speech recognizers exist, there is not an appropriate database for telephony speech recognizers. Most methods suggested for solving this problem are based on building new databases which tends to consume much time and many resources; or they used a filter which simulates circuit switch behavior to transform direct databases to telephony ones, in this case resulted databases have many differences with real telephony databases. In this paper we introduce a framework for creating telephony speech... 

    Preparation, Surface Modification and Application of Nanocomposite Membranes Based on Transition Metals- Dichalcogenide Nanoparticles in Forward Osmosis Desalination Process

    , Ph.D. Dissertation Sharif University of Technology Nikkhoo, Mohammad (Author) ; Bagherzadeh, Mojtaba (Supervisor) ; Ahadian, Mohammad Mahdi (Supervisor) ; Amini, Mojtaba (Supervisor)
    Different parts of this research are focused on developing FO membranes and improving their performance. For this purpose, thin film composite (TFC) membranes with fixed composition of polyethersulfone/polyamide (PES/PA) have been used to investigate the effect of nanocomposites containing transition metal dichalcogenides (TMDs) on their performance. The support layer in all cases is PES, which is prepared through the phase inversion process and does not contain any nanofillers. The modification process takes place in the polyamide layer by dispersing the desired nanoparticles in the aqueous monomer solution necessary to form this active layer. Identification and characterization of... 

    Synthesis and Study of Catalytic Activity of Iron (III)-bis(2-oxazolinyl) Methane complex by Urea Hydrogen Peroxide in Oxidation of Sulfides

    , M.Sc. Thesis Sharif University of Technology Kazem, Nasrin (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    Considerable effort has been directed in recent years towards the transition metal complex catalyzed oxidation of organic compounds. Herein the synthsis of the iron complex of bis(oxazoline) ligand as a novel catalyst is reported, and the catalytic activity of this complex in oxidation of sulfides is investigated. Bis(2-oxazolynil)methane as ligand is prepared by condensation of diethylmalonate with 2-aminoethanole in 1:2 molar ratio and finally corresponding complex is synthesized by the reaction between FeCl3.6H2O and Bis(2-Oxazolynil)methane in 1:1 molar ratio. The complex is characterized by using IR, UV-Vis, cyclic voltametery, conductometery and elemental analysis data. Moreover,... 

    Design of a Low Noise Amplifier without On-Chip Inductor

    , M.Sc. Thesis Sharif University of Technology Behmanesh, Baktash (Author) ; Atarodi, Mojtaba (Supervisor)
    In this project a wide-band inductorless Low Noise Amplifier (LNA) has been designed using 0.18 micrometer CMOS technology. The specification of this amplifier has been explored in frequency band of 330MHz to 10GHz. Wide-band input and output impedance matching, low Noise-Figure (NF), reasonable voltage gain and low power consumption are the main challenges of Low Noise Amplifier design. Without using an inductor a better overall performance of LNA in a wide frequency band as well as a lower chip area has been achieved. In this design a novel noise cancellation technique in common-gate topology has been used for lowering the Noise Figure of the LNA. Group Delay of the designed LNA, which is... 

    Synthesis, Structure and Catalytic Application of Mn, Fe and Mo Complexes with Schiff base and Oxazoline ligands and Theoretical Mechanistic Studies on the Role of Heme and non-Heme Iron(IV)-Oxo Species in Hydroxylation and Epoxidation Reactions

    , Ph.D. Dissertation Sharif University of Technology Tahsini , Laleh (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    The first part of this thesis describes the synthesis and characterization of several Mn, Fe and Mo complexes containing tridentate Schiff base and oxazoline ligands and their reactivities as catalysts in the oxidation of organic compounds like olefins and sulfides, as well. The crystal structures of newly prepared cis-dioxo-bis[2-(2′-hydroxyphenyl)-oxazolinato]molybdenum(VI), cis-[MoO2(phox)2] and (N-hydroxyphenyl-salicylidenamine)(acetylacetonato)ethanol iron(III), [FeIII(N-OPh-sal)(acac)EtOH] complexes have been described by X-ray crystallography. Due to the difficulties in the preparation of suitable single crystals of novel... 

    Designing and Fabricating the Active Phase Shifter

    , M.Sc. Thesis Sharif University of Technology asoodeh, Alireza (Author) ; Atarodi, Mojtaba (Supervisor)
    In this project, issues related to designing and fabricating active phase shifter blocks on the silicon substrate have been examined. Phase shifter circuits are designed in a way that have the most bandwidth and the less sensitivity to process characteristics changes and environmental conditions. The purpose of this research, is designing an active 6 bits phase shifter. The active phase shifter synthesizes the required phase using a phase interpolation process by adding quadrature phased input signals. It uses a new quadrature all-pass filter for quadrature signaling with a wide bandwidth. Also substitute structure has been suggested to this filter which is the main block in determining... 

    Wideband Frequency Synthesizer for Digital Video Tuners

    , Ph.D. Dissertation Sharif University of Technology Saeedi, Saeed (Author) ; Atarodi, Mojtaba (Supervisor)
    Integration of radio transceivers results in developing low power low cost wireless systems and allows delivery of multimedia contents to battery-powered mobile terminals. Portable reception of digital video for hand-held devices is one of the applications, for which, some telecommunications standards have been developed in the recent years. This research deals with the integrated implementation of the radio frequency parts of the digital video receiver, especially the frequency synthesizer. The key aspects of the digital video reception system are the required signal to noise ratio, which is relatively high, wide band input signals and strong interferers in the receiving band.

    Design and Fabrication of RFID Front END Transceiver single chip with 2.5W Output Power

    , Ph.D. Dissertation Sharif University of Technology Javidan, Javad (Author) ; Atarodi, Mojtaba (Supervisor)
    This thesis deals with the front-End of an Integrated RFID Reader operated in 860MHz to 960MHz, which integrates a RF transceiver including PA, LNA and Mixer. In the receiver part, a power amplifier was fabricated and measured and in the transmitter part, LNA and Mixer were designed. There is a growing interest in utilizing CMOS technologies for RF power amplifiers (PAs). Although several advances have been made recently to enable full integration of PAs in CMOS, it is still among the most difficult challenges in achieving a truly single-chip radio system in CMOS. This is exacerbated by supply voltage reduction due to CMOS technology scaling and on-chip passive losses due to the conductive... 

    Synthesis and Study of Catalytic Reactivity Oxo Vanadium (IV)& (V) Complexes with N,N'-Ethylenebis(Salicylimine)Ligand in Oxidation of Sulfides and Epioxidation of Olfins by Urea Hydrogen Peroxide (UHP) and Tert-Butyl Hydroperoxide (TBHP)

    , M.Sc. Thesis Sharif University of Technology Nadiri, Siheila (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    The selective oxidation of sulfides to sulfoxides is an important method in organic synthesis because sulfoxides are useful synthetic intermediates for the construction of various chemically and biologically significant molecules. To date, the most important method of preparation involves the oxidation of sulfides. Various oxidizing agents are used for this purpose. Oxovanadium(IV)(Salen) and oxovanadium(V)(Salen)Cl were synthesised and screened in the vanadium-catalysed oxidation of sulfides to solfuxides with urea hydrogen peroxide(UHP) as terminal oxidant. Both complexes showed good activity and selectivity trough the catalytic reaction.characterized by elemental analyses, IR, 1H and 13C... 

    Design and Implementation of Fully Integrated Frequency Synthesizer for Biomedical Applications

    , M.Sc. Thesis Sharif University of Technology Aghlmand, Fatemeh (Author) ; Atarodi, Mojtaba (Supervisor)
    Fully integrated frequency synthesizer is one of the important system-on-chips building blocks. Among this circuit’s remarkable applications, Bioelectronics field is very common. In these applications, advanced microelectronic circuits are used in order to diagnosis and treatment of diseases. The aim of this thesis is design and implementation a wideband frequency synthesizer in a 0.18um CMOS technology. The main usage of this circuit is in a fully integrated implantable biomedical sensory chip. This circuit generates two necessary local signals in sensory chip to stimulus cells and process the information.
    Frequency synthesizer is based on phased locked loop (PLL) circuit and produce... 

    Synthesis and Characterization of a novel Ruthenium(II) Complex With Bidentate O,N-donor OxazolineLigand and Study of Catalytic Oxidation of Sulfides and Alkanes

    , M.Sc. Thesis Sharif University of Technology Hosseini, Mojtaba (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    The 2-(2′-hydroxyphenyl)-oxazoline ligand (Hphox) is generated from 1:1 condensation of methyl salicylate with 2-aminoethanol. Novel [Ru(Hphox)2(H2O)2] (Hphox = 2-(2′-hydroxyphenyl)-oxazoline ) complex has been synthesized and characterized by physic-chemical methods. Oxidation of sulfides catalyzed by the mixed-ligand ruthenium(II) complex [Ru(Hphox)2(H2O)2]using urea-hydrogen peroxide (UHP) as oxidant was investigated under mild condition within 1 h. The results showed that mixed-ligand ruthenium(II) complex was effective catalyst in oxidation of sulfides in whichsulfoxideswere the only products. Using this catalytic system in the oxidation of alkanes, ketones were obtained as the main... 

    , M.Sc. Thesis Sharif University of Technology Hatami, Mojgan (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    Inert gold become catalytically active when dispersed in the form of nanoparticles. Isolated gold nanoparticles have demonstrated high catalytic activity for both oxidation and reduction reactions. In order to obtain high catalytic activity, gold nanoparticles are generally dispersed on support materials, among which oxides are commonly used. However, a substantial decrease in activity and selectivity of the immobilized catalysts is frequently observed due to the heterogeneous nature of these support materials in reaction media. In the course of our study on the metal-based catalysis for synthesis of organic compounds, we herein report that rod-shaped Au nanoparticles in aqua solution... 

    Preparation of Heterogeneous Catalysts by Immobilization of Molybdenum and Manganese-shiff Base Complexes into the Nanopores of Zeolite and SBA-15

    , Ph.D. Dissertation Sharif University of Technology Zare, Maryam (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    This thesisconsiders new fundamental approaches to yield heterogeneous catalysts in to three sections. The first section described the immobilization of the molybdenum-Schiff base complexes in pores of SBA-15 in two different methodologies depending on the actual structure of the complexes., (i) stepwise formation of the complex by initial covalent anchoring of one of the components and consecutive solid phase synthesis consisting of the condensation of the other components of the salen complex (iii) one-step complex immobilization by covalent binding through the ligand.Based on the first methodology, we report the preparation of ordered mesoporous silica SBA-15 containing a molybdenum... 

    Synthesis and Characterization of Various Transition Metal Complexes and the Application in Oxidation, Heck, Suzuki, Sonogashira and Olefin Metathesis

    , Ph.D. Dissertation Sharif University of Technology Amini, Mojtaba (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    In nature, catalysis is of vital importance in a wide variety of biochemical processes catalyzed by metalloenzymes. The functions performed by the metalloenzymes and their significance have inspired a range of biomimetic studies, and intense efforts have been concentrated on the synthesis of low molecular weight complexes to model the spectroscopic features of such enzymes. Concomitantly, a challenging frontier in the field of biomimetic chemistry is the development of highly reactive model compounds that are able to effect rapid and selective substrate conversion. Some important catalytic transformations that have gained attention in recent years involve the carbon-carbon coupling, olefin... 

    Synthesis of Core-Shell Nanoparticles Supported Iron and Vanadium Schiff Base and Their Application as a Catalyst for Oxidation of Sulfides, Alcohols and Olefins

    , M.Sc. Thesis Sharif University of Technology Payab, Ebrahim (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    In this work, synthesized Fe3O4 magnetic nanoparticles andcoated with SiO2 to prepare magnetic core-shell nanoparticles. Then immobilized Schiff baseof iron and vanadium complexes on magnetic core-shell nanoparticles was prepared as a recoverable magnetic nano catalysts. These catalysts were named Fe3O4@SiO2@L1@Fe, Fe3O4@SiO2@L2@Fe and Fe3O4@SiO2@L3@V. Furthermore,olefines epoxidation, sulfides and alcohols oxidation were studied with using iron and vanadium magnetic nano catalysts. The supported catalysts were characterized by atomic absorption, FT-IR and UV–Vis spectra.The catalytic performance of the synthesized iron catalyst was tested for the epoxidation of cyclohexene, styrene and... 

    Synthesis of Metal-Organic Frameworks and Self-supported Coordination Polymers of Transition Metals with Catalytic Potential as Template for Supported Pd Nanoparticles and Preparation of Metal Oxide Nanoparticles for Olefin Epoxidation and C-C Coupling Reactions

    , M.Sc. Thesis Sharif University of Technology Ashouri, Fatemeh (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    In this research, synthesis of new heterogeneous catalysts has been studied. These catalysts were prepared in three different areas of the synthesis of coordination polymers and metal-organic frameworks, supported palladium nanoparticles on these polymers, and production of metal oxide nanoparticles. At first, metal organic frameworks of cobalt and manganese transition metals were synthesized through hydrothermal method. In order to prepare these frameworks, 1,4-benzenedicarboxylic acid (terephthalic acid) and 2-amino-1,4-benzenedicarboxylic acid ligands were utilized as spacer ligands. X-ray analysis indicated that the structure of polymers is composed of secondary building units (SBUs) of...