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    Analysis of DNA Methylation in Single-cell Resolution Using Algorithmic Methods and Deep Neural Networks

    , M.Sc. Thesis Sharif University of Technology Rasti Ghamsari, Ozra (Author) ; Sharifi Zarchi, Ali (Supervisor)
    Abstract
    DNA methylation in one of the most important epigenetic variations, which causes significant variations in gene expressions of mammalians. Our current knowledge about DNA methylation is based on measurments from samples of bulk data which cause ambiguity in intracellular differences and analysis of rare cell samples. For this reason, the ability to measure DNA methylation in single-cells has the potential to play an important role in understanding many biological processes including embryonic developement, disease progression including cancer, aging, chromosome instability, X chromosome inactivation, cell differentiation and genes regulation. Recent technological advances have enabled... 

    The semi-analytical modeling and simulation of the VAPEX process of ""Kuh-e-Mond"" heavy oil reservoir

    , Article Petroleum Science and Technology ; Vol. 29, issue. 5 , Oct , 2009 , p. 535-548 ; ISSN: 10916466 Rasti, F ; Masihi, M ; Kharrat, R ; Sharif University of Technology
    2009
    Abstract
    The vapor extraction process (or VAPEX) uses vaporized solvents injected into a horizontal well to form a vapor chamber within the reservoir. Vapor dissolves in the oil and enhances the oil production by decreasing the oil viscosity in heavy oil reservoirs. To evaluate the process we conduct a simulation study on an Iranian heavy oil reservoir called Kuh-e-Mond. In addition, a semi-analytical investigation of the VAPEX process has been performed. The idea is to perform VAPEX simulation for a laboratory model and find a methodology to compare the results of the simulator with the semi-analytical Butler's model. In particular, a semi-analytical dimensionless correlation for production rate... 

    The semi-analytical modeling and simulation of the VAPEX process of "Kuh-e-Mond" heavy oil reservoir

    , Article Petroleum Science and Technology ; Volume 29, Issue 5 , 2011 , Pages 535-548 ; 10916466 (ISSN) Rasti, F ; Masihi, M ; Kharrat, R ; Sharif University of Technology
    2011
    Abstract
    The vapor extraction process (or VAPEX) uses vaporized solvents injected into a horizontal well to form a vapor chamber within the reservoir. Vapor dissolves in the oil and enhances the oil production by decreasing the oil viscosity in heavy oil reservoirs. To evaluate the process we conduct a simulation study on an Iranian heavy oil reservoir called Kuh-e-Mond. In addition, a semi-analytical investigation of the VAPEX process has been performed. The idea is to perform VAPEX simulation for a laboratory model and find a methodology to compare the results of the simulator with the semi-analytical Butler's model. In particular, a semi-analytical dimensionless correlation for production rate... 

    Shaping of Laser Pulse for Molecular Dissociation

    , M.Sc. Thesis Sharif University of Technology Rasti, Soroush (Author) ; Saddighi Bonabi, Rasoul (Supervisor)
    Abstract
    In this project, ionization and dissociation of nitrogen, methane and formaldehyde molecules through interaction by intense femto-second lasers have been investigated. The optimum shape of laser pulses for dissociation of methane and formaldehyde molecules for controlling the dissociation paths into desired products are obtained. Based on time dependent density functional theory and quantum optimal control theory, the calculations are carried out in intensities at the range of 1014-1016 Wcm-2 with pulse durations of 4 -20fs. Octopus package is used as a powerful computational program. By using, quantum optimal control theory, optimum laser pulses with manipulation of amplitude, phase and... 

    Preparation and characterization of ZnO nanoparticles by a novel sol-gel route

    , Article Materials Letters ; Volume 61, Issue 14-15 , 2007 , Pages 3265-3268 ; 0167577X (ISSN) Vafaee, M ; Sasani Ghamsari, M ; Sharif University of Technology
    2007
    Abstract
    In this study, ZnO nanoparticles with 3 to 4 nm size and spherical shape have been prepared. For the first time, TEA (triethanolamine) as a surfactant has been used for the preparation of ZnO nanoparticles. The best concentration of each component was adjusted through comparison between different sol absorption spectra. The best sol regarding its optical property was subjected to analysis by photoluminescence spectroscopy. TEM micrograph and electron diffraction pattern of these particles were obtained to represent the morphology and crystalline phase of the particles, respectively. Experimental results have shown that the prepared zinc oxide nanoparticles by this method have higher... 

    Optimal control of dissociation of nitrogen molecule with intense ultra-short laser pulse shaping

    , Article Journal of Molecular Structure ; Volume 1083 , March , 2015 , Pages 121-126 ; 00222860 (ISSN) Rasti, S ; Irani, E ; Sadighi Bonabi, R ; Sharif University of Technology
    Elsevier  2015
    Abstract
    (GraphPresented) The quantum optimal control theory in conjunction with time dependent density functional theory is used to optimize the laser pulse shape for dissociation of nitrogen molecule. For several initial peak intensities and frequency ranges, the optimum shapes are produced and compared to determine the most efficient pulse. Ehrenfest molecular dynamics model is also used to test the dissociation process. The corresponding snapshots of density and time dependent electron localization function are presented. It is noticed that when the frequency ranges of laser pulses are doubled, it leads to 60% faster dissociation of N2 molecule  

    Efficient photo-dissociation of CH4 and H2CO molecules with optimized ultra-short laser pulses

    , Article AIP Advances ; Volume 5, Issue 11 , 2015 ; 21583226 (ISSN) Rasti, S ; Irani, E ; Sadighi Bonabi, R ; Sharif University of Technology
    American Institute of Physics Inc  2015
    Abstract
    The fragmentation dynamics of CH4 and H2CO molecules have been studied with ultra-short pulses at laser intensityof up to 1015Wcm-2. Three dimensional molecular dynamics calculations for finding the optimized laser pulses are presented based on time-dependent density functional theory and quantum optimal control theory. A comparison of the results for orientation dependence in the ionization process shows that the electron distribution for CH4 is more isotropic than H2CO molecule. Total conversion yields of up to 70% at an orientation angle of 30o for CH4 and 65% at 900 for H2CO are achieved which lead to enhancement of dissociation probability  

    Context-Aware ontology-based security measurement model

    , Article Journal of Information Security and Applications ; Volume 67 , 2022 ; 22142134 (ISSN) Khaleghi, M ; Aref, M. R ; Rasti, M ; Sharif University of Technology
    Elsevier Ltd  2022
    Abstract
    Security measurement models (SMMs) and quantitative security metrics (QSMs) are crucial pillars of systematic security measurement. How to design the enhanced SMMs and effective QSMs has been seriously considered in recent years. However, to the best of our knowledge, a desirable SMM has not yet been provided to measure the security effectiveness of a national-level network (NLN) due to its specific attributes. NLN has three main attributes, including plurality and diversity of network components, continuous changes, and simultaneous functionalities. These attributes cause three major challenges to designing a desirable SMM for NLN, including complexity, dynamic measurement, and... 

    Comprehensive comparison of security measurement models

    , Article Journal of Applied Security Research ; 2022 ; 19361610 (ISSN) Khaleghi, M ; Aref, M. R ; Rasti, M ; Sharif University of Technology
    Routledge  2022
    Abstract
    Security measurement models (SMMs) and their corresponding derived metrics form the main pillars of a systematic security measurement. Providing a desirable SMM is very challenging and has been investigated over the past two decades, so that numerous SMMs have been proposed and several surveys on SMMs have been performed. However, to the best of our knowledge, neither a systematic taxonomy nor a comprehensive comparison has yet been proposed for SMMs. This paper focuses on the comprehensive comparison of SMMs relying on a feature-based approach. The plurality and diversity of the compared SMMs enable us to deduce all the open issues. © 2021 Taylor & Francis Group, LLC  

    Comprehensive Comparison of Security Measurement Models

    , Article Journal of Applied Security Research ; Volume 18, Issue 3 , 2023 , Pages 333-401 ; 19361610 (ISSN) Khaleghi, M ; Aref, M. R ; Rasti, M ; Sharif University of Technology
    Routledge  2023
    Abstract
    Security measurement models (SMMs) and their corresponding derived metrics form the main pillars of a systematic security measurement. Providing a desirable SMM is very challenging and has been investigated over the past two decades, so that numerous SMMs have been proposed and several surveys on SMMs have been performed. However, to the best of our knowledge, neither a systematic taxonomy nor a comprehensive comparison has yet been proposed for SMMs. This paper focuses on the comprehensive comparison of SMMs relying on a feature-based approach. The plurality and diversity of the compared SMMs enable us to deduce all the open issues. © 2021 Taylor & Francis Group, LLC  

    Plug and play augmented HQS: Convergence analysis and its application in MRI reconstruction

    , Article Neurocomputing ; Volume 518 , 2023 , Pages 1-14 ; 09252312 (ISSN) Rasti Meymandi, A ; Ghaffari, A ; Fatemizadeh, E ; Sharif University of Technology
    Elsevier B.V  2023
    Abstract
    Sparse recovery in the context of the inverse problem has become an enormously popular technique in reconstructing various degraded images in various applications. One of the well-known techniques in modularizing these particular inverse problems is the Plug and Play Half-Quadratic-Splitting (PnP-HQS). This method has been demonstrated to achieve good results in the literature; however, it is still too plain to be fully exploited for reconstruction. In this regard, we introduce an augmented version of this technique dubbed “PnP-AugHQS” to efficiently utilize its capabilities in image reconstruction. We provide a comprehensive convergence analysis of the proposed algorithm to ensure its... 

    Presentation of Knowledge Management Framework for Project-Based Organizations

    , M.Sc. Thesis Sharif University of Technology Ghamsari Esfahani, Narges (Author) ; Shadrokh, Shahram (Supervisor)
    Abstract
    Knowledge is an organization asset that if used in the direction of organization’s strategic mission, can provide values for the organization. Therefore, many organizations such as NASA, Siemens; and Microsoft have invested in order to improve their knowledge management practices. Many organizations have not been successful in implementing appropriate knowledge management and incurred by huge expenses, while others can use and improve their locations among their competitors in the business. The reason behind many of these organizations were ignoring factor(s) that have direct undeniable effect on result from organization’s knowledge management.
    The framework of knowledge management is a... 

    Semi-Analytical Modeling And Simulation Of Heavy Oil Recovery Through VAPEX Process

    , M.Sc. Thesis Sharif University of Technology Rasti, Fariba (Author) ; Masihi, Mohsen (Supervisor) ; Kharrat, Riyaz (Supervisor)
    Abstract
    VAPEX is a relatively new EOR process for the recovery of heavy oil. In this process solvent is used to form a vapor chamber within a reservoir. Vapor dissolves in the oil and diluted oil drains by gravity to a horizontal production well. The essential features of this recovery mechanism have been discussed in this study. Furthermore, a semi-analytical and a simulation study of VAPEX process have been performed on a specified Iranian heavy oil reservoir (such as Kuh-e-Mond). The aim of this study is to investigate an exponential functionality (correlation) witch incorporates all physical parameters that affect the production rate of VAPEX process in dimensionless form. The adjustable... 

    Determination of Stable Crystal Structure of Y358 New Superconductor and its Phonon and Electronic Structure using Density Functional Theory

    , M.Sc. Thesis Sharif University of Technology Rasti, Mohammad (Author) ; Khosroabadi, Hossein (Supervisor) ; Akhavan, Mohammad (Co-Advisor)
    Abstract
    Y-based Superconducting compounds (YBCO) with different stoichiometry have been considered by researchers for its transition temperature above the boiling temperature of liquid nitrogen, preparation of high quality samples, simple crystal and electronic structure and other advantages relative to the other high-Tc copper oxide superconductors. Reaching to higher transition temperature has been considered in the recent years. In 2009, new compound of this family with different stoichiometry Y3Ba5Cu8O18(Y358) and transition temperature above 100 K was synthesized which is 10 K higher than maximum transition temperature in this family. Confirming this transition temperature can be help us for... 

    Crack-free nanostructured BaTiO3 thin films prepared by sol-gel dip-coating technique

    , Article Ceramics International ; Vol. 40, issue. 6 , 2014 , pp. 8613-8619 Ashiri, R ; Nemati, A ; Sasani Ghamsari, M ; Sharif University of Technology
    2014
    Abstract
    In this report, crack-free nanostructured barium titanate thin films are prepared by a sol-gel processing method. Glacial acetic acid, barium acetate, titanium tetraisopropyl alkoxide, 2-propanol and deionized water are used as precursors for preparing stable precursor solution. Then very thin films (thickness=26 nm) are deposited on fused silica substrates. In order to prepare crack-free thin films of BaTiO3, much attention is given to solvent evaporation process and a controlled pre-drying process is developed. It is found that the control of the process, especially in the initial stage of drying process is crucial and important for preparation of the crack-free ultrathin nanostructured... 

    Sol stabilization in sol-gel process

    , Article The Sol-Gel Process: Uniformity, Polymers and Applications ; 2011 , Pages 787-818 ; 9781617613210 (ISBN) Ghamsari, M. S ; Mehranpour, H ; Radiman, S ; Sharif University of Technology
    Nova Science Publishers, Inc  2011
    Abstract
    The sol-gel process as a chemical route is widely used in the fields of materials science and engineering. Historically, the sol-gel techniques have been developed during the past 40 years as an alternative process for glasses and ceramics production [1]. It is reported that the sol-gel process had been introduced by Ebelman [2], who had prepared a transparent SiO2 thin film from slow hydrolysis of an ester of silicic acid in 1845. In comparison with other techniques such as CVD or sintering, the sol-gel technique is a very simple process with considerable advantages. This process is low cost, has high controllability and potential application for preparation of different materials and... 

    Effect of brookite presence on nanocrystalline anatase - Rutile phase transformation

    , Article International Journal of Nanotechnology ; Volume 6, Issue 10-11 , 2009 , Pages 961-972 ; 14757435 (ISSN) Mahshid, S ; Askari, M ; Sasani Ghamsari, M ; Sharif University of Technology
    2009
    Abstract
    TiO2nanocrystals were prepared by hydrolysis and peptisation of titanium isopropoxide under different pH values. The as-prepared powder of very fine anatase crystallites ranges from 8 nm in acidic solution of pH 3 to 10 nm in basic solution of pH 8. Heat treatment of the powders leads to grain growth and anatase - rutile transformation. Experimental results have shown that the anatase to rutile phase transformation in the heat-treated powders depend not only on primary crystallite size but also the presence of brookite phase. It is observed that in the powders with the same size the presence brookite phase would accelerate the anatase to rutile transformation. Furthermore it has been found... 

    Design of a Colorimetric Sensor Array Based on Aggregation of Gold Nanoparticles on the Surface of Probiotic Bacteria for Identification and Discrimination of Antiseptic Alcohols

    , M.Sc. Thesis Sharif University of Technology Ghamsari, Mahdi (Author) ; Hormozinezhad, Mohammad Reza (Supervisor)
    Abstract
    The occurrence of the COVID-19 pandemic and the subsequent rising demand for purchasing alcohol-based sanitizers led to a remarkable prosperity in supplying these hygiene products. Hence, the development of a straightforward and efficient analytical strategy for discrimination of antiseptic alcohols including methanol, ethanol and isopropanol is of great importance. By exploiting the alcohol-sensitive membranes of probiotic bacteria, this research aims to develop a colorimetric sensor array for discriminating methanol, ethanol and isopropanol. In this design, the aggregation of citrate-capped gold nanoparticles (Au NPs) on the thiol-modified surface of two probiotic bacteria, including... 

    Synthesis and Characterization of ZnO for Electron Transport Layer in Perovskite and CIGS Solar Cells

    , M.Sc. Thesis Sharif University of Technology Rasti, Noushin (Author) ; Taghavinia, Nima (Supervisor) ; Dehghani, Mehdi (Supervisor)
    Abstract
    The purpose of this study is the fabrication and characterization of ZnO nano particles and the application of ZnO in solar cells. Therefore, firstly we fabricate the high stable solution of ZnO nano particles and then characterize ZnO nano particles. In addition, we study sulfurzation and selenization of zinc oxide thin films. We use ZnO nano particles for fabrication of transparent conductive films. Transparent conductive films have many applications such as touch panels, displays and solar cells. The most applicable transparent conductive electrode is indium tin oxide , which is the most expensive layer in solar cells. But silver nanowires has some challenges such as high surface... 

    Probabilistic worth assessment of distributed static series compensators

    , Article IEEE Transactions on Power Delivery ; Vol. 26, issue. 3 , 2011 , p. 1734-1743 ; ISSN: 08858977 Dorostkar-Ghamsari, M ; Fotuhi-Firuzabad, M ; Aminifar, F ; Sharif University of Technology
    2011
    Abstract
    The deployment of flexible ac transmission system (FACTS) devices, despite miscellaneous benefits and applications, has been restricted mainly due to their large investment costs. Accordingly, the notion of distributed FACTS (D-FACTS) was recently proposed. Distributed static series compensators (DSSCs), as a new member of D-FACTS, are directly clamped to conductors of transmission lines. The possibility of controlling the compensation rate of DSSCs from the control center affords the active control of network power flow. This paper presents a comprehensive reliability model for the DSSC. The model is then reduced and a state-space representation is extracted for a transmission line with a...