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kalhor--hamidreza
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Investigating One-pot Three Component Synthesis of ß-Amino Carbonyl Compounds Exploiting Hydrolases: Protein Splicing Enzyme and N-Acetylmuramide Glycanhydrolase
, M.Sc. Thesis Sharif University of Technology ; Kalhor, Hamidreza (Supervisor)
Abstract
The application of biocatalysts in organic reactions refers to the use of enzymes, purified or crude, to increase the reaction rate. The usage of biocatalysts in organic reactions have many advantages, including biocompatibility, ease of separation, high yield, reusability without losing activity, high selectivity, and the use of water as the solvent. Furthermore, the carbon–carbon bond formation is one of the most important reactions in the synthesis of organic compounds, drugs, and biomolecules. Using enzymes in organic reactions can provide insightful information about the enzymes catalytic activities and paves the way for systematic investigation of their mechanisms. The enzymes...
Comparison of Switching Stream Cipher Systems
, M.Sc. Thesis Sharif University of Technology ; Daneshgar, Amir (Supervisor)
Abstract
In this thesis, we analyze and compare switching and CPSP cryptography systems. CPSP is a dynamic system which can act as synchronized or self-synchronized stream cipher under specific conditions. To do the comparison, first we have a brief review of cryptography fundamentals like stream cipher systems, synchronized stream ciphers, and self-synchronized ones. Then, we consider chaos systems in general form and then we present their role in cryptography systems, and in continue by introducing switching cryptography systems and also CPSP cryptography systems, and analyzing their relation with self-synchronized stream ciphers, we do our statistical tests on them
Application of Semi-Supervised Learning in Image Processing
, M.Sc. Thesis Sharif University of Technology ; Rabiee, Hamidreza (Supervisor)
Abstract
In recent years, the emergence of semi-supervised learning methods has broadened the scope of machine learning, especially for pattern classification. Besides obviating the need for experts to label the data, efficient use of unlabeled data causes a significant improvement in supervised learning methods in many applications. With the advent of statistical learning theory in the late 80's, and the emergence of the concept of regularization, kernel learning has always been in deep concentration. In recent years, semi-supervised kernel learning, which is a combination of the two above-mentioned viewpoints, has been considered greatly.
Large number of dimensions of the input data along with...
Large number of dimensions of the input data along with...
A General Theorem For Portfolio Generating Functions
, M.Sc. Thesis Sharif University of Technology ; Farhadi, Hamidreza (Supervisor)
Abstract
Portfolio generating functions are positive twice continuously differentiable functions of the common or ranked market weights. The return on such portfolios related to the market with a stochastic differential equation that has two components: the logarithmic change in the value of the generating function, and a drift process that is of bounded variation. The goal of this study is to generalized portfolio generating functions theorem for ’ functions, in order to cover some important functions in economic such as Gini coefficients
An Application of Algebraic Topology to Computer Sciences
, M.Sc. Thesis Sharif University of Technology ; Fanai, HamidReza (Supervisor)
Abstract
In this thesis we study one of the applications of algebraic topology to computer science and define some tools to analyze concurrent programs. For this purpose a geometric space is corresponded to every concurrent program and a partial order is considered on this space, so every path on it corresponds to an execution of the program. Some of these paths which are dihomotop (homotop in partial ordered spaces) with each other induce the same execution of the program. By defining “Fundamental Category” in which objects are points of the space and morphisms are dihomotopy classes, the space that should be analyzed shrinks to a smaller one. By defining component category in the next step, without...
A Survey Of Topological,Algebraic And C ∗-Algebraic K-Theory
, M.Sc. Thesis Sharif University of Technology ; Fanai, Hamidreza (Supervisor)
Abstract
In this thesis we study three versions of K−theory. The most well-known vesrsion is topological K−theory, a generalization of Grothendieck works on algebraic varieties to the topological setting by Atyiah and Hirzebruch. Since its birth it has been an indespensible tool in topology,differential geometry and index theory. In the early 1970s C∗−algebraic version of K−theory introduced through associating two abelian groups,K0(A)and K1(A)to a C∗−algebra like A. These functors proved to be a powerful machine, making it possible to calculate the K−theory of a great many C∗−algebras. At last,algebraic K−theory is dealig with linear algebra over a ring R by associating it, a sequence of abelian...
DNA Classification Using Optical Processing based on Alignment-free Methods
, M.Sc. Thesis Sharif University of Technology ; Koohi, Somayyeh (Supervisor)
Abstract
In this research, an optical processing method for DNA classification is presented in order to overcome the problems in the previous methods. With improving in the operational capacity of the sequencing process, which has increased the number of genomes, comparing sequences with a complete database of genomes is a serious challenge to computational methods. Most current classification programs suffer from either slow classification speeds, large memory requirements, or both. To achieve high speed and accuracy at the same time, we suggest using optical processing methods. The performance of electronic processing-based computing, especially in the case of large data processing, is usually...
Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies
, Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) ; Fattahi, A ; Sharif University of Technology
Nature Research
2022
Abstract
Designing drug delivery systems for therapeutic compounds whose receptors are located in the cytosol of cells is challenging as a bilayer cell membrane is negatively charged. The newly designed drug delivery systems should assist the mentioned drugs in passing the membrane barriers and achieving their targets. This study concentrated on developing novel ionic liquids (ILs) that interact effectively with cell membranes. These ILs are based on glucose-containing choline and are expected to be non-toxic. The binding energies of the known pharmaceutically active ionic liquids were calculated at the B3LYP/6-311++G(d,p) level in the gas phase and compared with those of our newly designed...
Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η
, Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) ; Fattahi, A ; Sharif University of Technology
Nature Research
2022
Abstract
DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of...
In silico design of novel anticancer drugs with amino acid and carbohydrate building blocks to inhibit PIM kinases
, Article Molecular Simulation ; Volume 48, Issue 6 , 2022 , Pages 526-540 ; 08927022 (ISSN) ; Fattahi, A ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
PIM-1 is a serine-threonine kinase mainly expressed in tissues like the Thymus, spleen, bone marrow, and liver. Overexpression of PIM kinases occurs in various types of human tumours, such as lymphomas, prostate cancer, and oral cancer. As a result, the design of drugs to inhibit PIM-1 in cancerous cells has attracted much attention in recent years. This study aimed to design the alternative inhibitors for PIM-1 kinase, which are based on carbohydrates and amino acids and are expected to be non-toxic with the same chemotherapeutic effects as the traditional known anticancer drugs. The combinatorial use of quantum mechanics (QM) and molecular dynamic simulation (MD) has enabled us to...
An Application of Stochastic Optimal Control in Solving the Mean-variance Portfolio Selection Problem
, M.Sc. Thesis Sharif University of Technology ; Farhadi, Hamidreza (Supervisor)
Abstract
In this essay, by putting in the framework of linear-quadratic optimal control (LQ),we study and solve the mean-variance portfolio selection problem. Two models will be studied in our work; in one we assume that the price process satisfies a diffusion stochastic differential equation, while in the second model, we assume it to satisfy a jump-diffusion stochastic differential equation. In both models, a formula for the efficient frontier is obtained. This essay is mainly obtained from the works of the following articles and books:
1)X.Y. Zhou and D. Li, Continuous-Time Mean-Variance Portfolio Selection:A Stochastic LQ Framework. Applied Mathematics and Optimization. 42(2000),...
1)X.Y. Zhou and D. Li, Continuous-Time Mean-Variance Portfolio Selection:A Stochastic LQ Framework. Applied Mathematics and Optimization. 42(2000),...
Customer Churn Prediction in Therapy Policy in Iran
, M.Sc. Thesis Sharif University of Technology ; Aslani, Shirin (Supervisor) ; Arian, Hamidreza (Supervisor)
Abstract
Using customer relationship management systems has led to the formation of databases containing businesses customer information. Increased competition in the markets, limited resources and high costs of attracting new customers compared to retaining existing customers have made customer retention an inevitable subject for business owners. Meanwhile, insurance companies, which due to their long history have suitable databases of product information and their customers, have resorted to using their databases to manage the relationship with their customers. In this research, while predicting customers churn in health insurance, as one of the most widely used products of domestic insurance...
Conversion of 3,6-O-dimethylfluorescein to fluorescein-based xanthylium derivative: characterization and covalent attachment to bovine serum albumin
, Article ChemistrySelect ; Volume 4, Issue 36 , 2019 , Pages 10681-10687 ; 23656549 (ISSN) ; Rezaei, M ; Sharif University of Technology
Wiley-Blackwell
2019
Abstract
Xanthene dyes, such as fluorescein and rhodamine, have played crucial rules in biological sciences especially covalent attachment of these organic compounds to biomolecules. 3-O-methylfluorescein and 3,6-O-dimethylfluorescein were synthesized and purified using a facile procedure. 3,6-O-dimethylfluorescein, which lacks fluorescence, was treated with sodium hydroxide and sulfuric acid solutions, giving rise to yellow and green fluorescent compounds, respectively. In both basic and acidic conditions, donor-acceptor structures were formed. The reaction of 3,6-O-dimethylfluorescein with acids, in a reversible manner, emitted green fluorescence, whereas its reaction with hydroxide ion,...
Investigating reliable conditions for hewl as an amyloid model in computational studies and drug interactions
, Article Journal of Chemical Information and Modeling ; Volume 59, Issue 12 , 2019 , Pages 5218-5229 ; 15499596 (ISSN) ; Jabbary, M ; Sharif University of Technology
American Chemical Society
2019
Abstract
A number of conformational diseases in humans have been associated with protein/peptide fibrillation known as amyloid. Although extensive studies have been conducted in understanding the molecular basis of amyloid formation, a detailed mechanism is still missing. Experimentally, HEWL (hen egg white lysozyme) has been exploited ubiquitously as a model protein for amyloid fibrillation and drug inhibition. However, computational studies investigating fibril formation of HEWL have been a difficult task to perform mainly due to high stability of lysozymes and the absence of crystal structures of HEWL fibril oligomers. In this study, we have examined various conditions of HEWL amyloid formation...
Identification of an aspidospermine derivative from borage extract as an anti-amyloid compound: A possible link between protein aggregation and antimalarial drugs
, Article Phytochemistry ; Volume 140 , 2017 , Pages 134-140 ; 00319422 (ISSN) ; Ashrafian, H ; Sharif University of Technology
Elsevier Ltd
2017
Abstract
A number of human diseases, including Alzheimer's and Parkinson's have been linked to amyloid formation. To search for an anti-amyloidogenic product, alkaloid enriched extract from borage leaves was examined for anti-amyloidogenic activity using Hen Egg White Lysozyme (HEWL) as a model protein. After isolation of the plant extract using rHPLC, only one fraction indicated a significant bioactivity. TEM analysis confirmed a remarkable reduction of amyloid fibrils in the presence of the bioactive fraction. To identify the effective substance in the fraction, mass spectrometry, FTIR, and NMR were performed. Our analyses determined that the bioactive compound as...
Investigating the effects of amino acid-based surface modification of carbon nanoparticles on the kinetics of insulin amyloid formation
, Article Colloids and Surfaces B: Biointerfaces ; Volume 176 , 2019 , Pages 471-479 ; 09277765 (ISSN) ; Yahyazadeh, A ; Sharif University of Technology
Elsevier B.V
2019
Abstract
Surface functionality of nanoparticles has been pivotal in defining interactions of nanoparticles and biomolecules. To explore various functionalities on the surface of nanoparticle through a facile procedure, various carbon-based nanoparticles, modified with a specific natural amino acid, were synthesized; the amino acids were chosen in order that almost all classes of amino acids were included. After characterizations of the nanoparticles using several spectroscopic methods, the effects of surface modification of nanoparticles were examined against amyloid formation, exploiting insulin as a model amyloidogenic polypeptide. Although most amino acids afforded carbon nanoparticles, only...
Probe into the molecular mechanism of ibuprofen interaction with warfarin bound to human serum albumin in comparison to ascorbic and salicylic acids: Allosteric inhibition of anticoagulant release
, Article Journal of Chemical Information and Modeling ; Volume 61, Issue 8 , 2021 , Pages 4045-4057 ; 15499596 (ISSN) ; Taghikhani, E ; Sharif University of Technology
American Chemical Society
2021
Abstract
The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned...
Experimental Removal of Diesel in Soil Using Indigenous Microorganisms Isolated Iran
, M.Sc. Thesis Sharif University of Technology ; Kariminia, Hamidreza (Supervisor) ; Yaghmaei, Soheila (Supervisor)
Abstract
Crude oil and petroleum products at the time of extraction, production and transportation cause serious contaminations in soil, water and environment. Biological methods have shown a promising effect for the cleanup of these hydrocarbon pollutants. Bioremediation employs the metabolic activity of microorganisms capable of using oil as their energy and carbon source. Biological methods are also less expensive than other cleanup technologies such as incineration and landfill. Large number of microbial stains have been discovered in nature, capable to degrade oil and petroleum products. Biological cleaning of oil contamination by microorganisms occurs naturally in the environment. It has been...
A Fine Grained Access Control Mechanism for Hybrid Mobile Applications in Android
, M.Sc. Thesis Sharif University of Technology ; Kharrazi, Mehdi (Supervisor) ; Rabiee, HamidReza (Co-Advisor)
Abstract
Hybrid mobile applications combine the features of Web technologies and native mobile apps. Like Web applications, they are implemented in portable, platform independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources. In these programs, web contents are loaded into a web component, called WebView, which can render HTML5 pages and execute JavaScript code. In order for the web content to access the system resources, which are isolated from the content inside Web-View due to its sandbox, bridges need to be built between JavaScript and the native code. developers usually use third party plug-ins for native side of application. hybrid...
Estimation of a Portfolio's Value-at-Risk Using Variational Auto-Encoders
, M.Sc. Thesis Sharif University of Technology ; Arian, Hamidreza (Supervisor) ; Talebian, Masoud (Supervisor)
Abstract
One of the most crucial aspects of financial risk management is risk measurement. Advanced AI-based solutions can provide the proper tools for assessing global markets, given the complexity of the global economy and the violation of typical modeling assumptions. A new strategy for quantifying stock portfolio risk based on one of the machine learning models known as Variational Autoencoders is provided in this dissertation. The suggested method is a generative model that can learn the stocks' dependency structure without relying on assumptions about stock return covariance and produce various market scenarios using cross-sectional stock return data with a higher signal-to-noise ratio. We...