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Evaluation of Base Calling Methods in Next Generation Sequencing
, M.Sc. Thesis Sharif University of Technology ; Hossein Khalaj, Babak (Supervisor) ; Motahhari, Abolfazl (Supervisor)
Abstract
In the mid twentieth century by discovering the existence of genetic strands and understanding their role in diseases and phenotypes of species, research initiated to decipher their content. Sequencing of the first human genome at early twenty-first century paved the way to study and even cure complex human deseases having genetic origin. Next Generation Sequencing (NGS) Technologies have significantly reduced the expenses and the timing complexity of DNA Sequencing and this has an improving trend. In this thesis, we evaluate Base Calling methods, a critical step in analyzing next generation sequencing information and deals with massive sequencing data. Base Calling tries to optimally detect...
Influences of Magnetic Nanoparticles and Magnetic Field on the Performance of the Redox Flow Batteries
, M.Sc. Thesis Sharif University of Technology ; Molaei Dehkordi, Asghar (Supervisor) ; Gharibi, Hossein (Supervisor)
Abstract
The novel concept of using magnetic nanofluidic electrolyte for redox flow batteries (RFBs) is demonstrated for the first time. In this regard, the stable magnetic nanofluidic electrolytes are prepared by dispersing magnetic modified multiwalled carbon nanotubes (MMWCNTs) in the positive electrolyte of a polysulfide-iodide redox flow battery at mass concentrations of less than 0.3 g L−1. The electrochemical behavior of magnetic nanofluidic electrolyte was examined using cyclic voltammetry at different mass concentrations of MMWCNTs with a carbon felt electrode. Higher and stable peak current densities were observed at larger mass concentrations of MMWCNTs. A polysulfide-iodide redox flow...
On competence of vendor managed inventory in supply chains using basic mathematical inventory models
, Article Scientia Iranica ; Vol. 21, issue. 3 , 2014 , p. 1061-1071 ; Haji, A ; Gharibi, M ; Sharif University of Technology
2014
Abstract
In this study, a two-echelon single-vendor supply chain is selected to do a cost-based comparison between short-term performances of a Vendor Managed Inventory (VMI) and a Retailer Managed Inventory (RMI). While the inventory costs include ordering and storing expenses, the rate of consumption and the price of goods are constant, the rate of production and pace of transportation are infinite and shortage is not allowed. This paper, after a comprehensive literature review, is followed by three cases of single retailer, n-retailer and two-retailer chains. Unlike the second case, in the first case, VMI shows an absolute superiority to RMI, and this is the reason for devising the third case in...
A Polypropylene-Based Microextraction Method Coupled with HPLC-FD for Determination of Fluoxetine in Human
, M.Sc. Thesis Sharif University of Technology ; Bagheri, Habib (Supervisor)
Abstract
Considering principles of both micro-solid phase extraction (µ-SPE) and stir-bar sorptive extraction (SBSE) techniques, in this study a microextraction technique was developed using a polypropylene sheet as extracting device for isolation of fluoxetine from biological samples. Being rather inexpensive and simple to prepare extracting device, elimination of time consuming sorbent synthesis step and memory effect are some of the advantages of the proposed method. The extraction process was performed using a polypropylene sheet as extracting device. Solvent desorption was performed in a microvial and then extractant was injected into HPLC system. The effect of various parameters including pH,...
Investigation of carbon monoxide tolerance of platinum nanoparticles in the presence of optimum ratio of doped polyaniline with para toluene sulfonic acid and their utilization in a real passive direct methanol fuel cell
, Article Electrochimica Acta ; Volume 97 , 2013 , Pages 216-225 ; 00134686 (ISSN) ; Amani, M ; Pahlavanzadeh, H ; Kazemeini, M ; Sharif University of Technology
2013
Abstract
Polyaniline fiber (PANI) was synthesized by chemical interfacial method and doped with para toluene sulfonic acid (PTSA) through a sequential doping-dedoping-redoping process resulting in PANI-PTSA. The doped material was utilized to fabricate Vulcan-polyaniline composite of C-PANI-PTSA. Next, through reduction, Pt particles were deposited on to this composite to produce a Pt/C-PANI-PTSA electrocatalyst. To investigate the PANI-PTSA interaction with the carbon support as well as, to consider its effect upon the catalytic activity of Pt/C-PANI-PTSA, electrocatalysts with different ratios of 10, 15, 20, 25 and 30 wt% were synthesized and their activity was compared with the Pt/C (Electrochem)....
Fabrication of MEA based on sulfonic acid functionalized carbon supported platinum nanoparticles for oxygen reduction reaction in PEMFCs
, Article RSC Advances ; 2015 , Pages 85775-85784 ; 20462069 (ISSN) ; Yasi, F ; Kazemeini, M ; Heydari, A ; Golmohammadi, F ; Sharif University of Technology
Royal Society of Chemistry
2015
Abstract
The Nafion ionomer affects the efficiency of the platinum (Pt) catalyst by blocking the active sites thereby restricting the gas permeability of the catalyst layer; but, there is a limitation in the quantity of Nafion ionomer that needs to be added without affecting the cell performance. Sulfonation of carbon-supported catalysts as mixed electronic and protonic conductors has been reported to be an efficient way to increase the triple-phase boundaries. In order to improve the utilization and activity of cathodic catalysts in the oxygen reduction reaction (ORR), Pt nanoparticles were loaded on a mixture of Vulcan XC-72R and MWCNTs, which were functionalized in a mixture of 96% sulfuric acid...
Novel magnetic flowable electrode for redox flow batteries: A polysulfide/iodide case study
, Article Industrial and Engineering Chemistry Research ; Volume 60, Issue 2 , 2021 , Pages 824-841 ; 08885885 (ISSN) ; Molaei Dehkordi, A ; Gharibi, H ; Roberts, E. P. L ; Sharif University of Technology
American Chemical Society
2021
Abstract
A novel approach named a magnetic flowable electrode (MFE) is proposed for the first time to enable enhancement of redox flow batteries (RFBs) performance. This approach enables the formation of a high active surface area electrode from magnetic nanomaterials, without the need to fabricate a self-supporting three-dimensional electrode structure. To form a simple MFE, magnetic modified carbon nanotubes are dispersed in the electrolyte, and permanent magnets are embedded behind the current feeder to apply a magnetic field across the flow cell channels. With circulating electrolyte, magnetic carbon nanotubes are aggregated on the graphite bipolar plate to form a well-structured nanoscale...
The potential therapeutic effects of Galbanic acid on cancer
, Article Pathology Research and Practice ; Volume 248 , 2023 ; 03440338 (ISSN) ; Vahedian, V ; Golshanrad, P ; Nahavandi, R ; Behshood, P ; Soltani, N ; Gharibi, M ; Rashidi, M ; Maroufi, N. F ; Sharif University of Technology
Elsevier GmbH
2023
Abstract
Galbanic acid (GBA), as a natural compound has potential anticancer properties. It has been documented that GBA shows promising therapeutic potential against various types of cancer, including breast, lung, colon, liver, and prostate cancer. Several mechanisms involve im anti-tumor effects of GBA include apoptosis induction, cell cycle arrest, inhibition of angiogenesis, suppression of metastasis, and modulation of immune responses. Furthermore, the synergistic effects of GBA along with chemotherapeutic agents led to has enhancing efficiency with reduction in toxicity. Moreover, GBA through antioxidant and anti-inflammatory properties possess indirect anti-tumor effects. In this review, we...
Calculation of the Energy Release Rate of Nano-Cracks in FCC Materials Via the Many Body Atomic Scale FEM
, M.Sc. Thesis Sharif University of Technology ; Mohammadi Shodja, Hossein (Supervisor)
Abstract
Since the classical continuum theory fails to deal with the problems associated with defects, stress concentrators, and relevant deformation phenomena in solids, alternative approaches that can detect the atomistic nature of materials' fracture are required. The deficiency of the capture the size effect which yields delusively high values for some components of the stress field right on the edge of the stress concentrators, and its weakness in describing the complex interaction between small inhomogeneities, cracks and the like when they are only a few nanometers apart, are among some of the disadvantages of the classical approach. In recent years, however, atomistic methods are emerging to...
Semisolid Stir Joining of As-Cast Silicon-Aluminum Bronze
, M.Sc. Thesis Sharif University of Technology ; Kokabi, Amir Hossein (Supervisor) ; Ashuri, Hossein (Supervisor)
Abstract
Aluminum Bronzes have many applications in marine environments. These alloys suffer from both hot cracking and cold cracking. In order to overcome the hot cracking and cold cracking, Semisolid Stir Joining method and a proper thermal cycle was used respectively. Effects of temperature, stirring rate, and tool type were investigated in Semisolid Stir joining method. In this method, butt joint design was used in order to place specimens, and the specimens were heated up to specific temperatures (920, 925, 930°C). A stirrer (Cylindrical and Grooved tool) with three rotational speeds (800, 1200, 1600 RPM) was introduced into the stir weld seam. Welded specimens were cooled to the 900°C...
The Study of Eliminating Gender Gap in Iran Labor Market on Participation Rate of Married Urban Women
, M.Sc. Thesis Sharif University of Technology ; Rahmati, Mohammad Hossein (Supervisor) ; Joshaghani, Hossein (Supervisor)
Abstract
The low female labor force participation rate in the Iranian labor market relative to the global average and even to countries that do not differ significantly from the socio-economic characteristics of our country is one of the important questions of the Iranian labor market. In this study, we seek to answer the question of whether the economic participation rate of married women will increase if the gender gaps in wages, job findings and job losses among women and men are eliminated in the Iranian labor market. To answer this question using household expenditure and income data and labor force data, we show that between the two categories of occupations, in terms of the share of women's...
Graph homomorphisms through random walks [electronic resource]
, Article Journal of Graph Theory ; 2003, Volume 44, Issue 1, pages 15–38 ; Hajiabolhassan, Hossein ; Sharif University of Technology
Abstract
In this paper we introduce some general necessary conditions for the existence of graph homomorphisms, which hold in both directed and undirected cases. Our method is a combination of Diaconis and Saloff–Coste comparison technique for Markov chains and a generalization of Haemers interlacing theorem. As some applications, we obtain a necessary condition for the spanning subgraph problem, which also provides a generalization of a theorem of Mohar (1992) as a necessary condition for Hamiltonicity. In particular, in the case that the range is a Cayley graph or an edge-transitive graph, we obtain theorems with a corollary about the existence of homomorphisms to cycles. This, specially, provides...
Unique list-colourability and the fixing chromatic number of graphs [electronic resource]
, Article Discrete Applied Mathematics ; Volume 152, Issues 1–3, 1 November 2005, Pages 123–138 ; Hajiabolhassan, Hossein ; Sharif University of Technology
Abstract
In this paper we introduce a chromatic parameter, called the fixing chromatic number, which is related to unique colourability of graphs, in the sense that it measures how one can embed the given graph G in G∪Kt by adding edges between G and Kt to make the whole graph uniquely t-colourable. We study some basic properties of this parameter as well as its relationships to some other well-known chromatic numbers as the acyclic chromatic number. We compute the fixing chromatic number of some graph products by applying a modified version of the exponential graph construction
Circular colouring and algebraic no-homomorphism theorems
, Article European Journal of Combinatorics ; Volume 28, Issue 6, August 2007, Pages 1843–1853 ; Hajiabolhassan, Hossein ; Sharif University of Technology
Abstract
In this paper, we apply some new algebraic no-homomorphism theorems in conjunction with some new chromatic parameters to estimate the circular chromatic number of graphs. To show the applicability of the general results, as a couple of examples, we generalize a well known inequality for the fractional chromatic number of graphs and we also show that the circular chromatic number of the graph obtained from the Petersen graph by excluding one vertex is equal to 3. Also, we focus on the Johnson–Holroyd–Stahl conjecture about the circular chromatic number of Kneser graphs and we propose an approach to this conjecture. In this regard, we introduce a new related conjecture on Kneser graphs and we...
Density and power graphs in graph homomorphism problem
, Article Discrete Mathematics ; Volume 308, Issue 17, 6 September 2008, Pages 4027–4030 ; Hajiabolhassan, Hossein ; Sharif University of Technology
Abstract
We introduce two necessary conditions for the existence of graph homomorphisms based on the concepts of density and power graph. As corollaries, we obtain a lower bound for the fractional chromatic number, and we set forward elementary proofs of the facts that the circular chromatic number of the Petersen graph is equal to three and the fact that the Coxeter graph is a core
Temperature dependence study of nonocontact AFM images using molecular dynamics simulations [electronic resource]
, Article Int. Journal of Modern Physics ; 2012, Vol. 5, pp. 418-432 ; Meghdar, Ali ; Sharif University of Technology
Abstract
The effect of temperature on the noncontact atomic force microscopy (NC-AFM) surface imaging is investigated with the aid of molecular dynamics (MD) analysis based on the Sutton-Chen (SC) interatomic potential. Particular attention is devoted to the tip and sample flexibility at different temperatures. When a gold coated probe is brought close to the Au (001) surface at high temperatures, the tip and surface atoms are pulled together and their distance becomes smaller. The tip and sample atoms displacement varies in the different environment temperatures and this leads to the different interaction forces. Along this line, to study the effect of temperature on the resulting images, we have...
Developing an Analytical Model for Predicting the Residual Stresses Induced by Shot Peening with Considering the Effect of Initial Surface Treatment
, Ph.D. Dissertation Sharif University of Technology ; Farrahi, Gholam Hossein (Supervisor) ; Mahmoudi, Amir Hossein (Co-Supervisor)
Abstract
Shot peening is a cold-working process commonly used in industry to improve the fatigue performance, stress corrosion resistance and surface nano-crystallization of metallic parts. This process extends fatigue life via two mechanisms: Preventing the crack growth due to compressive residual stresses and, preventing the crack initiation because of increased material hardness. These mechanisms are the results of the bombardment of the component's surface with small spherical particles. In this research, an analytical model is developed for estimating the residual stress distribution induced by shot peening process. The modifications of the developed analytical model are related to...
Combustible organic materials : determination and prediction of combustion properties
, Book
De Gruyter
2018
Evaluating Reliability of SSDs Against Power Outage
, M.Sc. Thesis Sharif University of Technology ; Asadi, Hossein (Supervisor)
Abstract
Solid-State Drives (SSDs) provide high performance, low power consumption, and hence are widely used in the I/O cache of enterprise storage systems and high performance servers. Although employing high performance SSDs in the I/O cache of storage systems significantly improves system performance, it comes with significant reliability threats for write operations upon power failures. In order to provide high level of reliability, storage architectures employ SSDs in I/O cache with RAID-1 configuration, however, such configuration only partially mitigates the reliability issues of the SSDs. In this thesis, we analyze the reliability of SSD-based I/O caches against power outage and high...
On the isoperimetric spectrum of graphs and its approximations [electronic resource]
, Article Journal of Combinatorial Theory, Series B ; Volume 100, Issue 4, July 2010, Pages 390–412 ; Hajiabolhassan, Hossein ; Javadi, Ramin ; Sharif University of Technology
Abstract
In this paper1 we consider higher isoperimetric numbers of a (finite directed) graph. In this regard we focus on the nth mean isoperimetric constant of a directed graph as the minimum of the mean outgoing normalized flows from a given set of n disjoint subsets of the vertex set of the graph. We show that the second mean isoperimetric constant in this general setting, coincides with (the mean version of) the classical Cheeger constant of the graph, while for the rest of the spectrum we show that there is a fundamental difference between the nth isoperimetric constant and the number obtained by taking the minimum over all n-partitions. In this direction, we show that our definition is the...