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nazari--aliakbar
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Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: Different hydrogen bonding preferences for thymine versus O-alkyl thymine
, Article Journal of Molecular Modeling ; Volume 19, Issue 8 , 2013 , Pages 2993-3005 ; 16102940 (ISSN) ; Fattahi, A ; Sharif University of Technology
2013
Abstract
In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these...
Conformational aspects of glutathione tripeptide: Electron density topological & natural bond orbital analyses
, Article Structural Chemistry ; Volume 24, Issue 1 , 2013 , Pages 147-158 ; 10400400 (ISSN) ; Fattahi, A ; Sharif University of Technology
2013
Abstract
Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density Δ2 ρ(r) from Bader's atom in molecules theory. Charge transfer energies based on...
Dynamical Systems Approach to Interacting Dark Energy Models
, M.Sc. Thesis Sharif University of Technology ; Abolhassani, Aliakbar (Supervisor)
Abstract
This thesis studies the possible solution to the H0 tension via a dynamical systems approach. The early dark energy (IDE) scenario can somewhat alleviate the Hubble constant tension. On the other hand, postulating a new subdominant EDE in the pre – recombination Universe can also resolve the H0 tension. We introduce a novel model to interweave the early dark energy(EDE) and interacting dark energy-dark matter (IDE) scenarios. In this scenario, the early dark energy emerges naturally by changing the topological class of the phase portrait of the universe dynamics. In particular, an EDE component contributing only 10% of the matter density of the Universe—preferably in the vicinity of the...
Mechanical Properties of TLP bonded SS304 by Two Steps Heating
, M.Sc. Thesis Sharif University of Technology ; Ekrami, Aliakbar (Supervisor)
Abstract
Austenitic stainless steels are the most common kinds of stainless steels. Although these alloys are generally very weldable, there are some problems in join- ing of them using fusion welding. Solidification and liquation cracking or corrosion at grain bound- aries in the heat-affected zone are examples of these problems. Transient liquid phase (TLP) bonding is an important variation of diffusion bonding that has the potential to overcome this problems. Two-step TLP bonding is an ingenious development to form non-planar interface. This method consists of a short-time high temperature heating to melt interlayer followed by isothermal solidification of liquid phase at a lower temperature. In...
Influence of metal complexation on acidity of cytosine nucleosides: Part I, Li +, Na + and K + cation
, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 535-545 ; 10263098 (ISSN) ; Fattahi, A ; Pourjavadi, A ; Sharif University of Technology
2012
Abstract
Gas-phase acidities of nucleosides, combined with the knowledge of deprotonation sites, could improve our understanding of chemical reactions to biological systems. In this paper, we mainly focus our attention on the influence of cation coordination on acidities of multiple sites in cytosine nucleosides. The acidities of multiple sites in M +-L (where L represents cytosine nucleosides and M + is an alkali metal ion, including Li +, Na + and K +) complexes have been investigated theoretically, employing B3LY P6-311++G(d,p) basis sets. The geometrical characters, gas-phase acidities, sugar puckering and electronic properties of non-deprotonated and/or deprotonated complexes have been...
Conformational behavior and potential energy profile of gaseous histidine
, Article Journal of Molecular Structure: THEOCHEM ; Volume 960, Issue 1-3 , November , 2010 , Pages 73-85 ; 01661280 (ISSN) ; Tavasoli, E ; Fattahi, A ; Sharif University of Technology
2010
Abstract
Histidine as a natural amino acid is found to be biologically important and is known to function as a nucleophile or enzyme co-factor, or in proton transfer process. The properties of gaseous aromatic amino acid histidine depend on the structural forms it may take in gas-phase. Ab initio method has been used to characterize the gas-phase conformer/tautomers of histidine. Wide range of possible structures for histidine was surveyed at the MM level, and then the geometries of the unique conformers were refined at the B3LYP/6-311++G (d,p) levels. At this theoretical level, 25 conformers were located for both tautomers of histidine i.e., His [NπH] and His [NτH]. The MM level provides a poor...
Warm Inflation Model in Effective Field Theory of Axion Monodromy
, M.Sc. Thesis Sharif University of Technology ; Abolhassani, Aliakbar (Supervisor)
Abstract
Temerature fluctuation of the Cosmic Microwave Background (CMB) is one of the key observebles of the modern cosmology. Today, it is widely believed that quantum fluctuation that are stretched to horizon scales during a period of acceleration expansion -- at the onset of evolution of the universe-- are responsible for these perturbations. In the simplest scenarios of the inflation, a scalar field is responsible for both nearly expansional expansion of the universe and the proimordial fluctuations. In this thesis, we investigate the models of inflation with an additional light degree of freedom. In particular, we employ the method of the Effective Field Theory to study the general structure...
Drop formation from a capillary tube: comparison of different bulk fluid on newtonian drops and formation of newtonian and non-newtonian drops in air using image processing
, Article International Journal of Heat and Mass Transfer ; Volume 124 , 2018 , Pages 912-919 ; 00179310 (ISSN) ; Zadkazemi Derakhshi, A ; Nazari, A ; Firoozabadi, B ; Sharif University of Technology
2018
Abstract
The formation of water drops as a Newtonian fluid and formation of a shear-thinning non-Newtonian fluid, Carboxyl Methyl Cellulose (CMC) from a capillary into different bulk fluids are experimentally investigated. A high speed camera is used to visualize the images of the drops and an image-processing code employed to determine the drop properties from each image. It was found that the properties of the water drops when they are drooped into the liquids bulk fluids such as toluene and n-hexane are almost the same while they differed substantially when they were drooped into the air bulk fluid. It is shown that during the formation of water drop in all three kinds of bulk fluids, the drop...
Computational investigation of thermochemical properties of non-natural C-nucloebases: Different hydrogen-bonding preferences for non-natural Watson-Crick base pairs
, Article Structural Chemistry ; Volume 24, Issue 4 , 2013 , Pages 1015-1025 ; 10400400 (ISSN) ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
2013
Abstract
In the present density functional theory study, we have compared intrinsic properties of non-natural nucleobases (acA, acG, acC, and acT nucleobases) such as proton affinities, gas phase acidities, tautomerization, and hydrogen-bonding properties with those in normal Watson-Crick nucleobases (A, G, C, T nucleobases). The hydrogen-bonding interactions in non-natural and Watson-Crick base pairs were studied at B3LYP/6-311++G (d,p) level regarding their geometries, energies, and topological features of the electron density. The quantum theory of atoms-in-molecule (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in base pairs. The...
DFT study of the interaction of cytidine and 2′-deoxycytidine with Li+, Na+, and K+: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond
, Article Carbohydrate Research ; Volume 344, Issue 6 , 2009 , Pages 771-778 ; 00086215 (ISSN) ; Fattahi, A. R ; Pourjavadi, A ; Sharif University of Technology
2009
Abstract
Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li+, Na+, and K+ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li+ to Na+ and K+ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were...
Non-linear Effects on "linear point" through Analytical Methods
, M.Sc. Thesis Sharif University of Technology ; Abolhassani, Aliakbar (Supervisor)
Abstract
By studying of simulations, it can be seen that the linear point (LP), a point lies midway between the scales associated with the peak and the dip in the correlation function on BAO scales, is a useful window into cosmology and large scale structures rather than baryonic echo peak. Some fundamental features of the LP, been unaffected by redshift space distortions and gravitational non-linear effects, has made it important. I want to find evidences to stability of the LP by utilizing Standard Perturbation Theory through my thesis
Microstructure and Mechanical Properties of Two-step TLP Bonded 304 Stainless Steel with a Cobalt base Interlayer
, M.Sc. Thesis Sharif University of Technology ; Pouranvari, Majid (Supervisor) ; Ekrami, Aliakbar (Supervisor)
Abstract
Considering the wide applications of 304 stainless steel in various industries and the existing literature on transient liquid phase bonding of stainless steels with a variety of interlayers, the present work aimed to reduce the bonding time by using a two step bonding method. Faster bonding reduces both energy consumption during bonding and the base metal grain growth. It also leads to a lower reduction in the base metal and joint strength.Due to the melting point of the interlayer, different durations and a temperature of 1200°C were selected for the first step. This temperature was maintained for a specified period of time before it sharply dropped to and remained at 1180°C (the...
Experimental Study of the β-CD-g-PG Hybrid Nanostructure On Phase Solubilityof Hydrophobic Drug
, M.Sc. Thesis Sharif University of Technology ; Saifkordi, Aliakbar (Supervisor) ; Vossoughi, Manouchehr (Supervisor)
Abstract
Some widely used drugs such as paclitaxel (PTX) are poorly water soluble. The clinical use of PTX with solubilizer causes side effects. These problems limited its application in treatments. In this work has been studied the effect of β-CD-g-PG (HPCD) hybrid nanomaterials, conjugated PG branches onto β-CD core, on the water solubility of PTX. First HPCD has been synthesized. Then the inclusion complex of PTX with HPCD was prepared. The inclusion complex efficiency for PTX:HPCD complex in 1:25 mole ratio was 87%. Then solubility of PTX with HPCD in water has been determined, showing Ap type phase solubility diagram. Then stability constants were calculated. The first order and second order...
Designing and Fabrication of a Wearable Colorimetric Biosensor Based on Polyvinyl Alcohol Hydrogel with the Help of Machine Learning to Detect Glucose Concentration and PH Level of Body Sweat
, M.Sc. Thesis Sharif University of Technology ; Simchi, Abdolreza (Supervisor) ; Ekrami, Aliakbar (Supervisor)
Abstract
Simultaneous detection of pH and glucose levels in sweat is a promising tool for early skin disease detection and diabetes diagnosis. Hydrogels have attracted a lot of attention in the field of wearable biosensors due to sweat absorption capability, biocompatibility, and the ability to store enzymes and reagents in their cavities. In this research, we have presented an innovative wearable colorimetric biosensor based on polyvinyl alcohol (PVA) hydrogel, which can simultaneously measure pH level (in the range of 3-9) and glucose concentration (in the range of 0.025-0.5 mM) of sweat with the help of machine learning (ML). This wearable sensor consists of two main parts: sensors and a patch, in...
Spot Resistance Welding of St12 and HSLA Steels in Different Thicknesses
, M.Sc. Thesis Sharif University of Technology ; Kokabi, Amirhosein (Supervisor) ; Ekrami, Aliakbar (Supervisor)
Abstract
High-strength low alloy (HSLA) E275 developed specifically for automotive application. Also St12 Steel is used in autobodies. On the other hand the resistance spot weld of dissimilar materials is generally more challenging than that of similar materials due to differences in the physical, chemical and mechanical properties of the base metals. The influence of the primary welding parameters affecting the heat input such as; current and time on the morphology, fracture mode, microhardness, and tensile shear load bearing capacity of dissimilar welds between HSLA E275 steel and St12 steel in two different thicknesses (1,2 mm) has been investigated in this study which consisted six group. The...
An Uplink Packet Scheduling Algorithm in Fixed PMP WiMAX Networks with TDD Frame Structure
, M.Sc. Thesis Sharif University of Technology ; Beigy, Hamid (Supervisor)
Abstract
Worldwide interoperability for Microwave Access (WiMAX) is one of the most dominant cell-based broadband wireless metropolitan access technologies. Packet scheduling algorithm specifies the packet transmission order. In WiMAX standard, packet scheduling algorithm is not defined and its efficient design is left for developers and researchers. The existing researches in the scope of uplink packet scheduling, which is the most challenging packet scheduling scheme, consider only one cell. However the uplink available resources might not be enough when there are many packets that should be scheduled. To solve this problem, we propose an algorithm that uses the load balancing mechanisms that are...
, M.Sc. Thesis Sharif University of Technology ; Shamsaei, Abolfazl (Supervisor)
Abstract
Entrance of air to close water conduits occurs in many ways. This phenomenon makes displeasing effects on water transport structures. Two-phase flows in closed conduits are studied experimentally, numerically and theoretically. Even after decades, due to the complexity of the subject, these studies still require development and reformation. Numerical and theoretical two-phase models are often limited to a special regime of flow."Volume Of Fluid"(VOF) is a model for non-mixing two-phase flows. "Fluent" software uses this model in this field of flows. Volume of fluid is used successfully in some problems like dam break or rising bubbles. Main disadvantage of this model is distribution of the...
A new distributed uplink packet scheduling algorithm in WiMAX newtorks
, Article Proceedings of the 2010 2nd International Conference on Future Computer and Communication, ICFCC 2010, 21 May 2010 through 24 May 2010 ; Volume 2 , May , 2010 , Pages V2232-V2236 ; 9781424458226 (ISBN) ; Beigy, H ; Sharif University of Technology
2010
Abstract
Worldwide interoperability for Microwave Access (WiMAX) is designed to support a wide range of Quality of Service (QoS) requirements for different applications. Unlike the single service networks, a priority based mechanism is needed for specifying the transmission order of packets belonging to different traffic sources according to their QoS characteristics, which is called packet scheduling. In WiMAX standard, packet scheduling algorithm is not defined and its design is left for researchers. In this work, we propose a distributed uplink packet scheduling algorithm. In the proposed algorithm, when uplink capacity cannot satisfy the required resource of connections, according to traffic...
Synthesis of Graphene Oxide-based Polymer Nanocomposites and Investigation of Their Ability in Dye Adsorption
, Ph.D. Dissertation Sharif University of Technology ; Pourjavadi, Ali (Supervisor)
Abstract
In this project, polymer nanocomposites containing graphene oxide were prepared and used for adsorption of several cationic and anionic dyes. In most cases, these nanocomposites were prepared as three-dimentional polymer networks which contain graphene oxide. Nanocomposites with direct grafting of polymer chains onto the surface of graphene oxide were also prepared. Graphene oxide is an oxidized carbonaceous material with unique properties. This material has high surface area, good mechanical strength and various functional groups. Polymeric compounds with different functional groups, structures and properties can be prepared and used. By preparing composites of graphene oxide and polymers,...
Design and Implementation of a Master Robot for a Fracture Reduction Robotic Telesurgery System
, M.Sc. Thesis Sharif University of Technology ; Farahmand, Farzam (Supervisor)
Abstract
Common fracture treatments include open reduction and intramedullary nailing technology. However, these methods have disadvantages such as intraoperative X-ray radiation, delayed union or nonunion and postoperative rotation. Robots provide a novel solution to the aforementioned problems while having new challenges. The robotic system used in the study by providing more precise motion and exerting higher amount of forces makes the operation procedure more straightforward. In a normal operation 300-400 N of extension force would be needed which is fully provided by the surgen which leads to physical his/her (khastegi), by using the robotic system however, this force is simply provided without...