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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) Aliakbar Tehrani, Z ; 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) Aliakbar Tehrani, Z ; 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 Pirayesh, Behnam (Author) ; 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... 

    Application of Damage Indices In Seismic Analysis of Concrete Frames Using Endurance Time Method

    , M.Sc. Thesis Sharif University of Technology Baniassadi, Arash (Author) ; Esmaeil Pourestekanchi, Homayoun (Supervisor)
    Abstract
    In most places in the world as it is in our country, structural vibration caused by earthquakes are among the most destructive menaces for the building. For this reason one of the main goals for civil engineers is constructing structures that can perform properly in an earthquake-exposed situation. For moving toward this goal it is necessary to estimate structural responses considering probable earthquake excitation and use these data for design of new structures or retrofitting of existing ones. In this research, the capability of a new method named Endurance Time analysis in seismic assessment of concrete moment frame is investigated in nonlinear range. ET is a new dynamic time history... 

    Mechanical Properties of TLP bonded SS304 by Two Steps Heating

    , M.Sc. Thesis Sharif University of Technology Bahrehmand, Mohammadreza (Author) ; 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... 

    Performance-Based Design of Steel Structures with Metallic damper Using Endurance Time Method

    , M.Sc. Thesis Sharif University of Technology Yousefian Moghadam, Sina (Author) ; Esmaeil Pourestekanchi, Homayoun (Supervisor)
    Abstract
    Preventing critical damages to structures and hence saving the lives and money is an inevitable work which a designer has to do. During the earthquake, huge amount of energy applies to the structure and finding a way to reduce transfer of this energy to main structure is crucial. For this purpose, Structural Control systems may be used. Metallic Dampers are one of those systems which absorb the earthquake input energy by having nonlinear deformations. In this Thesis, one type of this dampers which is innovated by Estekanchi, have been studied .Indeed, this damper is a connection between bracing and main frame. In this damper a U shape part acts as a sacrificing portion and absorbs energy by... 

    Seismic Performance and Cost Assessment of Concrete Bridges Designed by Iranian Bridge Code

    , M.Sc. Thesis Sharif University of Technology Haghani Baei, Ali (Author) ; Esmaeil Purestekanchi, Homayoun (Supervisor)
    Abstract
    The purpose of this study is to evaluate the performance and seismic costs for pre-designed bridges according to the Iranian Bridge Code, which maps and details are available in Code 294. In order to evaluate performance, seismic costs of a structures are determined over its life cycle and these costs are compared eventually. Seismic costs are divided into two parts of the initial cost and life cycle cost of the structure. The initial costs depend on the cost of constructing the bridge, but life cycle costs are depends on seismic damage for structure and its users over the useful life of the bridge. These damages include the cost of maintenance of the bridge over its useful life and the... 

    Seismic Analysis of Elevated Concrete Tanks with Endurance Time Method

    , M.Sc. Thesis Sharif University of Technology Ghasemi Khalafloo, Pouya (Author) ; Esmaeil Poorestekanchi, Homayoun (Supervisor)
    Abstract
    Elevated concrete tanks have a wide range of applications in storing drinking water, firefighting, sewage, oil, toxic chemicals, and similar fluids. Therefore, due to their usage, these tanks are usually placed in the category of very important structures and vital arteries. Consequently, their design against seismic loads and their proper performance during earthquakes are of great importance. The endeavor time Analysis is a seismic analysis method in which the structure is subjected to an increasing dynamic excitation whose intensity gradually increases over time. The structure's response over time is examined, and based on the corresponding response to various levels of excitation... 

    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) Aliakbar Tehrani, Z ; 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) Aliakbar Tehrani, Z ; 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 Ghomi Shurkai, Reza (Author) ; 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... 

    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) Aliakbar Tehrani, Z ; 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) Aliakbar Tehrani, Z ; 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 Farhadi Mahalli, Nematollah (Author) ; 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  

    Information-Theoretic Analysis of Coognitive Radio Networks

    , Ph.D. Dissertation Sharif University of Technology Charmmchi, Hosseein (Author) ; Hashemi, Homayoun (Supervisor) ; Nasiri Kenari, Masoumeh (Supervisor)
    Abstract
    In this thesis, the effect of cognition in wireless networks is studied. In a wireless communica-tion network, cognition is the ability of a device to sense the transmissions of neighboring nodes and adapt its own transmission to the sensed environment. Cognitive radios are very attractive be-cause of the increasing need for more efficient use of frequency spectrum. The goal of this thesis is the analysis of cognitive radio networks from an information theoretic perspective and to this end statistical models of the wireless medium with a limited and tractable number of devices are uti-lized. We consider three different models in three parts of the thesis. First, we consider a new... 

    Microstructure and Mechanical Properties of Two-step TLP Bonded 304 Stainless Steel with a Cobalt base Interlayer

    , M.Sc. Thesis Sharif University of Technology Amini, Ali (Author) ; 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... 

    A Front-End for an Integrated UHF RFID Reader

    , M.Sc. Thesis Sharif University of Technology Homayoun, Aliakbar (Author) ; Sharif Bakhtiar, Mehrdad (Supervisor) ; Atarodi, Mojtaba (Supervisor)
    Abstract
    The use of Radio Frequency Identification is increasing rapidly. The reason is the capability to transfer data wirelessly without line-of-sight necessity, high data rate and long read range. The main advantage of barcode is its lower cost which has ensured its existence for many years. The applications and materials that are identified by RFID increase as the price of RFID tags decrease. This Project deals with the front-end of an Integrated RFID Reader for the UHF band. The bottleneck of the design is the presence of a large interferer just hundreds of kilohertz apart from the desired signal which is at about 900 MHz. The key idea of the design is utilizing feedback in order to cancel... 

    Dynamics of a Viscoelastic Plate on a Viscoelastic Foundation Subjected to a Moving Mass

    , Ph.D. Dissertation Sharif University of Technology Foyouzat, Mohammad Ali (Author) ; Esmaeil Purestekanchi, Homayoun (Supervisor) ; Mofid, Masoud (Co-Advisor)
    Abstract
    This thesis investigates the dynamic response of a viscoelastic plate resting on a viscoelastic Winkler foundation subjected to the excitation of a moving mass. Through application of the Laplace transform, the governing equation of the problem is derived for a general viscoelastic material. Thereafter, an analytical-numerical method is proposed in order to determine the dynamic response of the viscoelastic plate. The method is based on transforming the governing partial differential equation into a new solvable system of linear ordinary differential equations. To that extent, the proposed solution proves to be applicable to plates made of any viscoelastic material and with various boundary... 

    Experimental Study of the β-CD-g-PG Hybrid Nanostructure On Phase Solubilityof Hydrophobic Drug

    , M.Sc. Thesis Sharif University of Technology Asadi, Farshid (Author) ; 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 Chenani, Hossein (Author) ; 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...