Sharif Digital Repository

DNA is big protein molecule consisting of two strands intertwining each others. Recently DNA molecule has drawn attention of researchers to be used in electronic circuits and molecule electronic field. Therefore, many experiments have been carried out to measure DNA conductivity in different temperature in single molecule or bundle mode with varying size and shape. In this thesis, metallic bundle DNA at normal room temperature is studied and their resistance characteristic is obtained and compared. In order to improve DNA conductivity Metal Ions like zinc are adulterated to each of its structure period. DNAs with these metallic impurities are called metallic DNAs.
Thus, golden electrodes... 

Many of the significant reactions in chemistry and biology are related to bimolecular nucleophilic substitution (SN2) reactions which have been studied first by Hughes and Ingold in the 1930s. Afterward, many organic chemists have continued this work. Up to now, numerous experimental kinetic and theoretical researches have studied the mechanism of these reactions. Since most SN2 reactions occur in solution, a large number of these studies have been devoted to the solvent effects. One of these effects that has been examined extremely is H-bonding via protic solvents that lowers the energy of an anionic nucleophile relative to the transition state, in which the charge is more diffuse, and... 

Lipid membranes are fundamental constituents of cell membranes and are now used in lap-on-a-chip technology. Membranes in living cells contain a significant fraction of proteins, which undergo lateral random movements due to thermal fluctuations and shear forces imposed by the solvent fluid. Prominent natural and biotechnological systems where membranes are highly sheared include the plasma membrane of endothelial cells, and membranes used in biosensors for high throughput screening of drug candidates, and in water purification devices. In these systems membrane is in direct contact with the mainstream suspension flow, which is driven by pressure gradients. The efficiency and function of... 

Different disadvantages associated with using fossil fuels as the main energy source including crisis of wells’ depletion and serious environmental problems, causing by the emission of large quantities of greenhouse gases (GHG), especially carbon dioxide (CO2), has increased attention to replacing them with renewable and clean fuels such as wind, solar, and geothermal energy sources. Hydrogen, as a clean energy carrier, is one of the best fuels in terms of the environment and cost. So, it is recently receiving increasing attention and it may one day replace fossil fuels for various applications such as in automobiles and power stations. The main subject of this thesis was surveying the... 

Water transportation through carbon nanotubes is key for designing nanodevices. The directed transport of water molecules through a rotating charged carbon nanotube (CNT) is investigated by molecular dynamics simulations. It is found that the net flux of continuous unidirectional water flow depended sensitively on the charge distribution, charge density and rotation of the CNT. we find that for a constant charge density, the water flux increases with the increase of the charge difference. Besides, we find that the water flux shows a nonlinear dependence on the angular velocity of the rotation. The rotation of the CNT with low angular velocities, can not generate a continuous water flux. The... 

Molecular nanomagnets, also known as Single Molecule Magnets (SMMs) are a class of molecules that at low temperature exhibit magnetic hysteresis of pure molecular origin and not related to a cooperative effect. In the past fifteen years they have attracted great interest for their potentiality to act as magnetic memory units and for the many quantum effects in the dynamics of their magnetization. Organization of SMM on surfaces is the first step in order to address the magnetic state of a single molecule or to connect the molecule to a conducting substrate. The complex nature of SMMs and the peculiar origin of their magnetic bistability have been representing for half a decade an obstacle to... 

Single molecule magnets due to their magnetic tunneling effect and the interaction they have with an external magnetic field are used widely in quantum computing and also the storage of data with high capacities. Polyoxometalates that are used as counter ions for cationic single molecule magnets, are able to affect their spin-couple nature via a magnetic exchange and also have an influence on the crystal accumulation in order to change the magnetic property of the molecule. In this research the probability of sedimenting a cationic single molecule magnet, [Mn4O2(CH3COO)7(bipy)2]+, with the use of anionic polyoxometalates with Keggin structures has been investigated. Thus, the single... 

Cancer diagnosis area has recently been in the limelight of the medical research and there exist an unremitting focus on the devices & technologies which enable cancer detection in its victims. Lately a genius diagnostic method based on isolation and entrapment of circulating tumor cells has been developed which pave the path for cancer identification. These circulating cells which are detached from the primary tumor are carried out through body by means of circulation system. They play key role in phenomenon called metastasis. Separating these rare cells from multifarious background blood cells, assessing their quantity can supply valuable information on the stage of disease as well as its... 

The X-ray attosecond pulses have many useful applications for studying atomic and sub-atomic scales phenomena in attosecond scale duration. Generation and optimization of high-order harmonics is an efficient way to produce such attosecond pulses which are studied in this thesis. There are several limitations in the attosecond pulse generation such as low efficiency of high-order harmonics, long duration of output pulses and the impossibility of producing an attosecond pulse with any desired wavelength in the x-ray region. Therefore, more investigations into high harmonic generation and fully control and optimization of this process is significant. In this thesis, high harmonic generation... 

In this thesis, the molecular dynamics simulation is used to investigate the melting transition of B-DNA molecule, via of configurational entropy, the fraction of broken hydrogen bonds (f-curve) and hydrogen bonding energy.We have performed molecular dynamics simulation on Drew-Dickerson oligomer with sequence of (CGCGAATTGCGC) at different temperatures, within the range of 280-400 K with the 20 K intervals. The simulation was done in two different mediums (pure water and 1 M NaCl), to see influences of water and salt in stabilizing the DNA molecule. At each temperature, configurational entropy is calculated by the Schlitter’s formula, using the Cartesian coordinate of all atoms. So, in each... 

This thesis is divided into three parts: In part I, conformational properties of neutral, anionic, cationic and zwitterionic forms of glutathione tripeptide were investigated by means of DFT-B3LYP method with 6-31+G (d,p) basis set. Results show that glutathione is a very flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond and its charge. Conformation of each amino acid in glutathione tripeptide depends on its orientation within the peptide sequence in addition to the conformation of other amino acids within the chain. Investigation of intramolecular hydrogen bonds in these conformers by means of AIM analysis demonstrates... 

This thesis is divided into three parts: In part I, interactions of neutral and anionic forms of histidine with coinage metal nano clusters M3 (M = Au, Ag and Cu) are investigated. Results demonstrate that nonconventional M…H-O hydrogen bonds and M-X bonds (X = N, O) play stabilization roles in interactions of histidine and metal nano clusters. Presence of negative charge in ligand leads to increase of binding energy of complexes. In the next step, the effects of coinage metal nano clusters on the gas-phase acidity of weak organic acid (histidine) have been explored. The acidity of isolated histidine is compared with the acidity of its Au3–, Ag3– and Cu3–complexed species. Moreover, pKa... 

The present research devoted to the application, development and implementation of clustering, classification and regression techniques for modeling of the biological activity of different drug and drug-like molecules. At first, the prediction ability of Bayesian regression techniques was evaluated for describing and predicting the inhibition behavior of Integrin antagonists. As a next step, the complementary local search techniques have been used for improving the performances of Bayesian regularized genetic neural network (BRGNN) algorithm. The results indicated that the pattern search algorithm has a great potential to be used as a feature selection method in Chemoinformatics. In line... 

In this project , the dissociation of methane in the presence of Ti:Sapphire laser with parameters of 1014wcm-2, 800nm wave lengths and 100fs pulse width have been investigated theoretically, by using the Gaussian03 package –computational chemistry program that is capable of predicting many properties of atomic and molecular systems. It is based upon the fundamental laws of quantum mechanism. By considering some limitations in approximate techniques and incapability of advancing them, numerical calculation of solving the time dependent Schrödinger equation in order to improve the results and find more quantum dynamic information is applied. Therefore at first, by Gaussian03 package some of... 

A general regularity has been found based on an effective pair potential of Lennard-Jones LJ (12, 6) for both dense nonmetallic and nonionic fluids and solids; namely, (Z-1)V2 linearly varies with respect to ρ2, this equation of state (EoS I) is known as LIR. The other equation of state (EoS II), according to wich the isotherm of (Z-1)V2 is linear in term of 1/ρ, wich gives a good description for the metallic and ionic fluids and solids. This equation of state was suggested based on an effective pair potential of LJ (6, 3). Unexpectedly, solid and liquid Ne indicates a significant deviations from EoS I. Recently, a general equation of state (EoS III) based on an effective near-neighbor pair... 

Conversion of Methane molecule to valuable heavier hydrocarbon and hydrogen by using of short pulse lasers is investigated. The dynamical information of molecule such as orientation, dipole moment variations with binding length, and potential energy levels are initially produced by using Gaussian software. Based on this information the Schrödinger wave equation for this polyatomic molecule is numerically solved. Then by selecting the various laser parameters and installing of them in the Hamiltonian of the mentioned system, the dependence of hydrogen transition and separation probability on these parameters are investigated. In this work by radiating of the laser beam along the C2 symmetry... 

Hydrogen bonding is an important weak interaction encountered in gas, liquid, as well as solid phases. The hydrogen bond plays a very vital role in many life processes and is one of the most frequently used terms in chemistry and biology.
Polyols or polyhydric alcohols are, strictly speaking, simply organic chemicals containing more than two hydroxyl groups. Each hydroxyl is attached to separate carbon atoms of an aliphatic skeleton.They may also contain ester, ether, amide, acrylic, metal, metalloid and other functionalities; along with hydroxyl groups. Polyols are obtained from many plant and animal sources and are synthesized by a variety of methods. Among important properties of... 

Ionization probability of Cl2 molecule is studied by irradiation of 800 nm Ti: Sapphire laser pulses at intensities of 1014 Wcm-2 to 1016 Wcm-2 with the Gaussian package. Molecular orbital symmetry and orientation of the molecule dipole moment with laser field polarization axis are very effective in ionization probability. The results show that the most ionization probability for the intensity of 1014 wcm-2 is at 900 and also 50 at intensity of 1016 wcm-2. Due to the lack of intrinsic dipole moment, variation of dipole moment with the intensity, bond length and time evolution of dipole moment are investigated. It is found that there is a linear dependance of these parameters with ionization... 

In this project, the ionization and dissociation of methane molecule by intense femto-second lasers has been studied. Dissociation probability is calculated for interacting CH4 molecule under Ti: Sapphire laser pulse with pulse durations of 10- 40fs in intensities at the range of 1014-1016 Wcm-2. Calculations are carried out with time-dependent density functional theory using Gaussian03 and Octopus packages as powerful computational chemical physics programs. Due to importance of the dependence of interaction dynamics to laser parameters, the effect of these parameters including different intensities, polarization, various pulse durations and pulse envelopes are investigated. The optimal... 

Polymerase chain reaction method is a conventional method for obtaining multiple copies of a specified segment in the DNA molecule and to amplify the DNA molecule itself. Therefore, this method has been of paramount importance in different fields of research and has been applied for different applications. PCR requires thermal cycling, or repeated temperature changes between two or three discrete temperatures to amplify specific nucleic acid target sequences. To achieve such thermal cycling, conventional bench-top thermal cyclers generally use a metal heating block powered by Peltier elements or benefit from forced convection heat transfer. Although efforts have been made in order to reduce...