Sharif Digital Repository

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... 

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... 

We present a systematic prescription for calculating cosmological correlation functions for models with derivative interactions through the wavefunction of the universe and compare this result with the "in-in"formalism - canonical approach. The key step in this procedure is to perform the path integral over conjugate momenta after which a straightforward generalisation of Feynman's Rules can be applied. We show that this integral recovers the classical action plus some additional divergent contributions which are necessary to cancel other divergences that arise due to loop diagrams involving time derivatives. As a side project, for the first time, we introduce the "off-shell"version of the... 

We try to clarify the relation of Feynman paths -which appear in the Feynman path integral formalism- with de Broglie-Bohm paths. To accomplish this, we introduce a Bohmian path integral and use it to obtain the propagator of a free particle and a general system  

We go over various view-points about wave-particle duality and criticize Schrödinger-type solution of this problem. In this framework we show that Barut's quantum theory of single events has some problems and that the non-linearization of the Schrödinger equation is of no help  

The definition of tunneling in the framework of Bohmian mechanics is used to select one of available definitions for quantum tunneling times (QTTs) within the standard interpretation as the best definition. It is demonstrated that due to experimental limitations, Bohmian mechanics leads to the same tunneling times  

Recently, people have calculated tunneling’s characteristic times within Bohmian mechanics. Contrary to some characteristic times defined within the framework of the standard interpretation of quantum mechanics, these have reasonable values. Here, we introduce one of the available definitions for tunneling’s characteristic times within the standard interpretation as the best definition that can be accepted for the tunneling times. We show that, due to experimental limitations, Bohmian mechanics leads to the same tunneling times. © 2000 The American Physical Society  

In this paper the possibility of generating large scale curvature perturbations induced from the entropic perturbations during the waterfall phase transition of the standard hybrid inflation model is studied. We show that whether or not appreciable amounts of large scale curvature perturbations are produced during the waterfall phase transition depends crucially on the competition between the classical and the quantum mechanical backreactions to terminate inflation. If one considers only the classical evolution of the system, we show that the highly blue-tilted entropy perturbations induce highly blue-tilted large scale curvature perturbations during the waterfall phase transition which... 

In this work, we study the anisotropic inflationary models. In these models, an abelian gauge field non-minimally coupled to the inflaton field plays a role in the inflation dynamicIn a gauge field,the backgroundanswer is anisotropic, in the form of metric Bianchi. In order for the model to be consistent with the observations, the level of anisotropy should be small. The anisotropy power spectrum is obtained by calculating cosmological perturbation using formalism. We show that the criticism levelled in [4] does not apply and we can repeat the calculations in the non-absorbence by calculating the anisotropy spectrum. Using the constraint on the quadrupole anisotopy, we show that the... 

According to the equivalence principal, the long wavelength perturbations must not have any dynamical effect on the short scale physics up to (k2 L/k2 s). Their effect can be always absorbed to a coordinate transformation locally. So any physical effect of such a perturbation appears only on scales larger than the scale of the perturbation. The bispectrum in the squeezed limit of the curvature perturbation in single-field slow-roll inflation is a good example, where the long wavelength effect is encoded in the spectral index through Maldacena's consistency relation. This implies that one should be able to derive the bispectrum in the squeezed limit without resorting to the in-in formalism in... 

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... 

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...