Sharif Digital Repository

In the present work, adsorption of hydrogen molecules over a metal organic framework (MOF-5) has been investigated by using first principles density functional theory (DFT). Different strategies have been applied for improving hydrogen storage, i.e. metal doping, boron substitution and functionalization. The metal atoms used for enhancing hydrogen adsorption include Li, Ca and Sc. It is found that the binding energy between these metal atoms and MOF is not enough to prevent clustering. Therefore a number of carbon atoms are substituted by boron atoms and it is indicated that boron substitution enhances the binding energies, significantly. Also the results reveal that boron substituted MOF... 

Chrysin is a bioflavonoid which possesses a wide range of important biological activities. In present study, we used a quantum mechanical approach to shed light on the antioxidant ability and antioxidant mechanism of chrysin to scavenge hydroxyl radical (˙OH) in solution phase. The analysis of the theoretical bond dissociation enthalpy (BDE) values and spin density of the radicals to determine the delocalization possibilities at B3LYP/6-311++G** level clearly shows the importance of the A-ring and the 7-OH group in antioxidant reactivity. In the next step, the inclusion of chrysin with β-CD has been investigated extensively using theoretical methods. Density functional theory (M05-2X)... 

In this paper, the bending modulus of a multi-layered graphene sheet is investigated using a geometrically based analytical approach. For this purpose, a bending potential energy is derived, based on the van der Waals interactions of atoms belonging to the two neighboring sheets of a double-layered graphene sheet. The inter-atomic spacing between the adjacent layers is determined along the line of action of the applied bending moments. The bending potential of the double-layered sheet is calculated by summing up the potentials at discrete hexagons over the length and width of the sheet. A multi-layered graphene sheet is considered as consisting of many stacking double-layers. It is observed... 

We provide a physically motivated definition for the binding energy (or bond dissociation) of a bipartite quantum system. We consider coherently applying an external field to cancel out the interaction between the subsystems, to break their bond and separate them as systems from which no work can be extracted coherently by any cyclic evolution. The minimum difference between the average energies of the initial and final states obtained this way is defined as the binding energy of the system. We show that the final optimal state is a passive state. We discuss how the required evolution can be realized through a sequence of control pulses. The utility of our definition is illustrated through... 

Molecular machines, such as nanocars, have shown promising potential for various tasks, including manipulation at the nanoscale. In this paper, we examined the influence of temperature gradients on nanocar and nanotruck motion as well as C60 - as their wheel - on a flat gold surface under various conditions. We also compared the accuracy and computational cost of two different approaches for generating the temperature gradient. The results show that severe vibrations and frequent impacts of gold atoms at high temperatures increase the average distance of C60 from the substrate, reducing its binding energy. Moreover, the temperature field drives C60 to move along the temperature variation;... 

Siligraphene belonging to the family of two-dimensional (2D) materials has great potential in optoelectronics due to its considerable excitonic effects. In this study, the strain effects on the electronic structure and the real-space exciton wave functions of g - SiC 7 are investigated using the first-principles calculations based on the ab initio many-body perturbation theory. Alongside the increase (decrease) of the bandgap with compressive (tensile) strain, our results show that the exciton in the siligraphene monolayer under in-plane biaxial compressive strains is much more localized than that in the case of tensile one, leading to the higher and lower exciton binding energies,... 

In the present work, the interaction of hydrogen molecules with defective graphene structures doped by transition metal (TM) atoms is investigated by using first principles density functional theory (DFT). Defective graphene structures include Stone-Wales (SW), 585 and 555-777 and transition metals include early TMs, i.e. scandium (Sc), titanium (Ti) and vanadium (V). It is found that in comparison with the pristine graphene, presence of defects significantly enhances the metal binding. Among three defects, 585 divacancy leads to the strongest binding between graphene and metal. Hydrogen adsorption is then evaluated by sequential addition of hydrogen molecules to the system. The results... 

We study the translocation of stiff polymers through a nanopore, driven by the chemical-potential gradient exerted by binding proteins (chaperones) on the trans side of the pore. Bound chaperones prevent backsliding through the pore and, therefore, partially rectify the polymer passage. We show that the sequence of chain monomers with different binding affinity for the chaperones significantly affects the translocation dynamics. In particular, we investigate the effect of the nearest-neighbor adjacency probability of the two monomer types. Depending on the magnitude of the involved binding energies, the translocation speed may either increase or decrease with the adjacency probability. We... 

Theoretical study of NH3(H2O) n=0,1,2,3 adsorption on (8, 0) carbon nanotube was performed at the X3LYP/6-31G* level of density functional theory (DFT). The tube-NH3 interaction was discussed in the terms of binding energy (EB), coupling energy (EC), charge density, molecular orbitals, and dipole moments. The results reveal that addition of water molecules to tube-NH3 system increases the interaction between tube and ammonia molecule  

In this paper by solving Dirac equation, we present an analytical solution to calculate energy levels and wave functions of mono- and bilayer graphene quantum dots. By supposing circular quantum dots, we solve Dirac equation and obtain energy levels and band gap with relations in a new closed and practical form. The energy levels are correlated with a radial quantum number and radius of quantum dots. In addition to monolayer quantum dots, AA- and AB-stacked bilayer quantum dots are investigated and their energy levels and band gap are calculated as well. Also, we analyze the influence of the quantum dots size on their energy spectrum. It can be observed that the band gap decreases as quantum... 

In this work, the generation of two-soliton and three-soliton molecules in a circular fiber array laser with an active optical central fiber is studied. Certain fibers of the array are excited by Gaussian and super-Gaussian pulses. The central fiber of the circular fiber laser is a rare-earth doped fiber. A circular fiber array is employed as a saturable absorber in a soliton mode locked fiber laser. Generation of two-soliton and three-soliton molecules are observed in our simulation. Numerical calculation of binding energy shows that the super-Gaussian pulse tends to be more stable, and therefore it would be a proper choice for the generation of soliton molecules in the circular fiber array... 

Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could... 

Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could... 

The existence of an energy gap of graphene is vital as far as nano-electronic applications such as nano-transistors are concerned. In this paper, we present a method for introducing arbitrary energy gaps through breaking the symmetry point group of graphene. We investigate the tight-binding approximation for the dispersion of π and π* electronic bands in patterned graphene including up to five nearest neighbors. As we show by applying special defects in graphene structure, an energy gap appears at Dirac points and the effective mass of fermions also becomes a function of the number of defects per unit cell. © 2008 IOP Publishing Ltd  

The X-ray photoemission (XPS) measurements of Cu1-xTlxBa2Ca2 Cu3-yZnyO10-δ (y = 0, 2.65) superconductors have been performed and compared. These studies revealed that the charge state of thallium in the Cu0.5Tl0.5Ba2O4-δ charge reservoir layer in Zn doped samples is Tl1+, while it is a mix of Tl1+ and Tl2+ in Zn free samples. The binding energy of Ba atoms in the Zn doped samples is shifted to higher energy, which when considered along with the presence of Tl1+ suggested that it more efficiently directed the carriers to ZnO2 and CuO2 planes. The evidence of improved inter-plane coupling witnessed in X-ray diffraction is also confirmed by XPS measurements of Ca atoms in the Zn doped samples.... 

An optical apta-nanosensor was designed and developed based on reduced graphene quantum dots (rGQDs) and multi-walled carbon nanotubes (MWCNTs) and applied for the selective detection of diazinon as one of the most widely used organophosphorus pesticides. Considering the GQDs and rGQDs high fluorescence emission and optical stability, efficient optical transducers could be designed and precise detection methods could be developed based on such transducers. Herein, by using rGQDs, diazinon specific aptamer, and MWCNTs, a simple economical fluorescence method has been introduced to detect and measure diazinon with the detection limit of 0.4 nM (0.1 μg/L) in the range of 4-31 nM, meeting the... 

Pattern-based sensing with multi-component sensor arrays, despite its merits, may be laborious and time-consuming. As an alternative approach, herein, a condition-based single component sensor array has been provided which represents an elegantly simple, low cost and minimally instrumented format for the quantification and classification of antidepressants (ADs). Tuning the pH and ionic strength enabled the single component probe to interact with the target analytes through different binding modes, providing the required cross-reactivity for multiplex detection. The analytical figures of merit verified that the condition-based sensor array is precise and accurate in both the discrimination... 

Interactions of α-D-glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM-B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α-D-glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M.H-O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy...