Sharif Digital Repository

We studied the mobility of p-carborane on a gold surface by analyzing the potential energy surfaces (PES) and simulating the motion of p-carborane using the classical molecular dynamics (MD) method. In the first section, we calculated the PES of p-carborane molecules on a gold surface during pure translation (sliding) and pure rotation independently and then employed this PES to predict the probable motion of p-carborane. These calculations were performed in several major orientations during sliding as well as different fixed positions during rotational movements to enable us to find the p-carborane motion threshold on a gold surface. In the second section, we use classical MD in isothermal... 

We present a method for high-order harmonics generation of N2 and CO molecules under two-color circularly polarized counter-rotating laser pulses at frequencies of and 2. Pulse envelope in this investigation is sin-squared and the intensity of each laser beam is with ten-optical cycle (o.c.). We show that an isolated pulse with a pulse duration shorter than 20 attosecond from the superposition of several harmonics can be generated. Both two-color linearly- and bicircularly-polarized laser pulses are considered. Our results have also been compared with the outcomes of the previous theoretical works as well as experiment observations. It is found that for CO molecule, the... 

The molecular behavior of some aniline derivatives as corrosion inhibitors of iron and copper in acidic media (HCl and H2 S O4) were investigated quantum-electrochemically by some recently developed models based on density functional theory and cluster/polarized continuum approaches. In this regard, electrical dipole moment, charges on hetero atoms and acidic hydrogen, electronic chemical potential, and extent of charge transfer were determined for both neutral and protonated forms of molecules inside an electrical double layer and correlated to their inhibitory powers. Good correlations were observed for both acidic media. The results were discussed via ion-pair hypothesis and deprotonation... 

Phonon detector can be designed by using colloidal silver nanoparticle (Ag NP) in presence of 1-Ethyl-3-methylimidazolium Hexafluorophosphate [EMim][PF6] ionic liquid (IL) via computational technique as the first time for many and high performance biosensors applications. Density functional theory as a quantum chemistry calculation method has been used to get the potential interaction between silver metal and ionic solvent. Molecular dynamics simulation shows that in small sizes of colloidal Ag NP in [EMim][PF6], electrical effect of IL makes one main phonon peak and in big size of colloidal Ag NP, splitting of phonon density occurs with two peaks due to the lower electrical field of IL with... 

An efficient method for synthesis of 2-iminium-1,3-dithiolane as a new family of ionic liquids with reaction of dithiocarbamates with methyl triflouromethanesulfonate was described. Theoretical study on the synthesized ionic liquids was also performed by quantum chemistry calculation. Geometry optimization on the ion pairs was carried out with the B3LYP/6-311++G(d,p) level of theory. The interaction energies were calculated, and corrected by the basis set superposition error (BSSE) calculated by the counterpoise method. The results of natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses indicate that the interactions occur via hydrogen bonding between oxygen... 

Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the... 

To control and utilize quantum features in small scale for practical applications such as quantum transport, it is crucial to gain a deep understanding of the quantum characteristics of states such as coherence. Here by introducing a technique that simplifies solving the dynamical equation, we study the dynamics of coherence in a system of qubits interacting with each other through a common bath at nonzero temperature. Our results demonstrate that depending on the initial state, the environment temperature affects coherence and excitation transfer in different ways. We show that when the initial state is incoherent, as time goes on, coherence and the probability of excitation transfer... 

In the present work, an efficient method is theoretically investigated for extending high-order harmonics and ultrashort attosecond pulse generation in N2 and CO molecules by using the time-dependent density functional theory approach. Our results show that by utilizing chirped laser field in the presence of a low frequency field, not only is the harmonic cutoff extended remarkably but also the single short quantum trajectory is selected to contribute to the harmonic spectra. When a low frequency field is added to the two-color chirped laser field, the long quantum trajectories are suppressed and only the short quantum trajectories contribute to the higher harmonic emission mechanism. As a... 

The reverse osmosis (RO) desalination capability of hydrogenated and hydroxylated graphene nanomesh membranes (GNMs) inspired by the morphology of carbon nitride (C2N) has been studied by using molecular dynamics simulation. As an advantage, water permeance of the GNMs is found to be several orders of magnitude higher than that of the available RO filters and comparable with highly strained C2N (S-C2N) as follows: 6,6-H,OH > 12-H > S-C2N > 5,5-H,OH > 10-H. The reverse order is found for salt rejection, regardless of S-C2N. The hydrophilic character of the incorporated -OH functional group is believed to be responsible for linking the water molecules in feed and permeate sides via the... 

The discrete-time quantum walk dynamics can be generated by a time-dependent Hamiltonian, repeatedly switching between the coin and the shift generators. We change the model and consider the case where the Hamiltonian is time-independent, including both the coin and the shift terms in all times. The eigenvalues and the related Bloch vectors for the time-independent Hamiltonian are then compared with the corresponding quantities for the effective Hamiltonian generating the quantum walk dynamics. Restricted to the non-localized initial quantum walk states, we optimize the parameters in the time-independent Hamiltonian such that it generates a dynamics similar to the Hadamard quantum walk. We... 

Quantum computing and quantum simulation can be implemented by concatenation of one- and two-qubit gates and interactions. For most physical implementations, however, it may be advantageous to explore state components and interactions that depart from this universal paradigm and offer faster or more robust access to more advanced operations on the system. In this article, we show that adiabatic passage along the dark eigenstate of excitation exchange interactions can be used to implement fast multiqubit Toffoli (Ck-NOT) and fan-out (C-NOTk) gates. This mechanism can be realized by simultaneous excitation of atoms to Rydberg levels, featuring resonant exchange interaction. Our theoretical... 

The nonlocal nature of unpaired Majorana bound states (MBSs) in topological superconductors can be exploited to create topologically protected qubits and perform gate operations fault-tolerantly via braidings. However, the time-dependent noises induced by coupling to an environment which is inevitable in any realistic system could spoil the topological protection. In this work, we study the effects of various dynamical noises such as Lorentzian, thermal, and quantum point contact on the MBSs in the recently proposed one-dimensional topological superconductors. We begin by investigating the Kitaev p-wave superconductors and examine the effects of long-range hopping and pairing on the... 

The aim of this research is to conduct atomistic investigations of physical interaction analysis of nanoscale objects manipulation. The system consists of tip, particle and substrate. The manipulation tool moves with a constant speed while pushing the particle in a desired direction. The focus of the research is on ultra-fine metallic nanoparticles. To perform this research, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behavior of the aforementioned system which is made from different transition metals. The effects of size, material type and temperature on the success of the process have been investigated by planar molecular dynamics. © 2008 IEEE... 

Theoretical calculations of structural parameters, 57Fe, 14N and 17O electric field gradient (EFG) tensors for full size-hemin group have been carried out using density functional theory. These calculations are intended to shed light on the difference between the geometry parameters, nuclear quadrupole coupling constants (QCC), and asymmetry parameters (ηQ) found in three spin states of hemin; doublet, quartet and sextet. The optimization results reveal a significant change for propionic groups and porphyrin plane in different spin states. It is found that all principal components of EFG tensor at the iron site are sensitive to electronic and geometry structures. A relationship between the... 

A state-of-the-art low-noise transimpedance amplifier (TIA) for 2.5 Gb/s family is presented using IBM 0.13-m CMOS technology. This TIA would be a part of a homodyne detector in a quantum key distribution (QKD) system. In this work a thorough design methodology based on a novel analytical noise optimization is presented. Also a unique method for eliminating the DC current of the input photodiodes (PDs) is proposed. The post-layout simulation results show bandwidth of 52 kHz to 1.9 GHz, average input referred noise of 1.93 pA/√Hz, and transimpedance gain of 80 db while dissipating 12 mW from a 1.5 V power supply, including the output buffer  

A computational approach to predict the main binding modes of two adrenalin derivatives, arachidonoyl adrenalin (AA-AD) and arachidonoyl noradrenalin (AA-NOR) with the β-lactoglubuline (BLG) as a nano-milk protein carrier is presented and assessed by comparison to the UV-Vis absorption spectroscopic data using chemometric analysis. Analysis of the spectral data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS) algorithm led to the pure concentration calculation and spectral profiles resolution of the chemical constituents and the apparent equilibrium constants computation. The negative values of entropy and enthalpy changes for both compound indicated... 

First principles density functional theory (DFT)-based molecular dynamics (MD) is used to study some physical and electronic properties of amorphous silicon (a-Si) samples, as-quenched and annealed containing dangling and floating bonds (pertinent to the threefold- and fivefold-coordinated defects, respectively) as well as distorted tetrahedral bonds. Surprisingly, except for the work of Pantelides (1986) who gave a rough estimate for the effective electron correlation energy, Ueff of a floating bond on the fivefold-coordinated Si, to date, there are no theoretical studies in the literature for the calculation of Ueff pertinent to this type of defect. In this work, Ueff for each type of... 

We performed density functional calculations aimed at identifying the atomistic and electronic structure origin of the valence and conduction band, and band gap tunability of halide perovskites ABX3 upon variations of the monovalent and bivalent cations A and B and the halide anion X. We found that the two key ingredients are the overlap between atomic orbitals of the bivalent cation and the halide anion, and the electronic charge on the metal center. In particular, lower gaps are associated with higher negative antibonding overlap of the states at the valence band maximum (VBM), and higher charge on the bivalent cation in the states at the conduction band minimum (CBM). Both VBM orbital... 

The current study demonstrates homogenous decorating of zinc oxide quantum dots (QDs) onto graphene oxide (GO) surface via simple chemical method. The AFM image exhibited that the prepared graphene was 0.8 nm thick and hence practically monolayer. Average size of the ZnO QDs was estimated by transmission electron microscopy around 3 nm. Instrumental and chemical analyses demonstrated formation of a strong bond between ZnO QDs and GO, through C-O-Zn and C-Zn bridges. The UV-visible spectra displayed that the introduction of graphene sheets to ZnO QDs resulted in higher absorption intensity of UV as well as widening of adsorption window toward visible light for ZnO-Graphene due to chemical... 

In this work, the antioxidant ability of fisetin was explored toward hydroxyl (•OH) radical in aqueous and lipid solution using density functional level of theory. Different reaction mechanisms have been studied: hydrogen atom transfer, single electron transfer followed by proton transfer, and radical adduct formation, and sequential proton loss electron transfer. Rate constants for all possible reaction sites have been calculated using conventional transition state theory in conjunction with the Collins-Kimball theory. Branching ratios for the different channels of reaction are reported for the first time. Results show that the reactivity of fisetin toward hydroxyl (•OH) radical takes place...