Sharif Digital Repository

In this paper, a new multi-scale technique is developed for concurrent coupling of atomistic-continuum domains in modeling nano-mechanical behavior of atomic structures. A Lagrange multiplier method is employed over an overlapping domain to coupling the continuum nodal velocities with atomic lattice velocities. The Hamiltonian method is applied to combine the continuum and molecular Hamiltonians with the same weight in the overlapping domain. The mass and stiffness matrices of the continuum domain are obtained using a linear bridging map of the atomic lattice displacement laid underneath the continuum grid to the element displacements. Numerical examples are performed by presenting the... 

The nature of alumazine⋯M (M = Li+, Na+, K+, Be2+, Mg2+, AND Ca2+) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical... 

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... 

Tungsten oxide thin films (deposited by thermal evaporation or sol gel method) were used for photocatalytic reduction of graphene oxide (GO) platelets (synthesized through a chemical exfoliation method) on surface of the films under UV or visible light of the environment, in the absence of any aqueous ambient at room temperature. Atomic force microscopy (AFM) technique was employed to characterize surface morphology of the GO sheets and the tungsten oxide films. Moreover, using X-ray photoelectron spectroscopy (XPS), chemical state of the tungsten oxide films and the photocatalytic reduction of the GO platelets were quantitatively investigated. The better performance of the sol-gel tungsten... 

Parkinson's disease (PD) is a neurodegenerative disease, which is not easily diagnosed using clinical tests and the discovery of proper methods would be a major step towards a successful diagnosis. In the present study, we employed metabolic profiling using proton nuclear magnetic resonance spectroscopy to find metabolites in serum, which are helpful for the diagnosis of PD. Classification of PD and healthy subject was done using random forest. Serum levels of selenium measured by atomic absorption spectrometry in PD group were lower than the serum selenium levels in the control group. The metabolites causing selenium changes in PD patients were identified using random forest, and a model... 

Graphene, a two-dimensional (2D) sheet of sp2-hybridized carbon atoms packed into a honeycomb lattice, has led to an explosion of interest in the field of materials science, physics, chemistry, and biotechnology since the few-layers graphene (FLG) flakes were isolated from graphite in 2004. For an extended search, derivatives of nanomedicine such as biosensing, biomedical, antibacterial, diagnosis, cancer and photothermal therapy, drug delivery, stem cell, tissue engineering, imaging, protein interaction, DNA, RNA, toxicity, and so on were also added. Since carbon nanotubes are normally described as rolled-up cylinders of graphene sheets and the controllable synthesis of nanotubes is well... 

In the present research, the introduction of multi-walled carbon nanotubes (MWCNTs) into the hydroxyapatite (HA) matrix and dip coating of nanocomposite on titanium alloy (Ti-6Al-4V) plate was conducted in order to improve the performance of the HA-coated implant via the sol-gel method. The structural characterization and electron microscopy results confirmed well crystallized HA-MWCNT coating and homogenous dispersion of carbon nanotubes in the ceramic matrix at temperatures as low as 500 C. The evaluation of the mechanical properties of HA and HA/MWCNT composite coatings with different weight percentages of MWCNTs showed that the addition of low concentrations of MWCNTs (0.5 and 1 wt.%)... 

A wide variety of carbon nanostructures were generated by a Q-switched Nd : YAG laser (1064 nm) while mostly nanodiamonds were created by an ArF excimer laser (193 nm) in deionized water. They were characterized by transmission electron microscopy, Raman spectroscopy and x-ray photoelectron spectroscopy. It was found that the IR laser affected the morphology and structure of the nanostructures due to the higher inverse bremsstrahlung absorption rate within the plasma plume with respect to the UV laser. Moreover, laser-induced breakdown spectroscopy was carried out so that the plasma created by the IR laser was more energetic than that generated by the UV laser  

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... 

Green tea-reduced graphene oxide (GT-rGO) sheets have been exploited for high efficiency near infrared (NIR) photothermal therapy of HT29 and SW48 colon cancer cells. The biocompatibility of GT-rGO sheets was investigated by means of MTT assays. The polyphenol constituents of GT-rGO act as effective targeting ligands for the attachment of rGO to the surface of cancer cells, as confirmed by the cell granularity test in flow cytometry assays and also by scanning electron microscopy. The photo-thermal destruction of higher metastatic cancer cells (SW48) is found to be more than 20% higher than that of the lower metastatic one (HT29). The photo-destruction efficiency factor of the GT-rGO is... 

Aim: This study evaluated serum levels of zinc in patient with CD compare to healthy subjects. Background: Celiac disease (CD) is characterized by small intestinal malabsorption of nutrients as a consequence of ingestion of wheat gluten. Zinc is an essential trace element that it has vital biological functions. Patients and methods: Sera of 30 celiac cases and 30 healthy normal cohorts as control group were obtained. Atomic absorption spectrophotometer was employed for estimating serum zinc level. Results: Zinc concentrations in patients diagnosed with CD were significantly lower than healthy subjects (75.97±12 compared with 92.83±18, P-value < 0.0001). Conclusion: The result of this study... 

Superparamagnetic Iron Oxide Nanoparticles (SPIONs) were synthesized and coated with pseudopolyrotaxanes (PPRs) and proposed as a novel hybrid nanostructure for medical imaging and drug delivery. PPRs were prepared by addition of α-cyclodextrin rings to functionalized polyethylene glycol (PEG) chain with hydrophobic triazine end-groups. Non-covalent interactions between SPIONs and PPRs led to the assembly of SPIONs@PRs hybrid nanomaterials. Measurements of the 1H Nuclear Magnetic Resonance (NMR) relaxation times T1 and T2 allowed us to determine the NMR dispersion profiles. Comparison between our SPIONs@PRs hybrid nano-compound and the commercial SPION compound, Endorem®, showed a higher... 

This paper deals with investigation of deformations and pull-in charges of the cantilever and doubly clamped carbon nanotubes (CNTs) with different geometries using molecular dynamics simulation technique. The well-known AIREBO potential for the covalent bonds between carbon atoms, Lennar-Jones potential for the vdW interaction and the Coulomb potential for electrostatic actuation are employed to model the nano electromechanical system. The results reveal that longer CNTs with smaller diameters have smaller pull-in charges in comparison with shorter CNTs possessing larger diameters. Furthermore, the pull-in charges of the doubly clamped CNTs are higher than the pull-in charges of the... 

WO3 thin film photoanodes containing different concentrations of Ag nanoparticles were synthesized by solegel method. Based on UV-visible spectra, presence of a surface plasmon resonance peak at 470 nm of wavelength indicated formation of silver nanoparticles in the WO3 films. According to atomic force microscopy (AFM) analysis, the highest value for surface roughness and the effective surface ratio was observed for the sample containing 2 mol% of Ag. X-ray diffraction (XRD) patterns revealed that WO 3 nanocrystalline structure was formed in the monoclinic phase with the average size of about 18.2 nm while Ag nanocrystals were determined in cubic phase. X-ray photoelectron spectroscopy (XPS)... 

The effect of etching time on the statistical properties of hydrophilic surfaces of SiO2/TiO2/glass nano bilayers has been studied using atomic force microscopy (AFM) and a stochastic approach based on a level crossing analysis. We have created rough surfaces of the hydrophilic SiO 2/TiO2 nano bilayer system by using 26% potassium hydroxide (KOH) solution. Measuring the average apparent contact angle allowed us to assess the degree of hydrophilicity, and the optimum condition was determined to be 10 min etching time. A level crossing analysis based on AFM images provided deeper insight into the microscopic details of the surface topography. With different etching times, it has been shown... 

A novel simple synthetic procedure for fabrication of high surface area nanostructured TiO2 electrode with uniform particles for photovoltaic application is reported. Modifying the TiO2 particulate sol by pH adjustment together with employment of a polymeric agent, so-called polymeric gel process, was developed. The polymeric gel process was used to deposit nanostructured thick electrode by dip coating incorporated in dye-sensitized solar cells (DSSCs). X-ray diffraction (XRD) analysis revealed that deposited film was composed of primary nanoparticles with average crystallite size in the range 21-39 nm. Field emission scanning electron microscope (FE-SEM) images showed that deposited film... 

In this study, the drastic influence of the boron atom on the acidity of alcohol has been considered. The calculated ΔHacid (320.9-338.1 kcal/mol) and pKa range of boron containing alcohol (-0.1-9.4) indicate that the boronation of alcohol leads to considerable enhancement of its acidity. For instance, we have obtained the ΔHacid values 338.1, 335.2 kcal/mol and the pKa values 4.12, 2.81 for BH 2CH2OH, BF2CH2OH alcohols, respectively, which are much smaller than that of CH3OH (with ΔHacid = 374.9 kcal/mol and pKa = 15). The increase in the acidity of boronated alcohol can be related to the stabilization of alkoxy ion due to overlap of unoccupied orbital of boron atom with the electron pairs... 

Considering high temperature and pressure during single bubble sonoluminescence collapse, a hot plasma core is generated at the center of the bubble. In this paper a statistical mechanics approach is used to calculate the core pressure and temperature. A hydrochemical model alongside a plasma core is used to study the bubble dynamics in two host liquids of water and sulfuric acid 85 wt % containing Ar atoms. Calculation shows that the extreme pressure and temperature in the plasma core are mainly due to the interaction of the ionized Ar atoms and electrons, which is one step forward to sonofusion. The thermal bremsstrahlung mechanism of radiation is used to analyze the emitted optical energy... 

The optical properties of a four-level atomic system via coherent and incoherent pumping fields are investigated. The giant Kerr nonlinearity with reduced linear and nonlinear absorption, which has a major role in decreasing the threshold of optical bistability (OB), can be obtained with subluminal light propagation via adjusting the intensities of coupling fields. An incoherent pumping field is noticed to be an extra parameter to reduce the threshold of OB and multistability, and it can be used as an effective parameter in producing lasing with or without population inversion. In this model, optical multistability is achieved simply by tuning the intensity of coupling laser fields.... 

Lipoproteins are biochemical compounds containing both proteins and lipids. These particles carry chemicals like cholesterol and triglycerides that are not soluble in aqueous solutions. This paper presents modeling of lipoprotein system using coarse grain molecular dynamics technique and stability analysis of this system in a water solution like blood. A high density lipoprotein (HDL) that consists of two annular monomers is modeled. Also there are lipid bilayers located in center of the rings, so the whole HDL and lipid bilayers are called lipoprotein system. First, all atom model is provided and then coarse-grain model is obtained using MARTINI technique. Modeling of the system in all atom...