Sharif Digital Repository

DNA supercoiling is a widespread phenomenon in biology. Here we introduce a coarse-grained DNA model and study supercoiled DNA rings via a rigid body molecular dynamics simulation. Our model allows us to investigate these structures in more detail than previously. The simulations are performed on rings of one to six kilobase pairs length and are compared to available experimental data and former simulation studies. The current study provides new additional information about some of the geometrical parameters of the supercoiled DNA rings. It also shows how enforcing a supercoiled DNA ring to two-dimensional space changes its geometrical parameters. Finally, our molecular dynamics method... 

By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA  

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the... 

The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use... 

Structural, half-metallic, magneto-optic, and thermoelectric properties of CrTiZ (Z = As, P) half-Heusleres compounds are investigated based on density functional theory. These compounds have mechanical stability in the ferromagnetic state with a high bulk modulus. They are often half-metallic with a large and integer magnetic moment and are very attractive in spintronics, magneto-optics applications. The magnetic moments of CrTiAs and CrTiP were 2.9865 μB and 3.00 μB, respectively, which were attributed to their ferromagnetic phase. Additionally, the positive sign of the phonon branches indicates the dynamic stability of these compounds. Applying both GGA and mBJ approximations, CrTiAs and... 

Purpose: The morphological stability of silicon single crystal wafers was investigated, after performing cleaning surface treatments based on moderate temperature annealing and plasma sputtering. Methods: The wafer surfaces were measured by Tapping mode atomic force microscopy in air, before and after the different treatments. The 3D images were segmented by watershed algorithm identifying the local peaks, and the stereometric parameters were extracted thereof. The analysis of variance allowed to better assess the statistically significant differences. Results: All the resulting quantities were critically discussed. It appeared that the different cleaning treatments affected differently the... 

In this study, ZrO2 coatings with different thicknesses were grown by the electron beam evaporation technique. The crystalline structure was studied by XRD analysis which suggested the tetragonal and monoclinic phases for ZrO2 coatings. Additionally, the film thickness slightly enhanced the crystallinity. The surface morphology and fractal features were analyzed using Scanning Electron Microscopy (SEM). The surface statistical parameters and the fractal geometry were employed to analyze the impact of the coating thickness and homogeneity on the morphology of the films. The statistical processing and fractal dimension revealed variations in the morphology parameters due to the electron beam... 

On silicon substrates, boron nitride nanosheets (BNNS) consisting of interconnected hexagonal boron nitride nano-layers were produced via chemical vapor deposition process at 1200 °C whose roughness's are at the micrometer- and nanometer-scale. The BNNS were functionalized in argon plasma admixed with ammonia or nitrogen or oxygen. The samples were characterized to investigate the surface chemistry and structural changes after plasma treatment using X-ray photoelectron spectroscope and Micro-Raman spectroscope techniques, respectively. While no significant changes in the surface features, upon plasma treatments of the BNNS, were noticed during SEM and TEM examination, the oxygen functional... 

Thin films of bismuth and iron oxides were obtained by atomic layer deposition (ALD) on the surface of a flexible substrate poly(4,4′-oxydiphenylene-pyromellitimide) (Kapton) at a temperature of 250°C. The layer thickness was 50 nm. The samples were examined by secondary-ion mass spectrometry, and uniform distribution of elements in the film layer was observed. Surface morphology, electrical polarization, and mechanical properties were investigated by atomic force microscope, piezoelectric force microscopy, and force modulation microscopy. The values of current in the near-surface layer varied in the range of ±80 pA when a potential of 5 V was applied. Chemical analysis was performed by... 

The micromorphology of tantalum pentoxide (Ta2O5) thin films, deposited on glass substrates by electron gun method, has been analyzed using atomic force microscopy (AFM), UV–Vis–NIR spectrophotometry and multifractal analyses. Two samples were grown at basic pressure of 7 × 10−6 mbar, work pressures of 1.3 × 10−4 and 2.0 × 10−4 mbar, and thicknesses of 0.38 μm and 0.39 μm, respectively. Subsequently, these samples were annealed at 300 °C for 2 h. The physical, structural and optical analyses were investigated by spectroscopic ellipsometry, spectrophotometry and AFM. The measured transmittance spectra were studied based on the Swanepoel method, whose results also yielded to the estimation of... 

The characterization of ion beam current density distribution and beam uniformity is crucial for improving broad-beam ion source technologies. The design of the broad ion beam extraction system directly affects these two parameters, therefore, depending on the application, the design and geometry of the source is changed. In this study, the effect of the presence or the absence of a neutralization process on the ion beam density was investigated. Also, the effect of the probe bias on the ion beam current measurement was evaluated. Eventually, using a flat probe, the ion beam profiles obtained from the extraction system of the ion source (Model RFIS 60, ACECR, Iran) were measured at energies... 

We recently reported an impressive cycling stability (over 20,000 cycles) of titanium nitride (TiN) electrodes with high specific capacitance. It is anticipated that nitrogen (β−N) doping in the oxidized surface of TiN film plays a crucial role in charge storage mechanism and stability of this material. In this work, we offer an evidence on the effect of β−N doping on improvement in specific capacitance of vacuum annealed TiN thin films. The annealing of the TiN films leads to the diffusion of the excess β−N from sub-surface to oxidized TiN film surface without further oxidation of the electrode surface. We demonstrate an increase in the TiN areal capacitance upon an increase in the amount...