Sharif Digital Repository

We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a salt-water medium with 1 M NaCl concentration to investigate salt effect on the denaturation process. At each temperature, configurational entropy is estimated using the covariance matrix of atom-positional fluctuations, from which the melting temperature (T m) was found to be 349 K. The calculated configuration entropy for different bases shows that the melting process involves more peeling (including fraying from the ends) conformations, and therefore the untwisting of the duplex and peeling states form the transition state of the denaturation process. There... 

The equilibrium crystal structure and electronic structure of BaFe2-x Cox As2 (x = 0,1, 2) superconductor have been investigated by using the pseudopotential Quantum Espresso code based on the ab initio density functional theory in the generalized gradient approximation. The equilibrium crystal structure for x = 1.0 has been determined by considering five different Fe/Co configurations. This study shows that the spin calculation is essential to obtain the experimental values at x = 0.0. The total and partial density of states, band structure, and Fermi surfaces of the three compounds has been calculated. Density of states calculation indicates the important... 

A quantum modeling of the CO adsorption on illuminated anatase TiO2 (0 0 1) is presented. The calculated adsorption energy and geometries of illuminated case are compared with the ground state case. The calculations were achieved by using DFT formalism and the BH and HLYP. Upon photoexcitation, an electron-hole pair is generated. Comparing of natural population in the ground state and the exited state, shows that an electron is trapped in a Ti4+ ion and a hole is localized in an oxygen ion. The photoelectron helps generation of a CO2 molecule on the TiO2 surface. As shown by optimization of these systems, the CO molecule adsorbed vertically on the TiO2 (0 0 1) surface in the ground state... 

Forced convective of a nanofluid that consists of water and Al2O3 in horizontal tubes has been studied numerically. Computed results were validated with existing well established correlation. Two-phase Eulerian model has been implemented for the first time to study such a flow field. A single-phase model and two-phase mixture model formulations were also used for comparison. The comparison of calculated results with experimental values shows that the mixture model is more precise. It is illustrated that the single-phase model and the two-phase Eulerian model underestimates the Nusselt number. Effects of nanoparticles concentration on the thermal parameters are also discussed  

Development of reliable and accurate models to estimate carbon dioxide–brine interfacial tension (IFT) is necessary, since its experimental measurement is time-consuming and requires expensive experimental apparatus as well as complicated interpretation procedure. In the current study, feed forward artificial neural network is used for estimation of CO2–brine IFT based on data from published literature which consists of a number of carbon dioxide–brine interfacial tension data covering broad ranges of temperature, total salinity, mole fractions of impure components and pressure. Trial-and-error method is utilized to optimize the artificial neural network topology in order to enhance its... 

Experimental values for surface tension of single and mixed electrolyte solutions were correlated using the models based on the perturbation theory. The Mean Spherical Approximation (MSA) model, coupled with the Ghotbi-Vera (GV) and the Mansoori et al. (BMCSL) equations of state, were used to correlate the experimental values of the surface tension. The results showed that the models can favourably correlate the experimental values for single electrolyte solutions. However, it was observed that the GV-MSA model can more accurately predict the surface tension for single electrolytes, especially at higher concentrations. Two different expressions for concentration dependency of cation hydrated... 

Metallic nanoclusters are interesting because of their utility in catalysis and sensors. The thermal and physical characteristics of metallic Pt nanoclusters with different sizes were investigated via molecular-dynamics simulations using Quantum Sutton-Chen (QSC) potential. This force field accurately predicts solid and liquid states properties as well as melting of the bulk platinum. Molecular dynamic simulations of Pt nanoclusters with 256, 456, 500, 864, 1372, 2048, 2916, 4000, 5324, 6912, 8788 atoms have been carried out at various temperatures. The Pt-Pt radial distribution function, internal energy, heat capacity, enthalpy, entropy of the nanoclusters were calculated at some... 

A numerical analysis is improved to study the effect of vibration on temperature history, heat generation, and mechanical properties during the friction stir welding process with different welding speeds. In this investigation, smoothed particle hydrodynamics (SPH) was applied to improve the 3D numerical analysis for simulation of the friction stir welding (FSW) process and friction stir vibration welding (FSVW) under different welding speeds. According to the experimental analysis, the grain size of the FSVW-ed sample is finer compared with that of the FSW-ed sample. The analysis was validated through a comparison of the simulated thermal cycles with the experimental results. There was a... 

In addition to its biological importance, DPhPC lipid bilayers are widely used in droplet bilayers, study of integral membrane proteins, drug delivery systems as well as patch-clamp electrophysiology of ion channels, yet their mechanical properties are not fully measured. Herein, we examined the effect of the ether linkage on the mechanical properties of ester- and ether-DPhPC lipid bilayers using all-atom molecular dynamics simulation. The values of area per lipid, thickness, intrinsic lateral pressure profile, order parameter, and elasticity moduli were estimated using various computational frameworks and were compared with available experimental values. Overall, a good agreement was... 

A genetic-based pore network extraction method from micro-computed tomography (micro-CT) images is proposed in this paper. Several variables such as the number, radius and location of pores, the coordination number, as well as the radius and length of the throats are used herein as the optimization parameters. Two approaches to generate the pore network structure are presented. Unlike previous algorithms, the presented approaches are directly based on minimizing the error between the extracted network and the real porous medium. This leads to the generation of more accurate results while reducing required computational memories. Two different objective functions are used in building the... 

Bridgehead C-H bond dissociation enthalpies of 105.7 ± 2.0, 102.9 ± 1.7, and 102.4 ± 1.9 kcal mol -1 for bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, and adamantane, respectively, were determined in the gas phase by making use of a thermodynamic cycle (i.e., BDE(R-H) = ΔH° acid(H-X) - IE(H •) + EA(X •)). These results are in good accord with high-level G3 theory calculations, and the experimental values along with G3 predictions for bicyclo[1.1.1]pentane, bicyclo[2.1.1]hexane, bicyclo[3.1.1]heptane, and bicyclo[4.2.1]nonane were found to correlate with the flexibility of the ring system. Rare examples of alkyl anions in the gas phase are also provided  

The properties of metallic nanorods vary due to changes in their composition, size and shape, which all depend on the aspect ratio of the nanorods. This work focuses on the optimization of the aspect ratio of silver nanorods using response surface methodology (RSM). Seed-mediated approach, which is the newest method with less difficulty, has been used for the synthesis of silver nanorods. First, silver ions were reduced with sodium borohydride in the presence of sodium citrate dehydrate, as stabilizer. Then, the prepared seeds were added to a solution containing more metal salts, a weak reducing agent (ascorbic acid) and a rod-like micellar template (cetyltrimethylammonium bromide, CTAB).... 

Statistically based experimental designs were applied to screen and optimize the bioleaching of spent hydrocracking catalyst by Penicillium simplicissimum. Eleven factors were examined for their significance on bioleaching using a Plackett-Burman factorial design. Four significant variables (pulp density, sucrose, NaNO3, and yeast extract concentrations) were selected for the optimization studies. The combined effect of these variables on metal bioleaching was studied using a central composite design (CCD). Second-order polynomials were established to identify the relationship between the recovery percent of the metals and the four significant variables. The optimal values of the variables... 

In the present study, a procedure was developed to determine the optimum reaction rate constants in generalized Arrhenius form and optimized through the Nelder-Mead method. For this purpose, a comprehensive mathematical model of a fixed bed reactor for dehydrogenation of heavy paraffins over Pt-Sn/Al 2O 3 catalyst was developed. Utilizing appropriate kinetic rate expressions for the main dehydrogenation reaction as well as side reactions and catalyst deactivation, a detailed model for the radial flow reactor was obtained. The reactor model composed of a set of partial differential equations (PDE), ordinary differential equations (ODE) as well as algebraic equations all of which were solved... 

In order to define a new temperature correction factor in this study, accurate experimental values were presented for permeability and diffusivity of carbon dioxide and methane in imidazolium-based room temperature ionic liquid: [bmim][PF6] (1-butyl-3-methylimidazolium hexafluorophosphate) immobilized on an inorganic membrane support. Results were presented as a function of temperature and pressure for temperatures within 300-320K and pressures below 50kPa. According to the literature, experimental values of permeability and diffusivity for CH4 in [bmim][PF6] vs. temperature are reported for the first time in this study. Results obtained for CO2 permeability revealed good agreement with data... 

The experimental 13C NMR chemical shift components of uracil in the solid state are reported for the first time (to our knowledge), as well as newer data for the 15N nuclei. These experimental values are supported by extensive calculated data of the 13C, 15N and 17O chemical shielding and 17O and 14N electric field gradient (EFG) tensors. In the crystal, uracil forms a number of strong and weak hydrogen bonds, and the effect of these on the 13C and 15N chemical shift tensors is studied. This powerful combination of the structural methods and theoretical calculations gives a very detailed view of the strong and weak hydrogen bond formation by this molecule. Good calculated results for the... 

Theoretical study of carbon monoxide adsorption on SixGe4 - x(x = 0-4) nano-clusters has been carried out using advanced hybrid meta density functional method of Truhlar (MPW1B95). MG3 semi-diffuse (MG3S) and correlation consistent valence basis sets with relativistic core potential were employed to improve the results. The agreement of the calculated ionization and dissociation energies with experimental values validates the reported structures of nano-clusters and justifies the use of hybrid meta density functional method. The geometry, adsorption energy, charge distribution, and vibrational frequency of CO adsorption on all possible structures were investigated. The maximum vibrational... 

The 3D simulation of the hydrodynamic behavior of a rotating disc contactor (RDC) by means of computational fluid dynamics (CFD) was investigated for the n-butanol-succinic acid-water (BSW) system. For the two-phase liquid-liquid flow, the velocity distribution of the continuous phase and drop size distributions were determined using the k-ω turbulence model in conjunction with the Eulerian-Eulerian approach and MUSIG model. In this system in which the holdup of the dispersed phase is low, the continuous phase velocity was computed by simultaneously solving the Navier-Stokes equations beside the different models of turbulence. The motions of the dispersed phase was calculated while... 

A modelling of the anaerobic digestion process of molasses was conducted in a 70-L multistage anaerobic biofilm reactor or hybrid anaerobic baffled reactor with six compartments at an operating temperature of 26 °C. Five hydraulic retention times (6, 16, 24, 72 and 120 h) were studied at a constant influent COD concentration of 10,000 mg/L. Two different kinetic models (one was based on a dispersion model with first-order kinetics for substrate consumption and the other based on a modification of the Young equation) were evaluated and compared to predict the organic matter removal efficiency or fractional conversion. The first-order kinetic constant obtained with the dispersion model was... 

CdS is conventionally used as the n-type buffer layer in chalcopyrite (CIG(S, Se)) and Kesterite (CZT(S, Se)) solar cells. CdS is toxic and there are wide attempts to find substitutes for it. Here, we suggest SnS2 as a possible alternative. SnS2 films were deposited by pulsed laser deposition (PLD), characterized to estimate carrier concentration and electron affinity values, and the obtained values were used to model a CZT(S, Se) solar cell. The experimental values of a benchmark CZT(S, Se) cell with efficiency of 12.3% were employed to obtain the density and energy position of defects in CZT(S, Se) and validating the model. We observed that SnS2 results in almost identical performance as...