Sharif Digital Repository

The 3A zeolite is an excellent adsorbent for natural gas dehydration due to low energy requirement in regeneration step and easy operation. To perform a reliable modeling, a good equilibrium adsorption isotherm is mandatory. Accordingly, water, methane, methyl mercaptan (M-mercaptan) and CO2 adsorption isotherms and also the competitive adsorption loading versus temperature are described for the system using molecular simulation and mathematical models. It is found that CO2 competes with water for adsorption on 3A and lower temperature is required for selective removal of water. The mathematical model results showed that M-mercaptan and CO2 quickly adsorb on 3A and capacity of 3A for water... 

For a set of 846 organic compounds, relevant in forensic analytical chemistry, with highly diverse chemical structures, the gas chromatographic Kovats retention indices have been quantitatively modeled by using a large set of molecular descriptors generated by software Dragon. Best and very similar performances for prediction have been obtained by a partial least squares regression (PLS) model using all considered 529 descriptors, and a multiple linear regression (MLR) model using only 15 descriptors obtained by a stepwise feature selection. The standard deviations of the prediction errors (SEP), were estimated in four experiments with differently distributed training and prediction sets.... 

The 3A zeolites are excellent adsorbents for industrial-scale gas dehydration because of the low energy required for regeneration and ease of operation. A computational study of the dehydration of an industrial feed stream containing ethane and water was performed using an in-house code that included an appropriate equilibrium adsorption isotherm. The validated computational model was used to examine the impact of particle size on the process dynamics and the corresponding pressure drop. The water concentration along the adsorption column was also investigated. To increase the process capacity, the packed adsorption bed was divided into two distinct layers, which were operated with different... 

Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of α -de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature Tf and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with Tf decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's... 

A simple model is proposed to estimate the critical properties of alkanes-temperature, pressure, and volume. This model is dependent on normal boiling and molecular weight of hydrocarbons. The model has been expanded based on a Taylor series in the form of a polynomial function of normal boiling. Because methane has the simplest structure among hydrocarbons, this model has been calculated around methane. The coefficients of this model were assumed in the form of a linear function of molecular weight. These parameters can be obtained from regression between experimental results and results from this model. By a comparison of this model and previous models, it is shown that this model is... 

In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements  

Molecular structural mechanics is implemented to model the vibrational behavior of defect-free single-layered graphene sheets (SLGSs) at constant temperature. To mimic these two-dimensional layers, zigzag and armchair models with cantilever and bridge boundary conditions are adopted. Fundamental frequencies of these nanostructures are calculated, and it is perceived that they are independent of the chirality and aspect ratio. The effects of point mass and atomistic dust on the fundamental frequencies are also considered in order to investigate the possibility of using SLGSs as sensors. The results show that the principal frequencies are highly sensitive to an added mass of the order of 1 0-... 

A lubrication model is used to study the dynamics of nanoscale droplets on wettability gradient surfaces. The effects of the gradient size, size of the nanodroplets and the slip on the dynamics have been studied. Our results indicate that the position of the center of mass of the droplets can be well described in terms of a third-order polynomial function of the time of the motion for all the cases considered. By increasing the size of the droplets the dynamics increases. It is also shown that the slip can considerably enhance the dynamics. The results have been compared with the results obtained using theoretical models and molecular dynamics simulations  

The synthesis and structures of two new octadentate, Schiff-base calixpyrrole macrocycles are presented in which modifications at the meso-substituents (L1) or the aryl spacer between the two pyrrole-imine donor compartments (L2) are introduced. The outcomes of these changes are highlighted in the structures of binuclear Pacman complexes of these macrocycles, [M2(L1)] and [M2(L 2)]. Both palladium and cobalt complexes of the fluorenylmeso- substituted macrocycle H4L1 adopt rigid, but laterally twisted geometries with enclosed bimetallic microenvironments; a consequence of this spatial constraint is an exo-exo-bonding mode of pyridine in the dicobalt complex [Co2(py)2(L1)]. In contrast, the... 

An Iron(lV)-oxo heme(+·) complex (Compound I, Cpd I) is the proposed active species of heme enzymes such as the cytochromes P450 and Is elusive; therefore, biomimetic studies on active site mimics give valuable Insight Into the fundamental properties of heme active species. In this work we present density functional theory (DFT) calculations on substrate hydroxylatlon by a Compound I mimic [FeIV=O(Por+̇)Cl] and its one-electron reduced form [FeIV=O(Por)Cl]-. Thus, recent experimental studies showed that [FeIV =O(Por)Cl]- is able to react with substrates via hydride transfer reactions [Jeong, Y. J.; Kang, Y.; Han, A.-R.; Lee, Y.-M.; Kotani, H.; Fukuzumi, S.; Nam, W. Angew. Chem., Int. Ed.... 

In this study, a multiplate shear model is developed for dynamic analysis of multilayer graphene sheets with arbitrary shapes considering the interlayer shear effect. By utilizing the model, then some free-vibration analysis is presented. According to the experimental results, the weak interlayer van der Waals interaction cannot maintain the integrity of carbon atoms in adjacent layers. Therefore, it is required that the interlayer shear effect is accounted to study multilayer graphene mechanical behavior. The governing differential equation of motion is derived for the multilayer graphene sheets utilizing a variational approach based on the Kirchhoff plate model. The essential and natural... 

To determine the outward permeability of retina-choroid-sclera (RCS) layer for different ophthalmic drugs and to develop correlations between drug physicochemical properties and RCS permeability. A finite volume model was developed to simulate pharmacokinetics in the eye following drug administration by intravitreal injection. The RCS permeability was determined for 32 compounds by best fitting the drug concentration-time profile obtained by simulation with previously reported experimental data. Multiple linear regression was then used to develop correlations between best fit RCS permeability and drugs physicochemical properties. The RCS drug permeabilities had values that ranged over 3 ×... 

An analytical model is proposed to study the effect of particle size on melting enthalpy and entropy of metallic nanoparticles (NPs). The Mott's and Regel's equations for melting entropy in the combination of core average coordination number (CAC) and surface average coordination number (SAC) of freestanding NPs are considered. Clusters of icosahedral (IC), body centered cubic (BCC), and body centered tetragonal (BCT) structure without any vacancies and defects are modeled. Using the variable coordination number made this model to be in good agreement with experimental and molecular dynamic (MD) results of different crystal structures. The model predicts melting entropy and enthalpy of... 

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... 

In this paper the two-point boundary value problem (BVP) of the cantilever deflection at nano-scale separations subjected to van der Waals and electrostatic forces is investigated using analytical and numerical methods to obtain the instability point of the beam. In the analytical treatment of the BVP, the nonlinear differential equation of the model is transformed into the integral form by using the Green's function of the cantilever beam. Then, closed-form solutions are obtained by assuming an appropriate shape function for the beam deflection to evaluate the integrals. In the numerical method, the BVP is solved with the MATLAB BVP solver, which implements a collocation method for... 

A mathematically rigorous, multiscale modeling methodology capable of coupling behaviors from the Kolmogorov turbulence scale through the full scale system in which a fiber suspension is flowing is presented. Here the key aspect is adaptive hierarchical modeling. Numerical results are presented focus of which are on fiber floe formation and destruction by hydrodynamic forces in turbulent flows. Specific consideration was given to molecular-dynamics simulations of viscoelastic fibers in which the fluid flow is predicted by a method which is a hybrid between direct numerical simulations and large eddy simulation techniques, and fluid fibrous structure interactions were taken into account. The... 

The classical methods utilized for modeling nano-scale systems are not practical because of the enlarged surface e ects that appear at small dimensions. Contrarily, implementing more accurate methods is followed by prolonged computations as these methods are highly dependent on quantum and atomistic models, and they can be employed for very small sizes in brief time periods. In order to speed up the Molecular Dynamics (MD) simulations of the silicon structures, Coarse-Graining (CG) models are put forward in this research. The procedure involves establishing a map between the main structure's atoms and the beads comprising the CG model and modifying the parameters of the system so that the... 

We explore the interplay between tunneling process and chiral interactions in the discrimination of chiral states for an ensemble of molecules in a biological environment. Each molecule is described by an asymmetric double-well potential and the environment is modeled as a bath of harmonic oscillators. We carefully analyze different time-scales appearing in the resulting master equation at both weak- and strong-coupling limits. The corresponding results are accompanied by a set of coupled differential equations characterizing optical activity of the molecules. We show that, at the weak-coupling limit, chiral interactions prohibit the coherent racemization induced by decoherence effects and... 

Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers,... 

We study the phase diagram of the anisotropic spin-1 Heisenberg chain with single ion anisotropy (D) using a ground-state fidelity approach. The ground-state fidelity and its corresponding susceptibility are calculated within the quantum renormalization group scheme where we obtained the renormalization of fidelity preventing calculation of the ground state. Using this approach, the phase boundaries between the antiferromagnetic Néel, Haldane and large-D phases are obtained for the whole phase diagram, which justifies the application of quantum renormalization group to trace the symmetry-protected topological phases. In addition, we present numerical exact diagonalization (Lanczos) results...