Sharif Digital Repository

We have investigated the water permeation through carbon nanotube (CNT) membranes as a model of peptide nanotube channels (PNCs). The effect of different charge configured CNTs which tailored based on some artificial ion channels on the water permeation through the channels have been studied. In addition, the temperature dependence of the permeation has been investigated. We have found that there is a jump in the permeation which is somehow related to the characteristics of each channel and the temperature of this permeation jump changes according to the channel configuration. Our investigation on the channels shows that the temperature at which the permeation jump occurs is related to the... 

The concept of effective pair potential (EPP), in which medium effects and contribution of long-range interactions are added to near-neighbor pair interactions, is a useful tool to derive and calculate the thermodynamic quantities. It has been shown that the extended Lennard-Jones (12, 6, 3) potential is an accurate EPP for many systems. However, the parameters of this EPP are not known for any systems. We introduce a new approach to use experimental pvT data of a fluid to calculate its EPP parameters. Such calculation has been carried out for some fluids at some temperatures. Unlike the isolated pair potential, it has been shown that the parameters significantly vary with temperature. We... 

A simple equation of state (EoS) has recently been introduced (J. Phys. Chem. B2009, 113, 11977-11987) as (Z - 1)v2 = e + f/ρ + gρ2, where Z ≡ pv/RT is the compressibility factor, v = 1/ρ is molar volume, and e, f, and g are temperature dependent parameters. This EoS has been found to be accurate for all types of nano and bulk solids and bulk fluids, in the entire temperature and pressure ranges for which experimental data are reported, except for the isotherms within 1 ≤ T r = T/Tc ≤ 1.1 for the spherical and near spherical species and for a wider temperature range for the cylindrical molecules. The aim of this work is to investigate the validity of a three-term expression similar to the... 

Water inside carbon nanotubes is an interesting confined system, and its theoretical and applied aspects have been studied extensively. The confinement in nanometer- and sub-nanometer-sized nanotubes gives rise to new molecular arrangements of water and affects its physical properties drastically. In order to study these new arrangements, Monte Carlo simulations of water inside carbon nanotubes have been performed. Simulations are carried out for water with a wide range of density inside carbon nanotubes with different diameters. It is observed that at constant temperature, the density of water dictates the presence of water clusters, filled states, and different ordered phases. The... 

A general regularity was found based on an effective pair potential of Lennard-Jones LJ (12, 6), for both dense, nonmetallic and nonionic fluids and solids according to which (Z-1) v2 linearly varies with respect to ρ2 for each isotherm, and this equation of state (EoS I) is known as LIR. However, despite the fact that Ne is a simple spherical species, unexpectedly, its solid and liquid phases both show a significant deviation from EoS I. In this work, we have investigated the accuracy of the EoS I for other systems, including quantum light molecules, such as D 2, H 2 and He, in both fluid and solid states at different temperatures. Like Ne, we have noticed that these systems do not well... 

Water inside carbon nanotubes as an example of nanoconfined water has gained noticeable attention, in both theoretical and applied aspects. Molecular simulation has played a major role in the studies in this field. Yet, there is a need for systematic study of simulation results and compilation of scientifically reliable predictive relations. Here we present Monte Carlo simulations of water inside carbon nanotubes with different radii. An equation of state which was derived on the basis of the extended Lennard-Jones (12,6,3) as the effective pair potential is chosen for the system of water inside the carbon nanotubes. The equation of state is modified to take the effects of anisotropic... 

The effect of electrostatic interactions on vibrational frequencies and thermodynamic properties of CO adsorbate on the Ni(111) surface is calculated by taking the first and second nearest-neighbour interactions into account. In order to obtain reasonable results, the cluster model of various surface adsorption sites with CO adsorbate is partially optimized, using Density Functional Theory and also the MP2 method for the hcp site. Comparison between DFT and MP2 results shows that DFT results are more reliable for this system. The stretching and bending frequencies of CO adsorbate are calculated using both Partial Hessian Analysis and Cluster-Adsorbate Coupling methods. Stretching and bending... 

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... 

In the framework of the Tsallis statistical mechanics, we study the change of the population of states when the parameter q is varied, for some model systems; the results show that the difference between predictions of the Boltzmann-Gibbs and Tsallis statistics can be much smaller than the precision of any existing experiment. Also, the relation between privilege of rare and frequent events and the value of q is restudied. It is shown that positive q privilege frequent and negative q privilege rare events. Finally, the convergence criteria of the partition function of some simple model systems, in the framework of Tsallis statistical mechanics, is studied. Based on this study, we conjecture... 

We have derived an analytical equation of state (EOS) based on the soft-core statistical mechanical perturbation theory for fluids, using the Weeks-Chandler-Andersen (WCA) theory recently developed by Ben-Amotz-Stell (BAS) for the choice of the hard-sphere diameter, but with a new algorithm for calculation of the pair and many-body interactions. We have used Carnahan-Starling expression with the Boltzmann factor criterion (BFC) as an effective hard-sphere diameter for the reference system, and also decomposed the perturbed pair potential to symmetric and asymmetric terms. The former term is due to the many-body interactions at high densities as was used in the linear isotherm regularity... 

The effect of repulsive steepness of the soft-core square well (SCSW) potential model on the second virial coefficient, critical behaviour (two- phase region and the position of critical point), and coordination number are investigated. The soft-core thermodynamic perturbation theory (TPT) presented by Weeks-Chandler-Anderson (WCA) recently developed by Ben-Amotz and Stell (BAS) has been used for the reference system, and the Barker-Henderson TPT for the perturbed system. The Barker-Henderson macroscopic compressibility approximation has been used for all order perturbation terms in which the second-order one is improved by assuming that the molecules in every two neighbouring shells are... 

The hydrogen abstraction reaction of the OH radical with CH 2FCH22F (HFC-152) is studied theoretically over the 150-3000 K temperature range. In this study, the two most recently developed hybrid density functional theories, namely, BBlK and MPWBlK, are applied, and their efficiency in reaction dynamics calculation is discussed. The BBlK/6-31+G(d,p) method gives the best result for the potential energy surface (PES) calculations, including barrier heights, reaction path information (the first and second derivatives of PES), geometry of transition state structures, and even weak hydrogen bond orientations. The rate constants were obtained by the dual-level direct dynamics with the... 

We present in this paper a simple method of obtaining various equations of state for hard sphere fluid in a simple unifying way. Using the first several virial coefficients of hard sphere fluid, we will guess equations of state by using the asymptotic expansion method. Among the equations of state obtained in this way are Percus-Yevick, Scaled Particle Theory, and Carnahan-Starling equations of state. Also by combining the Monte Carlo results on hard sphere fluid with the asymptotic expansion method many other equations of state for hard sphere fluid can be found where all of them give essentially similar results in the region of isotropic hard sphere liquid, i.e., up to η < 0.5, in which η... 

The effect of anharmonicity on the adsorption of CO molecules on the Ni(111) surface has been investigated. The DFT calculations are used to obtain the effective adsorption potential of the CO molecule on the Ni(111) surface. First, using an appropriate slab model, the geometry of adsorption system corresponding to hep, fcc, bridge, and on-top sites with p(2 × 2) arrangement and coverage of 0.25 ML is optimized by the DFT calculations using a plane wave basis set and ultrasoft pseudopotentials; this gives the hep site as the most stable site with De = 185 kJ/mol, for which the equilibrium distance of CO from the surface and C-O bond length on the surface are found to be 1.31 and 1.192 Å,... 

Using the newly introduced asymptotic expansion method to obtain equations of state for hard sphere fluid, new simple equations of state for hard disks based on known virial coefficients are derived. Comparison of the obtained equations of state with computer simulation data shows that they are accurate in the whole fluid region. © 2007 Elsevier B.V. All rights reserved  

A new potential function, which can in a simple and reasonable manner represent the molecular interaction of many kinds of hard-core fluids by varying the value of its parameter, is proposed. For prediction of thermodynamic properties of hard-core fluids such as the square-well (SW) and hard core Lennard-Jones (HCLJ), a simple perturbed equation of state (EOS) is derived by using the new potential function along with the Barker-Henderson perturbation theory. This method yields a simple and general analytical expression for each thermodynamic property of such fluids. The most important feature of these expressions is that they have no adjustable parameter and in some regions in which there is... 

The interaction potential energy and heat of sublimation of nanoparticles of HMX crystal polymorphs are studied by using molecular dynamics methods with a previously developed force field [Bedrov, et al., J. Comput.-Aided Mol. Des. 8 (2001) 77]. Molecular dynamics simulations of nanoparticles with 10, 20, 30, 40, 50, 60, 70, 80, 90, and 100 molecules of HMX are carried out at 300 K. The intermolecular, intramolecular and total interaction energies per mole for the nanoparticles are calculated at 300 K. Then, we have calculated sublimation enthalpy of HMX crystal polymorphs with different sizes. For the all sizes, the β-HMX is found to be the most stable phase, due to having the least total... 

In this paper the density and temperature dependencies of surface tension are investigated. Using the Lennard-Jones (12,6), as an effective pair interaction potential, a linear expression is derived for isotherms of γ /ρ 2 versus ρ 2 for some normal and ChloroFluoroCarbons (CFCs) fluids, where is surface tension and ρ = 1/v is molar density. The linearity behavior of the derived equation is well fitted onto the experimental data of surface tension for monatomic, diatomic, nonpolar, polar, hydrogen-bonded and chlorofluorocarbons. In addition, the temperature dependence of surface tension for 20 different fluids is examined, in which the contributions of both terms of the average effective... 

Continuing an ongoing study, molecular dynamics (MD) simulations were performed to investigate the effects of methanol concentration on Nafion morphology, such as the size of solvent cluster, solvent location, and polymer structure via the sandwich model. Our survey shows that high methanol concentrations resulted in increment of solvent cluster size in Nafion membrane. The sulfonic acid clusters also befall much in order as subsequent layers of such ionic clusters are formed. The number of neighbouring hydronium ions around a sulfur atom is independent of methanol concentration, but the first shell of hydronium and water around sulfonic acid clusters is broader. Although methanol would... 

Ising models in nanosystems are studied in the presence of a magnetic field. For a one-dimensional (1-D) array of spins interacting via nearest-neighbour and next-nearest-neighbour interactions we calculate the heat capacity, the surface energy, the finite-size free energy and the bulk free energy per site. The heat capacity versus temperature exhibits a common wide peak for systems of any size. A small peak also appears at lower temperatures for small arrays when the ratio of magnetic field spin interaction energy over the nearest-neighbour spin-spin interaction energy, f, is within 0 < F ≤ 0.10 . The peak becomes smaller for longer array and eventually vanishes for long arrays,...