Sharif Digital Repository

Stochastic simulation is carried out to investigate intracellular viral reaction kinetics and the time evolution of the average particle number ( N̄) and coefficient variation (CV) for genome, template, and structural protein. The coefficient variation of these components is found to be ordered as: CV template > CV structural protein > CVgenome. The average particle number is also calculated via a deterministic approach. The magnitude value of the difference between the stochastic and deterministic approaches is found to be N̄ template ̃ N̄ structural protein > N̄ genome. The Poisson algorithm has been used to investigate the number of particles in the dynamics of intracellular viral... 

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... 

Molecular dynamics simulations are performed to obtain insight into the structural properties of hydrated Nafion using the sandwich model of the polymer membrane. It is shown that a larger distance between the sulfonate groups of a chain leads to the polymer forming a better inverted micelles structure. Water- and hydronium-polymer interfaces are investigated. Comparing our results with others indicates that, from the perspective of distance, the formation of shells of water and hydronium ions is independent of the model and monomer type, but depends on both if the coordination number is considered. The behaviour of water molecules and hydronium ions is also studied dynamically. Our survey... 

As the delay time and hence nuclei formation play a crucial role in the pathophysiology of sickle cell disease, MD simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations have been performed on three systems of hemoglobin; namely dimer of hemoglobin with valine (Hb S), tryptophan (Hbβ6W), and phenylalanine (Hbβ6F) at β6 position. The structural changes due to these aromatic substitutions are investigated. It is shown that β subunits have significant impact on the differences between a dimer and other crystal structures. Transition from a dimer to polymer for Hb S system affects the donor molecule more than that of the acceptor. In the case of donor and... 

A method is developed to calculate the critical line of two dimensional (2D) anisotropic Ising model including nearest-neighbor interactions. The method is based on the real-space renormalization group (RG) theory with increasing block sizes. The reduced temperatures, Ks (where K=J/kBT and J, kB, and T are the spin coupling interaction, the Boltzmann constant, and the absolute temperature, respectively), are calculated for different block sizes. By increasing the block size, the critical line for three types of lattice, namely: triangular, square, and honeycomb, is obtained and found to compare well with corresponding results reported by Onsager in the thermodynamic limit. Our results also... 

We compute fractal dimension and permutation entropy for healthy and people who have experienced heart failure. Our result shows that permutation entropy is a suitable approach as well as detrend fluctuation analysis (DFA). The result of DFA shows that the fractal dimensions for healthy and heart failure are different as well as the permutation entropy result. The fluctuation value for permutation entropy for an individual who has experienced heart failure is bigger than for a healthy person. There is some specific change in the interbeat signal of a person who has experienced heart failure, but there is not previous trend for a healthy person  

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... 

We investigate a one-dimensional (1-D) Ising model for finite-site systems. The finite-site free energy and the surface free energy are calculated via the transfer matrix method. We show that, at high magnetic fields, the surface free energy has an asymptotic limit. The absolute surface energy increases when the value of f (the ratio of magnetic field to nearest-neighbor interactions) increases, and for f ≥10 approaches a constant value. For the values of f ≥0.2, the finite-site free energy also increases, but slowly. The thermodynamic limit in which physical properties approach the bulk value is also explored  

To solve the controversy, regarding the existence of an analytic solution to the 1-D Ising model with nearest-neighbor (NN) and next-nearest-neighbor (NNN) interactions in the presence of a magnetic field, we apply the transfer matrix method to solve the 1-D Ising model in the presence of a magnetic field, taking both NN and NNN interactions into account. We show that it is possible to write a transfer matrix only if the number of sites is even. Even in such a case, it is impossible to diagonalize the transfer matrix in an analytic form. Therefore, we employ a numerical method to obtain the eigenvalues of the transfer matrix. Moreover, the heat capacity, magnetization, and magnetic...