Sharif Digital Repository

Phonon detector can be designed by using colloidal silver nanoparticle (Ag NP) in presence of 1-Ethyl-3-methylimidazolium Hexafluorophosphate [EMim][PF6] ionic liquid (IL) via computational technique as the first time for many and high performance biosensors applications. Density functional theory as a quantum chemistry calculation method has been used to get the potential interaction between silver metal and ionic solvent. Molecular dynamics simulation shows that in small sizes of colloidal Ag NP in [EMim][PF6], electrical effect of IL makes one main phonon peak and in big size of colloidal Ag NP, splitting of phonon density occurs with two peaks due to the lower electrical field of IL with... 

Molecular dynamic simulation was performed to calculate the configurational entropy and the free energy for colloidal silver nanoparticles (Ag NPs) in 1-Ethyl-3-methylimidazolium Hexafluorophosphate [EMim][PF6] ionic liquid (IL). Furthermore, the density functional theory (DFT) was used to get the potential interaction between the metal surface and ion in IL. The effect of size and temperature on the configurational entropy and the free energy of colloidal Ag NPs were investigated. Then, it was compared with the gas phase. The Tsallis nonextensivity of entropy was investigated for different sizes of colloidal Ag NPs and it was shown that sub-extensivity of entropy occurs for colloidal Ag... 

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... 

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... 

MD simulations were used for investigation on the kinetic formation of Ni-Pd nanoalloys at different simulation times. We have examined excess energies and bond order parameters for initial gas phase compositions including pure Ni, and Pd, and also Ni0.2Pd0.8, Ni0.4Pd0.6, Ni0.6Pd0.4, Ni0.8Pd0.2 concentrations. Excess energies for created Ni-Pd nanoalloys exhibit more instabilities for larger nanoparticles. Also, bond order results demonstrate amorphous structures for all of created nanoclusters. Moreover, number of formed clusters for pure Ni at 5 ns is more than pure Pd nanoclusters and number of formed clusters decreases when Pd is doped in pure Ni nanocluster. © 2017 Elsevier B.V  

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  

The energetics and kinetic energy barriers of vacancy/atom exchange in a 37-atom truncated octahedron Ag-Pt binary cluster in the Ag-rich range of compositions are investigated via a first-principles atomistic approach. The energy of the local minima obtained considering various distributions of a single vacancy and a few Pt atoms within the cluster and the energy barriers connecting them are evaluated using accurate density-functional calculations. The effects of the simultaneous presence of a vacancy and Pt atoms are found to be simply additive when their distances are larger than first-neighbors, whereas when they can be stabilizing at low Pt content due to the release of strain by the... 

We present an approach for constant-pressure molecular dynamics simulations. This approach is especially designed for finite systems, for which no periodic boundary condition applies. A molecular dynamics (MD) simulation for Ni nanoclusters is used to calculate their pressurevolumetemperature (pvT) data for the temperature range 200 K≤T≤400 K, and pressures up to 600 kbar. Isothermal sets of pvT data were generated by the simulation; each set was fitted by three equations of state (EoSs): Linear Isotherm Regularity-II (LIRII), BirchMurnaghan (BM), and EOS III. It is found that the MD data are satisfactorily reproduced by the EoSs with reasonable precision. Some features of the EoSs criteria,... 

We have investigated the size dependence of a nano-cavity properties produced in a Xe fluid using molecular dynamics simulations. We have created a nano-cavity of different sizes at 170 and 200 K (cavities diameters are within 1-10 nm). Liquid pressure, vapor pressure and surface tension of the nano-cavity for some given values of diameter are calculated. Within 1-10 nm cavity diameter, we have observed two opposite behavior for dependency of surface tension on the cavity diameter: for the range of 1-5 nm, it increases with the diameter, while, for the range of 5-10 nm remains constant. Also, the value of liquid pressure becomes less negative, when the size of cavity increases. Vapor...