Sharif Digital Repository

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  

A familiarity with denaturation process is highly significant in understanding the DNA replication, manipulation, and interactions involving DNA double helix stability. We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. At each temperature, configurational entropy was estimated using the covariance matrix of atom-positional fluctuations. By plotting the configuration entropy versus temperature, we calculated the melting temperature which was found to be 329.7 K. We also calculated the hydrogen bonding energy and heat capacity for the atoms participating in the hydrogen bonding between two strands of DNA. Moreover, their temperature... 

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... 

Molecular dynamics (MD) simulation was used to study of mechanical properties of NiTiCu with different content of copper. It was shown that the percent composition of copper are significantly affects the stress-strain curves curve. The results showed that as the Cu content increased, the Yield Strength and Young's modulus decreased. © 2017 Elsevier Ltd  

DNA supercoiling is a widespread phenomenon in biology. Here we introduce a coarse-grained DNA model and study supercoiled DNA rings via a rigid body molecular dynamics simulation. Our model allows us to investigate these structures in more detail than previously. The simulations are performed on rings of one to six kilobase pairs length and are compared to available experimental data and former simulation studies. The current study provides new additional information about some of the geometrical parameters of the supercoiled DNA rings. It also shows how enforcing a supercoiled DNA ring to two-dimensional space changes its geometrical parameters. Finally, our molecular dynamics method... 

In this paper we have studied the motion of a nanocar and nanotruck on gold substrate using the classical molecular dynamics method. Analyzing the motion regime of the nanocar at different temperatures is one of the main goals of this paper. In the past years, similar molecules such as Trimmer, Z-car and nanotruck have been simulated by Konyukhov and Akimov. To increase the modeling accuracy in this paper we have used classical molecular dynamics contrary to previous works which used a rigid body molecular dynamics method. The result of our simulations were compared qualitatively to the experimental tests performed by Zhang et al. [12]. There was a good agreement between the results achieved... 

In this paper, four coarse-graining (CG) models are proposed to accelerate molecular dynamics simulations of FCC metals. To this aim, at first, a proper map between beads of the CG models and atoms of the all-atom (AA) system is assigned, afterwards mass of the beads and the parameters of the CG models are determined in a manner that the CG models and the original all-atom model have the same physical properties. To evaluate and compare precision of these four CG models, different static and dynamic simulations are conducted. The results show that these CG models are at least 4 times faster than the AA model, while their errors are less than 1 percent. © 2018 Polish Society of Theoretical... 

Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on stepped surfaces. Five surface forms are considered in the simulations. The system parts are made of pure transition metals and Sutton-Chen many-body potential is used as interatomic potential. The conditions which are subjected to change in the tests include: materials used for particles and substrate, and surface step conditions. In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Simulation results show the effect of the aforementioned working conditions on... 

Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on double-layer surfaces. The system parts are made of transition metals. The conditions which are subjected to change in the tests are material combinations for cluster, main substrate and lubricant layer (adlayer). In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Obtaining this sort of knowledge is highly beneficial for further experiments in order to be able to plan the conditions and routines, which guarantee better success in the manipulation process  

A molecular dynamics simulation study has been performed to investigate the solidification and remelting of aluminum using Sutton - Chen many body potential. Different numbers of atoms from 108 to 2048 atoms were considered to find an adequate size for the system. Three different cooling and heating rates, i.e. 1 0 12 K/s, 10 13 K/s and 10 14 K/s, were used. The structure of the system was examined using radial distribution function. The melting and crystallization temperatures of aluminum were evaluated by calculating the variation of heat capacity during the phase t ransformation. Additionally, Wendt – Abraham parameters were calculated to determine the glass transition temperature. It is... 

One of the most popular constitutive rules that correlate the continuum and atomic properties in multi-scale models is the Cauchy–Born (CB) hypothesis. Based on this constitutive law of continuum media, it assumes that all atoms follow the deformation subjected to the boundary of crystal. In this paper, the validity and failure of CB hypothesis are investigated for the silicon nano-structure by comparison of the continuum and atomic properties. In the atomistic level, the stresses and position of atoms are calculated using the molecular dynamics (MD) simulation based on the Tersoff inter-atomic potential. The stresses and strains are compared between the atomistic and continuous media to... 

The surface, edge and corner effects have significant influences in the electrical and optical properties of silicon nano-structures. In this paper, a novel hierarchical temperature-related multi-scale model is presented based on the boundary Cauchy-Born method to investigate not only the surface but also the edge and corner effects in thermal properties of diamond-like structures such as silicon nano-structures at finite temperature. A combined finite element method and molecular dynamics are respectively employed in macro- and micro-scale levels. The temperature-related Cauchy-Born rule is applied using the Helmholtz free energy, as the energy density of equivalent continua relating to the... 

Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on stepped surfaces. Five surface forms are considered in the simulations. The system parts are made of pure transition metals and Sutton-Chen many-body potential is used as interatomic potential. The conditions which are subjected to change in the tests include: materials used for particles and substrate, and surface step conditions. In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Simulation results show the effect of the aforementioned working conditions on... 

In the recent years a great attention of research deals with different physical and biological aspects of the BBB structure, a robust shield that separates the blood and brain, a recent research held by the authors of this paper has focused on figuring out computing the diffusion coefficient of endothelial cell membrane. In this study, the major efforts have been concentrated on calculating a standardized measure for the amount of permeability and diffusion of this barrier. As a result, this work is dedicated to molecular dynamics (MD) simulation of calculating the interaction force between nano-particle and BBB membrane. data is recorded by using steered molecular dynamics simulation and... 

Due to the growing applications of silicon in nano-scale systems, a molecular dynamics approach is employed to investigate thermal properties of silicon. Since simulation results rely upon interatomic potentials, thermal expansion coefficient (TEC) and lattice constant of bulk silicon have been obtained using different potentials (SW, Tersoff, MEAM, and EDIP) and results indicate that SW has a better agreement with the experimental observations. To investigate effect of size on TEC of silicon nanowires, further simulations are performed using SW potential. To this end, silicon nanowires of different sizes are examined and their TEC is calculated by averaging in different directions ([100],... 

The study of the surface free energy (SFE) of metal at nanoscale is far from perfection and the obtained results are approach dependent. Despite the extensive investigations, there is still a lack of a complete model for the surface energy of metallic nanoparticles which could be able to consider effects of the particle size and shape. Most studies emphasize the size dependence of the melting characteristics, rather than considering the lattice deformation and the surface energy of nanoclusters. This research aimed at computation of SFE of copper nanoclusters depending on temperature over a wide range of sizes, containing 147 to 10179 atoms. We employed molecular dynamics simulation by using... 

Control over the wettability of reservoir rocks is of crucial importance for enhancing oil and gas recovery. In order to develop chemicals for controlling the wettability of reservoir rocks, we present a study of functionalized silica nanoparticles as candidates for wettability alteration and improved gas recovery applications. In this paper, properties of fluorinated silica nanoparticles were investigated in water or decane-loaded pores of mineral silica using molecular dynamics simulation. Trifluoromethyl groups as water and oil repellents were placed on the nanoparticles. Simulating a pore in the presence of trapped water or decane molecules leads to liquid bridging for both of the... 

Fibrillation of amyloid beta (Aβ) peptide is the hallmark of Alzheimer's disease. Given that interactions at the bio–nano interface affect the fibrillation tendency of this peptide, an understanding of the interactions at Aβ peptide–inorganic surfaces on the microscopic level can help to determine the possible neurotoxicity of nanoparticles. Here, the interactions between a fibril-forming peptide, Aβ25–35, and (111) and (100) facets of gold and silver surfaces have been studied by conducting atomistic molecular dynamics simulations. The obtained results indicate that the adsorption onto gold and silver surfaces force the peptide into the β-sheet-rich conformations, which is prone to... 

Nanomanipulation as a new emerging area enables precise manipulation, interaction and control at the nanoscale. Currently, the modeling schemes are based on continuum mechanics approaches. A main consideration in the nanomanipulation process is the fact that surface attraction forces are greater than gravitational forces at the nanoscale. In other words, surface area properties dominate volume properties. Especially at the nanoscale (i.e. the manipulation of fine nanoparticles with size of about 5 nm) the physical phenomena have not been completely understood. Along this line of reasoning, the aim of this paper is to conduct an atomistic investigation of physical interaction analysis of... 

Molecular dynamics (MD) simulation was utilized to study the role of asphaltene extracted from Gachsaran (an Iranian oilfield) at the synthetic oil-water interface. In agreement with experimental data, IFTs predicted by MD simulation for heptol/brine system showed a minima at around 50 vol.% n-heptane, reflecting the highest contribution of asphaltene into the interface. At greater n-heptane fractions, IFT was increased steadily. Simulation results suggest the asphaltene propensity for remaining in the bulk heptol phase rather related to the fraction of toluene in the mixture. Heptol ingredients, i.e., toluene and heptane, act differently with respect to asphaltene, where former tends to...