Sharif Digital Repository

The effect of temperature on the noncontact atomic force microscopy (NC-AFM) surface imaging is investigated with the aid of molecular dynamics (MD) analysis based on the Sutton-Chen (SC) interatomic potential. Particular attention is devoted to the tip and sample flexibility at different temperatures. When a gold coated probe is brought close to the Au (001) surface at high temperatures, the tip and surface atoms are pulled together and their distance becomes smaller. The tip and sample atoms displacement varies in the different environment temperatures and this leads to the different interaction forces. Along this line, to study the effect of temperature on the resulting images, we have... 

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  

Based on the fact that the manipulation of fine nanoclusters calls for more precise modelling, the aim of this paper is to conduct an atomistic investigation for interaction analysis of particle-substrate system for pushing and positioning purposes. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviours. Performing the planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is reduced extremely in comparison to 3D simulations. To perform this study, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behaviour of the aforementioned system. Pushing of... 

We investigate the effect of wall roughness on water electrolyte transport characteristics at different temperatures through carbon nanotubes by using nonequilibrium molecular dynamics simulations. Our results reveal that shearing stress and the nominal viscosity increase with ion concentration in corrugated carbon nanotubes (CNTs), in contrast to cases in smooth CNTs. Also, the temperature increase leads to the reduction of shearing stress and the nominal viscosity at moderate degrees of wall roughness. At high degrees of wall roughness, the temperature increase will enhance radial movements and increases resistance against fluid motion. As the fluid velocity increases, the particles do not... 

We investigate the effect of wall roughness on water electrolyte transport characteristics at different temperatures through carbon nanotubes by using nonequilibrium molecular dynamics simulations. Our results reveal that shearing stress and the nominal viscosity increase with ion concentration in corrugated carbon nanotubes (CNTs), in contrast to cases in smooth CNTs. Also, the temperature increase leads to the reduction of shearing stress and the nominal viscosity at moderate degrees of wall roughness. At high degrees of wall roughness, the temperature increase will enhance radial movements and increases resistance against fluid motion. As the fluid velocity increases, the particles do not... 

In this study, sandwich beam model (SM) is proposed for free vibration analysis of bilayer graphene nanoribbons (BLGNRs) with interlayer shear effect. This model also takes into account the intralayer (in-plane) stretch of graphene nanoribbons. The molecular dynamics (MD) simulations using the software LAMMPS and Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential are done to validate the accuracy of the sandwich model results. The MD simulation results include the two first frequencies of cantilever BLGNRs with different lengths and two interlayer shear moduli, i.e., 0.25 and 4.6GPa. These two interlayer shear moduli, 0.25 and 4.6GPa, can be obtained by sliding a small... 

A molecular dynamics simulation of the shock-wave propagation in the face-centered cubic (FCC) structured C60 fullerene along the <100>, <110> and <111> crystallographic directions is performed. For this purpose, the response of the material under different shock-wave loadings is studied through Hugoniot curves. Three regimes of the material behavior have been observed from fully elastic to elastic-plastic to plastic. The Hugoniot elastic limit and the phase transition are also investigated along different crystallographic directions. It is shown that the shock wave travels faster along the <110> and <111> directions than in the <100> direction in the material. Comparing the results with the... 

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... 

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were... 

Fire events and the related toxicants such as CO are responsible for many fatalities in the current century. These hazardous events are much more dangerous when they occur in enclosed spaces. In the present study, a theoretical relation is developed for horizontal distribution of CO in a large tunnel fire. Then, the developed criterion is used to study the effect of some rudimentary parameters such as the heat release rate (HRR) of fire and tunnel's aspect ratio (AR) on CO and temperature stratification. Theoretical results of various heat release rates and aspect ratios for horizontal distribution of CO are compared with numerical results using fire dynamics simulator (FDS5.5). It is found... 

One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of... 

A brass vortex tube with changeable parts is used to obtain the optimum nozzle intake numbers and diameter. The effects of inlet pressure and CF (cold fraction) are also investigated. Results illustrate that increasing the number of nozzles causes a temperature drop and the optimum nozzle diameter corresponds to quarter of vortex tube diameter. The distance between cold end orifice and nozzle intakes is investigated in this work and it is found that for a better performance, this distance should be decreased. A series of experiments conducted to investigate the CF effect on VT performance and an optimum amount for this parameter is found. A two-dimensional computational fluid dynamics... 

We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, the subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein-lipid complexes within the membrane voids,... 

A molecular dynamics (MD) simulation is employed to study the phase transition process in argon induced by shock wave transmission. Deriving the relation between the shock and piston velocities, the theoretical equation of state for argon is presented. Also, argon equation of state is obtained by measuring the quantities directly from simulations to be able to detect the phase transitions. The phase transition is also detected by using argon phase diagram and free energy calculations. A comparison shows good agreement between the theoretical and MD results for the phase transitions. Based on these simulations, it is concluded that under a shock wave transmission with suitable energy, the... 

The overall design of cold gas propulsion systems is pretty complicated when considering the mission requirements, operating constraints and functional limitations imposed by the mechanical components. To address this complication, a precise design process is proposed, which attempts to optimize the cost of operation as well as to minimize the waste volume and weight by using multi-objective trade-off analysis. This analysis is based on a set of ordinary differential equations that are solved iteratively to describe the optimal behavior of the system. Therefore, a numerical code is being developed to give insight on the design sensitivity with respect to uncertainties on the design... 

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the... 

Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used... 

The current paper uses the Extended Kantorovich Method (EKM) to analytically solve the problem of squeezed film damping in micromirrors. First a one term Galerkin approximation is used and following the extended Kantorovich procedure, the solution of the Reynolds equation which governs the squeezed film damping in micromirrors is reduced to solution of two uncoupled ordinary differential equation which can be solved iteratively with a rapid convergence for finding the pressure distribution underneath the micromirror. It is shown that the EKM results are independent of the initial guess function. It is also shown that EKM is highly convergent and practically one iterate is sufficient for... 

The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use...