Sharif Digital Repository

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... 

An accurate molecular dynamics simulation of the nanocavity flow cannot be achieved without considering correct thermal treatments for the molecules both distributed in the flow and located at the cavity walls and without including their interactions correctly. In this study, we specify constant temperature at the nanocavity vertical walls; however, we examine three different thermal wall models, including a rigid wall, a controlled-temperature flexible wall, and a noncontrolled-temperature flexible wall, to model the horizontal wall behaviors. Comparing the results of these three models with each other, it is possible to evaluate the effect of wall model on the resulting temperature and... 

Water molecules are one of the important molecules in nanofluidics. Its structure and its behavior can change with Temperature and cut-off distance parameters. In this study temperature and cut-off distance effects on the nano-scale water molecules behavior are investigated by molecular dynamics simulations. Many water molecular models have been developed in order to help discover the structure of water molecules. In this study, the flexible three centered (TIP3P-C) water potential is used to model the inter- and intramolecular interactions of the water molecules. In this simulation, we have been studied 512 water molecules with periodic boundary conditions and in a simulation box with 25... 

This Paper presents the simulation of electroosmotic flow in nanochannels using the dissipative particle dynamics (DPD) method. Most of the past electroosmotic phenomenon studies have been carried out using the continuum flow assumptions. However, there are many electroosmotic applications in nanoscales NEMS and microscales MEMS, which need to be treated using non-continuum flow assumptions. We simulate the electroosmotic flow within the mesoscopic scale using the DPD method. Contrary to the ordinary molecular dynamics method, the DPD method provides less computational costs. We will show that the current DPD results are in very good agreement with other available non-DPD results. To expand... 

In this study, we apply a novel numerical technique for modeling the propagation of mechanical wave in the human arteries using the multiscale method. We define a particle region characterized by molecular dynamics (MD) method which is surrounded by a continuous region characterized by a finite element (FE) method. The interface between the two models are defined so as to minimize spurious reflections at the interface. This is a preliminary work for the modeling of the mechanical stability of atherosclerosis plaques using multiscale method. The model offered has extensive application in cell mechanics  

We use the dissipative particle dynamics (DPD) method to simulate the non-Newtonian electroosmotic flow (EOF) through nanochannels. Contrary to a large amount of past computational efforts dedicated to the study of EOF profile, this work pays attention to the EOF of non-Newtonian fluids, which has been rarely touched in past publications. Practically, there are many MEMS/NEMS devices, in which the EOF behaviour should be treated assuming both non-continuum and non-Newtonian conditions. Therefore, our concern in this work is to simulate the EOF through nanochannels considering both non-Newtonian fluid properties and non-continuum flow conditions. We have chosen DPD as our working tool because... 

The use of superhydrophobic surfaces is one the most promising methods for reducing the friction and increasing the flow rate in fluid transfer systems. Because in such systems the surface structure plays a key role, in this study, we explore the performance of the hierarchical nanostructures. These nanostructures are inspired by the superhydrophobic surface of the lotus leaf. We consider a flow between two walls with hierarchical nanostructures and simulate the system via the molecular dynamics method. The size of the nanostructures and the distance between them have been studied to find whether a design with a maximum flow rate exists. The nanostructures have two parts, a bigger part on... 

The use of superhydrophobic surfaces is one the most promising methods for reducing the friction and increasing the flow rate in fluid transfer systems. Because in such systems the surface structure plays a key role, in this study, we explore the performance of the hierarchical nanostructures. These nanostructures are inspired by the superhydrophobic surface of the lotus leaf. We consider a flow between two walls with hierarchical nanostructures and simulate the system via the molecular dynamics method. The size of the nanostructures and the distance between them have been studied to find whether a design with a maximum flow rate exists. The nanostructures have two parts, a bigger part on... 

The ever-increasing growth of nano-technology has elevated the necessity for development of new computational methods that are capable of evaluating large systems at nano-scale. The existing techniques, such as the molecular dynamics, lack the ability to simulate large systems of practical size and time scales. In order to provide a realistic simulation of large models, the multi-scale methods such as coarse-graining, have therefore become very popular. The coarse-grained models have mostly been used to simulate large biomolecules, such as proteins, lipids, DNA and polymers. In this paper, the Iterative Boltzmann Inversion (IBI) coarse-graining technique is applied to FCC nano-crystals; the... 

Superhydrophobic surfaces have been used for reducing friction in micro- and nanochannels. In the present work, water flow between two carbon walls with nanostructures made of poly(N-isopropylacrylamide) via the molecular dynamics method has been studied. The structure of this polymer can change based on the temperature of the environment, so that by increasing the temperature the structure becomes hydrophobic. This property has been studied and the effect of multiple factors on the slip length is presented. The effects of the number of monomers in the polymer, the distance between the polymers, and the temperature on the flow field are investigated. The results reveal that the slip length... 

Understanding the motion characteristics of fullerene clusters on the graphene surface is critical for designing surface manipulation systems. Toward this purpose, using the molecular dynamics method, we evaluated six clusters of fullerenes including 1, 2, 3, 5, 10, and 25 molecules on the graphene surface, in the temperature range of 25 to 500 K. First, the surface motion of clusters is studied at 200 K and lower temperatures, in which fullerenes remain as a single group. The trajectories of the motion as well as the diffusion coefficients indicate the reduction of surface mobility as a response to the increase of the fullerene number. The clusters show normal diffusion at the temperature... 

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... 

Models capable of accurate simulation of the microcantilever dynamics coupled with complex tip-sample interactions are essential for interpretation of the imaging results in non-contact atomic force microscopy (AFM). In the present research, a combination of finite element and molecular dynamics methods are used for modelling the AFM system to overcome the drawbacks of conventional approaches that use a lumped system with van der Waals interaction. To illustrate the ability of the proposed scheme in providing images with atomic resolution, some simulations have been performed. In the conducted simulations, a diamond tip is interacting with nickel samples having different surface plane... 

Predominance of nano-scale effects observed in material behavior at small scales requires implementation of new simulation methods which are not merely based on classical continuum mechanic. On the other hand, although the atomistic modeling methods are capable of modeling nano-scale effects, due to the computational cost, they are not suitable for dynamic analysis of nano-structures. In this research, we aim to develop a continuum-based model for nano-beam vibrations which is capable of predicting the results of molecular dynamics (MD) simulations with considerably lower computational effort. In this classical-based modeling, the surface and core regions are taken to have different... 

The Poiseuille flow through slit-like nanochannels is investigated using the nonequilibrium molecular dynamics simulations. To drive a dense flow through the channel, we use two self-adjusting vertical plates strategy. These plates force the liquid to flow through the nanochannel under adjustable inlet and outlet boundary conditions. Comparing with the dual-control-volume grand-canonical molecular dynamics method, the current strategy provides many advantages. The current strategy does not need particle insertion and deletion, therefore, the system dynamics would not be affected at all. Moreover, the number of particles in the simulation system is fixed due to inserting the two... 

The crack growth process in columnar nanocrystalline samples is simulated using the molecular dynamics method. The effects of grain size, grain boundary, crystallographic orientation and crack tip position on the crack growth behavior are investigated. Different sets of samples with mean grain sizes ranging from 4 nm to 14 nm are prepared. Samples with a similar number of grains and identical dimensions are considered for examining the impact of grain boundary and crystallographic orientation. To assess the effect of the grain boundary, no constraint is considered on the position and orientation of grains, while only the grain orientations are changed to examine the effect of... 

In this paper, the uniaxial cold compaction process of metal nano-powders is numerically analyzed through the Molecular Dynamics (MD) method. The nano-powders consist of nickel and aluminum nano-particles in the pure and mixed forms with distinctive contributions. The numerical simulation is performed using the different number of nano-particles, mixing ratios of Ni and Al nano-particles, compaction velocities, and ambient temperatures in the canonical ensemble until the full-dense condition is achieved. In the MD analysis, the inter-atomic interaction between metal nano-particles is modeled by the many-body EAM potential, and the interaction between frictionless rigid die-walls and metal...