Sharif Digital Repository

The Cauchy-Born hypothesis has been used to concurrently bridge atomistic information to continuum model. It has been a prevalent assumption in computational nano-mechanics during the past decade. This kinematic assumption relates the deformation of the continuum to the deformation of its underlying crystalline structure. The main objective of this paper is to investigate the validity of this hypothesis by means of direct atomistic simulations and the continuum mechanic calculations. In fact, we intend to determine under which strain or stress state the crystalline structure undergoes inhomogeneous deformation due to a small perturbation of the homogeneously deformed system. Two failure... 

A coiled carbon nanotube (CCNT) can be formed from the distortion of parent toroidal carbon nanotube with a uniform pitch length and a uniform spring rise angle. In this research molecular dynamics simulation was carried out to assess the tensile properties of three CCNT having indexes of (3,3), (4,4), and (5,5). The results indicated that Stone-Wales defects are necessary for thermodynamic stability of the CCNTs. The stress-strain curves showed that the yield stress, yield strain, and failure strain are decreased with increase in temperature. The force-displacement curves revealed that the spring constant of these materials is highly depended on the tube diameter and rising angle, while it... 

Desalination of sea saline water seems a successful solution to supply clean water. For desalination, novel nanoporous membranes have been proposed as a substitute for the classic reverse osmosis (RO) membranes. The one-atom-thick graphyne membrane has shown great potential in water desalination. By applying functional groups (FGs) into the pores of the monolayer graphyne membranes, the water permeability and the ion rejection were passively increased. The effects of applying various FGs such as Hydrogen, Fluorine, Carboxyl and Amine, effect of the salt concentration, the applied pressure, and the effective diameter of the graphyne pores were determined by molecular dynamics (MD)... 

The efficiency of water flooding methods is known to improve by applying ion-tuned water injection. Although there is a consensus that such improvement happens through reversing reservoir wettability characteristics to more water-wet state, the true impact of ions is still ambiguous among contradictory debates. The well-known molecular dynamics (MD) simulation techniques would shed light on such ambiguities to gain deep atomic-scale understanding of the process. Results from MD simulations show that the presence of Na+ and Cl¯ ions leads to the formation of an electrical double layer in adjacency of calcite surface while Mg2+ ions dominantly make complexes with hydrocarbons throughout the... 

Molecular dynamics simulation was applied in this study to scrutinize the interfacial properties of water nano-film confined between calcite mineral and hydrocarbon layer, as two intrinsically different media. Such system resembles the environment experienced by water molecules in the pore spaces of underground carbonate reservoirs. The interplay between water film and confining phases, oil and mineral, strongly influences hydrocarbon production process; however, there is a lack of detailed understanding of the involved interactions. MD simulations indicate development of several layers with different water densities in the confined brine. Water molecules form well-ordered structure in three... 

Analytical and molecular dynamics simulation approaches are used in this paper to study free-vibration behavior of multilayer graphene-based nanoresonators considering interlayer shear effect. According to experimental observations, the weak interlayer van der Waals interaction cannot maintain the integrity of carbon atoms in the adjacent layers. Hence, it is vital that the interlayer shear effect is taken into account to design and analyze multilayer graphene-based nanoresonators. The differential equation of motion and the general form of boundary conditions are first derived for multilayer graphene sheets with rectangular shape using the Hamilton’s principle. Then, by pursuing an... 

The main concern in Molecular Dynamics (MD) simulations is the computational cost, and coarse-graining methods accelerate simulations by reducing the degrees of freedom in the system. Yet, the utilization of these methods should be carefully followed. In this paper, we presented an energy-based coarse-graining method for Tersoff and Stillinger-Weber potential functions. The presented coarse-graining method is based on the domain mapping and modification of potential function. The focus of this paper is on Carbon and Silicon materials; however, this method can be applied to model other materials for which Tersoff and Stillinger-Weber potentials are defined. This method has been validated by... 

Metallic nanoclusters are interesting because of their utility in catalysis and sensors. The thermal and physical characteristics of metallic Pt nanoclusters with different sizes were investigated via molecular-dynamics simulations using Quantum Sutton-Chen (QSC) potential. This force field accurately predicts solid and liquid states properties as well as melting of the bulk platinum. Molecular dynamic simulations of Pt nanoclusters with 256, 456, 500, 864, 1372, 2048, 2916, 4000, 5324, 6912, 8788 atoms have been carried out at various temperatures. The Pt-Pt radial distribution function, internal energy, heat capacity, enthalpy, entropy of the nanoclusters were calculated at some... 

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... 

A very important part of the living cells of biological systems is the lipid membrane. The mechanical properties of this membrane play an important role in biophysical studies. Investigation as to how the insertion of additional phospholipids in one leaflet of a bilayer affects the physical properties of the obtained asymmetric lipid membrane is of recent practical interest. In this work a coarse-grained molecular dynamics simulation was carried out in order to compute the pressure tensor, the lateral pressure, the surface tension and the first moment of lateral pressure in each leaflet of such a bilayer. Our simulations indicate that adding more phospholipids into one monolayer results in... 

In this paper the classical molecular structural mechanics model of graphene is modified to improve its accuracy for the analysis of transverse deformations. To this aim, a sample graphene sheet under a uniform pressure is modeled by both molecular dynamics and molecular structural mechanics methods. The sectional properties of the beam element, by which the covalent bonds are modeled, are modified such that the difference between the results of the molecular mechanics model and molecular dynamics simulation is minimized. Using this modified model, the buckling behavior of graphene under a uniform edge pressure is investigated subjected to different boundary conditions for both zigzag and... 

Computational methods to understand interactions in bio-complex systems are however limited to time-scales typically much shorter than in Nature. For example, on the nanoscale level, interactions between nanoparticles (NPs)/molecules/peptides and membranes are central in complex biomolecular processes such as membrane-coated NPs or cellular uptake. This can be remedied by the application of e.g. Jarzynski's equality where thermodynamic properties are extracted from non-equilibrium simulations. Although, the out of equilibrium work leads to non-conservative forces. We here propose a correction Pair Forces method, that removes these forces. Our proposed method is based on the calculation of... 

Various thermodynamic and structural properties of amino acid ionic liquids (AAILs), comprising 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C 2 OHmim] + ) cation mixed with Glycinate [Gly], Serinate [Ser], Alaninate [Ala], and Prolinate [Pro] AA anions are explored using molecular dynamic (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis. In general, the simulated thermodynamic results are in good agreement with the reported experimental data. Structural dependence of vdW- and electrostatic energies of AAILs is [Pro] > [Ala] > [Ser] > [Gly] and [Gly] > [Ala] > [Pro] > [Ser], respectively. The similar trend of electrostatic energies is found for their interaction... 

In this paper, a hierarchical multi-scale technique is developed to investigate the thermo-mechanical behavior of nano-crystalline structures in the presence of edge dislocations. The primary edge dislocations are generated by proper adjustment of atomic positions to resemble discrete dislocations. The interatomic potential used to perform atomistic simulation is based on the Finnis-Sinclair embedded-atom method as many-body potential and, the Nose-Hoover thermostat is employed to control the effect of temperature. The strain energy density function is obtained for various representative volume elements under biaxial and shear loadings by fitting a fourth order polynomial in the atomistic... 

2D minerals are among key elements of advanced systems, but the need for understanding their interactions/reactions with materials and systems in which they are involved necessitates tracking their molecular and atomic monitoring. Zeolitic structures are microporous materials formed in the nature through volcanic activities or synthesis. Because of their outstanding physicochemical properties like cation exchange capacity and excellent adsorption properties, zeolites have found application in diverse chemical processes, e.g., gas adsorption, water purification, and wastewater treatment. Prediction of zeolite performance for a targeted application saves time and expense as such projection... 

Seawater, which has been frequently applied in cooling and injection water systems, imposes severe pitting corrosion to mild steel. Addition of green and sustainable inhibitors based on renewable sources is one of the promising methodologies for restricting metal corrosion in chloride-containing electrolytes. In this study, for the first time, from both theoretical and experimental faces, the role of Juglans regia green fruit shell (JRS) extract as a sustainable potent corrosion inhibitor for mild steel was studied. The chemical structure of the JRS extract was deliberated by Fourier transform infrared spectroscopy (FT-IR). By electrochemical techniques including polarization, EIS and...