Sharif Digital Repository

Mg-based metallic glasses are promising materials for biodegradable implants. Understanding atomistic mechanism behind glass formation in these glasses plays a critical role in developing them for future applications. In the present work, we perform a set of molecular dynamics simulations to study structural origin behind glass form ability of Mg-based Mg-Zn metallic glasses at a wide range of compositions. Pair distribution function, Voronoi tessellation and dynamical analysis were adopted to characterize local structures in these glasses. Structural analysis was performed considering both topological and chemical short-range orders. It was found that structure of Mg-Zn metallic glasses... 

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... 

In the present study, we employ all-atom molecular dynamics simulations to investigate the dynamic behaviors and structural properties of the native and modified cellulose chains in the bulk, aqueous, and organic media. Particular attention has been directed to the role of different hydrophobic and hydrophilic functional groups as linear and branched aliphatic and also cyclic pendent groups on the solubility and packing of the cellulose chain. The various properties related to density profile, mean squared displacement, intramolecular entropy, radius of gyration, and radial distribution function were calculated. The results showed that the chain tendency toward crystallinity decreased when... 

Molecular dynamics, MD, simulation of calcite (CaCO3) is selected to compare the p-v-T behaviour of some universal equations of state, UEOS, for the temperature range 100 K ≤ T 800 ≤ K, and pressures up to 3000 kbar. The isothermal sets of p-v-T data generated by simulation were each fitted onto some three- and two-parameter EOSs including Parsafar and Mason (PM), Linear Isotherm Regularity (LIR), Birch-Murnaghan (BM), Shanker, Vinet, Baonza and Modified generalized Lennard-Jones (MGLJ) EOSs. It is found that the MD data satisfactorily fit these UEOS with reasonable precision. Some features for a good UEOS criteria such as temperature dependencies of coefficients, pressure deviation,... 

This research provides an atomistic picture of the role of ions in modulating the microstructural features of an oil-contaminated calcite surface. This is of crucial importance for the rational design of ion-engineered waterflooding, a promising technique for enhancing oil recovery from carbonate reservoirs. Inspired by a conventional lab-scale procedure, an integrated series of molecular dynamics (MD) simulations were carried out to resolve the relative contribution of the major ionic constituent of natural brines (i.e., Na+, Cl-, Mg2+, Ca2+, and SO42-) when soaking an oil-bearing calcite surface in different electrolyte solutions of same salinity, namely, CaCl2, MgCl2, Na2SO4, MgSO4, and... 

Introduction: Nanotube-based drug delivery systems have received considerable attention because of their large internal volume to encapsulate the drug and the ability to penetrate tissues, cells, and bacteria. In this regard, understanding the interaction between the drug and the nanotube to evaluate the encapsulation behavior of the drug in the nanotube is of crucial importance. Methods: In this work, the encapsulation process of the cationic antimicrobial peptide named cRW3 in the biocompatible boron nitride nanotube (BNNT) was investigated under the Canonical ensemble (NVT) by molecular dynamics (MD) simulation. Results: The peptide was absorbed into the BNNT by van der Waals (vdW)... 

The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned... 

In this paper, a multiplate nonlocal shear model and molecular dynamic simulations are presented to investigate the effects of interlayer shear and nonlocality on the natural frequencies of multilayer graphene sheets (MLGSs). From one aspect in the optimal design of such structures, the interaction between graphene layers, which can significantly vary the static and dynamic behavior due to lack of solidity of layers stack, should be considered. On the other hand, it is requied that the nonlocality phenomenon which has an effective role in the mechanical analysis of nanostructures is taken into account. To this aim, the equation of motion along with corresponding boundary conditions is... 

SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans... 

The high concentration of zinc metal ions in Aβ aggregations is one of the most cited hallmarks of Alzheimer's disease (AD), and several substantial pieces of evidence emphasize the key role of zinc metal ions in the pathogenesis of AD. In this study, while designing a multifunctional peptide for simultaneous targeting Aβ aggregation and chelating the zinc metal ion, a novel and comprehensive approach is introduced for evaluating the multifunctionality of a multifunctional drugs based on computational methods. The multifunctional peptide consists of inhibitor and chelator domains, which are included in the C-terminal hydrophobic region of Aβ, and the first four amino acids of human albumin.... 

Lithium ions play a crucial role in the energy storage industry. Finding suitable lithium-ion-conductive membranes is one of the important issues of energy storage studies. Hence, a perovskite-based membrane, Lithium Lanthanum Titanate (LLTO), was innovatively implemented in the presence and absence of solvents to precisely understand the mechanism of lithium ion separation. The ion-selective membrane’s mechanism and the perovskite-based membrane’s efficiency were investigated using Molecular Dynamic (MD) simulation. The results specified that the change in the ambient condition, pH, and temperature led to a shift in LLTO pore sizes. Based on the results, pH plays an undeniable role in... 

Understanding the effect of crystallographic orientation on the twinnin/detwinning mechanisms in NiTi shape memory alloys at an atomistic scale can help to control and tune the mechanical properties and failure behavior of such materials. In this work, we employed classical molecular dynamics (MD) and density functional theory (DFT) computational methods to better understand how twinning and detwinning occurs through a combination of slip, twin, and shuffle on 〈0 1 0〉, 〈1 1 0〉, and 〈1 1 1〉 crystallographic orientations under uniaxial tensile test. Elastic constants including Young's Modulus (E), Bulk modulus (B), Poisson's ratio (ν), and Shear Modulus (G) are obtained and computed for... 

Nanocars have been proposed to transport nanomaterials on the surface. Study of the mechanism of the motion of nanocars has attracted a lot of interests due to the potential ability of these nano-vehicles in the construction of nanostructures with bottom-up approach. Using molecular dynamics simulations, we study the motion of two nano-vehicles named “Nanocar” and “Nanotruck” on hexagonal boron-nitride monolayer. The obtained results reveals that, boron-nitride is an appropriate option to obtain higher mobility of nanocars compared with metal substrates. Considering different temperatures reveals that nanocars start to move on the BN at 200 K, while long range motions are observed at 400 K... 

In this paper, a multiplate nonlocal shear model and molecular dynamic simulations are presented to investigate the effects of interlayer shear and nonlocality on the natural frequencies of multilayer graphene sheets (MLGSs). From one aspect in the optimal design of such structures, the interaction between graphene layers, which can significantly vary the static and dynamic behavior due to lack of solidity of layers stack, should be considered. On the other hand, it is requied that the nonlocality phenomenon which has an effective role in the mechanical analysis of nanostructures is taken into account. To this aim, the equation of motion along with corresponding boundary conditions is... 

This paper focuses on the influences of the tip mass ratio (the ratio of the tip mass to the cantilever mass), on the excitation of higher oscillation eigenmodes and also on the tip-sample interaction forces in tapping mode atomic force microscopy (TM-AFM). A precise model for the cantilever dynamics capable of accurate simulations is essential for the investigation of the tip mass effects on the interaction forces. In the present work, the finite element method (FEM) is used for modeling the AFM cantilever to consider the oscillations of higher eigenmodes oscillations. In addition, molecular dynamics (MD) is used to calculate precise data for the tip-sample force as a function of tip... 

The effects of incorporating the ester functional group (-C=OO-) into the side chain of the 1-alkyl-3-methylimidazolium cation ([C1COOCnC1im]+, n = 1, 2, 4) paired with [Br]-, [NO3]-, [BF4]-, [PF6]-, [TfO]-, and [Tf2N]- anions on the various thermodynamic properties and interaction energies of these biodegradable ionic liquids (ILs) were investigated by means of molecular dynamics (MD) simulations combined with ab initio calculations in the temperature range of 298-550 K. Excluding the simulated density, the highest values of the volumetric properties such as molar volume, isobaric expansion coefficient, and isothermal compressibility coefficient can be attributed to the largest cation... 

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... 

We investigate heat transfer between parallel plates separated by liquid argon using two-dimensional molecular dynamics (MD) simulations incorporating with 6-12 Lennard-Jones potential between molecule pairs. In molecular dynamics simulation of nanoscale flows through nanochannels, it is customary to fix the wall molecules. However, this approach cannot suitably model the heat transfer between the fluid molecules and wall molecules. Alternatively, we use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the... 

As the delay time and hence nuclei formation play a crucial role in the pathophysiology of sickle cell disease, MD simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations have been performed on three systems of hemoglobin; namely dimer of hemoglobin with valine (Hb S), tryptophan (Hbβ6W), and phenylalanine (Hbβ6F) at β6 position. The structural changes due to these aromatic substitutions are investigated. It is shown that β subunits have significant impact on the differences between a dimer and other crystal structures. Transition from a dimer to polymer for Hb S system affects the donor molecule more than that of the acceptor. In the case of donor and... 

In this article, a multiscale modeling procedure is implemented to study the effect of interphase on the Young's modulus of CNT/polymer composites. For this purpose, a three-phase RVE is introduced which consists of three components, i.e., a carbon nanotube, an interphase layer, and an outer polymer matrix. The nanotube is modeled at the atomistic scale using molecular structural mechanics. Moreover, three-dimensional elements are employed to model the interphase layer and polymer matrix. The nanotube and polymer matrix are assumed to be bonded by van der Waals interactions based on the Lennard-Jones potential at the interface. Using this Molecular Structural Mechanics/Finite Element...