Ionic liquids which are known as green solvents have specific physical and chemical properties and include great potential applications in various industries. In other hand, carbon nanotubes due to their outstanding mechanical, thermal and electronic properties have been extensively studied during the last two decades. It has been indicated that the systems containing ionic liquids and other components such as nanostructures and carbon nanotubes have properties which have reduplicated the importance of ionic liquids and carbon nanotubes. In the present paper, recent investigations on the systems containing various ionic liquids and carbon nanotubes by molecular dynamics simulation is reviewed and simulation details and computational methods for performing molecular dynamics simulation of some systems are presented. Using molecular dynamics simulation, it can be demonstrated how ionic liquids disperse the carbon nanotubes. Also, molecular dynamics simulation can be used for investigating the structural and dynamical behaviors of confined ionic liquids inside the carbon nanotubes.

Molecular dynamics simulations are used to study the mechanical properties of single-walled carbon nanotube reinforced polyvinyl pyrrolidone matrix. The effects of nanotube diameter and chirality on the elastic moduli of carbon nanotube reinforced nanocomposites are studied. It is shown that zigzag nanotube reinforced polymers have higher longitudinal elastic modulus than their armchair counterparts. For example, embedding (5,5) and (9,0) SWCNTs whose diameters are close to eachother in polymer matrix lead to the elastic modulus of 78.43 and 81.55 GPa, respectively. Besides, increasing diameter results in decreasing longitudinal Young’s modulus. Because of disability of the existing finite element approaches to study the behavior of polymers containing atom types other than carbon, based on molecular dynamics simulations, a finite element method is proposed. The results of the proposed method are in good agreement with the results of molecular dynamics simulations. The correlation coefficient of diameter and Young's modulus obtained from molecular dynamics simulations is equal to -0.8375. Moreover, the correlation coefficient of diameter and Young's modulus computed by finite element method is obtained as -0.8781.

Molecular dynamics simulation is an appropriate method for microscpoic modeling of materials and is widely used in several fields of science and technology. Experimental measurement of thermodynamic properties of many materials is not economic due to time consuming and high cost of instruments. Using simulation methods such as molecular dynamics, thermodynamic properties of these materials can be computed and compared with experimental data. One of the important arguments in molecular dynamics simulation is application of appropriate combination ruls for dissimilar pair interactions. In this study, volumetric properties of 1-butyl-3-methylimidazolium hexafluorophosphate inonic liquid, acetonitrile, and their mixture are studied by molecular dynamics simulation and using three different combination rules for dissimilar pair interactions. Then the results are compared with experimental data inorder to evaluate validity of the applied combination rules.

The interactions of 6twk protein with Ectoine drug, Polyamidoamine (PAMAM) /Ectoine and histidine modified PAMAM/Ectoine were investigated using molecular docking and molecular dynamics simulation. Based on the results of molecular docking increasing of binding energy and the decreasing of inhibition constant of the compounds, increase their inhibitory activity. Protein stability in complex with these ligands was investigated using molecular dynamics simulation approach. Results molecular dynamics simulation displayed that histidine modified PAMAM/Ectoine with the lowest mean square displacement (MSD) is the better suitable to deliver the ectoine drug. This causes the most controlled/diffusion of ectoine drug molecule. So, histidine modified PAMAM/Ectoine conjugate can be introduced for further investigations on interaction of ectoine drug and 6twk protein.

In this research, the molecular dynamics simulation for interactions between molecules of meclortamine in pure state, in aqueous medium, with single-walled carbon nanotubes of the armchair type (6, 6) and with carbon nanotubes functionalized with (COOH) has been investigated. Using the OPLS force field, molecular dynamics simulations were performed to determine the structural and dynamic properties of this drug with nanotubes. Using molecular dynamics simulations of microscopic properties and dynamic properties such as density, total energy, and radial distribution function (RDF), mean time-dependent displacement squares (MSD) and diffusion of drug molecules in aqueous medium with carbon nanotubes and functionalized nanotubes have been calculated. The results of RDF showed that the adsorption between the molecules of mechlorethamine on the surface of carbon nanotubes is affected by the functional group. Also, the results of MSD and RDF indicate that hydrogen bonds play an essential role in the structural and dynamic properties of this molecule.

In this study, phosphorus trichloride (PCl3) and phosphorus triiodide (PI3) as the condensed inorganic materials were investigated based on the molecular dynamics simulation. To this purpose, molecular dynamics simulations were performed by applying force field parameters derived from the quantum chemistry approach. The potential energy data were computed at the B3LYP/6-31+G (d) and B3LYP/dgdzvpd levels of theory for different configurations of PCl3 and PI3, respectively. To determine force field parameters, a four-site all-atom force field model was used to correlate the potential energy data. Therefore, the force field parameters were applied to perform the molecular dynamics simulations. The MD simulations were performed to obtain the atomic number density, enthalpy, heat capacity, and radial distribution function in the NPT and NVT ensembles for PCl3 and PI3 dimers. There is a good consistency between the experimental data and simulation results over a wide range of experimental conditions.

The molecular dynamics simulation technique can be used to examine systems that are difficult to achieve the experimental The molecular dynamics simulation technique can be used to examine systems that are difficult to achieve the experimental values of some of their characteristics in unconventional conditions. In this work, molecular dynamics simulation methods of removal of heavy metals (zinc and copper) were evaluated by zeolites. The structural parameters, the adsorption of heavy metals of zinc and copper well as the adsorption energies were analyzed. Calculating the mean square displacements on zeolites, the amount of diffusion coefficient was calculated. The amount of diffusion coefficient in zeolite A is less than that of zeolite X, which indicates that the metal has less diffusion in zeolite and remains in the effluent and its removal by zeolite A is better. Heavy metal adsorption efficiency is 99.9% based on simulation and experimental data. The results show that Zn removal from zeolite surface requires more energy than copper since absorbed ions exhibit high stability at adsorbent surfaces.

In this article, the study of the time history of the displacement of the central point of single-layer graphene nanosheets under the passage of moving mass has been studied. In order to analyze the passage of the nanoparticle on the graphene sheet, the non-local theory of elasticity was used and finally the governing equations were extracted by the special function expansion method. Also, by using molecular dynamics simulation, the time history of the displacement of the central point of single-layer graphene sheets under different boundary conditions and the passage of metal nanoparticles with different geometries (such as square cubes, spheres and blades) along the length and through the middle of these sheets, including There are parameters that are effective in changing the behavior of graphene, and the results of theoretical calculations have been compared with the relevant molecular dynamics simulations. In addition, the results of the molecular dynamics simulation for a single-layer graphene sheet have been compared with the results of the corresponding non-local elasticity theory, and a non-local coefficient has been proposed for the model. As a result, the comparison of the results obtained from the relevant theory and simulation will provide more confidence to validate the response of the graphene sheet.

Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work all-atom molecular dynamics simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chloride (GdmCl) at 273-395 K by molecular dynamics simulation. Analysis of surface area, radial distribution function, radius of gyration, heat capacity, hydrogen bond, helix, coil and beta contents showed that an intermediate appears on the way of helix to coil transition. GdmCl at low concentration increases the midpoint of transition temperature (Tm), number of solvent molecules in the hydration layer and interapeptide hydrogen bond as well as decreases in rate of helix to coil transition. Thus, the role of guanidine at low concentration is same as osmolytes which decreases the beta form, increases hydration layer and the polypeptide thermal stability.

Molecular dynamics (MD) simulation is a well-known subject in the field of bioinformatics. MD simulations study the complexity of biological processes in the aqueous dynamic environment similar to the cellular world at the nanoscale. Over the last five decades since the first molecular dynamics simulations were performed on a protein, the biological understanding of the mechanism of molecular processes has been transformed from several perspectives by these simulations. In this review article, the most important molecular dynamics simulation studies on the biological systems are discussed. While reviewing the most important studies, the focus would be on the three main breakthroughs in this field. These Three turning points include: protein folding, the role of the cell membrane in the function of the cell receptors and the effect of water molecules in MD simulations. Finally, the means of determining the simulation time and the number of atoms in the system are discussed.