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Molecular Dynamics Simulations for the Extraction of Aromatics and Pesticide
Published in Papu Kumar Naik, Nikhil Kumar, Nabendu Paul, Tamal Banerjee, Deep Eutectic Solvents in Liquid–Liquid Extraction, 2023
Papu Kumar Naik, Nikhil Kumar, Nabendu Paul, Tamal Banerjee
After successful completion of the production run, the trajectory file was obtained, which contains the trajectory of the molecules of the system. The parameter file and the trajectory files were then inserted in the VMD software package [55]. The non-bonded interaction energy, average hydrogen bonding, and radial distribution function on the specifications of the requisite criteria were obtained directly using the tools provided in VMD. TRAVIS package [56] was used to obtain the combined distribution function (CDF) and the spatial distribution function (SDF) where the final coordinate file was used as the input. Specific molecules and atoms, along with required criteria such as reference molecule and observed molecule, were selected to get the CDF datasheet SDF coordinate file. The data were then plotted on graph sheet. Proper isovalue was set to display the three-dimensional SDF. The MSD curve was obtained by solving Einstein’s equation of self-diffusivity through VMD. The diffusion coefficient was obtained from the linear slope of the MSD curve.
Montmorillonite swelling properties with various surfactants based on molecular simulation
Published in Journal of Dispersion Science and Technology, 2023
Ying Liu, Guangsheng Cao, Qingchao Cheng, Yujie Bai, Ning Zhang, Shengbo Zhai
Mean Squared Displacement (MSD) refers to the evolution of particle coordinates over time, and its instantaneous position is a measure of the deviation from its initial position.[21] where N is the number of particles, square brackets represent the ensemble average, and is the coordinate of particle i at time t. MSD is to find the average square displacement at a specific time interval during the traversal time, Å2. The diffusion coefficient of particles is proportional to MSD: where D is the diffusion coefficient, cm2/s, and d is the dimension of motion space. In this study, d = 3.
Distributed charge models of liquid methane and ethane for dielectric effects and solvation
Published in Molecular Physics, 2021
Atul C. Thakur, Richard C. Remsing
To the extent that liquid structure determines dynamic properties in equilibrium, the above results suggest that the DC models should yield liquid dynamics similar to the dipole-free OPLS models. To characterise the single-particle translational dynamics of each liquid, we compute the mean-squared displacement (MSD) in each system. The MSD is related to the diffusion coefficient, D, through the Einstein relation, , such that similar MSDs in two systems imply similar diffusion coefficients. The MSDs are shown in Figure 5 for all systems under study. The dynamics of the DC methane models are slightly slower than the OPLS models, which can be attributed in part to the slightly higher density of the DC models. The slower dynamics of the DC models is reflected in the diffusion coefficients, which we obtained by linear fitting the long-time behaviour of the MSD to 6Dt + c. This yields diffusion coefficients of and for the OPLS and DC models of methane, respectively. Both models predict diffusion coefficients that are slightly smaller than that obtained at T = 95.94 K by Oosting and Trappeniers at coexistence [63], .
Study of diffusion characteristics of asphalt–aggregate interface with molecular dynamics simulation
Published in International Journal of Pavement Engineering, 2021
Man Huang, Hongliang Zhang, Yang Gao, Li Wang
MSD is just a scalar quantity and the diffusion coefficients calculated using the MSD can only reflect the activity of the particles in the system, and it cannot directly reflect the direction of the movement of particles. In order to bridge this large gap, diffusion of asphalt in the Z-axis direction of the interface was computed and analysed. The radial distribution function can be interpreted as the ratio of system’s local density to bulk density. The local density in the vicinity of the reference molecules is different from the bulk density of the system. However, the local density of the region far from the reference molecules should be the same as the bulk density, that is, the value of the radial distribution function should approach 1 when the value of r is larger. Therefore, the calculation method for radial distribution function using MD is represented as Equation (8):where N denotes the total number of molecules; T denotes the total calculation time (steps); denotes the designed difference in distance and denotes the number of molecules within the interval of