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Diffusion of rejuvenator in RAP binder observed at molecular scale
Published in Eyad Masad, Amit Bhasin, Tom Scarpas, Ilaria Menapace, Anupam Kumar, Advances in Materials and Pavement Performance Prediction, 2018
In this study, all molecular models were prepared by the Materials Studio package version 7.0, and all following MD simulations were performed by the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) (Plimpton 1995). The bonded and non-bonded potentials parameters were calculated using the Optimized Potentials for Liquid Simulations (OPLS) force field. This force field has been validated for predicting adsorptive properties for abroad range of substances, such as such as most common organics, small inorganic molecules, and polymers (Jorgensen et al. 1996). The time step of 1.0 fs was selected considering the balance between accuracy of simulation results and simulation time. A cut-off distance of 15.5 Å was used for van der Waals between molecules. As for the electrostatic interaction, Ewald summation method with a 6 Å cutoff distance was used. In all MD simulations, the Nosé-Hoover thermostat and Berendsen barostat were employed to control the temperature and pressure, respectively.
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Published in Sarhan M. Musa, Computational Finite Element Methods in Nanotechnology, 2013
Lutz Nasdala, Andreas Kempe, Raimund Rolfes
In contrast to bond stretch, the long-range van der Waals, hydrogen, and Coulomb interactions connect an atom to a multitude of atoms. In theory, each atom has a direct connection to all atoms of the same structure. For practical applications, it is recommended to introduce cutoff distances or special algorithms in order to reduce the numerical effort of an MDFEM analysis: Since interaction forces approach zero for large distances, bondings that exceed a certain range, for example, three times the natural length, can be neglected.For a geometric nonlinear analysis, the selection should be revised in regular intervals as the interatomic distances are supposed to change.For very large structures and long-range interactions that decay slowly with distance, it is necessary to bundle long-range interactions using special algorithms. For instance, the Ewald summation has been derived for the fast treatment of electrostatic interactions and is often used in biomolecular systems such as proteins and enzymes in a crystalline state, whereas methods based on multipole expansions are often used for nonperiodic systems, such as an enzyme in solution. For details, see Schlick (2002).
Molecular Simulations for Nanofluids
Published in Victor M. Starov, Nanoscience, 2010
Interactions between nonbonded ions or atoms in molecules that carry charges, Qi, are typically modeled by Coulomb’s law as: EQQ(r)=Q1Q24πε0r, where ε0 is the dielectric constant of a vacuum. This interaction presents a particular challenge in molecular simulation as its spatial decay is very gradual compared with the dispersion and other short-ranged interactions (e.g., hydrogen bonding). If treated naively, evaluation of charge–charge interactions would require very large volumes (compared with that of a molecule) and the evaluation of extremely large numbers of pair interactions. Both problems can be significantly mitigated, however, by adopting the Ewald summation, fast multipole expansion, or particle-mesh algorithms (Frenkel and Smit 2002)—the first of these is generally more efficient for N < 105, while the latter are more competitive for larger numbers of particles (Frenkel and Smit 2002). Although now less commonly used, electrostatic interactions between molecules or parts of molecules can also be modeled using the multipole expansion—this is, for example, done in the PE models of Allinger et al. (1989). If this is done, the charge–dipole and dipole–dipole interactions all decay slower than rD, where D is the dimension of the system, necessitating Ewald summation to be used.
Synthesis and characterization of ionic liquids [C12mim]Cl, [C14mim]Cl and [C16mim]Cl: experimental and molecular dynamics simulations
Published in Liquid Crystals, 2022
Zhihao Li, Chuandong Ma, Meng He, Qingbiao Wang, Hao Yu, Xiaofang You, Lin Li
The simulation was carried out on an NVT ensemble at 298, 303 and 313 K. A Nosè-Hoover thermostat was used in the simulation with a relaxation time of 100 fs. The Ewald summation method was used to express the long-distance electrostatic interaction. After using the van der Waals interaction with a cut-off value of 12.5, the time step was set to 1.0 fs. The duration of the simulation was 1 ns. In addition, according to the 250 ps simulation result after the balance phase, the final result calculation was completed. The constructed single IL chemical model and crystal cells are shown in Figure 2 and 3.
Numerical and experimental evaluation of adhesion properties of asphalt-aggregate interfaces using molecular dynamics simulation and atomic force microscopy
Published in Road Materials and Pavement Design, 2021
Bingyan Cui, Xingyu Gu, Hao Wang, Dongliang Hu
All the modelling and simulations were conducted by Materials Studio 7.0 at 298.15K. Canonical ensemble NVT (constant number of atoms, volume and temperature) and isothermal-isobaric ensemble NPT (constant number of atoms, pressure and temperature) were used with the time step of 1 fs. For the van der Waals interaction, the atom-based summation method with a cutoff distance of 15.5 Å was used. For the electrostatic interaction, Ewald summation method was used. Meanwhile, Nose–Hoover thermostat and Berendsen barostat was employed to control the temperature and pressure, respectively.
Study on the stability of emulsion based on molecular dynamics
Published in Journal of Dispersion Science and Technology, 2021
Hongxin An, Guangsheng Cao, Yujie Bai, Daye Wang, Fansong Meng
The model adopts periodic boundary, the intermolecular interaction potential adopts Lennard-Jones potential, and the cutoff radius is 12.5 Å. The long-range coulomb force is calculated by PPPM algorithm, and the simulation accuracy is 1.0 e−4. The pppm style invokes a particle-particle particle-mesh solver which maps atom charge to a 3d mesh, uses 3d FFTs to solve Poisson’s equation on the mesh, then interpolates electric fields on the mesh points back to the atoms. It is closely related to the particle-mesh Ewald technique (PME) used in AMBER and CHARMM. The cost of traditional Ewald summation scales as N3/2 where N is the number of atoms in the system. The PPPM solver scales as N log N due to the FFTs, so it is almost always a faster choice.[20] In previous studies, the CVFF force field correctly described the dynamics of polyhydrocarbons and surfactants.[21] The water molecules are described by SPC model. The surfactant and crude oil components were described by CVFF force field. After the initial model is constructed, the Shake method is used to make the crude oil component vibrate near its geometric position to fix the crude oil component at the geometric position. The local potential energy of the simulation system in all simulation processes is minimized by iteratively adjusting the atomic coordinates. The iteration terminates when a stop standard (such as energy, force, maximum number of iterations, and maximum number of force/energy assessments) is satisfied. The initial velocity adopts Gaussian random method. The system is first relaxed for 2 ns. Then 5 ns dynamic simulation is carried out under NVT ensemble. The system temperature was controlled to 333.15 K by Nose-Hoover thermostat. The interval was 0.5 ps.