Aspherical particle models for molecular dynamics simulation

Nguyen, Trung Dac; Plimpton, Steven J.

doi:10.1016/j.cpc.2019.05.010

Cited by 28 publications

(17 citation statements)

References 49 publications

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“…In the case of atomistic simulations, such methods have been used to constrain the high-frequency motions of atoms in small molecules using algorithms such as SHAKE and RATTLE that allow longer time steps and an increased speed of the simulations. For larger rigid particles, many time-reversible and symplectic algorithms for rigid-body dynamics have been developed. ,− In our model, the forces and torques exerted on the magnetic core of the MNP are calculated as the sum of the respective terms experienced by the magnetic dipole moments of the core, an approach similar to the one described in ref . Given the presence of a dipole moment defined by eq embedded in the MNP core, the magnetic dipolar force and torques can be calculated for the rigid core by eq , and in an external magnetic field, the forces due to Zeeman interactions can be similarly computed.…”

Section: Results and Discussionmentioning

confidence: 99%

“…While we have shown here the use of spherical and cubic MNPs, additional shapes such as an ellipsoid, rod, lobe, and so forth with different sizes can be used in the model. Furthermore, the relative distance between the atoms of the rigid core is kept fixed, which provides added benefits such as the ability to turn off intrabody interactions to save time in computations . Another major advantage of the model is the ability to define and tune the strength and orientation of the magnetic dipole moments of the modeled MNP(s) using eq and the scaling factor, β.…”

Section: Results and Discussionmentioning

confidence: 99%

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All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles

Mahmood

Yingling

2022

J. Chem. Theory Comput.

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Magnetic nanoparticles (MNPs) can organize into novel structures in solutions with excellent order and unique geometries. However, studies of the self-assembly of smaller MNPs are challenging due to a complicated interplay between external magnetic fields and van der Waals, electrostatic, dipolar, steric, and hydrodynamic interactions. Here, we present a novel all-atom molecular dynamics simulation method to enable detailed studies of the dynamics, self-assembly, structure, and properties of MNPs as a function of core sizes and shapes, ligand chemistry, solvent properties, and external field. We demonstrate the use and effectiveness of the model by simulating the self-assembly of oleic acid ligand-functionalized magnetite (Fe 3 O 4 ) nanoparticles, with spherical and cubic shapes, into rings, lines, chains, and clusters under a uniform external magnetic field. We found that the long-range electrostatic interactions can favor the formation of a chain over a ring, the ligands promote MNP cluster growth, and the solvent can reduce the rotational diffusion of the MNPs. The algorithm has been parallelized to take advantage of multiple processors of a modern computer and can be used as a plugin for the popular simulation software LAMMPS to study the behavior of small MNPs and gain insights into the physics and chemistry of different magnetic assembly processes with atomistic details.

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Section: Results and Discussionmentioning

confidence: 99%

Section: Results and Discussionmentioning

confidence: 99%

All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles

Mahmood

Yingling

2022

J. Chem. Theory Comput.

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“…In this work, a time step of 2 fs was used as recommended by Brown et al (2008) for coarse-grained simulations. MD simulations were performed using LAMMPS code (Nguyen & Plimpton, 2019).…”

Section: Polyethylene Modelmentioning

confidence: 99%

Analysis of elastic deformation of amorphous polyethylene in uniaxial tensile test by using molecular dynamics simulation

Le¹

2020

cmms

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In this paper, the linear elastic response to uniaxial tension of amorphous polyethylene was investigated by using Molecular Dynamics (MD) simulation. The polymeric system was initiated using a Monte Carlo-based technique and then equilibrated by a relaxation sequence at temperature of 100 K under a NPT control. Uniaxial tension test was carried out by modifying the corresponding component of the pressure tensor, with a loading rate of 0.5 bar/ps. The results showed that at 100 K (which is smaller than the glass transition temperature), the amorphous polymeric material exhibited a linear elastic response to uniaxial tension. The obtained Young's modulus and Poisson's ratio were also compared with values reported in the literature. Finally, parametric studies were performed on the stress-strain curve as a function of loading axis, number of chains and number of monomer units, respectively.

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“…Several CG models of water have been proposed during the last two decades, following different approaches for the mapping process. − However, current CG models often do not provide an adequate description of intermolecular interactions due to the lack of many-body contributions, which are particularly important for the accurate description of, for example, water properties . Instead, the MOLC model uses finite-size aspherical particles connected with directional bonds. The particles are decorated with virtual sites representing point charges.…”

Section: Introductionmentioning

confidence: 99%

Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations

Bellussi

Roscioni²,

Ricci³

et al. 2021

J. Phys. Chem. B

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Water models with realistic physical–chemical properties are essential to study a variety of biomedical processes or engineering technologies involving molecules or nanomaterials. Atomistic models of water are constrained by the feasible computational capacity, but calibrated coarse-grained (CG) ones can go beyond these limits. Here, we compare three popular atomistic water models with their corresponding CG model built using finite-size particles such as ellipsoids. Differently from previous approaches, short-range interactions are accounted for with the generalized Gay–Berne potential, while electrostatic and long-range interactions are computed from virtual charges inside the ellipsoids. Such an approach leads to a quantitative agreement between the original atomistic models and their CG counterparts. Results show that a timestep of up to 10 fs can be achieved to integrate the equations of motion without significant degradation of the physical observables extracted from the computed trajectories, thus unlocking a significant acceleration of water-based mesoscopic simulations at a given accuracy.

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Aspherical particle models for molecular dynamics simulation

Cited by 28 publications

References 49 publications

All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles

All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles

Analysis of elastic deformation of amorphous polyethylene in uniaxial tensile test by using molecular dynamics simulation

Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations

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