Parameters (σ, ε) of Lennard-Jones for Fe, Ni, Pb for Potential and Cr based on Melting Point Values Using the Molecular Dynamics Method of the Lammps Program

Maghfiroh, C Y; Arkundato, Artoto; Misto,; Maulina, Wenny

doi:10.1088/1742-6596/1491/1/012022

Cited by 20 publications

(12 citation statements)

References 5 publications

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“…Table 4 gives the Lennard–Jones 6–12 parameters and partial charges for PbO, which were taken from Refs. 62 , 63 . We first tested the PbO force field parameters by determining internal energies of departure as a function of temperature.…”

Section: Resultsmentioning

confidence: 99%

Modeling thermophysical properties of glasses

Lucia

Gregory

2023

Sci Rep

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Metal oxide glasses are important in various industries because their properties can be tailored to meet application-specific requirements. However, there are few rigorous modeling tools for predicting thermomechanical properties of these materials with acceptable accuracy and speed, yet these properties can play a critical role in material design. In this article, a general multi-scale modeling framework based on Monte Carlo simulation and a cubic equation of state for predicting thermomechanical properties is presented. There are two novel and fundamental aspects of this work: (1) characterization of glass transition and softening temperatures as adjacent saddle points on the heat capacity versus temperature curve, and (2) a new moving boundary equation of state that accounts for structure and ‘soft’ repulsion. In addition, modeling capabilities are demonstrated by comparing thermomechanical properties of a pure B2O3 glass and PbO–B2O3 glass predicted by the equation of state to experimental data. Finally, this work provides a rigorous approach to estimating thermophysical properties for the purpose of guiding experimental work directed at tailoring thermomechanical properties of glasses to fit applications.

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Section: Resultsmentioning

confidence: 99%

Modeling thermophysical properties of glasses

Lucia

Gregory

2023

Sci Rep

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“…The interatomic interactions within and between the ILs were described by the OPLS-AA force field based on LigParGen . Interactions within the iron substrate were modeled using the Lennard–Jones (LJ) potential with ϵ = 0.2007 eV and σ = 2.4193 Å . Interactions between the substrate and the ILs were modeled using the LJ potential combining the Fe parameters with the LJ parameters of OPLS-AA using geometric mixing rules …”

Section: Methodsmentioning

confidence: 99%

“…65 Interactions with the iron substrate were modeled using the Lennard-Jones (LJ) potential with ϵ ss = 0.2007 eV and σ ss = 2.4193 Å. 66 Interactions between substrate and ILs were modeled using the LJ potential, combining the Fe parameters with the LJ parameters of OPLS-AA using geometric mixing rules. 67 It has been found that contact angle generally increases linearly with droplet size until it converges to a constant values after a critical number of ions or droplet radius is reached.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

Effect of Ion Pair on Contact Angle for Phosphonium Ionic Liquids

2022

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The wettability of ionic liquids (ILs) is relevant to their use in various applications.However, a mechanistic understanding of how the cation-anion pair affects wettability is still evolving. Here, focusing on phosphonium ILs, wettability was characterized in terms of contact angle using experiments and classical molecular dynamics simulations.Both experiments and simulations showed that contact angle was affected by the anion and increased as benzoate < salicylate < saccharinate. Further, the simulations showed contact angle decreased with increased alkyl chain length for these anions paired with five different tetra-alkyl-phosphonium cations. The trends were explained in terms of adhesive and cohesive energies in the simulations, and then correlated to the atomic scale differences between the anions and cations.

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“…The [NiFe] cofactor had bond constraints placed across the CN and CO ligands as well as between the iron atom and two bound sulfur atoms. Lennard-Jones parameters were taken from the Charmm36m [89,90] forcefield where appropriate, with exception of the cyanuric carbon [95] with the iron parameters taken from physical data to have a non-zero epsilon value [96]. The QL molecular oxygen model developed by Javanainen et al [97] was chosen to better define the quadrupole within the molecule.…”

Section: Molecular Dynamics Parameterization and Simulationmentioning

confidence: 99%

Energy extraction from air: structural basis of atmospheric hydrogen oxidation

Grinter

Kropp

Venugopal

et al. 2022

Preprint

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Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival. This recently discovered yet globally significant process regulates the composition of the atmosphere, enhances soil biodiversity, and drives primary production in certain extreme environments. Atmospheric H2 oxidation has been attributed to still uncharacterised members of the [NiFe]-hydrogenase superfamily. However, it is unresolved how these enzymes overcome the extraordinary catalytic challenge of selectively oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2, and how the derived electrons are transferred to the respiratory chain. Here we determined the 1.52 angstroms resolution CryoEM structure of the mycobacterial hydrogenase Huc and investigated its mechanism by integrating kinetics, electrochemistry, spectroscopy, mass spectrometry, and molecular dynamics simulations. Purified Huc is an oxygen-insensitive enzyme that couples the oxidation of atmospheric H2 at its large subunit to the hydrogenation of the respiratory electron carrier menaquinone at its small subunit. The enzyme uses a narrow hydrophobic gas channel to selectively bind atmospheric H2 at the expense of O2, while three [3Fe-4S] clusters and their unusual ligation by a D-histidine modulate the electrochemical properties of the enzyme such that atmospheric H2 oxidation is energetically feasible. Huc forms an 833 kDa complex composed of an octamer of catalytic subunits around a membrane-associated central stalk, which extracts and transports menaquinone a remarkable 94 angstroms from the membrane, enabling its reduction. These findings provide a mechanistic basis for the biogeochemically and ecologically critical process of atmospheric H2 oxidation. Through the first characterisation of a group 2 [NiFe]-hydrogenase, we also uncover a novel mode of energy coupling dependent on long-range quinone transport and pave way for the development of biocatalysts that oxidize H2 in ambient air.

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Parameters (σ, ε) of Lennard-Jones for Fe, Ni, Pb for Potential and Cr based on Melting Point Values Using the Molecular Dynamics Method of the Lammps Program

Cited by 20 publications

References 5 publications

Modeling thermophysical properties of glasses

Modeling thermophysical properties of glasses

Effect of Ion Pair on Contact Angle for Phosphonium Ionic Liquids

Energy extraction from air: structural basis of atmospheric hydrogen oxidation

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