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adaptive intermolecular reactive empirical bond order.
For the inner atoms of the indenter and the graphene film, the energy function was described by adaptive intermolecular reactive empirical bond order (AIREBO) potential.
We modify the adaptive intermolecular reactive empirical bond order (AIREBO) potential to account for the excess-charge-induced change in equilibrium bond length of the carbon atoms.
The C60/graphene system was simulated using the large-scale atomic/molecular massively parallel simulator (LAMMPS) code [23] and the adaptive intermolecular reactive empirical bond order AIREBO potential [24].
Molecular dynamics simulations with the adaptive intermolecular reactive bond order (AIREBO) potential are performed to study the high-temperature (T) behavior of monolayer graphyne and graphdiyne (MGY and MGDY).
In the second part of the 'Results and discussion' section entitled 'Comparison with classical molecular dynamics', we perform classical molecular dynamics (CMD) calculations with two state-of-the-art bond order hydrocarbon potentials, reactive empirical bond-order (REBO) [20] and adaptive intermolecular reactive empirical bond order (AIREBO) [21].
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By use of the Dissipative Particle Dynamics (DPD) simulation technique mixtures of star-branched (arm number F = 4) and linear chains in athermal (good) solvent are analyzed regarding probabilities for intermolecular contacts of various reactive sites within different polymer coils.
This makes the phenoxyphenol oxygen poorly reactive for intermolecular interactions including hydrogen bonding.
A challenging example is that all four cysteines in SOD1 have been found to be reactive in the intermolecular crosslinking by disulfide bonds, leading to SOD1 aggregation under oxidative conditions in vitro (6).
Upon exposure to inducers, the reactive cysteine residues form intermolecular disulfide bonds and change its conformation which leads to dissociation of Nrf2 from Keap1, translocating Nrf2 into the nucleus, and activating the expression of phase 2 genes [ 26].
Further, it has also been shown that certain 2′-OH groups can be hyper-reactive, owing to their intermolecular interactions with RNA functional groups nearby in space that transiently deprotonate the 2′-OH for activation (McGinnis et al, 2012).
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