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We present a new coupling method for hybrid simulations in which the system is partitioned into covalently linked quantum mechanical (QM) and molecular mechanical (MM) regions.
Basal parts 10-200 mm regions from the root-shoot junction) of the adventitious roots were sliced into 80-μm-thick sections, and were incubated in lactic acid saturated with chloral hydrate at 70°C for 1 h for clearing.
Mapping was done for each sample on several 40 mm × 40 mm regions, each one containing 400 points with an acquisition time of 5 s for each point (result presented in the Additional file 1: Figure S2).
The electronic embedding was used in order to take into account electrostatic interaction between the QM and MM regions, i.e., the atoms of the QM region were treated by TD-DFT calculations, while the atoms of the MM region were treated as partial charges contributing to the quantum-mechanical Hamiltonian.
Our method, called the "link molecule method (LMM)," is substantially different from the link atom methods in that LMM is free from the delicate issue of how to remove the additional degrees of freedom with respect to the position of the virtual atoms linking the QM and the MM regions.
Grid sizes of 50 µm×50 µm and 200 µm×200 µm were used at the lesion site and 1 mm regions, respectively.
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Slip: Slip is observed by 2.0 mm, region A to B in Figure 17.
A spatial resolution of 8.6 mm in FWHM within a ±50 mm region (field of view) and a linear response of a 0.3 mm standard deviation within a ±200 mm region were obtained.
A 5 mm × 10 mm region of interest (ROI) cursor is placed during real-time B-mode scanning.
In this paper, the root-mean-square of residual ripple in the 50 mm × 50 mm region is defined as the RMS value of residual ripple (RMSr).
The QM/MM-specific task (QMMMTask) references the same parameter set since these definitions are necessary to describe the computational method to treat the MM region.
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