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The structural optimization is allowed to relaxed until the maximum force on each atom becomes at least less than 0.01 eV/Å and the maximum energy change between two steps is smaller than 10−5 eV.
The lattice parameters and atomic positions are fully relaxed under Broyden-Fletceher-Goldfarb-Shanno (BFGS) [68] scheme until the energy difference between two steps is smaller than 5 × 10−6 eV/atom, and the maximum force is smaller than 0.01 eV/Å.
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Convergence for the EM algorithm was chosen to be when either the difference in log likelihood function value between two steps was smaller than 0.1 or after a maximum of 1,000 iterations.
Finally, according to Fig. 3c from Koenig, et al. [ 28], only 10 OTUs with 36 time points between four steps were selected for analyzing using our RMN algorithm (Additional file 3).
The process of exchangin informations between the two steps is then iterated until convergence to a fixed point.
The main difference between the two steps is the widths of synchronization pulses transmitted by master node.
The path between these two steps is not fully understood; however, variables such as pressure, temperature, composition, and the velocity generally influence this process.
In an industrial process, filtration and washing of the material between the two steps is difficult, as it should be performed at high pressure to reduce energy demand.
For this critical frequency and the standard signal parameters, the relationship between the standard rate constant of the first step, the transfer coefficient of this step and the difference between standard potentials of two steps is calculated.
Therefore, the average Amean between the two steps was used to compute SFAF.
The final refined theoretical structure of M antigen was achieved by a harmonic constraint with 20 steps of steepest descent in all residues followed by 1,000 steps of steepest descent and conjugated gradient minimization methods until the energy difference between the two steps was below 0.01 kJ/mol.
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