Sentence examples for simulation as implemented from inspiring English sources

The stereochemistry was improved using spatial restraints and CHARMM energy terms, followed by a conjugate gradient simulation, as implemented in the Modeller software [ 28].

Haplotype statistics (number of haplotypes, frequency of the commonest haplotype, haplotype configuration) were calculated using DNAsp, and their probability under a neutral model of evolution assessed by coalescent simulation as implemented in Haploconfig [ 44], conservatively assuming no recombination within loci.

The phonon transport is studied using the nonequilibrium molecular dynamics [NEMD] simulations as implemented in the LAMMPS software package (Sandia National Laboratories, Livermore, CA, USA)[16].

To correct for multiple comparisons, we conducted Monte Carlo simulations as implemented in AlphaSim [28].

A threshold adjustment method based on Monte-Carlo simulations as implemented in AFNI function Alphasim was used to guard against identifying false positive areas of activation [30].

Statistical significance of D and Fs was estimated with coalescent simulations as implemented in this program.

Significance was determined using 10,000 coalescent simulations as implemented in DNAsp version 5 (Rozas et al. 2003).

To do this, we calculated pairwise nucleotide differences (θπ; Tajima 1989) and the number of segregating sites (θw; Watterson 1975) for each population and assessed significance using coalescent simulations as implemented in the program SITES (Hey and Wakeley 1997).

The resulting PARP-1 8-mer structure and that of unliganded PARP-1 8-merthen subjected to energy minimization and equilibration in a box of water using molecular dynamics simulations as imPARP-1 8-mer the NAMD structurepandage.

Performances of rW, rQG, and rK were evaluated using a simulation approach as implemented in PEDAGOG [ 31].

Because hierarchical structuring, as observed in our data, can lead to an excess of false positives if not accounted for in outlier tests (Excoffier et al. 2009), we supplemented the bayescan results with simulations under the hierarchical fdist model as implemented in arlequin 3.5 (Excoffier and Lischer 2010).