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To enable a direct comparison between the topologies measured from simulations and the experimental results, we convert the experimentally-measured cell activities from Seppälä et al. (2010) to the fraction of Ncyto/Ccyto topologies by assuming a linear relationship between cell growth and the population of antiparallel EmrE dimers.
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Variation was measured from coevolutionary simulations on smooth single-peak landscape (e.g. Figure 2H) using ensembles of simulation runs to account for stochastic effects.
In Figs 3(c) and 3 d) the dotted lines represent the ideal response expected from the object and the solid lines show the response measured from the simulations.
We demonstrate that the Spatial Markov model, an upscaled random walk model that enforces correlation between successive jumps, can reproduce breakthrough curves measured from microscale simulations that explicitly resolve all pertinent processes.
The values of elastic modulus of both prion and non-prion fibrils are comparable to the elastic modulus of Aβ fibrils (i.e., ~15 GPa) [55] measured from SMD simulations.
While the tilt angle of FK1TMD in the more complex GA membrane was 23.6 ± 8°, this is intermediate between the tilts observed for the DPPC/DLPC and POPC bilayers but similar to the tilt angle of 25.5° measured from our simulations of FK1TMD in pure POPS.
Figures 8 and 9 respectively show the number of packets in the network and the average lifetime of the nodes, measured from our simulation.
The number of false positive readings measured from our simulation of 50 calcium imaging experiments was acceptably low at a threshold of 3.5 standard deviations above baseline (corresponding to 1.8 false positive transients h−1).
The elastic moduli of prion and non-prion fibrils measured from our SMD simulations are an order of magnitude larger than those estimated from ENM simulations reported in our previous work [19].
As a consequence, for StK= 2.2, particle number density and RUE spatial distribution predicted by the mesoscopic Eulerian approach are more smooth with respect to the ones measured from the Lagrangian simulations results.
Variation of the free energy, ΔG, with ξ was determined using the adaptive biasing force (ABF) method [24], which relies on the integration of the average force acting along ξ measured from unconstrained MD simulations.
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