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The dimensions of the simulation cells and their initial configurations were adopted using the experimental lattice parameters and geometries at corresponding temperatures.
The dimensions of the simulation domain are similar to those of a typical laboratory sample (a few centimeters in each direction).
In general, scaling the dimensions of the simulation space up or down does not affect the ecology as long as food density is not changed.
In the simulations with the PTEN bound to one leaflet of the bilayer, the dimensions of the simulation box were 14.5 nm × 14.5 nm × 13 nm, containing ∼14500 CG waters.
For the simulations with the PTEN and the Ci-VSP displaced from the bilayer, the dimensions of the simulation box were 12.5 nm × 12.5 nm × 28 nm, containing ∼30000 CG waters.
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The second model consists of finite chain stems, whose lengths are determined by the z-dimension of the simulation box.
The dimensions of the periodic simulation boxes were 34 × 34 × 34 3, which were constructed by 2 × 2 × 2 unit cells.
The dimensions of the exposure simulation chamber were 1800 × 700 × 700 mm and it was made of acrylic, as shown in Fig. 1.
Figure 4b shows the dimensions associated with the compression simulations for a spherical particle of radius R. Figure 4 Applied compression using plate above and below the particles, and dimensions of the compression simulation.
To calculate the fractal dimensions of the KMC simulation data, we use the same methods and in-house software as for the medical data, i.e. we use the box-counting algorithm described in the "Fractal and multifractal analysis" section to calculate the d f from the simulations, for direct comparison with the results from the PET/CT images.
The simulation box of two IGF1R TM helices for the two simulations of 12 µs and 34 µs is of 65 Å × 65 Å × 86 Å in dimensions and the simulation box of four IGF-1R transmembrane helices for the other two simulations of 24 µs and 36 µs is of 81 Å × 81 Å × 93 Å in dimensions.
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