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A cutoff of 10 Å using a switching function beginning from 8.5 Å was employed.
We combine the HLLC and HLL schemes in a single framework using a switching function.
Nonbonded van der Waals interactions were treated by using a switching function at 10A and reaching zero at 12 Å distance.
Non-bonded van der Waals interactions were treated by using a switching function at 10 Å and reaching zero at a distance of 12 Å.
All nonbonded interactions were truncated using a switching function between 12 and 14 Å, and the dielectric constant was kept at unity.
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We model this sulfur source as dependent on available protein and oxygen levels using a switch function to specify that fermentation only occurs during anaerobiosis, ω < ωp (Happe et al., 2002).
This assumption is realized by using a switch function to stipulate that protein is only produced when sufficient sulfur (s > s1), thus sufficient Rubisco, allows the Calvin cycle to function (White and Melis, 2006; Zhang et al., 2002) (see Disussions and Conclusions section).
The electrostatic potential (Eelec) was calculated by using a shift function, while a switching function (between 6.5 and 8.5 Å) was used to define the Van der Waals potential (Evdw).
All conditions are established for any switching using a switched Lyapunov function and a common Lyapunov function.
For the non-bonding interaction cut-off distance of 10 Å was used with a switching function turned-on at 8 Å.
To include long-range effects of the solvent on the solute's interior, the SASA solvation model has been further refined by a volume term [ 26] using a SASA/VOL switch function g (r → i ) (3) V s o l v V O L (r → ) = ∑ i σ i V O L ⋅ g (r → i ) ⋅ 4 3 π R i 3 and by recalibrated contributions of cavity formation and van der Waals interactions [ 27,28].
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