Concentration of nitrogen molecules needed by nitrogen nanobubbles existing in bulk water

Developing Martini Coarse-Grained Nitrogen Gas Model for Lipid Nanobubble Simulations

“…In this work, coarse-grained parametrization of gas within Martini force field is mainly based on reproducing gas density (1.091 g/L) [24] at body temperature (~310K), atomistic simulations of nanobubbles [23] and -lipid membrane interaction systems [12] . The obtained coarse-grained gas model was further validated in lipid nanobubble self-assembly simulations, which needs to be consistent with the experiments [4,27] .…”

“…In other words, the total simulation time for this part is 13×10×8×50 ns=52 µs. As shown in Table S3, LJ parameters of =0.36 nm, =1.6 kJ/mol for G1-G1 and =0.42 nm, =1.4 kJ/mol for G1-P4 enable the reproduction of the critical gas concentration for the nanobubble formation observed in all-atom MD simulations [23] . Using this parameter set, we could also obtain comparable the gas density within the nanobubble as Zhang et al's work [23] (Fig.…”

“…Considering the value of energy parameter is especially critical to the nanobubble formation process, while the value of distance parameter is less sensitive to the assemble states of gas in this range, we finally chose =0.36 nm and ∈[0.7, 1.9] kJ/mol, which will be further determined in the following nanobubble formation benchmark simulations. Optimized parameters ( is 1.6 and 1.4 kJ/mol for G1-G1 and G1-P4 LJ interactions respectively) enable better reproduction of the critical concentration for gas nucleation and gas density within the nanobubble in Zhang et al's work [23] . (c) Optimized parameters ( is 1.4, 1.4, 1.7 and 2.0 kJ/mol for G1-Q0, G1-Qa, G1-Na and G1-C1 LJ interactions respectively) well reproduce the preferred localization of in DPPC lipid bilayer [12] .…”

“…In other words, modified value of will be needed. Hence, LJ parameters =0.36 nm, ∈[0.7, 1.9] kJ/mol for G1-G1 and =0.42 nm, ∈[1.1, 2.0] kJ/mol for G1-P4 (Table S3) were carefully calibrated to obtain the optimized energy parameters which can well reproduce the critical gas concentration (22 kg/m 3 ) necessary for the nanobubble formation [23] . For each LJ parameter set (13×10=130 in total), the 50ns benchmark simulations (11 different initial gas concentrations from 10 kg/m 3 to 30 kg/m 3 , ∆ =2 kg/m 3 , Table S4) were performed.…”

“…In this work, based on previous available results of gas from atomistic MD simulations [12,23] and experiments [24][25] (main reason for the choice of gas), we developed MARTINIcompatible coarse-grained model of gas ( Fig. 1), which can well reproduce the lipid nanobubble self-assembly process and overcome possible artifacts of lipid monolayer (e.g.…”