16 Interactions Between Carbon-Based Nanostructures and Biomembranes. . .
279
[44]. DMPC molecules were modeled using CHARMM27 force field [45, 46]. To
improve the sampling of state space, all simulations were repeated several times, and
the results presented in this work are the averages over all independent simulation
runs.
The simulations were performed as follows:
1. Firstly indentation using two armchair CNTs (10, 10) and (12, 12) was executed
with the speed equal to 1.5 m/s.
2. Next part of simulations was to use capped (10, 10) CNT as a nanoindenter. The
CNT was moving through bilayer with the speed v = 2 m/s.
3. Thirdly we used heterogeneous (10, 10) SiCNT nanotube, which pierced the
membrane with speed equal to 1.5 m/s.
4. We also used 56 × 32 Å graphene sheet. The graphene sheet was moved with the
speed equal to 2 m/s.
5. Last part of our simulations was extraction process for the open-ended (10, 10)
CNT with the pullout speed equal to 1.5 m/s.
The results of these simulations are presented and discussed in the above order.
16.3 Results
16.3.1 Indentation of the Membrane by (10, 10) and (12, 12)
CNTs
Figure 16.1 shows the initial configuration (Fig. 16.1a) for the (12, 12) CNT and the
final configuration of this system (Fig. 16.1b).
In the Fig. 16.1b, one can observe that some lipids were pulled out of the
membrane, but its consistency is saved. Moreover, the deflection of the membrane
is observed after indentation process. Figure 16.2 presents the average dislocation
of C2 carbon atoms from the phospholipid glycerol backbones with respect to the
distance from nanotube main axis. The bending was calculated with respect to the
positions of glycerol backbone C2 atoms at the edges of simulation cell. In case of
nanotube with larger diameter, the deflection is larger because it is more difficult
to accommodate the change imposed by moving (12, 12) CNT. In case of (12, 12)
CNT, the C2 atoms located close to the nanotube surface were displaced about 2–
3 Å deeper into the bilayer comparing to (10, 10) CNT. The C2 atoms located close
to the CNT surface experience larger dislocation comparing to these located at the
edges of simulation cell.
The average force required to insert the nanotube into bilayer, as a function of
the indentation depth, is shown in Fig. 16.3. It can be seen that force required to
indent phospholipid bilayer is larger in case of CNT with larger diameter. The
higher amount of the force required is clearly observed mainly in the last part of
indentation process where the bilayer is almost pierced by CNT. The maximums of
279
[44]. DMPC molecules were modeled using CHARMM27 force field [45, 46]. To
improve the sampling of state space, all simulations were repeated several times, and
the results presented in this work are the averages over all independent simulation
runs.
The simulations were performed as follows:
1. Firstly indentation using two armchair CNTs (10, 10) and (12, 12) was executed
with the speed equal to 1.5 m/s.
2. Next part of simulations was to use capped (10, 10) CNT as a nanoindenter. The
CNT was moving through bilayer with the speed v = 2 m/s.
3. Thirdly we used heterogeneous (10, 10) SiCNT nanotube, which pierced the
membrane with speed equal to 1.5 m/s.
4. We also used 56 × 32 Å graphene sheet. The graphene sheet was moved with the
speed equal to 2 m/s.
5. Last part of our simulations was extraction process for the open-ended (10, 10)
CNT with the pullout speed equal to 1.5 m/s.
The results of these simulations are presented and discussed in the above order.
16.3 Results
16.3.1 Indentation of the Membrane by (10, 10) and (12, 12)
CNTs
Figure 16.1 shows the initial configuration (Fig. 16.1a) for the (12, 12) CNT and the
final configuration of this system (Fig. 16.1b).
In the Fig. 16.1b, one can observe that some lipids were pulled out of the
membrane, but its consistency is saved. Moreover, the deflection of the membrane
is observed after indentation process. Figure 16.2 presents the average dislocation
of C2 carbon atoms from the phospholipid glycerol backbones with respect to the
distance from nanotube main axis. The bending was calculated with respect to the
positions of glycerol backbone C2 atoms at the edges of simulation cell. In case of
nanotube with larger diameter, the deflection is larger because it is more difficult
to accommodate the change imposed by moving (12, 12) CNT. In case of (12, 12)
CNT, the C2 atoms located close to the nanotube surface were displaced about 2–
3 Å deeper into the bilayer comparing to (10, 10) CNT. The C2 atoms located close
to the CNT surface experience larger dislocation comparing to these located at the
edges of simulation cell.
The average force required to insert the nanotube into bilayer, as a function of
the indentation depth, is shown in Fig. 16.3. It can be seen that force required to
indent phospholipid bilayer is larger in case of CNT with larger diameter. The
higher amount of the force required is clearly observed mainly in the last part of
indentation process where the bilayer is almost pierced by CNT. The maximums of