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P. Raczy´ nski et al.
deflection is discussed. We compare the results with capped (10, 10) CNT. We
also present results for heterogeneous nanotube, namely, silicon-carbide nanotube
(SiCNT). Recent studies show that SiCNT might have some advantages when
compared to CNTs, because they exhibit larger reactivity and they can be applied
in hydrogen storage components [31, 32]. Also graphene sheet was taken into
consideration as it is a novel material and its interaction with biological samples
is still relatively not well known.
The damage of phospholipid bilayer is equivalent with the death of the cell, and
the nanostructure used during indentation process should not destroy the membrane
if it is to be considered as possible drug carrier. To assess the impact of nanostructure
on the membrane, we performed a set of simulations of removing the (10, 10) CNT
from the membrane. During extraction process, we examined self-sealing abilities
of phospholipid bilayer.
16.2 Materials and Methods
Molecular dynamics simulations were performed with NAMD 2.8 simulations code
[33], with the all-atom CHARMM force field. VMD 1.9.2 was used to visualize the
simulated systems [34]. The studied systems consisted of nanostructure, phospholipid (DMPC), and cholesterol molecules, which play in membrane an important
role in the context of its fluidity [1, 2, 35–37]. Moreover, all simulations were
performed in a water environment (TIP3P adapted CHARMM model of water
[38, 39]).
All systems were initially equilibrated in NPT ensemble. The pressure was set to
1 atm and controlled using Langevin barostat implemented in NAMD. Next the
systems were equilibrated in NVT ensemble, and after these initial runs, where
the nanostructures were kept at constant positions, the indentation simulations were
started. All indentation simulations were performed in NVT ensemble.
Nanoindentation of a phospholipid bilayer was modeled by means of SMD
simulations. In case of nanotubes, the springs were added between the most distant
from bilayer ring of nanotube and imaginary points moving with constant velocity
perpendicularly to bilayer surface. For graphene sheet springs were added at the
closest to bilayer carbon atoms due to the fact that it was difficult to keep the sheet
perpendicularly to bilayer surface when the springs were added to the atoms most
distant from the bilayer.
The simulated systems consist of approximately 130,000 atoms. All simulations
were performed at physiological temperature equal to 310 K. The integration time
step was set to 0.5 fs. During equilibration process, the distance between the
closest to the bilayer nanostructure atoms and average positions of phospholipid
heads was approximately equal to 0.8 nm. All interactions were described with
CHARMM potential. The CHARMM-adapted parameters and topologies for CNTs
and graphene sheet were taken from [40–42] and for silicon-carbide nanotube from
[43]. The atomic charges and model for cholesterol molecule were taken from
P. Raczy´ nski et al.
deflection is discussed. We compare the results with capped (10, 10) CNT. We
also present results for heterogeneous nanotube, namely, silicon-carbide nanotube
(SiCNT). Recent studies show that SiCNT might have some advantages when
compared to CNTs, because they exhibit larger reactivity and they can be applied
in hydrogen storage components [31, 32]. Also graphene sheet was taken into
consideration as it is a novel material and its interaction with biological samples
is still relatively not well known.
The damage of phospholipid bilayer is equivalent with the death of the cell, and
the nanostructure used during indentation process should not destroy the membrane
if it is to be considered as possible drug carrier. To assess the impact of nanostructure
on the membrane, we performed a set of simulations of removing the (10, 10) CNT
from the membrane. During extraction process, we examined self-sealing abilities
of phospholipid bilayer.
16.2 Materials and Methods
Molecular dynamics simulations were performed with NAMD 2.8 simulations code
[33], with the all-atom CHARMM force field. VMD 1.9.2 was used to visualize the
simulated systems [34]. The studied systems consisted of nanostructure, phospholipid (DMPC), and cholesterol molecules, which play in membrane an important
role in the context of its fluidity [1, 2, 35–37]. Moreover, all simulations were
performed in a water environment (TIP3P adapted CHARMM model of water
[38, 39]).
All systems were initially equilibrated in NPT ensemble. The pressure was set to
1 atm and controlled using Langevin barostat implemented in NAMD. Next the
systems were equilibrated in NVT ensemble, and after these initial runs, where
the nanostructures were kept at constant positions, the indentation simulations were
started. All indentation simulations were performed in NVT ensemble.
Nanoindentation of a phospholipid bilayer was modeled by means of SMD
simulations. In case of nanotubes, the springs were added between the most distant
from bilayer ring of nanotube and imaginary points moving with constant velocity
perpendicularly to bilayer surface. For graphene sheet springs were added at the
closest to bilayer carbon atoms due to the fact that it was difficult to keep the sheet
perpendicularly to bilayer surface when the springs were added to the atoms most
distant from the bilayer.
The simulated systems consist of approximately 130,000 atoms. All simulations
were performed at physiological temperature equal to 310 K. The integration time
step was set to 0.5 fs. During equilibration process, the distance between the
closest to the bilayer nanostructure atoms and average positions of phospholipid
heads was approximately equal to 0.8 nm. All interactions were described with
CHARMM potential. The CHARMM-adapted parameters and topologies for CNTs
and graphene sheet were taken from [40–42] and for silicon-carbide nanotube from
[43]. The atomic charges and model for cholesterol molecule were taken from