Biomedical Engineering Reference
In-Depth Information
Fig. 1.36
The influence of
larger damping coefficient
( D
0.1 ps
1
)onthe
manipulation.
X
-coordinate of
the center of mass of the
GNNQQNY peptide (in
red
)
and the peptide-water
mixture (in
green
) vs. time,
together with the
x
-coordinate
of the external charge (in
black
)forthecaseofSystem
Iwhen
q
0.5
e
.Asa
comparison, Fig.
1.9
shows
the manipulation when
D 0.01 ps
1
DC
time (see Fig.
1.36
). We note that, in this case, the peptide or peptide-water mixture
gets behind the external charge in most of time due to the larger Langevin damping
force; in contrast, in the case of
D
0.01 ps
1
, the peptide or peptide-water mixture
usually goes ahead of the external charge due to thermal fluctuation. Moreover,
we have also carried conventional MD simulation: the controllable manipulation
abilities are consistent with the results presented here.
The aforementioned design can be regarded as an “indirect” approach, which
manipulates the position of biomolecule through manipulating the position of
water molecules surrounding it. We also propose a “direct” approach, which can
manipulate the position of biomolecule with charged residue(s) inside a water-filled
nanotube directly. To demonstrate this design, we have built another system, namely,
System II. It contains a peptide called Aˇ
16-22
[
71
] (Ace-KLVFFAE-NMe) inside a
(29, 0) zigzag SWNT with dimensions of 8.33 nm in length and 2.24 nm in diameter
(see Fig.
1.37
). This peptide is an Alzheimer's disease-related peptide, having a
lysine (K) residue with one positive charge (
C
1
e
) at one end and a glutamic acid
(E) residue with one negative charge (
1
e
) at the other. The other space in SWNT
is fully filled with water. The SWNT is aligned along the
x
-axis in a periodic box of
8.4
12
12 nm
3
. A group of external charges that contained 12 charges forming a
3
4 array is allocated 3.5 A from the SWNT wall and initially above the glutamic
acid residue of the peptide. The distance between the nearest adjacent charges is
2.88 A. This charge pattern is very similar to the Au (100) crystal face. We note
that other patterns of the external charge group do not change much the conclusion
we have obtained here provided that the external charges are densely packed in two
dimensions. The quantity of each charge is also denoted by
q
. The corresponding
counterions are constrained at the right edge of the box to make the system neutral.
For the case of System II, Fig.
1.38
shows a typical example of the
x
-coordinate
of the COM of the peptide as a function of time, together with the
x
-coordinate of
the geometrical center of the external charges for
q
DC
0.5
e
per atom. The peptide
