A Molecular Dynamics study of interfaces from pure liquids to biological membranes
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description
a PhD thesis in computational biology
Transcript of A Molecular Dynamics study of interfaces from pure liquids to biological membranes
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-100 -50 0 50 100
z axis (Å)
0
0.2
0.4
0.6
0.8
ρ ( g . c m - 3 )
SKS modelexperiment
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300 350 400 450 500Temperature (K)
0.4
0.45
0.5
0.55
0.6
0.65
ρ ( g . c m - 3 )
SKS modelOPLS modelGibbs-ensembleAlejandre et alExperimental
400 450 500 550 600Temperature (K)
0.4
0.45
0.5
0.55
0.6
0.65
ρ ( g . c m - 3 )
SKS modelOPLS modelGibbs-ensemble
500 550 600 650 700Temperature (K)
0.4
0.45
0.5
0.55
0.6
0.65
ρ ( g . c m - 3 )
SKS modelOPLS modelGibbs-ensemble
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273 293 313 333 353Temperature (K)
0.6
0.65
0.7
0.75
0.8
ρ
( g . c m - 3 )
C16 exp.C16 sim.C10 exp.C10 sim.C6 exp.C6 sim.
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250 300 350 400 450 500
Temperature (K)
0
2
4
6
8
10
12
14
16
18
γ
( m N . m
- 1 )
SKS modelOPLS modelAlejandre et al
0.4 0.5 0.6 0.7
ρ (g.cm-1
)
0
2
4
6
8
10
12
14
16
18
γ
( m N . m
- 1 )
SKS modelOPLS modelAlejandre et al
400 450 500 550 600Temperature (K)
0
2
4
6
8
10
γ
( m N . m
- 1 )
SKS modelOPLS model
0.4 0.5 0.6 0.7
ρ (g.cm-1
)
0
2
4
6
8
10
γ
( m N . m
- 1 )
SKS modelOPLS model
500 550 600 650 700Temperature (K)
0
2
4
6
8
10
γ
( m N . m
- 1 )
SKS modelOPLS model
0.4 0.5 0.6 0.7
ρ (g.cm-1
)
0
2
4
6
8
10
γ
( m N . m
- 1 )
SKS modelOPLS model
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260 280 300 320 340 360 380Temperature (K)
12
14
16
18
20
22
24
26
28
30
γ
( m N . m
- 1 )
C16 exp.C16 sim.C10 exp.C10 sim.C6 exp.C6 sim.
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-50 -40 -30 -20 -10 0 10 20 30 40 50coordinates along z axis (Å)
0
0.2
0.4
0.6
0.8
1
d e n s i t y ( g . c m - 3 )
hexanewaterwater+hexane
-10 -5 0 5 10 15z (Å)
n o r m a l i z e d t o t a l d e n s i t y p r o f i l e
283 K303 K323 K343 K
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-4 0 4 8 12distance from the interface (Å)
-0.2
-0.1
0
0.1
0.2
o r d e r p a r a m e t e r
283 K303 K323 K343 K
-12 -8 -4 0 4distance from the interface (Å)
-0.2
-0.1
0
0.1
0.2
o r d e r p a r a m e t e r
283 K303 K323 K
343 K
dipole
normal
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-8 -4 0 4 8distance from the interface (Å)
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
1.2
P n -
P t ( a r b i t r a r y
u n i t s )
283 K303 K323 K343 K
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-30 -20 -10 0 10 20 30
Position from the interface (Å)
-0.03
-0.02
-0.01
0
0.01
0.02
0.03
( g . c m )
- 3
waterhexanetotalcomposite
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0 5 10 15 20 ξ (Å)
0
5
10
15
s q u a r e d w i d t h ( Å
2 )
σCW
(sim)σ comp(sim)
σ (exp)σ CW
(exp)
ξ"
σ02=R
g2
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S−base
S−top
S−height
O L−Leu D−Leu L− Asp
L−ValC1H2
CH
CO L−Glu L−Leu D−leu
CH3−(CH2)10−CH
CO L−Glu L−Leu D−leu
O L−Leu D−Leu L− Asp
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-40 -20 0 20 40z axis (Å)
0
0.2
0.4
0.6
0.8
1
1.2
1.4
ρ
( g . c m - 3 )
HexaneSurfactin headgroupWater
A
-48 -44 -40 -36 -32 -28 -24 -20 -16 -12z axis (Å)
0
0.2
0.4
0.6
0.8
1
1.2
1.4
ρ
( g . c m - 3 )
B
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-20 -10 0 10 20 coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
AAAAAAAAAAAA
-20 -10 0 10 20 coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
AAAAAA
-20 -10 0 10 20 coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å ) BBB
-20 -10 0 10 20 coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å ) B
-20 -10 0 10 20 coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
CC
-20 -10 0 10 20 coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
CC
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-20 -10 0 10 20coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
A
-20 -10 0 10 20coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
A
-20 -10 0 10 20coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
B
-20 -10 0 10 20coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
B
-20 -10 0 10 20coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
C
-20 -10 0 10 20coordinates along x axis (Å)
-20
-10
0
10
20
c o o r d i n a t e s a l o n g y a x i s ( Å )
C
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5 7.5 10 12.5 15 17.5 20 22.5R (Å)
0
0.5
1
1.5
2
2.5
g ( R )
16 molec./interf.12 molec./interf.9 molec./interf.4 molec./interf.
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0 30 60 90 120 α
dih
0
0.2
0.4
0.6
0.8
1
16 molec./interf.
12 molec./interf.
9 molec./interf.
A
0 30 60 90 120 α
dih
0
0.2
0.4
0.6
0.8
1
4 molec./interf.
2 molec./interf.
1 molec./interf.
B
0 30 60 90 120α
dih.
0
0.2
0.4
0.6
0.8
1
clustered to 2 other surfactin molecules
tumbled over or clustered to 1 other surfactin
free molecules not tumbled
C
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-90 -60 -30 0 30 60 90angle between S
heightand xy plane
0
0.2
0.4
0.6
0.8
1
16 molec./interf.12 molec./interf.9 molec./interf.
A
-90 -60 -30 0 30 60 90angle between S
heightand xy plane
0
0.2
0.4
0.6
0.8
1
4 molec./interf.2 molec./interf.1 molec./interf.
B
-90 -60 -30 0 30 60 90angle between S
heightand xy plane
0
0.2
0.4
0.6
0.8
1
saddle up moleculessaddle down molecules
C
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-90 -60 -30 0 30 60 90S
baseangle (degree)
0
0.2
0.4
0.6
0.8
1
16 molec./interf.12 molec./interf.9 molec./interf.
A
-90 -60 -30 0 30 60 90S
topangle (degree)
0
0.2
0.4
0.6
0.8
1
16 molec./interf.12 molec./interf.9 molec./interf.
A
-90 -60 -30 0 30 60 90S
baseangle (degree)
0
0.2
0.4
0.6
0.8
1
4 molec./interf.2 molec./interf.1 molec./interf.
B
-90 -60 -30 0 30 60 90S
topangle (degree)
0
0.2
0.4
0.6
0.8
1
4 molec./interf.2 molec./interf.1 molec./interf.
B
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2 3 4 5 6 7 8 9 10S base vector length (Å)
0
0.2
0.4
0.6
0.8
1
16 molec./interf.12 molec./interf.9 molec./interf.
A
2 3 4 5 6 7 8 9 10S top vector length (Å)
0
0.2
0.4
0.6
0.8
1
16 molec./interf.12 molec./interf.9 molec./interf.
A
2 3 4 5 6 7 8 9 10S base vector length (Å)
0
0.2
0.4
0.6
0.8
1
4 molec./interf.2 molec./interf.1 molec./interf.
B
2 3 4 5 6 7 8 9 10S top vector length (Å)
0
0.2
0.4
0.6
0.8
1
4 molec./interf.2 molec./interf.1 molec./interf.
B
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NH(1)-CO(5)NH(2)-CO(5)
NH(5)-CO(2)NH(5)-NH(4)
0
100
200
300
400
500
l i f e t i m e ( p s )
A(a) (a)
(a)
(a)
(a) embedded molecules
(c)
(c)
(b)
(c)
(b)
(c)
(b) ending molecules(c) free molecules
NH(1)-CO(5)NH(2)-CO(5)
NH(5)-CO(2)NH(5)-NH(4)
0
100
200
300
400
500
l i f e t i m e ( p s )
B
(a)
(a)
(a)
(a)
(a) saddle up molec.
(b)
(b)(b)
(b)
(b) saddle down molec.
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0 5 10 15 20 25 30l(l+1)
0
1
2
3
4
5
6
7
8
9
- 1 / τ
( n s
- 1 )
1 molec./interf.2 molec./interf.4 molec./interf.9 molec./interf.12 molec./interf.16 molec./interf.
A
0 10 20 30 40 50time (ps)
-40
-30
-20
-10
0
( l n < P l c o s θ > ) / l ( l + 1 )
( 1 0 -
3 )
l=1l=3l=5
B
a
b
c
d
e
f
0 4 8 12 16Number of surfactin molecules per interface
0
0.05
0.1
0.15
0.2
0.25
R o t a t i o n a l d i f f u s i o n c o e f f i c i e n t ( n s - 1 )
C
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0 10 20 30 40 50z axis (Å)
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O O
O O
O
OHO
HO OHO
OH POO
OH
HOHCCH2OH
O
OO
O
OOHO
HO OHO
OH POOOH
HOHCCH2OH
O
O
O O OO
HO
HO OHO
OH
POOOH
HOHCCH2OH
O
OO
O
O
OHO
HO OHO
OH
PO
O
OH
HOHCCH2OH
O O
O O
O
OHO
HO OHO
OHPOOOH
HOHCCH2OH
MPL
0200
0202
1202
1212
chain 1
chain 2
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-40 -30 -20 -10 0 10 20 30 40z (Å)
0
0.2
0.4
0.6
0.8
1
1.2
1.4
m a s s d e n s i t y ( g . c m - 3 )
-40 -30 -20 -10 0 10 20 30 40z (Å)
0
0.2
0.4
0.6
0.8
1
1.2
1.4
m a s s d e n s i t y ( g . c m - 3 )
-40 -30 -20 -10 0 10 20 30 40z (Å)
0
0.2
0.4
0.6
0.8
1
1.2
1.4
m a s s d e n s i t y ( g . c m - 3 )
-40 -30 -20 -10 0 10 20 30 40z (Å)
0
0.2
0.4
0.6
0.8
1
1.2
1.4
m a s s d e n s i t y ( g . c m - 3 )
-40 -30 -20 -10 0 10 20 30 40z (Å)
0
0.2
0.4
0.6
0.8
1
1.2
1.4
m a s s d e n s i t y ( g . c m - 3 )
-40 -30 -20 -10 0 10 20 30 40z (Å)
0
0.1
0.2
0.3
0.4
e l e c t r o n i c d e n s i t y ( e - . A
- 3 )
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-16 -12 -8 -4 0 4 8 12 16
carbon number
-0.4
-0.2
0
0.2
0.4
0.6
0.8
o r d e r p a r a m e t e r
C--C chain 2
C--C chain 1
C--H chain 2
C--H chain 1
-16 -12 -8 -4 0 4 8 12 16
carbon number
-0.4
-0.2
0
0.2
0.4
0.6
0.8
o r d e r p a r a m e t e r
C--C chain 2
C--C chain 1
C--H chain 2
C--H chain 1
-16 -12 -8 -4 0 4 8 12 16
carbon number
-0.4
-0.2
0
0.2
0.4
0.6
0.8
o r d e r p a r a m e t e r
C--C chain 2
C--C chain 1
C--H chain 2
C--H chain 1
-16 -12 -8 -4 0 4 8 12 16
carbon number
-0.4
-0.2
0
0.2
0.4
0.6
0.8
o r d e r p a r a m e t e r
C--C chain 2
C--C chain 1
C--H chain 2
C--H chain 1
-16 -12 -8 -4 0 4 8 12 16
carbon number
-0.4
-0.2
0
0.2
0.4
0.6
0.8
o r d e r p a r a m e t e r
C--C chain 2
C--C chain 1
C--H chain 2
C--H chain 1
-16 -12 -8 -4 0 4 8 12 16
carbon number
-0.4
-0.2
0
0.2
0.4
0.6
0.8
o r d e r p a r a m e t e r
C--C chain 2
C--C chain 1
C--H chain 2
C--H chain 1
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0 5 10 15 20 25 300,00
0,02
0,04
0,06
0,08
0,10
0,12
0,14
0,16
a r b i t r a r y
u n i t s
Tilt angle (degree)
0000
0200
0202
1202
1212
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0 10 20 30 40 50 60 70 80 90 100
slabs
-3
-2
-1
0
1
2
3
L a t e r a l p r e s s u r e p r o f i l e
0 10 20 30 40 50 60 70 80 90 100
slabs
-3
-2
-1
0
1
2
3
L a t e r a l p r e s s u r e p r o f i l e
0 10 20 30 40 50 60 70 80 90 100
slabs
-3
-2
-1
0
1
2
3
L a t e r a l p r e s s u r e p r o f i l e
0 10 20 30 40 50 60 70 80 90 100
slabs
-3
-2
-1
0
1
2
3
L a t e r a l p r e s s u r e p r o f i l e
0 10 20 30 40 50 60 70 80 90 100
slabs
-3
-2
-1
0
1
2
3
L a t e r a l p r e s s u r e p r o f i l e
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