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MOLECULAR DYNAMICS STUDY OF LIPOSOMES WITH A NEW COARSE-GRAINED - - PowerPoint PPT Presentation
MOLECULAR DYNAMICS STUDY OF LIPOSOMES WITH A NEW COARSE-GRAINED - - PowerPoint PPT Presentation
MOLECULAR DYNAMICS STUDY OF LIPOSOMES WITH A NEW COARSE-GRAINED MOLECULAR MODEL Wataru SHINODA AIST 2010/08/26 MULTI-SCALE MODELING phenomenological modeling molecular modeling CONTENTS 1. COARSE-GRAINED MOLECULAR MODELING II. VESICLES
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CONTENTS
- 1. COARSE-GRAINED MOLECULAR MODELING
- II. VESICLES
- A. MORPHOLOGY OF LIPID ASSEMBLY
- B. LIPID MIXING EFFECT
- III. EFFECT OF CARBON NANOPARTICLES
(FULLERENES) ON THE MEMBRANES
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SCALE ISSUE FOR MOLECULAR SIMULATION
!"#$%&'(#)*& All atom +,-).#&/)-"0#%&
+ ,
- )
. # & / )
- "
" / & 12-3#& 4"5#&
!"#!$%&#!$"#!$'$%&#!$#!$#!$'(%#!$#!()
!"#$%!&'#$()&*#(+',
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COARSE GRAINING PROCEDURE
MULTI-PROPERTY FITTING
Shinoda et al. Mol. Simul. (2007); Soft Matter (2008); J. Phys. Chem. B (2010).
Target properties: Surface/interfacial tension, density, compressibility, Solvation free energy, transfer free energy, Radial distribution functions from all-atomic model Simple potential functions Intramolecular : harmonic Intermolecular : Coulomb + (LJ12-4 or LJ9-6) Versatility, transferability
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WHAT WE GAIN ... ?
- Mesophase structure
- Self-assembly
- Phase transition
- Correct molecular partition(oil/water)
- Transferability
- Bulk solution
- Interfaces (air/water, oil/water, solid/water etc.)
- Systematic parameterization
- Multiscale(AA-CG) / reverse mapping
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ALKANE MODEL
RDF: Dodecane CT2-CM CT2-CT2 CT-CT CT-CM CM-CM
LJ9-6
CT! CM! CT2!
CH3CH2CH2-
- CH2CH2CH2-
CH3CH2-
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ALKANE-WATER INTERACTION
interface pair interfacial t cial tension interface pair exp MD water/hexane CT-W 49.96 50.0 water/nonane 51.21 51.9 water/dodecane CM-W 52.14 52.9 water/pentadecane
- 52.9
water/heptane CT2-W 50.30 50.1
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ALKANE-WATER INTERACTION
TRANSFER FREE ENERGY
density profile across the hexane/water interface
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SOLUTE-W INTERFACTION
Hydration free energy
ε
Ex) Ethylene glycol - water Steered MD / Jarzynski or Thermodynamic Integration
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C12E2 LAMELLAR PHASE
!"#$%!"#$%&'(')$**+,'-./0'1233456' 7489:'/2;<;,';3=6>'?','2'$9@' !%&%'()'%*+,%-%"%&%.(/)%*+% 01$% !%&%'()'%*+,%-%"%&%.(23%*+%
!!" #$"
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PHASE DIAGRAM C12E6
!" !" !"
Jonsson et al., ‘Surfactants and Polymers in Aqueous Solution’
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PHOSPHATIDYLCHOLINE(PC): LIPID BILAYER
CG-MD has carried out for 100ns in the NPT ensemble
T [K] A [Å A [Å2] d [Å] d [Å] KA [dyn/ [dyn/cm] ϰ [10- [10-20 J] T [K] MD Expt. MD Expt. MD Expt. MD Expt. DMPC 310 62.0 60.6 60.0 ⎯ 226 234 6.90 5.6, ~10 DPPC 323 63.8 64 66.9 67 233 ⎯ 6.41 ~10 POPC 303 64.6 64 66.2 ⎯ 296 ⎯ 5.68 ⎯
Area per lipid: A, repeat spacing: d, area expansion modulus: KA, bending modulus: ϰ
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PHOSPHATIDYLETHANOLAMINE(PE) POPE BILAYER
T [K] A [Å A [Å2] d [Å] d [Å] KA [dyn/ [dyn/cm] ϰ [10- [10-20 J] T [K] MD Expt. MD Expt. MD Expt. MD Expt. POPE 308 60.3 60 67.7 ⎯ 296 ⎯ 6.45 ⎯ !"#$%&#$'()*&+,-./& /0)1(%&#$'()*&22-./ 34"505$#$67&%(')$67&"8&+,&)(9:('6)& 0#"'9&&61(&5$#07(4&'"4:0# ;0%$0#&%$)64$5<6$"'&8<'=6$"'& 0:"'9&1(0%94"<>&)(9:('6)
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ORDER PARAMETER PROFILES
!"#$%&'()$*&+'',+#"-(.&/!& 0"'(%&'()$*&."+12$,31+()$%&/! !
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MAKING A VESICLE
long time.......
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MORPHOLOGY OF LIPID AGGREGATE (VESICLE, BICELLE)
DMPC 1512 DMPC 1000
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VESICLE FORMATION (LARGER SYSTEMS)
DMPC 3500 DMPC 5000
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MORPHOLOGY CHANGE (DMPC)
DMPC1000 DMPC1512 DMPC2500 DMPC3500 DMPC5000
Bicelle (disk) Closed vesicle Energy cost at the bilayer edge vs Bending free energy
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BISTABILITY OF AGGREGATE
DMPC 1512 Closed Vesicle
- Microsec. MD
Bicelle
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ACKNOWLEDGMENTS
T2K, Tsukuba Univ. Next Generation Supercomputer Project CREST-JST
✴CG modeling
- Prof. Michael L Klein (Temple Univ.)
- Prof. Russell DeVane (Temple Univ.)
✴Implementation of CG model to LAMMPS
- Prof. Axel Kohlmeyer (Temple Univ.)
✴Free energy analysis
- Prof. Steven Nielsen (Univ. Texas at Dallas)
- Dr. Takenobu Nakamura (AIST)