First French-Japanese Workshop Petascale Applications, Algorithms and Programming(PAAP). A grand challenge application for the next-generation supercomputer in the soft nano-science. Fumio Hirata Institute for Molecular Science. Grand challenge applications in nano-science
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First French-Japanese Workshop
Petascale Applications, Algorithms and Programming(PAAP)
A grand challenge application
for the next-generation supercomputer in the soft nano-science
Institute for Molecular Science
Grand challenge applications in nano-science
(The next-generation Integrated Nanoscience Simulations)
（１）Material science for the information technology
（post-silico electronic devise)
molecular switch, nano-wire, etc.
（２）Material science for the biotechnology
virus, cancer drug, drug delivery, etc.
（3）Material science related to effective use of the solar energy
(environment and energy shortage)
solar cells, enzyme (cellulase), super capacitor, etc.
These problems are “grand challenges” in dual senses.
1. important for the society (economy, medicine, environment…)
2. unsolved scientific problems
What is “nanoscience”?
Why makes “nanoscience” so challenging?
(10-11〜10-8 M)(10-9〜10-6 M) (10-6〜 )
micro chip (IC, LSI)
Multi-scale & multi-physics
Molecular (microscopic) theories to be applied to nano-phenomena
Hard nano-phenomena: (ex. electron conduction in molecular wire)
Band theory, DFT, Hubbard model,
ab-initio MD (Car-Parrinello), QED
Soft nano-phenomena: (ex. Enzymatic reactions)
Molecular simulation (MC, MD), Car-Parrinello method
Generalized ensemble method (Replica exchange, etc.)
Statistical mechanics of liquids (RISM, ….)
Molecular orbital(MO) theory (FMO, DFT, ONIOM)
“None of a single theory can explain an entire nano-phenomenon”
Enzyme to decompose
・human being does not have
・exist in bacteria (yeast)
We use the peta machine to design an enzyme to decompose
What is the enzimatic reaction?
Why is it difficult to treat by theory?
accelerate a reaction
catalysts：enhances reaction rate dramatically.
(1000 to 1 million times）
example: binap by Prof. Noyori
enzyme（biocatalyst）：catalyses almost all
chemical reactions occurring in our body
（１）it works in water（theory of water is essential）
（２）it should accommodate substrate molecules
in the active-site（molecular recognition）
The reaction to alcohol from cellulose （２ steps）
Enzymes concern both reactions, but the mechanism
of the first step has not been well understood.
In any case, “water (solvent) plays essential role”
RISM-SCF theory predicts chemical reactions in solutions
H3N + CH3Cl H3N+–CH3 + Cl–
oprotein structureprotein data bank(PDB)
o the solute-solvent interactions, uuv(r)
o the correlation functions of solvent, wvv(r), hvv(r)
o temperature,b= 1/kBT;the density of solvent, r
gO(r) > 2
Isosurface representation of the 3D-distribution function of water oxygen
The distribution function of solvent atoms normalized by solvent density
gg(r) =hg(r) + 1 gg(r) = rg(r) / r
Results (1-1) Cavity 1: 3D distribution
(Imai, Hiraoka, FH， JACS communcation,
o Hydration structure in Cavity 1
determined by 3D-RISM is in
excellent agreement with the
gO(r) > 8
gH(r) > 8
(a) 3D distribution functions of water
(b) Hydration model reproduced from (a)
(c) X-ray structure
Aquaporin (water channel)
Works in our body to control water concentration
(kidney, eye, etc.)
Questions asked for aquaprins.
What is the conduction mechanism of aquaporin?
What is the gating mechanism of the channels?
Why aquaporin does not permeate proton?
Does aquaporin permeate Ions? How and what extent?
What is the role of c-GMP in aquaporin as an ion
Ion channel ?
Enzymatic reaction to decompose cellulose
“Water is one of reacting species (substrate)”
“The position of water molecule in the reaction
Pocket is essential.”
The finding so far is a big step toward final solution, but not
quite enough to predict entire enzymatic reaction.
Huge amount of calculation should be made.
Key words,“3D-FFT” and “Eigen-value-problem”
Just a multiplication
in the Fourier space
Solute-solvent interaction potential
1.Potential parameter for solute and solvent molecules
2. Calculate the interaction potential energy
3. Initial value of
4. Convert by 3D-FFT
5. Solve 3D-RISM in k-space
6. Inverse transform of c by
7. Solve HNC eq. to get
8. Go back to 4 if is not converged
9. Calculate 3D-distribution function from and c
for fragment pair
Fragment pair SCF
“Fast eigen-value-problem solver
If this became reality, the protein folding can be done.
We do not “simulate” the earth, but
try to “save” it from the energy and
But, in order make it reality, we need 3D-FFT and
eigen-value-problem solver well tuned for the next
Thank you for your attention.