Report Nagaoka

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JST Basic Research ProgramsC R E S T

(Core Research for Evolutional Science and Technology)

Annual Report for Research Work in the fiscal year 2006

Research Area :High Performance Computing for Multi-scale and Multi-physics Phenomena

Research ThemeMulti-scale Simulation of Condensed-phaseReacting Systems Developing Coarse-Graining

Theory and Reconstruction Method of Large-scale Atomic DataName of Research Director, Belonging and Title:

Masataka Nagaoka , Professor, Graduate School of Information Science, Nagoya University


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Outline of Research Work

It is a big aim of this project to develop a basic technology on the simulation of condensed-phasechemically reacting systems (CpCRS). At current year, both a few necessary basic techniques and

the interface QM/MM-IF that enables us to execute ab initio QM/MM-molecular dynamics (MD)

simulation, were developed. The first stage of them will be accomplishment by the end of 2007

fiscal year. Next, for the purpose to develop a new coarse-grained theory, a number of

coarse-graining techniques that enable us to extract some coarse-grained parameters from a

large-scale computational information of atomic motion, were developed, and the construction of the

coarse-graining theory was partially advanced. Because this is a basic and theoretical

development, another three years are expected for its full accomplishment. Finally, to achieve the

CpCRS simulation, both the ensemble MD (EMD) method and the concurrent computing technique

were advanced. Because a satisfactory progress has been achieved, in 2006 fiscal year, as it was

planned, the accomplishment in its first stage should, therefore, be expected at the end of 2007 fiscal

year.

Content of Research Work# Research Work Item: (Theme I) Development of Basic Technology of Condensed-phase

Chemically Reacting Systems Simulation

To develop a basic technology of the condensed-phase chemically reacting systems (CpCRS)

simulation, first, some parameter-preparing tools for constructing QM/MM Hamiltonians were

developed. Second, the algorithm to implement the structural optimization scheme via the free

energy gradient method on the semi-empirical QM/MM-molecular dynamics (MD) simulation

program (ROAR2.1), was examined. Third, a technical, basic policy to develop the interface

QM/MM-IF of ab initio molecular orbital (MO) method program GAUSSIAN and an MD program

AMBER, was fixed to realize ab initio QM/MM-MD simulation, and its -version was made.

# Research Work Item: (Theme II) Development of Coarse-grained Theory based on

Condensed-phase Chemically Reacting Systems Simulation

For the purpose to develop a new coarse-grained theory, the QM/MM-MD simulations were

applied to some examples (HF aqueous solution and ammonia aqueous solution, etc.). At the

same time, the coarse-graining technique for extract some coarse-grained parameters (i.e., number

density distribution and temperature distribution, etc.) from a large-scale computational information

of atomic motion (i.e., time series data of positions and momenta of individual atoms, etc.), was

studied and developed. Taking the space-time number density distribution thus obtained as an


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initial input distribution, the development of systematic reconstruction techniques of space-time

distributions started on the basis of the maximum entropy principle, and a partial construction of the

coarse-grained theory was also started.

# Research Work Item: (Theme III) Realization of Condensed-phase Chemically Reacting

Systems Simulation by Concurrent Computing Technique

A basic architecture of the ensemble MD (EMD) method was developed utilizing a number of

MD calculations. Assuming a lot of initial conditions chosen systematically from an initial

phase-distribution corresponding to a real thermodynamic state, a number of MD trajectories were

executed concurrently to achieve the CpCRS simulation by the computer server that consists of

multi-CPUs, (nodes, or cores). The concurrent computing technique was developed as well.

Formation of Research Work(1) Nagaoka group

i) Research investigatorsName Affiliation Title Terms

MasatakaNagaoka

Graduate School ofInformation Science,

Nagoya University

Professor H18.10-H19.3

Nobuaki Koga Graduate School ofInformation Science,Nagoya University


Katsuya Ishii Information Technology

Center,

Nagoya University


Toshio Asada Graduate School of

Science,

Osaka PrefectureUniversity

Associate

Professor

H18.10-H19.3

Takuya Okamoto Graduate School ofInformation Science,

Nagoya University

Postdoctoral

Fellow

H18.10-H19.3

Yoshiyuki Koyano Graduate School of

Information Science,

Nagoya University

D3 H18.10-H19.3

Masayoshi

Takayanagi

Graduate School of


Nagoya University

D3 H18.10-H19.3

Yusuke Ohta Graduate School of


Nagoya University

D2 H18.10-H19.3

Kenta Yamada Graduate School ofInformation Science,

Nagoya University

D2 H18.10-H19.3

Norio Takenaka Graduate School of D1 H18.10-H19.3


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Nagoya University

ii)Research Work Items# Research Work Item: (Theme I) Development of Basic Technology of Condensed-phase

Chemically Reacting Systems Simulation

1. Development of the parameter-calibrating software for QM/MM-MD simulation (Part I)2. Implementation of the free-energy gradient method for QM/MM-MD simulation (Part I)3. Development of the QM/MM-MD simulation interface

# Research Work Item: (Theme II) Development of Coarse-grained Theory based on

Condensed-phase Chemically Reacting Systems Simulation

1. Development of the coarse-graining theory of MD simulation data2. Development of the reconstruction technique on the basis of maximum entropy method

# Research Work Item: (Theme III) Realization of Condensed-phase Chemically Reacting

Systems Simulation by Concurrent Computing Technique

1. Technique development and its efficiency improvement of statistical information generation

through concurrent computing

Publication of Research Results Publication of Thesis (The original Work) Number of Publications ( 0 times-Domestic, 2 times-International) Detailed Information of Thesis

1. T. Asada, T. Takahashi, S. Koseki, Theoretical Study of Environmental Effects for Proton

Transfer Reaction through the Peptide Bond in a Model System, Theoretical Chemical Accounts,

2007, in press.

2. M.Takayanagi, H.Okumura, M.Nagaoka Anisotropic Structural Relaxation and Its Correlation

with the Excess Energy Diffusion in the Incipient Process of Photodissociated MbCO:

High-Resolution Analysis via Ensemble Perturbation Method, Journal of Physical Chemistry B,

111, 4, 864-869Feb. 2007

Patent Application Cumulative Number

1) Patent Applications in the fiscal year 2006 (Domestic- 0 Cases, Oversea- 0 Cases)2) Cumulative number of Patent Applications for the research period of CREST

(Domestic- 0 Cases, Oversea- 0 Cases)

3) Details for this fiscal year


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a) Domestic Application (0 cases)b) Oversea Application (0 Cases)

Documents

Report Nagaoka