JST Basic Research Programs C 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 Theme Multi-scale Simulation of Condensed-phaseReacting Systems Developing Coarse-Graining Theory and Reconstruction Method of Large-scale Atomic Data Name of Research Director, Belonging and Title: Masataka Nagaoka , Professor, Graduate School of Information Science, Nagoya University

Outline of Research Work

It is a big aim of this project to develop a basic technology on the simulation of condensed-phase chemically 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

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 investigators Name Masataka Nagaoka Nobuaki Koga Affiliation Graduate School of Information Science, Nagoya University Graduate School of Information Science, Nagoya University Information Technology Center, Nagoya University Graduate School of Science, Osaka Prefecture University Graduate School of Information Science, Nagoya University Graduate School of Information Science, Nagoya University Graduate School of Information Science, Nagoya University Graduate School of Information Science, Nagoya University Graduate School of Information Science, Nagoya University Graduate School of Title Professor Terms H18.10-H19.3

Professor

H18.10-H19.3

Katsuya Ishii

Professor

H18.10-H19.3

Toshio Asada

Associate Professor

H18.10-H19.3

Takuya Okamoto

Postdoctoral Fellow D3

H18.10-H19.3

Yoshiyuki Koyano

H18.10-H19.3

Masayoshi Takayanagi Yusuke Ohta

D3

H18.10-H19.3

D2

H18.10-H19.3

Kenta Yamada

D2

H18.10-H19.3

Norio Takenaka

D1

H18.10-H19.3

Information Science, 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 data 2. 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

a) b)

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