ACCESS MAP

2. Establishment of the Research System for Computational Science
High Performance Computing Development

Sanyo Shinkansen(bullet train) line

KOBESannomiya station

Port-Liner line
RIKEN Advanced Institutefor Computational Science

Supercomputational Life Science

Kobe Port Island
K computer Mae station

BayShuttle

KansaiInternational
AirportTo Sannomiya▲

Konan
University

K computer Mae station

Computational
Science Center
Building

Kobe
University
KachoenWe provide support programs for human resource
development in high schools, universities and industries.

RIKEN
AICS
To Kobe Airport▼

SCLS Supercomputer System(Public invitation for research theme proposals)

We offer a K computer-compatible supercomputer
system, “SCLS supercomputer system” to encourage
researchers in life sciences to make active use of the K
computer and the HPCI environment.

Human Network

We hold symposia and seminars to introduce our activities
in the HPCI programs to life science communities. We
plan to support researchers in Japan and abroad in theuse of the K computer.

● JR Shinkansen (Bullet) Train (Arriving at Shin-Kobe Station)
JR Shin-Kobe
Station

Kobe City Subway
2 minutes

Sannomiya Port-Liner line K computer MaeStationstation
15 minutes
3 minutes

RIKEN
AICS

● FlightKansaiInternational
AirportOsakaInternational
AirportBay Shuttle Ferry
30 minutes
Limousine Bus
65 minutes
Limousine Bus
40 minutes

KobeAirport

Port-Liner line
5 minutes

Sannomiya Port-Liner line
Station15 minutes

K computer Maestation

3 minutes

RIKEN
AICS

RIKEN HPCI Program for
Computational Life Sciences
Planning and Coordination Group

Public Relations

We carry out public relations activities aimed atcommunicating our project to the public and gaining
long-term support.

Strategic Programs for Innovative Research Field 1

Osaka Bay

Kobe Airport

Education and Outreach

Education

Osakastation

OSAKA

K computer-use support

Advanced skills and capabilities for parallel programmingare required to use the K computer. Thus, we provide highly
skilled technical staff, and offer technical workshops
including parallel programming and usage of software, tobest utilize computational resources.

Kyoto
station

Kobe City Subway

JR Kobe line

Management of computational resources

We are working to operate and maintain computing
environments required for the efficient use of computational
resources offered by the High Performance Computing
Infrastructure, with the K computer as a primary resource
for a number of researchers (including members of healthcare and pharmaceutical industries) to realize the potentialof researchers in Strategic Field 1.

Shin-Osaka station

Shin-Kobe station

7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 JAPANphone:+81-78-940-5692 fax:+81-78-304-8785 Email: senryaku1@riken.jp

http://www.kobe.riken.jp/stpr1-life/en/
2013.2.28

RIKEN 2013-034

Strategic organization

RIKEN

Computational Life Sciences
Biological phenomena are understood as the result oflarge and complex systems consisting of a variety ofelements (these systems form various levels of biologicalhierarchy such as genomes, biomolecules, cells, andorgans). Our approach involves the simulation ofbiological phenomena by constructing suitable models
based on experimental information on the biologicalsystems, and then inputting these models into thecomputer. The applicability of a given simulation isusually limited by the performance of the computer
employed, making it necessary to divide the system into
subsystems, to coarse-grain the model, and/or to deal
with only short-term phenomena. The K computer
makes it possible to simulate a whole system without
such limitations. The simulation results obtained by the K
computer will reveal the principles of biologicalphenomena that are hidden behind experimental
information and, as a result, will enable greater prediction
and control of biological phenomena. In particular,
focusing on disease as the target problem, we have set
our sights on the ultimate goal of contributing to medicalcare and drug design using the simulations.
Participants ; RIKEN, Nagoya Univ., The Univ. of Tokyo, JAEA, OIST,Tokyo Tech., AIST, Osaka Univ., NIG, Yokohama City Univ.,
Kyoto Univ., ISM (abbreviated, in no particular order)
The "Strategic Programs for Innovative Research" is a five-year
program of the Ministry of Education, Culture, Sports, Science andTechnology (MEXT), aimed at yielding significant social and academic
breakthroughs in five ‘strategic fields’: 1. Supercomputational LifeScience, 2. New Materials and Energy Creation, 3. Projection of globalchange toward the mitigation of natural disasters, 4. Industrial
Innovations, 5. The Origin of Matter and the Universe (utilizing the K
computer system as a primary resource).
The program was launched in April 2011. RIKEN is a representative
organization of Strategic Field 1, and has been developing appliedcomputational life sciences, collaborating with other universities andresearch institutes in Japan.
In addition, we plan to offer a number of technical workshops andseminars to the social and academic communities, and to contributeto the formation of human networks in computational life sciences.

1.Research and Development

1

Simulations of biomolecules
under cellular environments

By using multi-scale molecular dynamics simulations andsingle-particle simulations as research tools, we aim toinvestigate biomolecular structures and functions undercellular environments. Molecular transport acrossbiological membranes, protein/DNA interaction, and signaltransduction are representative targets in the project. We
expect that these simulation studies will contribute to drug
design and understanding of cellular functions.

23

Hierarchical integrated simulation
for predictive medicine

We plan to combine the whole-body musculoskeletal-nervous
system simulator, thrombus simulator, heart simulator, andwhole-body vascular network simulator, and construct anintegrated simulator that can help us understand complex
biological phenomena more thoroughly, and can be applied to awide range of diseases. We expect that these studies willcontribute to the development of effective medical treatments(including those for cardiac diseases such as angina pectoris andmyocardial infarction, and neurological diseases), as well as to theevaluation of drug efficacy, and prognostic prediction.

Simulation applicable todrug design

We plan to construct a methodology
for designing new compounds, and toestablish a method for identifying
protein-compound binding sites; andthen to design and verify drugcandidates against several target
proteins. In addition, we will develop
a method for predicting ligand binding
to proteins with flexible binding sites.
A highly efficient method of drug
design is expected to be establishedthrough this research.

4Large-scale analysis of life data

We will develop a methodology for large-scale analysisof data obtained by cutting-edge technologies such as
the next-generation sequencer, to understand diseases
and biodiversity, investigate characteristics of cells andcancer, and understand the network of biomolecules. We
expect that this research will contribute to personalized
medicine and industrial use of genomic information.