RIKEN Center for Computational Science

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All-atom Molecular Dynamics Simulation of the Bacterial Cytoplasm

How biomolecules behave in crowded cellular environments has been an important question in life science. Researchers at RIKEN and Michigan State University made an atomic model of the bacterial cytoplasm using the existing experimental information. They also developed highly-parallelized MD software, GENESIS, and carried out large-scale MD simulations of the model by using GENESIS on K computer. From detailed analysis of the simulation trajectories, they discovered strange behaviors of biomolecules in the cytoplasm.

Post-K Priority Issue 1: Innovative drug discovery infrastructure through functional control of biomolecular systems (Only in Japanese)

RIKEN Channel (4'53'')


Into the Future with the Post-K Computer -Solutions to Global Challenges-

The K computer has been a powerful scientific tool that has made possible many world-leading research results. RIKEN AICS is now developing a new supercomputer, the post-K computer, scheduled to be launched around 2020. This video introduces what the post-K computer is expected to achieve and how it will be used for advanced scientific research as well as for solving challenging issues affecting society.

Post-K Supercomputer Project

RIKEN Channel (8'39'')


A Better Future with the Post-K Computer(for Children)

The K computer is a powerful scientific tool that is being used for world-leading research. RIKEN AICS is now developing a new supercomputer, the Post-K, scheduled to be launched around 2020. This video introduces to children in an easy and understandable manner what the Post-K computer is expected to achieve and how it will be used for solving challenging issues people face.

Post-K Supercomputer Project

RIKEN Channel (6'37'')


K computer Simulation: Prevention and Mitigation of Natural Disasters (full ver.)

This video gives an overall picture of the integrated total city simulation that is being developed in cooperation with local governments with the goal to prevent or mitigate damage from earthquakes using the K computer, which has made many world-class achievements, as well as the types of research that will be carried out on the post-K computer.

Short or digest version (RIKEN Channel (2'10'')

RIKEN Channel (9'55'')


Multi Scale Modeling of Chromatin and Nucleosomes

Double-stranded DNA in which genetic information is encoded is folded into compact protein-DNA complex structures, called “chromatin", in a nucleus of cell. When DNA is transcribed into RNA for gene expression, chromatin has to be in relaxed conformations. These conformational changes are regulated by chemical modifications of histones and so on. To study the complicated mechanism of life, three-dimensional structures of nucleosomes that compose the chromatin were constructed virtually and molecular dynamics (MD) simulations based on physical laws such as the equation of motion were conducted using the K computer. Such MD calculations enable us to simulate and observe dynamic behaviors of chromatin structures precisely.

Strategic Programs for Innovative Research Field 1 Supercomputational Life Science

SCLS-Channel (5'00'')


K computer Simulation: Lithium-ion Battery -From a Universe of Molecules to Batteries of the Future-

Have you ever seen the inside of lithium-ion battery? Using Japanese supercomputer K, the 1st supercomputer which exceeds 10peta FLOPS in the world, scientists observed atomic-scale processes at the electrode of lithium-ion batteries, allowing them to identify a material that could improve the charging time, voltage capacity and reliability of these batteries for long-term and renewable energy storage solutions.
This video was created for outreach purpose and introduces how lithium-ion battery works and what kind of challenges the scientists are facing as well as the simulations at the molecular level of the inside of the battery.
The scientists were awarded Gottfried Wagener Prize 2015 Energy & Industry.

Short or digest version (RIKEN Channel (1'53'')

RIKEN Channel (7'51'')


K computer: Automobile Aerodynamic Simulation -Catch the wind of the next generation-(full ver.)

Supercomputer K is a powerful tool for science. This video explains how K is being used for aerodynamic simulation to design autos. It also shows wind tunnel experiments at a car manufacturer which is usually closed to the public. Researchers talk about their efforts to strengthen Japan’s international competitiveness by using supercomputers for aerodynamic analysis.

Short or digest version (RIKEN Channel (2'03'')

RIKEN Channel (8'28"")


Multi-scale Multi-physics Heart Simulator UT-Heart

The heart is a pump circulating blood containing nutrients and oxygen to the whole body. In the heart simulator, contraction and relaxation of muscle are reproduced based on the statistical behavior of molecules, which in turn are strongly coupled with the computation of blood flow and pressure. By reproducing a highly realistic human heart whose behavior strictly follows the physical and physiological principles in the computer, the simulator can help doctors choose a treatment option for heart disease patients by accurately predicting its outcome. In fact, projects to determine the optimal operative strategy for individual patients by performing in silico tailor-made cardiac surgeries have already been under way in collaboration with the cardiac surgeons.
Win an award for the BEST VISUALIZATION OR SIMULATION at SIGGRAPH 2015, the 42nd annual Computer Animation Fetival

Strategic Programs for Innovative Research Field 1 Supercomputational Life Science

SCLS-Channel (5'15'')


The Development of the K computer

Development on the K computer began in 2006, and was completed in June 2012. The supercomputer was opened for public use at the end of September. With its phenomenal performance of 10 petaflops, meaning 10 quadrillion operations per second, this machine promises to create a new future. This video presents a picture of the development, manufacture, and installation of the supercomputer, along with an explanation of the new network structure that was developed for it.
Full version video is available during the K computer site tour in Kobe, Japan and some international events.

RIKEN Channel (3'54"")