Strategic Programs for Innovative Research Field 1 Supercomputational Life Science10

2014.3 Vol.
CONTENTS
Open Up SPECIAL TALK

Discussion meeting

Toward integrated simulation of
biological systems beyond hierarchy

Developing models for reproducing and predicting biologicalphenomena of all scales, from molecular motions to behaviors
of tissues and organs
Kazuya Shimizu ／ Naoto Yamamura ／ Takumi Washio
The University of TokyoZOOM IN

2

Close-up on SCLS Research

Theme 1 Simulations of biomolecules under cellular environments

Exploring the biomolecular world throughmolecular dynamics free energy calculation
Yoshiteru Yonetani

Japan Atomic Energy Agency

4

Theme 3 Hierarchical integrated simulation for predictive medicine

Integrated simulation of whole-body
musculoskeletal-nervous system
Ko Ayusawa

The University of Tokyo

5

Theme 4 Large-scale analysis of life data

Towards elucidation and control of the functionsof brown adipocytes which contribute to energy
expenditure
Hiromi Daiyasu

Osaka University

6

SCLS Gotcha!

HPCI Human Resources Fostering Programsby the AIST Computational Biology Research Center
Short Lecture at the K computer Booth in SC1377

Discussion meeting

Toward integrated simulation of
biological systems beyond hierarchy

Developing models for reproducing and predicting biological phenomena of all scales,from molecular motions to behaviors of tissues and organs

Theme 3 “Hierarchical integrated simulation for predictive medicine” (leader: Prof. Shu Takagi, The University ofTokyo) aims to integrate simulators of biological systems (thrombosis, heart, muscles and skeleton, cerebral nervous
system, etc.) that were separately developed in the grand challenge program that ended last spring in order toreproduce the complicated processes involved in various diseases including myocardial infarction, and contribute to
the prediction of pathology and treatment of these diseases. The new integrated simulation model to be developed
is required to achieve simultaneous reproduction on both the multi-scale (reproduction of biological phenomenaof all scales from molecular level to the entire body) and multi-physical (including mechanical, biochemical andelectrical phenomena) levels by making effective use of the powerful computer resources of the K computer. We
interviewed three researchers who are working toward the development of a simulation system for Theme 3 while
confronting many issues.
Research Associate, School of Engineering, The University of Tokyo
Research Associate, School of Engineering, The University of Tokyo
Research Associate Professor, Graduate School of Frontier Science, The University of Tokyo

Models to be constructed by hierarchical integration− In what actual research are you engaged?

Shimizu: Dr. Yamamura and I are developing
an integrated nervous and musculoskeletal
simulation model of the entire human body,which can reproduce micro- to macro-scale
activities that occur in the body, aiming toelucidate motor dysfunctions caused byneurological disorders, such as Parkinson’s
disease. The motor command from the brain
is modified in various ways in the signaling pathway, such as the spinal cord, andfinally induces motion, such as contractionof a muscle and articular movement. Oneof our goals is to reproduce such a series ofprocesses with a computer, and contributeto unveiling the causes and treatment of diseases. I am mainly in charge of constructing
a neural network model in the spinal cord.
Yamamura: I am developing a finite element simulator of the musculoskeletal
system. The musculoskeletal simulator
receives motor commands from the spinal
cord and generates a joint movement asa result of muscle contraction. Our collaborators are developing simulators of
the central nervous system for generating

the motor commands. We will finally integrate simulators of the brain, spinal cord
and musculoskeletal system.
Washio: Our group is developing a heart
simulator (UT-Heart), which can reproduce
a living heart by using the K computer. At
present, we are modeling cardiac beat. Basically, we are trying to reproduce the pulsation of the heart by solving equations
that follow the laws of physics based on
the movements of each molecule. However, individual molecules do not movealone, but affect each other and are also
affected by peripheral muscles. Thus, it isdifficult to find equations that describe
average movements of the molecules. Besides, we need to not only reproduce themovements of the myocardia by calculating the forces acting on the molecules
and larger macroscopic entities, but also
to solve the interactions between the
blood, which is fluid pumped out fromthe heart, and the ventricular wall. The
flow of blood cannot be calculated only
for the heart alone - the flow in the entire
body needs to be reproduced. Therefore,
the huge capacity of the K computer is re-

Basic information for modeling is difficult to acquire− What are the most difficult points
for constructing the simulators?

Shimizu: Before getting involved in life science, I mainly studied simulation of fluids.
For example, in engineering simulation,
basic and detailed blueprints are available, and it is relatively easy to performmaterial tests for collecting information
required for modeling, such as resistanceand thermal conductivity. But in the case

2 BioSupercomputing Newsletter Vol.10of the human body, we cannot open the
body and measure the values; and thus itis difficult to obtain basic information.
Yamamura: I had developed a simulator
for sheet metal forming process before I
started to study living bodies, and I also
know the difficulty of collecting basic dataon the human body. We particularly wantto measure the “living human body”, andwant to use non-invasive measurement

Kazuya Shimizu
Naoto Yamamura
Takumi Washio

quired to achieve consistent computationfrom molecular motions to systemic circulation, otherwise we cannot reproduce
the phenomena well.
Yamamura: We are also developing models for skeletal muscle contraction fromthe molecular level, like the myocardialmodel which Dr. Washio developed.
Shimizu: Neurons exchange electrical signals by closing and opening channels on
the membranes of cells, and changing ion
concentrations. Thus, for signal transmission simulation, we are also constructing
models which may not be as small as molecules, but are much smaller than cells.
Compared to the simulation of the brain,
we do not need large computer resources
for calculating the necessary signaling
for moving a joint. However, when we
think about reproducing movements thatinvolve the entire body, such as “walking
and running”, even the spinal cord model
will need a considerably large computerresources.

methods, but it is difficult. The differencesamong individuals are also large. We areusing MRI data for the shapes of skeletal
muscles, but MRI does not show the thin
aponeurosis, which transmits the force ofmuscle contraction to the bone. We haveto consult anatomical references for datathat we cannot measure.
Shimizu: I think the nervous system iseven more difficult to measure.

Kazuya Shimizu

Simulation science has big
possibilities. It can surely play animportant role in the progress oflife science and medicine.

Naoto Yamamura

Our simulators will
reveal the mechanismsof living bodies that wecannot see now, and thisis one of the pleasures of
R&D for me.

Takumi Washio

I would like to achieve early
implementation, and create a new
age when physicians will senddata about heart disease patientsto be analyzed by the simulator,
and use the results for predicting
risks and deciding treatment.

Simulator of the cerebral
nervous system

Ventricles reproducedby the heart simulator(UT-Heart)
Simulator of
the cerebrospinal
nervous system

Simulator of
the musculoskeletal
systemSchematic diagram of an integrated simulationof the musculoskeletal and nervous system

Washio: The difficulty is the same for theheart. For example, CT and MRI data are
available for the shape of the heart, but
the heart is always beating. We do notknow the accurate natural shape of theliving human heart, and it varies amongindividuals. Myocardia also have a very

we need to dissect the body or stop theheart. What we can do now is to collectas much data and experimental results as
possible, and construct a model that can
reproduce all characteristic phenomena.

complicated structure with myofibers
running through them while making
twists. The heart has a very clever structure, and ejects about 60% of the blood
just by 15% contraction of the myocardia.
In order to know its detailed structurewith current measurement techniques,

Toward development of simulators that can contribute to society
Washio: Luckily, the K computer has improved the reliability of heart simulation. It
has aroused interest among experimental
molecular biologists and cardiac surgeonsin simulation. Cooperative relations withthem are expanding, and they are helping us in experiments and providing data.
There have also been inquiries about theavailability of simulation for deciding an
operational method for treating patientswith an innate heart defect. A challenge
has already started to unveil the mechanism of developing hypertrophic cardiomyopathy by using the heart simulator.
I believe that the heart simulator will be
useful for both clinical and basic medicine,and the results will further improve thesimulation models.

Yamamura: It is wonderful that simulation scientists are cooperating with medical personnel and molecular biologists,and enhance each other. The integrated
simulator for the nerves and entire musculoskeletal system is still in the stage ofdeveloping models, but I believe it will
attract the attention of medical personnel
and scientists.
Shimizu: For example, the mechanism
by which Parkinson’s disease develops is
not fully understood. The situation will
be greatly altered if simulators reveal themechanism and provide useful information for deciding treatment plans. It is
one of our important roles to show thatcomputer simulation is useful for develop-●See the URL below for more detailed information on this report.
http://www.kobe.riken.jp/stpr1-life/en/newsletter/Vol.10/openup.html

ment of new medicines and new medical
treatments.
Washio: Hierarchical integrated simulation may connect physicians in medical
settings and molecular biologists, between whom there is little communication at present. For this, it is important toimprove the reliability of simulators.
Yamamura: So we have to produce reliable results that can contribute to society.
Washio: I think it is the goal for us, who
are involved in this project, to develop
and elaborate simulators that are notmere tools for writing research papers,
but are acknowledged by people as a useful technology.

BioSupercomputing Newsletter Vol.10 3

Close-up on SCLS Research

Theme 1 Simulations of biomolecules under cellular environments

Exploring the biomolecular world through molecular
dynamics free energy calculation
Quantum Beam Science Directorate, Japan Atomic Energy Agency

Yoshiteru Yonetani

Free energy is an important quantity forbiological functions. Fig. 1 shows our recent

densed molecular systems. For example,

ing the molecular dynamics method called

understanding various phenomena of conliquid water is transformed into ice as tem-

calculation on a protein, lac repressor. UsAdaptive Biasing Force [1], we revealed not

perature decreases. This is because the free

only the dissociation process of the DNA-

that in the liquid sate. Free energy calcula-free energy changes [2].

energy in the ice state becomes lower thantion using molecular dynamics simulation*

protein complex, but also the accompanied
Our result is significant in the following

allows us to predict such molecular phenom-

two points. One is that we gained an un-

The biomolecular world in cells, including

binding proteins move around DNA?” Ourena.

DNA and proteins, follows the same physicalrule. Thus, by calculating the free energy, we
can understand various biological phenom-

ena such as molecular recognition, structureformation and molecular transportation,
However, in biological systems, free energy
is difficult to calculate. This is because themolecular structure is very complex and ischanging with a large fluctuation. It takes

derstanding of the question, “How do DNA-

free energy result found that dissociation of
the protein from DNA is rare, and that theprotein is likely to slide on the DNA. This find-ing concerns an unsolved problem, “Howdo DNA-binding proteins find their target
sequence?” This problem is one of the most
attractive topics in biology, and many researchers are puzzling over the problem.

The other significant point of our study isquite a long computing time to reproduce

about the DNA sequence recognition. The

Thanks to the recent increase of comput-

bases, A, T, G and C. Among them, the lacsuch various molecular structures.

ing power such as the K computer, biomolecules became an attainable target of the freeenergy calculation, and many researchers aretackling related problems. We are particularlyinterested in the interaction between DNA
and proteins. By calculating the free energy,

we will reveal the molecular behavior andsequence of DNA consists of four kinds ofprotein binding. The result is considered to

be useful for elucidating various intracellular
events such as gene expression.

There remain several problems to besolved. Present computer simulation cantreat only a small part of the protein andDNA, but next-generation Exa-scale super-computing will enable us to treating muchlarger molecules. For example, the simulation of a compactly folded DNA structure,
nucleosome, will become possible. Exa-scale
supercomputing will reveal the atomic-level

behavior of such larger molecules, and provide us with a more realistic picture of the
DNA-protein interactions.

repressor protein binds specifically to theregion with GTGAGCG. This has been clarified experimentally. However, the reason* Molecular dynamics simulation: Computer simulation
method to derive trajectories of many-particle systems
by solving Newton's equations of motion.

sequence-dependent binding? Our free

References

remained unclear. What is the origin for theenergy results answered this question by
providing an atomic-level picture of DNA-

[1] E. Darve, D. Rodríguez-Gómez, A. Pohorille, J. Chem.
Phys., 128, 144120 (2008).
[2] Y. Yonetani, H. Kono, J. Phys. Chem. B, 117, 7535 (2013).

Lac repressor

Fig. 1: Dissociation process of the DNA-lac repressor complex●See the URL on the right for detailed information on this report. http://www.kobe.riken.jp/stpr1-life/en/newsletter/Vol.10/zoomin01.html

4 BioSupercomputing Newsletter Vol.10

Close-up on SCLS Research

Theme 3 Hierarchical integrated simulation for predictive medicine

Integrated simulation of whole-body
musculoskeletal-nervous system
Department of Mechano-Informatics,
Graduate School of Information Science and Technology, The University of TokyoKo Ayusawa

One of our major goals is to understandresearch groups with different researchputing using a supercomputer. Parkinson’s

Our group has actually been working on hu-

Parkinson’s disease through numerical comdisease causes a wide spectrum of disorders

including tremor in a limb, muscle rigidityand difficulty in maintenance of posturalbalance. Insufficiency of a neurotransmitter

called dopamine in the brain is considered
to be the cause. However, the mechanism

responsible for systemic disturbance of

motor function by dopamine insufficiency
in the brain is still poorly understood. This
study aims to elucidate the pathway fromintracerebral phenomena to whole-body

motion, and tries to clarify the mechanismof neurological disorders responsible forbackgrounds are cooperating on the project.
manoid robots. To study a humanoid robot
is to understand human beings. Throughmodeling of the human skeleton, muscles

and nerves based on robot technologies, it
is possible to estimate muscular tension andidentify neural reflex networks from human

it to a skeletal muscle model consisting of

oped a whole-body musculoskeletal model

model which combines the simple muscle

motion measurements. Our group has devel-with 53 bone links and 1,206 segmentalizedmuscles and tendons, which makes it possible to estimate muscular tension during
exercise on a real-time basis (Fig. 1).

In regard to the aforementioned musculo-

motor dysfunction through a large-scale

skeletal model, we are trying to connect

and whole-body musculoskeletal system. A

level muscle activity simulation and asimulation integrating the brain, spinal cordsupercomputer is necessary for such a largescale simulation.

In whole-body integrated simulation, vari-

ous simulations including the cerebrospinal
nervous system, cellular-level muscle con-traction and whole-body musculoskeletalmotion are integrated. Therefore, several

a detailed muscle model to a cellular-

cerebrospinal nerve system simulation incooperation with other research groups.
Since the aforementioned model assumes
usual computational calculation, a simple
wire model is used for muscles. In thisresearch, we construct a spinal nerve system

network throughout the body, and connect

Fig. 1: Example of visual representation of muscle tension
estimation. Red-colored muscles are more active than green ones.

muscle fibers. Simulation using an upper arm

model and the spinal nerve system network

can reproduce a phenomenon called the
myotatic reflex on the muscles of the upperarm (Fig. 2). This phenomenon is a reflexive
muscle contraction caused by muscle

stretch. When a neural signal for muscle

stretch reaches the spinal cord, anothersignal to contract the muscle is sent via
the spinal cord. Only a simulation throughconnection of the musculoskeletal model tothe spinal nerve network could reproduce

such a phenomenon. By connecting it
further with a brain model, we plan to realize
a simulation in which brain signals activate
skeletal muscles throughout the body.

Fig. 2: Simulation connecting a musculoskeletal model of the upper arm and a spinal nerve model.

●See the URL on the right for detailed information on this report. http://www.kobe.riken.jp/stpr1-life/en/newsletter/Vol.10/zoomin02.html

BioSupercomputing Newsletter Vol.10 5

Close-up on SCLS Research

Theme 4 Large-scale analysis of life data

Towards elucidation and control of the functions of brown
adipocytes which contribute to energy expenditure
Department of Bioinformatic Engineering,
Graduate School of Information Science and Technology, Osaka University

Hiromi Daiyasu

Adipocytes, usually regarded as a nui-a beige adipocyte, and contributes to heat

white adipocytes and brown adipocytes.

cyte (Fig. 1). However, both the browningsance, are roughly divided into two types,

production together with the brown adipo-

White adipocytes play a role in accumula-mechanism and the relationship between

tion of fat which acts as an energy source, asbrown adipocytes and beige adipocytes arewell as in secretion of bioactive substances.

still unknown. It is thought that there are

Brown adipocytes are known to have theseveral pathways leading to lipolysis, butfunction of consuming energy through li-

both the master gene that dominates thepolysis for heat production to regulate bodytemperature. Human brown adipocytes

whole system of energy metabolism and theregulatory relationship, which characterize

tem remain to be clarified. The elucidation of

to analyze expression data measured every

overall mechanisms which regulate the sys-

were believed to disappear after birth, but
it has been revealed recently that they ex-these mechanisms would enable control of

ist in adults, and their metabolism is closely

the system, which would lead to the preven-involved in common diseases includingtion of common diseases and improvement

obesity and diabetes. Therefore, they are be-of symptoms.

ing intensively investigated from the aspects

It is known that human brown adipocytesof both basic and clinical sciences. Previous

share several characteristics with mouseof the genes and mechanisms involved in li-function of brown adipocytes and regulatory

studies using mice have uncovered the parts

beige adipocytes. Our group elucidates thepolysis by brown adipocytes. The sympathetic nervous system stimulates β-adrenergic

which results in heat production in mito-

brown adipocyte has been identified, whichby cold stimulation (browning). It is called

powers of conventional computers. The K

computer can process this massive data, andenables estimation of the gene regulatory
network (Fig. 2).

Our analyses with the K computers sug-from those in brown adipocytes, rapidly in-work in beige adipocytes, which are different
duce UCP-1 to regulate fat metabolism.

We aim to obtain knowledge useful forgene expression from the adipose tissues of

the remedy of common diseases by eluci-

microarray and RNA-seq. Our group analyzed

functioning in adipocytes with the approachmice reared under cold stimulation (4ºC) by

is differentiated from the white adipocyte

the processing of such data is beyond thecolleagues of the Graduate School of Agriculgating adipocytes using mice, and measured

1. In addition, a third adipocyte similar to thecomputational resources are required, andgest that the genes and the pathways atture, Kyoto University. Kawada’s lab is investi-

chondria by a membrane protein called UCP-

few hours on about 25,000 genes, enormousmechanisms of energy metabolism in collaboration with Prof. Teruo Kawada and his

receptors to activate its signaling pathway,

white, brown and beige adipocytes. In orderthese data to identify the genes and theirMesenchymal stem cell

Beige adipocyte

dating the regulatory relationships of genes
described above.

Brown adipocyte

Brown preadipocyte

White preadipocyte
Mitochondria
NucleusFat droplet

White adipocyte

Beige adipocyte

Fig. 1: Classes of adipocytes and their differentiation
Dots in mitochondria show UCP-1.

Brown adipocyte

Fig. 2: Regulatory network of two types of adipocytes under cold stimulation
Genes with large differential expression are shown by circles. The red line and blueline show relationships for up-regulation and down-regulation, respectively.
Blue circles show a gene detected in both networks.

●See the URL on the right for detailed information on this report. http://www.kobe.riken.jp/stpr1-life/en/newsletter/Vol.10/zoomin03.html

6 BioSupercomputing Newsletter Vol.10

SCLS
HPCI Human Resources Fostering Programs by the
AIST Computational Biology Research Center
The Computational Biology ResearchCenter (CBRC) of the National Institute ofAdvanced Industrial Science and Technology(AIST) conducts SCLS’s human resources
fostering programs in Odaiba in Tokyo, an
artificial island which has an appearance
very similar to the Port Island in Kobe. The
results of research using large-scale computer
systems are often reported in various meetings held in many parts of Japan. However,
it is still not easy for researchers in the fieldof life science to use large-scale computing
systems even though they wish to try themout. Therefore, CBRC decided to promote

HPCI tutorialhuman resources development with the aim ofincreasing the number of users of such computing systems, and fostering people who can
carry out research using large-scale computing systems like the K computer.
The main feature of human resources fostering programs conducted here is a welldeveloped educational system that offers fourlearning styles:“workshops”that transmit
the outcome and prospects of research about
large-scale computing systems to the generalpublic;“seminars”given by many leading-edge
researchers;“tutorials”that provide handson training using one personal computer perperson; and“e-learning courses”which participants can take in their spare time.
In particular, seminars are not only open to
the public but also designated as a subject
for which a credit may be awarded in cooperation with the Graduate School of Frontier
Sciences, the University of Tokyo. They are
distributed to three campuses of the University of Tokyo via video-conferencing systems.
In the hope of inspiring students who listen to

SCLS

Example of an e-learning screen: Slides
are changed according to the progress ofa lecture video.

the same lecture as professional researchersdo, including company employees, we holdthese seminars every year.
The curriculum of tutorials is focused onoffering practical exercises. It ranges from giving basic knowledge to how to analyze various biological data according to commonlyused analysis pipeline.
In the e-learning course, about 60 lectures
on various topics from basics to advanced
applications are available (as of January2014), and new lecture videos are added every
year. We hope you will join us.
For more details, please see our website at:
http://hpci.cbrc.jp/

SCLS short lecture

Short Lecture at the K computer
Booth in SC13The Supercomputing Conference 2013
(SC13) was held in Denver, United States,in November 18 to 22. The RIKEN HPCI
Program for Computational Life Sciences
sent two people to the conference: Atsushi
Miyauchi, a research scientist of the High
Performance Computing Development Team,and Erika Jinnai, a member of the Planningand Coordination Team, to collect information on supercomputers in the world.
,
SC13 is the world s biggest international

Staff members explaining research activities
at our K computer boothconference on high-performance computing
technology, and the year marked the 25thyear since it was first held. It has provided
opportunities for information exchange,
discussion and collaboration, which help
promote utilization of high-performancecomputing (HPC), and which are useful for
research and education aimed at scientificdevelopment and greater knowledge.
In this conference, in addition to sessions
and thesis presentations, the supercomputer
ranking“Top 500”and the Gordon Bell
Prize are announced, and exhibitionbooths of universities, research institutions and companies are set up.
The RIKEN Advanced Institute for
Computational Science, which operates
and manages the K computer, set up
an exhibition booth as it did last year
to demonstrate research activities using
the K computer, and held short lecturesby lecturers from related organizations(including the Strategic Programs forInnovative Research).
SCLS held a lecture titled“Collaborationof Education and Outreach Activities”witha desire to share our activities and knowledge, and provide an opportunity to globally develop collaborative relations in joint
research, education and outreach activities.
After the lecture, we received questions
about education in bioinformatics and othersubjects, and were able to share information with U.S. government agencies whichwere concentrating on outreach activities.
In addition, the lecture helped us to have interactions with organizations which showedinterest in our activities, as well as Japanese
education and outreach activities. Throughthe lecture, we became aware of possibilities
to expand our activities.

BioSupercomputing Newsletter Vol.10 7

News & EventsFirst call for research theme proposals for access to the SCLS supercomputer system during FY 2014

We will provide the computational resources of the SCLS supercomputer system, which is compatible with the K computer, to biologists andbioengineers at no charge. We will entertain research theme proposals as follows.
⃝Application period: February 3 (Mon) - March 3 (Mon)⃝Notification to successful applicants: Late March⃝Period of use: April 1 (Tue) - March 31 (Tue) 2015

For more details, please visit our website (http://www.kobe.riken.jp/stpr1-life/).

On-site classes in high schools

To promote education in the computational life sciences, SCLS offers classes on computational life sciencefor high school students and teachers throughout Japan to foster understanding of the latest science andtechnology. These classes can be given in schools and social educational institutions. In addition, seminars
can be presented in science and technology promotion events.
For more details, please visit our website (http://www.kobe.riken.jp/stpr1-life/), or contact the Planning and
Coordination Group of the HPCI Program for Computational Life Sciences by e-mail (senryaku1@riken.jp).

Exercise using base sequence puz zle at
Okayama Prefectural Tamashima High School

Hokkaido University -RIKEN Joint SymposiumStudent 5-minute Session

Computer Simulation of Life Science toward Future Medicine:
Challenge of the High Performance Computers to Medical
Applications

The symposium entitled “Computer Simulation of Life Science Toward Future Medicine:
Challenge of the High Performance Computers to Medical Applications” was held jointly
by the Creative Research Institution of Hokkaido University and SCLS at the Hokkaido
University Conference Hall on Thursday, August 1, 2013. Researchers engaged in cuttingedge research on utilization of the K computer and invited researchers in biomechanics,
biological systems, and physiology presented potential applications of high performancecomputing in medical technology and diagnosis.

We also sponsored a student workshop open to undergraduate and graduate students
from across Japan, entitled “What kind of medical applications will you do researchon if you could use the K computer?” We would like to express our gratitude to the six
participating graduate students for delivering excellent short presentations.

Speakers:(From left) Mr. Kenta Yahata (Saitama Univ. Graduate School), Mr.
Sunao Tomita (Hokkaido Univ. Graduate School), Ms. Stephanie
Nix (Tohoku Univ. Graduate School), Mr. Naoki Takeishi (Tohoku
Univ. Graduate School), Mr. Tomohiro Otani (Osaka Univ. Graduate
School), and Mr. Masataka Arai (Kyushu Univ. Graduate School)

Strategic Programs for Innovative Research:
Field 1 & Field 2 Symposium in Nagoya University

Computational studies of complex biomolecular systems to understand the role ofintermolecular interactions

Strategic Programs for Innovative Research Field 1: SCLS and Field 2: CMSI held an interdisciplinary symposium, focusedon the potential of high performance computing for studies of biomolecular complexes to understand intermolecularinteractions, at the Lecture Hall of Building IB, Nagoya University on Tuesday, December 17, 2013.

Although the symposium was targeted primarily at researchers studying biomolecules, presentations were made byscientists from diverse backgrounds. Active question-and-answer sessions provided ample opportunities for interdisciplinary
discussion.

Third Japan High School Championship at Kagaku no Koshien: Science Olympiad (March 21 (Fri)-24 (Mon))SCLS will organize an exhibition booth at the Kagaku no Koshien (March 23 (Sun)): Science Olympiad, which is a contest that tests scientific knowledge
and skills of student teams from high schools all over Japan.

Strategic Programs for Innovative Research Field 1

Supercomputational Life Science

SPIRE (Strategic Programs for Innovative Research) is a MEXT program aiming to produce ground-breaking results in computer science
technology by maximizing the benefits of the HPCI (High Performance Computing Infrastructure) centered on the supercomputer K computer,and encouraging developments in five research fields that need to be strategically addressed.
“Supercomputational Life Science” has conducted research with the mission of understanding and predicting life phenomena based on largescale simulation and advanced data analysis, and to apply these results to design and implement medicine and medical care with its research.

BioSupercomputing Newsletter Vol.10 2014.3
RIKEN HPCI Program for Computational Life Sciences
7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe Hyogo 650-0047, Japan
Tel:+81-78-940-5692 Fax:+81-78-304-8785 http://www.kobe.riken.jp/stpr1-life

Issued: March 2014

RIKEN 2014-023