Strategic Programs for Innovative Research Field 1 Supercomputational Life Science

12

2015.3 Vol.

CONTENTS

Open Up SPECIAL TALK

Discussion meeting

Toward a reproduction of biomolecular functionsin intracellular environments through large-scale
simulation utilizing the high computational
capabilities of the K computer

Hisashi Ishida Japan Atomic Energy Agency ／ Isseki Yu RIKEN ／Motoshi Kamiya Kyoto University ／ Ryo Kanada Kyoto University ／Kazunari Iwamoto RIKEN ／ Yuichi Kokabu Yokohama City University

SCLS Eyes

2

S-cruise From the field of software development

Reproducing the processes of blood clot formationand growth by focusing on platelet activation
Norio Shimamoto

The University of Tokyo

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ZOOM IN Close-up on SCLS Research
Theme 1 Simulations of biomolecules under cellular environments
Exploring a chemical reaction in an intracellular crowded
environment by the QM/MM method
Motoshi Kamiya

Kyoto University

Theme 3 Hierarchical integrated simulation for predictive medicine

Multi-scale simulation of platelet aggregation
in initial stage of thrombogenesis
Seiji Shiozaki Tokai University School of Medicine
Theme 4 Large-scale analysis of life data

Simulating cancer evolution to understand principles
generating intratumor heterogeneity
Atsushi Niida

The University of TokyoSCLS Gotcha!

Remote Interactive Lectures “Foundations of Computational Life Sciences”
Further Sophistication to Make Effective Useof the High Performance Computing Infrastructure

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Discussion
meeting

Theme1: Simulations of biomolecules under cellular environments

Toward a reproduction of biomolecularfunctions in intracellular environments throughlarge-scale simulation utilizing the highcomputational capabilities of the K computer
To transition from molecular level simulations to cellular functions, andconnect with understanding and predicting biological phenomena
The introduction of the K computer is about to open a path for reproducing the behavior of a biomolecule under conditions
close to those of an actual intracellular environment, which has been considered difficult due to the limitations of hitherto
computational capabilities. The aim of Theme 1, "Simulations of biomolecules under cellular environments" (leader: Yuji
Sugita, Principal Investigator of RIKEN), is to go from molecular level computations to "whole-cell simulation", which is directed
to understanding and predicting biological phenomena. Today, we are hearing from six investigators who are undertaking
research in the simulation of biomolecules under cellular environments, which is key to achieving this goal.

On the basis of a loose collaboration, the theme of each investigator is tackled● What type of research are you
currently undertaking in Theme 1?

Yu: The aim of the Sugita team ist o r e p r o d u c e , i n a c o m p u t e r, t h ebehavior of biomolecules under cellularenvironments, through large-scale
molecular dynamics calculations using
the K computer. In this process, wehave a bacterium called mycoplasma as
the target, and we have created a cell
environment model at an atomic level,in which almost all the proteins andmetabolites involved in its metabolic
network coexist at concentrations
that are close to those inside an actual
cell. Currently, we are carrying out allatom molecular dynamics simulations
using this model. The interior of a cell is

2 BioSupercomputing Newsletter Vol.12

extremely crowded with biomolecules,
and there are a large number ofproteins, small molecules, ions, and soon, in a melee, similarly to a packed
commuter train. What type of dynamics
and interactions the proteins and small
molecules display in such a packed
environment is an important questionin biology as well, but it is not wellunderstood, due to the difficulties in
obtaining experimental measurements.
The objective is to elucidate this aspect.
Iwamoto: What our team is doing ismodeling and simulation of intracellularsignal transduction pathways, whichtake the intracellular environment into
consideration. A cell responds suitably
to a change in the environment. This

response is called signal transduction,
which pathways are biochemical
reaction networks among a number of
intracellular proteins. A large number ofsuch signal transduction pathways exist
inside a cell. Well known among themis the epidermal growth factor (EGF)signal transduction pathway. It has therole of receiving EGF ligand stimulationfrom the external environment
communicating the information to
the cell interior, and prompting thecell to grow, divide or differentiate.
We are currently undertaking cell
simulations pertaining to the networks
in this pathway. The cell simulation isa method for simulating a cell virtuallyin a computer, and one importantHisashi Ishida
Senior Researcher, Quantum Beam Science
Center, Japan Atomic Energy Agency

Participating in the round-table talk again
made me realize the importance of multiscale simulation that links the broadness andhierarchy of the scale at which biologicalphenomena are handled. At the same time, I
strongly felt the various developments in thefield of simulation.

Isseki Yu
Research Scientist, RIKEN Theoretical
Molecular Science Laboratory

Motoshi Kamiya

I strongly felt that all the members who
participated in the round-table talk were
undertaking research toward the elucidationof a theme with passion and a sense of
mission. Going forward, I think that it isimportant to undertake the elucidation of
biological phenomena on multiple scales while
effectively sharing the data obtained with one
another.

Program-Specific Researcher, Department ofchemistry, Graduate School of Science, Kyoto
University

The calculations I am performing tend to haveaspects that inevitably require the size of the system
to be modest, so, I felt a sort of admiration in regard
to the large-scale computation that the people who
participated in the round-table talk are carrying
out with the K computer. In addition, I strongly
agree with the discussion on the importance ofcollaboration with experimental people.

Ryo Kanada

Kazunari Iwamoto

Program-Specific Researcher, Department ofBiophysics, Division of Biological Sciences,
Graduate School of Science, Kyoto University

Postdoctoral Researcher, RIKEN Quantitative
Biology Center

Listening to everyone's story, I realized once
again that my own research was closely
related to other people's research. I think thatby deepening collaborative relationships
and exploiting findings and data obtainedon different scales, progress in each other'sresearch can be made more effectively.

I truly feel that, in order to utilize the K computer
effectively, it is important to have a good handle on
knowledge regarding parallelization, and on thecharacteristics of the calculator itself. Meanwhile,
today, coordination with experimental systems is
also important; so, arrangements may need to bemade to have investigators of experimental systems
participate.

Yuichi Kokabu
Postdoctoral Researcher, Computational Life
Science Laboratory, Graduate School of Medical Life
Science, Yokohama City University

Listening to the people who participated in the roundtable, I am beginning to see where my research stands
in the ongoing large-scale simulations. In addition,
thinking about the maximizing the efficiency of thecomputational capabilities of the K computer, I truly
felt that simulation research geared toward gigantic
systems will become more and more important.

feature of our method is that the highcomputational capabilities of the K
computer are utilized so that the cell
shape and structures are included anddiffusion, collision, reaction fluctuation,and so on, are represented at themolecular resolution.

Kamiya: Intracellular signal transduction
is mainly carried out throughphosphorylation reactions by several
kinases. The reaction activity of a kinase
is a chemical process that is key tointracellular signal transduction, andelucidating the molecular mechanismof reaction activity in a cellularenvironment is important in establishinga molecular platform oriented
toward understanding and control of
intracellular signal transduction. For
this purpose, our team is carrying out
research and development related to

BioSupercomputing Newsletter Vol.12 3

Discussion
meeting

Toward a reproduction of biomolecular functions in intracellular environments throughlarge-scale simulation utilizing the high computational capabilities of the K computer
reactivity analysis of kinases in signaltransduction pathways. As mentioned
by Dr. Yu, the interior of a cell is anextremely crowded environment. In
order to elucidate what kind of chemical
reaction is occurring in such a crowded
environment and how different it is froma conventional reaction occurring inwater, we are performing analyses using
the QM/MM method, which combines
quantum chemical (QM) computationand molecular mechanical (MM) computation.
Kanada: We are using the coarse-grained
molecular dynamics simulation program(CafeMol) which has been developedby our research team to carry out
research focused on the MAPK system
phosphorylation cascade (a series ofreactions), which is a representativemodel for signal transduction pathways.
As already mentioned by Dr. Iwamoto
and Dr. Kamiya regarding signaltransduction, in the mammalian MAPK
system cascade, upon stimulation fromthe exterior, the upstream protein MEK1
(MAPKK) activates the downstream
protein ERK2 (MAPK) by phosphorylating
it, leading to a transmission of the signal,
finally the signal is transmitted to theinterior of the nucleus. However, thedetails of the molecular mechanism forphosphorylation are not understood,
and need to be elucidated. Therefore,
based on the individual monomeric
structures of MEK and ERK, which havebeen resolved experimentally, we areinvestigating the MEK-ERK complex
structure and the dynamics of its

formation. Another target is related to
the ERK protein translocated into the
nucleus after phosphorylation. Applying
coarse-grained simulation, we would
like to elucidate the dynamical behaviorof the ERK protein in an intranuclear
crowded environment where chromatin
is present in high concentration.
Ishida: We are dealing with nucleosomes.
The DNA from eukaryotes, including
humans, has a fundamental structure
called a nucleosome, which is DNA
wound around a core of proteins calleda histone, and many of them are aligned
to form a chromosome, which is housed
inside the nucleus in a compact form. This
nucleosome is deeply involved in gene
regulation, and known to change structure
or position in relation to DNA metabolism
such as transcription, replication, andrepair. In order to elucidate the mechanismof movement, structural stability and soon, of the nucleosome, we are using total
atomic models to calculate the extent of
DNA winding and unwinding around thehistones in each of the systems including
conventional canonical histones andvariants that constitute the nucleosome.
More specifically, we simulate a slow
pulling and peeling of the DNA and use
the K computer to calculate the structure
distribution in so doing, called a freeenergy profile in expert terms, i.e., whether
the free energy of the pulled and peeled
DNA is high or low. We are trying to go as
far as seeing, at the total atomic level, howdifferent the ease of peeling becomeswhen a component of the nucleosome ischanged.

Kokabu: As explained by Dr. Ishida, theintranuclear DNA has a nucleosome
structure in which DNA is woundaround histone proteins, and adopts astructure in which several nucleosomes
have condensed. In our laboratory, we
are undertaking research regarding
the functional dynamics of these
intranuclear DNA-binding proteins, using
molecular simulation, while linking withexperimental systems. In this process,we have been undertaking program
development for the coarse-grained MDSAXS method. The SAXS (small-angle
X-ray scattering method) is a method inwhich a protein in solution is irradiatedby X-rays, and the overall shape ofthe molecule is measured from its
scattering pattern, and it allows a protein
structure that fluctuates to be seen.
Meanwhile, MD (molecular dynamics)
simulation can predict, on the total
atomic level, the behavior of a biologicalmacromolecule such as a protein bysolving an equation of motion. However,in the case of a gigantic molecule suchas the nucleosome, a total atomic MD
simulation would require too muchcomputation time, so that a coarsegrained (CG) MD is used, in which anamino acid is substituted with a particle,
to predict the structure, and from thisresult, the SAXS scattering pattern iscomputed theoretically. The computation
result and the SAXS experimental data
are compared and examined; if theycorrespond, then the simulation result
can be deemed appropriate.

Undertaking research with a dream● What is your impression afterusing the K computer?

Ishida: We are doing a large computation
using 4,800 nodes for an all-atomsimulation of peeling a nucleosome
consisting of approximately 500,000
atoms. The calculations simulate thebehavior of about 50,000,000 atoms
in total. Such a simulation is indeed
impossible if not for the K computer, andI really have the feeling of doing cuttingedge computation, which could not be
carried out so far. While we are currently
in the middle of analyses, we are starting
to learn about what is needed in order

4 BioSupercomputing Newsletter Vol.12

to do high-precision analyses throughultra-large system simulations.
Yu: Even in such an extremely small
bacterium as mycoplasma, when you
try to include all the proteins related toa metabolic network at realistic number
density ratios, the total number will
end up being about 1,500 at least. Since
the simulation of one to a few large
proteins is common at a conventional
laborator y level, I indeed think thisresearch would be impossible without
the K computer. In terms of impression
after actual use, in addition to the factthat it is crowded with jobs, determining

an optimal number of nodes requireda bit of trial-and-error. If the numberof no des se cure d is to o large, thewait time becomes extremely long;
conversely, if the number of nodes is
too small, although jobs can be placed
at a good pace, the trade-off is that thetime available for simulation is shorter.
I struggled to find the most balanced
number of nodes in the beginning.
Kamiya: The K computer is indeed
attractive for handling large systems.
R e g a r d i n g M D, w e a r e a l s o u s i n g
the mole cular dynamic s simulator"GENESIS", which is used by Dr. Yu'sgroup as well. It is extremely efficient,and helpful to us. The ability to run MDof a large-scale system at high-speed isindeed important. As for QM/MM, while
it can be run, there is the fact that the
input has become very complicated,
and there are many failures, which is an
issue. In addition, since job submission
has to be reiterated several times, thewait time to do so is long, which is a real
problem.
Kanada: When investigating the
dynamic s of the ERK protein in an
intranuclear crowded environment, weare including in the system a chromatin
structure consisting of 20 nucleosomes
to per form the calculations. My
impression is that, since this is an
ex tremely large system for coarse grained simulation by CafeMol, utilizing
the K computer is extremely helpful toproceed with large-scale calculations
efficiently and systematically.
Iwamoto: I too think that the ability tolook at large systems in fine detail is
what makes the K computer attractive.
I am dealing with a whole cell. Ideally, I
would like to bring the grid size to thesize of one protein molecule, i.e. about
5 nanometers, but there is not enoughmemory in PC clusters such as those inconventional laboratories. On this point,
the K computer allows you to proceedwith no problem at all.
Kokabu: In my case, since I use coarsegrained simulation, the to-be-computed
system itself is not that large, but inorder to examine various conditions, I
am doing simulation with 90 conditions
f o r o n e n u c l e o s o m e. I n a d d i t i o n ,even for coarse-grained simulation,
enough conformational space cannot
be searched in only one round, andthe same computation is repeatedabout 100 times. I feel that using the K
computer is extremely important forthis purpose as well.

● Going for ward, what t ype of
research would you like to carry on?
Ishida: I have been doing simulation

After SPECIAL TALK

research on biological macromolecularsystems that exceed 1,000,000 atoms.
Calculators have been developed, which
possess high computational capabilities,
such as those of the K computer, andsimulation accurac y also has been
increasing dramatically compare dto the past. In this context, I would
like to keep my interest in simulation
techniques, and carry out research thatnicely links the best part of coarsegrained simulation with the best part of
all-atom simulation. In addition, I thinkthat ultimately connecting with drug
development and such, may be a theme
in simulation research, but I personallywould like to carry on steadily with
fundamental research.
Yu: In contrast, I would like to expandin the direction of medicine anddrug development. T he research I
am currently undertaking has strong
basic science aspects, and while thisobviously remains important to me, inthe future, I would like to contributeto the development of drug design
processes that take the cellularenvironment into account. Currently,
computer-assisted drug development
focuses mainly on the affinity between
a protein and a drug; to this, I would liketo add the influence of the intracellularenvironment. For example, intracellularw a te r h a s d i f f e r e nt v is co s i t y a n ddielectric constant from pure water,and I believe there is also a significant
i n f l u e n ce o n t h e b i n d i n g a f f i n i t y
between a target and a drug. If a generalcellular environment mo del could
be built by gathering such findings,
wouldn't it lead to a more realistic drug
development process?
Kamiya: My "root" being chemistr y,
I would like to continue by properly
handling the chemical reactions uponwhich the field of life science is based.
While setting my aim in such a direction,
I would like to contribute to society
though drug development, or the like.

the simulation program "CafeMol". I am
thinking that whole-cell simulation will
also become possible with "CafeMol" in
the future. By running high performance
calculators such as the K computer overan extended time period, using not only
protein models but also DNA and lipid
models, it should be possible to simulate
an entire cell. While my current main
targets are proteins related to signaltransduction, I would like to contributealso to research on systems including
DNA and lipids.
Iwamoto: To b e brief, I to o would
like to achieve whole-cell simulation.
However, I do not mean coarse-grained
simulation; I would like to achieve
whole - cell simulation including allof the numerous functions that a cellpossesses in order to respond to various
stimuli from the environment, such as
those involved in signal transduction
and metabolism. About two years ago,
an article came out about an American
research group having simulated all the
mycoplasma reaction systems. Progressis also being made in whole-simulation
research with Escherichia coli and thelike. I would also like to proceed in sucha direction.
Kokabu: We happen to collaborate
with molecular biologists in theexperimental field, and when we learn
that a prediction by our simulation
turned out to be correct through anactual experiment, we are sometimes
overjoyed. For such reasons, I would
like to continue placing an importanceon collaboration with experimenters. I
think that findings through simulation
are also extremely useful to molecularbiologists conducting experiments. I
would also like to do research that can
support experimental projects, throughsimulation.

Kanada: I would like to reproduce thebehavior of large systems by utilizing
After the interview, the interviewees
answered questions from and talked freely
with young researchers and students. Visit
the URL below for more information.

●See the URL on the right for longer version of this discussion meeting. http://www.scls.riken.jp/eng/newsletter/Vol.12/openup.html

BioSupercomputing Newsletter Vol.12 5

SCLS Eyes S-cruise From the field of software development

Reproducing the processes ofblood clot formation and growthby focusing on platelet activation
Multiscale thrombus simulator “EX-THROM”
Researcher, Department of Mechanical Engineering, The University of Tokyo

Norio Shimamoto

Theme 3 “Hierarchical integrated simulation for predictive medicine” (leader: Prof. Shu Takagi, Graduate School ofEngineering, The University of Tokyo) aims to elucidate the complicated onset process of heart diseases and motor
dysfunction by integrating simulations of the circulatory, muscoskeletal and central nervous systems to provide optimum
medical support to each and every individual. A multiscale thrombus simulator “EX-THROM” is being developed as apart of the project. Developed by expanding “ZZ-THROM”, which was developed in a grand challenge program “NextGeneration Integrated Simulation of Living Matter (ISLiM)” (until March 2013) and is a simulator for reproducing the initial
phase of thrombus formation, “EX-THROM” aims to reproduce thrombus growth. We interviewed Dr. Shimamoto, andasked about the simulator and its development.

Focusing on ADP stimulation in thrombus growth─ How does a thrombus actuallyform?
Shimamoto The mechanism of thrombus formation is basically the same as thatof blood coagulation at hemastasis, which
is a defensive mechanism against damage
to blood vessels. The coagulation system
is an important response for maintaining
life; but the blood clot may grow, hinder
the flow of blood, block up a vessel andcause ischemia or infarction. This is called
thrombosis.
Platelets play the key role in thrombus
formation. When a vascular wall isdamaged due to some reason, it triggers
von Willebrand factor (vWF) on thewounded site to bind with protein
GPIbα on a platelet, resulting in theplatelet adhering to the vessel wall. The
activated protein GPIIb/IIIa present on theplatelet binds with vWF and fibrinogen,and causes the platelet to successively
adhere with other platelets and a platelet
thrombus, which is an aggregate ofplatelets, to form. Then, a series ofmultistage chain reactions by 12 blood
coagulation factors takes place. During
the process, a network structure calledfibrin mesh is formed and entraps blood
cells such as erythrocytes, making thethrombus to grow further and a stable“fibrin clot” to be formed.

6 BioSupercomputing Newsletter Vol.12

─ Your team is developing EXTHROM. What kind of application
software is it?
Shimamoto ZZ-THROM, which is amultisimulator for reproducing the initial
phase of thrombosis, was developed in
the grand challenge program based ona new fluid-structure coupling method(ZZ-EFSI). It reproduces the processes ofplatelet adhesion on a damaged vascularwall. We are now developing EX-THROM,
which is a multiscale thrombus simulator,
to reproduce the activation process ofadhered platelets and the subsequent
thrombus formation processes by
expanding the functions of ZZ-THROM.
A number of substances are involved inthrombus formation compositely andat various stages. The processes arestill not fully understood. To develop
the thrombus simulator, we need toincorporate minute reactions, but weare thinking of narrowing targets first,
creating a framework that reproduces thecharacteristic movements of platelets, andthen moving into minute reactions.
─ What are the important targets
for building the framework?
Shimamoto During the processes ofplatelet aggregation, platelet-inducing

substances, which binds with receptors
on the platelet surface and stimulate andpromotes activation of the platelet, play

important roles. Adenosine diphosphate(ADP) is one of such substances. It has

been experimentally revealed thatplatelets aggregate and dissociate
depending on ADP concentration.

Activated platelets release ADP contained

in dense granules, and the “ADP positive
feedback mechanism”, which is a chain
reaction that amplifies activation, occurs.

Therefore, we are focusing on andmodeling the activation of platelets by
ADP, which is a key process in platelet

aggregation. In concrete terms, we are
reproducing the activation of GPIIb/

IIIa, which is induced by ADP binding
to ADP receptors P2Y12 and P2Y1 andsubsequent activation reactions. Using

this model, we are going to investigate
how the activations of P2Y12 and GPIIb/
IIIa on the platelet surface undergo
time sequential changes in a condition

where ADP, vWF and fibrinogen diffuse
advectively and undergo concentration

changes. Obviously, ADP alone does

not stimulate the entire process. Various
substances are involved in an integrated
manner. We will be expanding thefunctions of the model by adding theirinvolvement.

SCLS Eyes
● We also aim to use the model to evaluate a thrombosis therapeutic agent
─ What are the important points
in modeling?
Shimamoto The important point is
to well reproduce the characteristics ofthe actual phenomena. There are many
substances involved; but if we incorporate
them all blindly, we would not be able
to understand what is happening. On
this point, we are receiving advice from
Professor Shinya Goto of Tokai University
School of Medicine, who is a specialist in
thrombosis, as well as other specialists.
We are going to create a model consistent
with experimental data by also including
the reactions of thrombin, serotonin andthromboxane A2 as well as ADP stimulus.
─ We have heard that your study
project also aims to use the model
to evaluate a thrombosis therapeutic
agent.
Shimamoto Yes. We are now investigating clopidogrel, which blocks P2Y12of the ADP receptor and inhibits binding,also difficult deciding how to refine theplatelets together.

the model so as to fit the knowledge thatand an inhibitor of GPIIb/IIIa, which binds

─ Have you already obtained thecomputation results from the K
computer?

Goto and his team of medical specialists
by continuously giving feedback.

─ Please tell us about yourprospects.

─ What was the most difficult
point in modeling?

agent. For example, if we can reveal

ShimamotoWe have just advanced

from the stage of aggregation to thestage of coagulation. We are now also

investigating coagulation. Our goal is toreproduce the actual process of thrombus

formation. We also aim to contribute toevaluation of a thrombosis therapeutic
how much should be administered andShimamoto I am originally from anengineering school, and had difficulty
understanding the medical information.
Moreover, much is left unveiled in themechanism of thrombus formation. It is

at which timing of thrombus formation

by simulation, we would be able tocontribute to thrombosis treatment.

Fig. 1: Mechanism of thrombus formation. Von
Willebrand factor (vWF) in the damaged vascularendothelium binds with protein GPIbα present on
a platelet, resulting in the platelet adhesion. Whenthe platelet is activated by a signal transduction of
stimulus, it releases ADP, inducing further activationof itself and other platelets, and the procedure toadvance to aggregation and coagulation.

Activated

Rolling

BindingSignaling

has experimentally been acquired by Prof.

Shimamoto We are still in the phaseof testing calculation. Actual calculation
using the K computer will be the next
step. We will be calculating the processof platelet activation inter-connectedly
with blood flow calculation including
erythrocytes, which was developed in ZZTHROM.

PlateletShear stressmodel. At present, I’m trying to improve

FibrinReleaseMicroparticle

Activation

Adhesion

Aggregation

Modification of an illustration cited from Platelet Biology(in Japanese) edited by Ikeda and Maruyama (Medical
Review Co., Ltd.)

Coagulation

Platelet

Vascular wall
Ligands

ADP : Adenosine diphosphate
VWF: Von Willebrand factor
FIB : Fibrinogen

Receptors

P2Y1: ADP receptor
P2Y12: ADP receptor
GPIIb/IIIa : Adhesive protein

Antagonists

CLO : Clopidogrel
IGP : GPIIb/IIIa inhibitor

Fig. 2 : Reaction model of platelet activation● See the URL on the right for detailed information on this report

Fig. 3 : Calculation example of P2Y12 activation. During the timecourse in which ADP undergoes advective diffusion, the P2Y12
molecules on the surface of the platelets bind with ADP, anddeactivated molecules (blue) become activated (red).

http://www.scls.riken.jp/eng/newsletter/Vol.12/sclseyes.html
BioSupercomputing Newsletter Vol.12 7

Close-up on SCLS Research

Theme 1 Simulations of biomolecules under cellular environments

Exploring a chemical reaction in an intracellular
crowded environment by the QM/MM method
Theoretical Chemistry Laboratory, Department of Chemistry, Graduate School of Science,
Kyoto University

Motoshi Kamiya
Various chemical reactions

continuously occur in the living

body. Knowledge of those chemical
reactions is essential to understand life

phenomena and go further. The QM/
MM method we use (a combinationof quantum chemistr y and classicalphysics to deal with a chemical reaction

in a complex system with a high degreeof accuracy) is a very important method
to g a i n k n o w l e d g e o f a c h e m i c a lreaction in a complex environment likea biological system. In 2013, Dr. Karplus,

D r. Lev i t t a n d D r. Wa r sh e l sha r e d

the Nobel Prize in Chemistry for thedevelopment of the QM/MM method. Itshows how important and promising it
is.

Although the QM/MM method is

a very excellent method to deal withchemical reactions, it has a problem
of requiring very high computational
capacity. Recently developed computers
can now deal with an isolated protein

floating in water (Fig. 1). However, theircapacity is not sufficient to handle invivo chemical reactions. For example,
a real living cell is packed with various
proteins (Fig. 2). It is much different fromthe too ideal environment shown in
Fig. 1. However, conventional QM/MM
computation does not take account ofsuch a crowded cellular environment
at all. On top of that, temperature isanother important and sensitive factor
for living organisms. Although thermal
fluctuation of protein conformation
always occurs, its impact has not beenhandled properly. However now, thanks
to the K computer and other largescale computers, QM/MM computationin the environment shown in Fig. 2 has
become possible. We also can deal withtemperature efficiently to some extent
by the method our group has developed
recently (QM/MM RWFE SCF method).
Honestly speaking, how things change
in the very complex environment shownin Fig. 2 has been poorly understood.
Even imagining it is difficult, but now
we can study it anyway.
Now we are studying the reaction

Fig. 1： Ideal protein (Ras/GAP complex) floating in water (red dot:water molecule)● See the URL on the right for detailed information on this reportand profile of the author.

8 BioSupercomputing Newsletter Vol.12

by which GTP (guanosine triphosphatecommonly found in functional

regulation of a living organism) breaks
down into GDP (guanosine diphosphate)

in a system called the Ras/GAP complex

in the environment shown in Fig. 2. BothRas and GAP proteins are involved incanceration as well as in life. Although

we have just started computing and,there are many things we still don t

understand, we will discover, bit bybit, how a more realistic environment(temperature, crowded environment,etc.) works, and how things are affectedby such an environment.

Fig. 2：Ras/GAP complex in schematic cell environment (watermolecules omitted. Gray dots represent other proteins)

http://www.scls.riken.jp/eng/newsletter/Vol.12/zoomin01.html

Close-up on SCLS Research

Theme 3 Hierarchical integrated simulation for predictive medicine

Multi-scale simulation of platelet aggregation
in initial stage of thrombogenesis
Division of Cardiovascular Medicine, Department of Internal Medicine,
Tokai University School of Medicine

Seiji Shiozaki
When blood vessels are damaged
by injury, etc., platelets clump together
at the site of injury to stop bleeding.
When the inner wall of a blood vessel
is damaged due to arterial sclerosis,
platelets also agglutinate and form ablood clot inside the blood vessel. Suchblood clots cause thrombosis including
heart infarction and cerebral infarction,
which are major cardio circulator ydiseases and rank fourth as a cause ofdeath in Japanese people. Platelets
agglutinate in a blood vessel throughinteraction between glycoprotein Ib
alpha (GPIb alpha) found on platelets
and the von Willebrand factor (VWF)
adhering to the wall of an injured
blood vessel. A few dozen GPIb alphaVWF couples are formed on the joining
surface of the platelet to stick platelets
together. On a larger scale, the dynamic
action of erythrocytes in blood plays acrucial role in adhesion of platelets.
Fig. 1 shows the binding site structureof the GPIb alpha-VWF couple obtainedby the molecular dynamics method.
The molecular dynamics method candetermine the momentary position of
every atom by solving Newton’s equationof motion for all atoms constituting
the protein molecules and water. By
this method, we can calculate the force
working bet ween the proteins andthe potential energy of the system wecalculate. It enables us to model reaction
rates of bond formation and dissociationof a protein couple. Fig. 2 shows a gridmodel of a platelet surface. In this model,
the behavior of a membrane proteinon the platelet surface is analyzed bya statistical approach called the Monte
Carlo method to find the momentarybond number and adhesion force of theprotein. In the calculation area, 1.5μm
on a side, which is equivalent to about
one fifth part of the platelet surface area,
there are 4,000 GPIb alpha and 3,600
VWF binding sites. Each dot in Fig. 2
represents one GPIb alpha molecule. We
presumed that GPIb alpha is scatteredon the platelet surface whereas VWF isanchored to the blood vessel wall, andthat GPIb alpha molecules bound to VWF
are neither scattered nor move over themembrane. We also presumed that GPIb
alpha near VWF forms a bond with VWF
at a certain combination rate, and theFig. 1：Binding site structure of N-terminal of platelet
membrane protein GPIb alpha (blue) and A1 domain of
VWF (red)bond is dissociated at a certain bonddissociation rate. As those rates, we canuse a model modeled by the molecular
dynamics method. By introducing thenumber of protein bindings and theiradhesion force into an Eulerian approachfor fluid-hyperelastic body interaction by
the finite difference method, it becomes
possible to reproduce a phenomenon
in which platelets adsorb onto a
blood vessel wall in the presence of[1]erythrocytes .
By performing a multi-scale simulationfrom the protein scale to the bloodstream
scale in this way, we are studying further
to elucidate the clotting mechanism, andin the future we will construct a usefulmodel for the discovery of an antiplatelet
drug, and predictive and personalized
medicine.
Reference:：[1] BioSupercomputing Newsletter, Vol. 7, p. 7.

Fig. 2：Platelet surface grid model. Red dots represent bound GPIb alpha, and blue dots represent
free GPIb alpha which moves over the platelet surface.

●See the URL on the right for detailed information on this reportand profile of the author.

http://www.scls.riken.jp/eng/newsletter/Vol.12/zoomin02.html

BioSupercomputing Newsletter Vol.12 9

Close-up on SCLS Research

Theme 4 Large-scale analysis of life data

Simulating cancer evolution to understand principles
generating intratumor heterogeneity
Human Genome Center, The Institute of Medical Science,
The University of Tokyo

Atsushi Niida
Cancer results when cells abnormally
proliferate by genetic mutation. It is
known that every patient has his or her
own different cancer-causing genetic
mutation. Fur thermore, it has been
revealed that even a single cancer in apatient has multiple cell populations
with various combinations of genetic
mutation. This phenomenon is called
intratumor heterogeneity, and thought
to play a role in resistance to anti-cancer
therapy. Provided that a tumor consists ofa large number of cell A which responds
to treatment and small numbers oftreatment-resistant cell B, the tumor
temporarily shrink s with treatment
due to the decrease of cell A. However,when cell B grows, before long, thetumor recurs. Therefore, it is a clinicallyimportant task to clarify the principles
generating intratumor heterogeneity.
We first worked with Kyushu University
Beppu Hospital to investigate the tumor
heterogeneity of colorectal cancer. We
took DNA samples from multiple sites ofa single colorectal tumor and analyzed
their genomes with the Next Generation
Sequencer. As a result, we found a
genetic mutation shared by all samples.

Meanwhile, it was revealed that eachsample has its own genetic mutation,
which causes high heterogeneity.
Next, we tried to clarif y the princ i p l e g e n e r at i n g su c h i nt r at u m o r
h etero g en eit y, an d co ns tr uc te d asimulation model of cancer evolution,
the Branching Evolutionary Process (BEP)
model. When cells are allowed to growby mutating multiple genes randomly,
cells accumulating driver mutations
that increase proliferation rate are
selected. As a result, they evolve into acell population with high proliferating
ability. In such an evolutionary process,the cells branch into cell populations
with different mutations under a certain
condition and acquire heterogeneity.
We simulated cancer evolution undervarious conditions with the K computerin an exhaustive search for a condition
which generates high heterogeneity.
We found that if we postulate a highgene mutation rate and the existence ofcancer stem cells, we can reproduce thegene mutation patternwith high heterogeneity
obser ved in the above
experimental results

Fig. 1：Visualized simulation of cancer evolution. (A) Growing cancer, (B) Growth curve, (C)Genetic mutation pattern●See the URL on the right for detailed information on this reportand profile of the author.

10 BioSupercomputing Newsletter Vol.12

using colorectal cancer. In addition, theresults of our simulation suggested thatdriver genes are shared by all tumor cells,
while most heterogeneity-producing
mutations are neutral mutations which
do not affect the cell growth rate.
As above, in our study, some evolutionary principles generating intratumor
heterogeneity were elucidated by genome analysis of colorectal cancer andsimulation of cancer evolution with the
K computer. From now on, we plan toestablish a treatment strategy based ona study to overcome treatment-resistantcancers.

Fig. 2：Genetic mutation patterns with high heterogeneity obtainedby simulation of cancer evolution (A, B) and genome analysis ofcolorectal cancer (C, D)

http://www.scls.riken.jp/eng/newsletter/Vol.12/zoomin03.html

Remote Interactive Lectures“Foundations of Computational Life Sciences”
From the tangent point of life andengineering sciences to applications
in society

L i fe s c i e n ce s , s u c h a s b i o l o g y,
medicine, pharmacy and agriculturalscience, developed dramatically inthe latter half of the 20th century.
In the 21st century, which is called“the era of life sciences,”scientists
are required not only to investigate
the fundamental theories of physics
a n d c h e m i s t r y b u t a l s o to c a r r y
out research based on enormous
databases related to life sciences,which have accumulated all over theworld. It is also increasingly required
to apply the fundamental theories ofphysics, chemistry and engineering inlife sciences.
SCLS is giving a series of a courseof basic lectures on computational
life science, which forms the tangent
point of life and engineering sciences,
jointly with the Education Centeron Computational Science andEngineering of Kobe University forundergraduates, graduate students
and working members of society.
The course, which star ted in
October 2014, consists of 15 lectures

Held by : Education Center on Computational
Science and Engineering, Kobe University
Co-held by : RIKEN HPCI Program for
Computational Life Sciencesin three categories ranging from thetangent point of life and engineeringsciences to applications in society;they are“Life Sciences Viewed fromthe Genome,”“Life Sciences Viewed
from the Protein,”and“Life Sciencesin Medicine and Drug Discovery.”The
lectures are easy to attend as auditing
students can attend the lectures via
their own personal computer.
All lectures are given by scientists
active in various fields at universities,
companies, and others. The lecturers
overview computational life science,
introduce technologies of data mining,mention gene expression databases,
and briefly explain methods ofcalculating and analyzing molecular
dynamics simulations of proteins, andthe present states and prospects ofcomputational life science in the fieldsof medicine and drug development.
About 260 undergraduates,
graduate students and researchers ofcompanies have registered and areattending the lectures. We believethat they will form a community ofcomputational life science researchers,t r a n s fo r m Ko b e , w h i c h i s n o w asupercomputer center, into a basefor transmitting computational life
science information, and propel thedevelopment of computational life
science into the future.
Th e F Y2014 cou rse will en d o n
February 3 (Tuesday), 2015; but thecourse is scheduled to be held also
in FY 2015. We look forward to yourattendance.

Further Sophistication to Make
Effective Use of the High PerformanceHigh Performance Computing
Development Group, RIKEN HPCI
Computing Infrastructure
Program for Computational Life Sciences
The High Performance Computing
Development Group of RIKEN HPCIP ro g r a m fo r C o m p u t a t i o n a l L i f e
Sciences, which is a representative
organization of SCLS, has its
head q uar ters in R IKEN Advanced
Institute for Computational Sciencein Port Island, Kobe. It is in charge ofproviding support services to users,
and help them use the computing
i nf ra s t r u c t u re a n d e xe cu te t h e i r
research tasks smoothly. Our work
can be broadly classified into twoparts: 1) to manage the computing
infrastructure efficiently, and 2) toprovide research support and assist
users to use the K computer. As forthe fo rmer, we have co nstruc ted
and are operating an originalcomputer environment called the
SCLS supercomputer system, which
supplements the High Performance
Computing Infrastructure (HPCI), sothat researchers who actually work on
the task and related medical and drug

development can make full use of the
K computer and other constituentsof H P CI . T h e o p e rati n g p o l i c y isdetermined by a steering committee
established to deliberate each andevery issue. For the convenience ofusers, open software has also been
ported into the environment, and arebeing used by many users mainly for
preparation before calculation using
the K computer and also for postprocessing work. As for the latter
category of our work, we have actively
collected and accumulated know-how,such as advanced parallel computing
and programming techniques
necessary for using the K computer,at academic conferences and study
meetings, and from various kinds ofinformation available on the Internet.
The information has been transferredto persons in charge of theme studies
and is used for improving the parallel
computing per formance of the
program for analyzing intracellularsignal transduction. To disseminate
study results to the public, we also
give a short course on the use of the
new programs whenever appropriate.
To cultivate human resources who
have advanced knowledge and skills
sufficient for making use of the HPCI
environment, we are al so holding
various kinds of lecture meetingsa n d s e m i n a rs j o i ntly w it h R I K E N
Advanced Institute for Computational
Science, other strategic fields, and theRegistered Institution for Facilities Use
Promotion of the K computer.

A scene from a lecture meeting on mu2lib

BioSupercomputing Newsletter Vol.12 11

We released a video of the “Multi-scale, Multi-physics Heart Simulator UT-Heart”

We created a video describing the “Multi-scale, Multi-physics Heart Simulator UT-Heart” which runs on the K computer and reproduces theactual movements of the heart. With many varied camera techniques as well as music and sound effects, the video depicts the movementsof the heart in an easy-to-understand manner.
The UT-Heart aims to reproduce the heart of a person on a computer, which moves physically and physiologically identically with the realheart, for practical application in the medical setting. The K computer calculates the flows of blood, blood pressure and electrocardiogram,enabling physicians to precisely investigate remedies, correctly predict conditions after treatment,
virtually practice heart operations, and thus decide the optimum surgical method.
The video shows heart beats, heart muscle contractions and the movements of myosin molecules insarcomere in an easy-to-understand manner not only for professionals but also for ordinary people.
The video has been released onthe Web page, Strategic Programs for Innovative Research Field 1“Supercomputational Life Science (SCLS).” Please visit the page.

⃝Dates of release : July 11, 2014 (Japanese version), October 20, 2014 (English version)

SCLS issued a brochure on its research
SCLS is working on four themes:“Simulations of biomole cules undercellular environments,” “Simulation
applicable to drug design,” “Hierarchicalintegrated simulation for predic tive
medicine,” and “Large-scale analysis
of life data.” The brochure introduces
researchers and their research, trying toconvey the appeal of computational life
science.

Bio Japan 2014 World Business Forum

Bio Japan 2014 World Business Forum was held on October 15(Wednesday) to 17 (Friday), 2014, at Pacifico Yokoyama. SCLS
exhibited panels at RIKEN’s booth also this year and showed resultsof simulations applicable to drug design and other activities.

RIKEN KOBE Campus Open Day(Kobe: RIKEN Advanced Institute for
Computational Science)

RIKEN KOBE Campus Open Day was held on Saturday October25, 2014. At “Kagaku-no-Hiroba” open to the public, five research
institutes that are using the K computer exhibited their researchin various ways. At the exhibition hall, panels were exhibited
describing the research. Visitors of all ages, from children to theelderly, enjoyed making paper crafts shown in the illustration,
which helped them understand the hierarchical system of ourbody.
Besides the exhibitions at “Kagakuno-Hiroba,” there were tours to see
the K computer and brief lecturesdescribing the research. About 2,500
visited the institute on the day.

A short course on GHOST-MP (a parallel sequence similarity search tool) and a drill
using the SCLS supercomputer system (compatible with the K computer) will be held.
⃝Date and time : March 20 (Friday), 2015, 1:00 p.m. - 4:30 p.m.
⃝Location : 8F, AIST Tokyo Waterfront Annex⃝Number of trainees invited : 10

GHOST-MP is a software that parallelizes the GHOSTX’s search algorithm, which is a rapid sequence similarity search tool, for a distributed
memory system. A vast amount of short base or amino-acid sequences obtained by a next-generation sequencer, etc., can be searched
for sequence similarity to those in an amino-acid sequence database in a short period of time. The software is useful for metagenome
analysis, etc. The short course will explain the structure and methods of using GHOST-MP, and participants will practice metagenome
data analysis by using GHOST-MP in the drill. For inquiries, please contact: scls-mado@riken.jp.

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, andencouraging 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 large-scale
simulation and advanced data analysis, and to apply these results to design and implement medicine and medical care with its research.

BioSupercomputing Newsletter Vol.12 2015.3

www.scls.riken.jp/en/

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

Issued: March 2015

RIKEN 2015-020