CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

CCS Report: PART II

Research Activities, Results, Collaborations and Plan
2004 - 2007

October 2007

Center for Computational Sciences
University of Tsukuba-1-

CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007-2-

CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Table of Contents
1. Division of Particle Physics and Astrophysics: Computational Particle
Physics Group ................................................................................................... 7
1.1 Research Activity.......................................................................................... 7
1.2 Research Results .......................................................................................... 7
1.3 Collaboration .............................................................................................. 10
1.4 Future Plan ................................................................................................ 11
1.5 Publications ................................................................................................ 11
1.5.1 Journal Papers..................................................................................... 11
1.5.2 Proceedings .......................................................................................... 13
2. Division of Particle Physics and Astrophysics: Computational Astrophysics
Group .............................................................................................................. 17
2.1 Research Activity........................................................................................ 17
2.2 Research Results ........................................................................................ 17
2.2.1 Dedicated Computer and Numerical Methods ................................... 17
2.2.2 Large-Scale Numerical Simulations ................................................... 18
2.3 Collaboration .............................................................................................. 20
2.4 Future Plan ................................................................................................ 20
2.5 Publications ................................................................................................ 20
2.5.1 Journal Papers..................................................................................... 20
2.5.2 Proceedings .......................................................................................... 21
3. Division of Materials and Life Sciences: Computational Condensed Matter
Science Group ................................................................................................. 23
3.1 Research Activity........................................................................................ 23
3.2 Research Results ........................................................................................ 24
3.3 Collaboration .............................................................................................. 28
3.4 Future Plan ................................................................................................ 28
3.5 Publications ................................................................................................ 29
3.5.1 Journal Papers..................................................................................... 29
3.5.2 Proceedings .......................................................................................... 33
4. Division of Materials and Life Sciences: Computational Life Science Group35
4.1 Research Activity........................................................................................ 35-3-

CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

4.2 Research Results ........................................................................................ 36
4.3 Collaboration .............................................................................................. 39
4.4 Future Plan ................................................................................................ 39
4.5 Publications ................................................................................................ 41
4.5.1 Journal Papers..................................................................................... 41
4.5.2 Proceedings .......................................................................................... 42
5. Division of Materials and Life Sciences: Quantum Many-Body Systems Group......................................................................................................................... 43
5.1 Research Activity........................................................................................ 43
5.2 Research Results............................................................................................. 45
5.3 Collaboration .............................................................................................. 48
5.4 Future Plan ................................................................................................ 48
5.5 Publications ................................................................................................ 49
5.5.1 Journal Papers..................................................................................... 49
5.5.2 Proceedings.............................................................................................. 53
6.

Division of Global Environment and Biological Sciences: Global
Environmental Science Group ....................................................................... 56
6.1 Research Activity........................................................................................ 56
6.1.1 Activity in 2005.................................................................................... 56
6.1.2 Activity in 2006.................................................................................... 58
6.1.3 Activity in 2007.................................................................................... 59
6.2 Research Contributions.............................................................................. 61
6.3 Collaboration .............................................................................................. 61
6.4 Future Plan ................................................................................................ 62
6.5 Publications ................................................................................................ 63

7. Division of Global Environment and Biological Sciences: Biological Science
Group .............................................................................................................. 65
7.1 Research Activity. ....................................................................................... 65
7.2 Research Results ........................................................................................ 67
7.2.1 Testing the monophyly of red algae and green plants ....................... 67
7.2.2 Monophyly between cryptophytes and haptophytes .......................... 67
7.2.3 Phylogenetic position of Centrohelida ................................................ 68
7.2.4 Origin of chlorophyll-c containing plastids......................................... 68-4-

CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

7.2.5 Sisterhood between Cercozoa and Foraminifera ................................ 69
7.2.6 New excavate flagellates ..................................................................... 69
7.3 Collaboration .............................................................................................. 70
7.4 Future Plan ................................................................................................ 70
7.5 Publications ................................................................................................ 71
8. Division of High Performance Computing Systems ....................................... 73
8.1 Research Activity ....................................................................................... 73
8.2 Research Results ........................................................................................ 74
8.3 Collaboration .............................................................................................. 75
8.4 Future Plan ................................................................................................ 76
8.5 Publications ................................................................................................ 77
8.5.1 Journal Papers..................................................................................... 77
8.5.2 Proceedings .......................................................................................... 79
9. Division of Computational Informatics: Computational Intelligence Group 84
9.1 Research Activity........................................................................................ 84
9.1.1 Infrastructure for Information Integration ........................................ 84
9.1.2 Data Mining and Knowledge Discovery.............................................. 85
9.1.3 XML and Web Programming............................................................... 87
9.1.4 Meteolorogical Databases.................................................................... 88
9.2 Research Results ........................................................................................ 89
9.3 Collaboration .............................................................................................. 91
9.4 Future Plan ................................................................................................ 91
9.5 Publications ................................................................................................ 92
9.5.1 Journal Papers..................................................................................... 92
9.5.2 Proceedings .......................................................................................... 93
10. Division of Computational Informatics: Computational Media Group..... 97
10.1 Research Activity...................................................................................... 97
10.2 Research Results ...................................................................................... 98
10.2.1 Network Transmission and Interactive Display of Live 3D Video................. 98
10.2.2 Visual augmentation for pedestrians using surveillance cameras .................. 99
10.2.3 Visual Augmentation of Drivers by Dynamic Sensing of Environment........ 100
10.2.4 Autonomous Cooperation of Multimedia Sensor Arrays Tightly Connected over
Network (Massive Sensing) ...................................................................... 101-5-

CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

10.2.5 Privacy Considering Video Surveillance System by Combining the Advantagesof Mobile and Environmental Cameras ...................................................... 102
10.3 Collaboration .......................................................................................... 103
10.4 Future Plan............................................................................................. 103
10.5 Publications ............................................................................................ 104
10.5.1 Journal Papers................................................................................. 104
10.5.2 Proceedings ...................................................................................... 105-6-

CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

1. Division of Particle Physics and Astrophysics: Computational Particle Physics
Group
1.1 Research Activity
Computational Particle Physics group has performed researches in lattice QCD, using
mainly massively parallel computer CP-PACS, constructed and operated at Research Centerfor Computational Physics, the precursor of our center. In addition to CP-PACS, otherresources such as SR8000 at our center, VPP5000 at Academic Computing andCommunications Center, University of Tsukuba, SR8000 at High Energy Accelerator
Research Organization (KEK) and the Earth Simulator at The Erath Simulator Center havebeen employed for our researches.
Our research activities for the past 3 years are summarized below.
①. Calculation of hadron spectra and determination of fundamental parameter in QCD
such as quark masses via numerical simulations in lattice QCD with dynamicalquarks
②. Dynamical properties of hadorons such as the pion scattering in lattice QCD③. Determination of hadornic matrix elements in lattice QCD, necessary to test thestandard model and beyond④. Lattice QCD at finite temperature and density⑤. The nuclear force from lattice QCD
1.2 Research Results
Our research group has obtained many results in the areas of the above research activities.
Main results for the past 3 years are given below item by item.
①. Calculations in lattice QCD with light dynamical up and down quarks have been
performed by using CP-PACS and finished in 2003. We have found that a discrepancyof hadron masses from experimental values, which is about 10% in quenched QCD, ismuch reduced in 2 flavor QCD. We then have started the “complete QCD” (2+1 flavor
QCD), which includes dynamical quark effects of a heavier strange quark as well as
up and down quarks. Results obtained in the calculation are as follows.
(a) We have made a test of our simulation algorithm and a choice of the gauge action
performing preliminary simulations in a small volume.
(b) In order to remove the lattice artifact liner in the lattice spacing a, we havedetermined the clover coefficient in 3 flavor QCD non-perturbatively.
(c) After preparations mentioned above、we have proceeded to a 2+1 flavor QCD-7-

CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

simulation in which we treat heavier strange quark dynamical in addition to light up
and down quarks. Meson masses extrapolated to the continuum limit turn out to beconsistent with experiment. All available computational resources such as CP-PACS,
SR8000, VP5000 and the Earth Simulator have been devoted to this calculation.
Although no clear effects of dynamical strange quarks are observed, determinationof the meson spectrum for QCD without quenching approximation is an event ofgreat significance in the history of lattice QCD simulations.
(d) In the 2+1 flavor simulation above, calculations have been made for up and downquark masses heavier than 70 MeV and results is extrapolated to the physical up anddown quark masses of about 3 MeV. This long chiral extrapolation causes a possible
systematic error. In order to overcome these difficulties, we have just started
simulations with much lighter up and down quark masses down to 6 MeV on a large
lattice of 3.2 fm. The simulation was carried out using the PACS-CS computer, a
successor of CP-PACS, developed at our center. Fig. 1 shows results for the hadron
spectrum, compared with those obtained for quenched and 2 flavor QCD. A
consistency of all measured hadron masses with experiment is observed only for our
new 2+1 flavor QCD results, though errors are still large and the results are obtained
only at one lattice spacing.
(e) The masses of light quarks are fundamental parameters of QCD. It is known thatquark masses in 2 flavor QCD are smaller those in quenched QCD by 20-30%. We
have calculated quark masses in 2+1 flavor QCD and obtained a result that they arealmost unchanged from those in 2 flavor QCD.
(f) Wilson chiral perturbation theory, which is a theoretical guideline of chiralextrapolation for the Wilson or clover quark action, has been extended topseudo-scalar meson masses and vector meson masses in 2+1 flavor QCD.

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CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Fig.1: Hadron mass spectrum obtained from 2+1 flavor QCD simulations withvery light up and down quark masses. Results for quenched QCD and 2 flavor QCD
are overlaid. Horizontal bars represent experimental values.
②. Dynamical properties of hadrons.
(a) Calculation of scattering phase shift is an important step for expanding ourunderstanding of strong interactions based on lattice QCD beyond the hadron mass
spectrum. For scattering lengths, which are the threshold values of phase shifts,
several studies have already been carried out. However there is none for the
scattering phase shift. We calculated the I=2 S-wave two-pion scattering phase shift
in the quenched QCD and the full QCD. We show that the results in the full QCD
in the continuum limit are consistent with the experiments.
(b) The U(1) problem, which is to derive the flavor U(1) pseudo-scalar meson mass
much heavier than the pion, is one of the longstanding issues in particle physics. We
have carried out an 2+1 flavor QCD calculation, taking account of a mixing effect ofU(1) and other mesons. So far, calculations are completed only at one lattice spacing
and we obtain the U(1) meson mass roughly consistent with the experimental value.
③. Hadronic matrix elements(a) We have calculated proton decay matrix element in lattice QCD with the quenched-9-

CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

approximation. Values obtained in the continuum limit is larger by about 3 times
than the smallest prediction among various QCD models. This implies stronger
constraints on models for the grand unified theories(GUTs).
(b) Matrix elements of hadrons which include heavy quarks are important to restrict
parameters of the standard model. However it is difficult to put a heavy quark on thelattice. Therefore we have proposed a new formulation for a heavy quark on thelattice to overcome the difficulty. A quenched QCD simulation we have performed
has shown that our formulation for a heavy quark works well.
④. Under usual conditions, quarks and gluons are confined within hadrons. However, attemperatures higher than about 1012 K, hadrons are expected to turn into thequark-gluon plasma phase. These unconventional states of matter are relevant to theearly evolution of the Universe and maybe the structure of the central core of neutronstars. We have studied the quark number susceptibility and static quark free energy in
2 flavor QCD at zero chemical potential. From the static quark free energy in various
color channels, we have found that the inter-quark force for quark-antiquark(quark-quark) pairs is attractive for color singlet (triplet) channels while it is repulsive
for octet (sextet) channels. We are extending the study to finite chemical potentials.
⑤. It is one of the most important problems in nuclear physics to understand aninteraction between nucleon (nuclear force). In particular, repulsion at short distance(repulsive core) necessary to explain stability of a nuclei has been theoretically lessunderstood. We have proposed a new method to calculate a potential between hadrons,
and applying it to nucleons we have calculated the nucleon potential in quenched QCD.
Our result at one lattice spacing shows that not only repulsive core but also attraction
at long and intermediate distances are reproduced.
1.3 Collaboration
Recognizing that gauge configurations generated in dynamical QCD simulations arevaluable,
we are now constructing ILDG (International Lattice Data Grid) incollaboration with Grid and Networks group in High Performance Computing Systems
division, to share gauge configurations worldwide through internet. This year, supported by
CSI (Cyber Science Infrastructure) project at National Institute of Informatics, we haveconstructed JLDG for domestic data sharing. We have also closely cooperated with System
Architecture group in High Performance Computing Systems division, to develop andconstruct PACS-CS. We are currently collaborating with several peoples in High
Performance Computing Systems division, for development and tuning of simulation codes
on PACS-CS.
- 10 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

1.4 Future Plan
With the encouraging results in 2+1 flavor QCD at one lattice spacing, we plan to
calculate the hadron spectrum at the physical up and down quark masses at the same
spacing, so that no chiral extrapolation is necessary. We then will proceed to simulations
for finer lattices, which will finally establish the QCD mass spectrum. Using gauge
configurations generated in 2+1 flavor QCD simulations, we will investigate hadroninteractions, hadronic matrix elements and nuclear force. In addition a lattice QCD study at
finite density is also planed.
1.5 Publications
1.5.1 Journal Papers
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Y. Maezawa, N. Ukita, S. Aoki, S. Ejiri, T. Hatsuda, N. Ishii and K. Kanaya, Heavy-Quark Free
Energy, Debye Mass, and Spatial String Tension at Finite Temperature in Two Flavor Lattice
QCD with Wilson Quark Action, Phys.Rev.D75, ref.074501 (2007)
Y. Kayaba, S. Aoki, M. Fukugita, Y. Iwasaki, K. Kanaya, Y. Kuramashi, M. Okawa, A. Ukawa,T.Yoshie, First Nonperturbative Test of a Relativistic Heavy Quark Action in Quenched Lattice
QCD, JHEP702, 019 (2007)
E. Shintani, S. Aoki, N. Ishizuka, K. Kanaya, Y. Kikukawa, Y. Kuramashi, M. Okawa, A. Ukawa,T. Yoshie. Neutron electric dipole moment with external electric field method in lattice QCD,
Phys.Rev.D75, ref.034507 (2007)
Sinya Aoki, Hidenori Fukaya, Shoji Hashimoto, Tetsuya Onogi, Finite volume QCD at fixed
topological charge, Phys.Rev.D76, ref.054508 (2007)
H. Fukaya, S. Aoki, T.W. Chiu, S. Hashimoto, T. Kaneko, H. Matsufuru, J. Noaki, K. Ogawa, T.
Onogi, N. Yamada, Two-flavor lattice QCD simulation in the epsilon-regime and chiral Random
Matrix Theory, Phys.Rev.D76, ref.054503 (2007)
T.Kaneko, S.Aoki, M.Della Morte, S.Hashimoto, R.Hoffmann, R.Sommer, Non-perturbative
improvement of the axial current with three dynamical flavors and the Iwasaki gauge action,
JHEP704, 092 (2007)
H. Fukaya, S. Aoki, T.W. Chiu, S. Hashimoto, T. Kaneko, H. Matsufuru, J. Noaki, K. Ogawa, M.
Okamoto, T. Onogi, N. Yamada, Two-flavor lattice QCD simulation in the epsilon-regime withexact chiral symmetry,. Phys.Rev.Lett.98, ref.172001 (2007)
S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T.
Kaneko, Y. Kuramashi, M. Okawa, S. Takeda, Y. Taniguchi, N. Tsutsui, A. Ukawa, N. Yamada,T. Yoshie. Nonperturbative $O(a)$ improvement of the Wilson quark action with therenormalization-group-improved gauge action using the Schr¥""odinger functional method,
Phys.Rev.D73, ref.034501 (2006)
Sinya Aoki, Oliver Bar, Automatic O(a) improvement for twisted-mass QCD in the presence of
spontaneous symmetry breaking,Phys.Rev.D74, ref.034511 (2006)
S. Aoki, O. Baer, S. Takeda, Vector meson masses in 2+1 flavor Wilson Chiral Perturbation
Theory, Phys.Rev.D73, ref.094501 (2006)
S. Aoki, O. Baer, T. Ishikawa, S. Takeda, Pseudo scalar meson masses in Wilson Chiral
Perturbation Theory for 2+1 flavors, Phys.Rev.D73, ref.014511 (2006)
Hiroshi Suzuki and Yusuke Taniguchi, Two dimensional N=(2,2) super Yang-Mills theory on thelattice via dimensional reduction, JHEP510, 082 (2006)
Yusuke Taniguchi, Schroedinger functional formalism with domain-wall fermion, JHEP610, 027(2006)- 11 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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住元真司, 大江和一, 久門耕一, 朴泰祐, 佐藤三久, 宇川彰, 複数 Gigabit Ethernet を用いた
PACS-CS のための高性能通信機構の設計と評価, 情報処理学会論文誌コンピューティン
グシステム vol.47,No.SIG12(ACS 15), 25-34 (2006)
S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T.
Kaneko, Y. Kuramashi, M. Okawa, N. Tsutsui, A. Ukawa, N. Yamada, T. Yoshie, Bulk first-orderphase transition in three-flavor lattice QCD with $O(a)$-improved Wilson fermion action at zerotemperature, Phys.Rev.D72, ref.054510 (2005)
E. Shintani, S. Aoki, N. Ishizuka, K. Kanaya, Y. Kikukawa, Y. Kuramashi, M. Okawa, Y.
Tanigchi, A. Ukawa, T. Yoshie, Neutron electric dipole moment from lattice QCD, Phys.Rev.D72,
ref.014504 (2005)
S. Aoki, M. Fukugita, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T. Kaneko, Y.
Kuramashi, M. Okawa, A. Ukawa, T. Yamazaki, T. Yoshie, $I=2$ Pion Scattering Length from
Two-Pion Wave Functions, Phys.Rev.D71, ref.094504, (2005)
N. Yamada, S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K.
Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, Y. Taniguchi, N. Tsutsui, A. Ukawa, T.
Yoshie, Non-perturbative $O(a)$-improvement of Wilson quark action in three-flavor QCD withplaquette gauge action, Phys.Rev.D71, ref.054505 (2005)
Norikazu Yamada, Sinya Aoki and Yoshinobu Kuramashi, Perturbative Determination of Mass
Dependent Renormalization and Improvement Coefficients for the Heavy-Light Vector and
Axail-Vector Currents with Relativistic Heavy and Domain-Wall Light Quarks,Nucl.Phys.B713,
407 (2005)
Yusuke Taniguchi, Schroedinger functional formalism with Ginsparg-Wilson fermion, JHEP512,
037 (2005)
N. Tsutsui, S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K.
Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, T. Onogi, Y. Taniguchi, A. Ukawa, T. Yoshie,
Lattice QCD calculation of the proton decay matrix element in the continuum limit, Phys.Rev.D70,
ref.011501(R) (2004)
S. Takeda, S. Aoki, M. Fukugita, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T. Kaneko,
Y. Kuramashi, M. Okawa, Y. Taniguchi, A. Ukawa, T. Yoshie, Scaling study of the step scaling
function in SU(3) gauge theory with improved gauge actions, Phys.Rev.D70, ref.074501 (2004)
K. Ide, S. Aoki, R. Burkhalter, M. Fukugita, S. Hashimoto, K-I. Ishikawa, T. Ishikawa, N.
Ishizuka, Y. Iwasaki, K. Kanaya, T. Kaneko, Y. Kuramashi, V.I. Lesk, M. Okawa, Y. Taniguchi,
T. Umeda, A. Ukawa, T. Yoshie, Non-perturbative renormalization of meson decay constants inquenched QCD for a renormalization group improved gauge action, Phys.Rev.D70, ref.074502(2004)
Y. Namekawa, S. Aoki, M. Fukugita, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T.
Kaneko, Y. Kuramashi, V.I. Lesk, M. Okawa, A. Ukawa, T. Umeda, T. Yoshie, Light hadron
spectroscopy in two-flavor QCD with small sea quark masses, Phys.Rev.D70, ref.074503 (2004)
T. Yamazaki, S. Aoki, M. Fukugita, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T.
Kaneko, Y. Kuramashi, M. Okawa, A. Ukawa, T. Yoshie, $I=2$ $¥pi¥pi$ Scattering Phase Shiftwith two Flavors of $O(a)$ Improved Dynamical Quarks, Phys.Rev.D70, ref.074513 (2004)
S. Aoki, M. Fukugita, N. Ishizuka, Y. Iwasaki, K. Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa,Y. Taniguchi, A. Ukawa, T. Yoshie, Non-perturbative calculation of $Z_V$ and $Z_A$ indomain-wall QCD on a finite box, Phys.Rev.D70, ref.034503 (2004),
S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T.
Kaneko, Y. Kuramashi, M. Okawa, N. Tsutsui, A. Ukawa, N. Yamada, T. Yoshie, Heavy quark
expansion parameters from lattice NRQCD, Phys.Rev.D69, ref.094512 (2004)
S.Takeda, S.Aoki, M.Fukugita, K-I.Ishikawa, N.Ishizuka, Y.Iwasaki, K.Kanaya, T.Kaneko,
Y.Kuramashi, M.Okawa, Y.Taniguchi, A.Ukawa and T.Yoshie, A Scaling Study of the Step
Scaling Function in SU(3) Gauge Theory with Improved Gauge Actions, Phys.Rev.D70,
ref.074510 (2004)
Sinya Aoki, Yasuhisa Kayaba and Yoshinobu Kuramashi, Perturbative Determination of Mass
Dependent O(a) Improvement Coefficients for the Vector and Axial Vector Currents with a- 12 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Relativistic Heavy Quark Action, Nucl.Phys.B689, 127 (2004)
Sinya Aoki, Yasuhisa Kayaba and Yoshinobu Kuramashi, Perturbative Determination of Mass
Dependent O(a) Improvement Coefficients in a Relativistic Heavy Quark Action, Nucl.Phys.B697,
271 (2004)
Sinya Aoki, Oliver Baer, Twisted-mass QCD, O(a) improvement and Wilson chiral perturbation
theory, Phys.Rev.D70, ref.116011 (2004)
B0 - ANTI-B0 MIXING IN UNQUENCHED LATTICE QCD
JLQCD Collaboration: S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, N. Ishizuka, Y.
Iwasaki, K. Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, T. Onogi, N. Tsutsui, A. Ukawa, N.
Yamada, T. Yoshie, Phys.Rev.Lett.91, ref.212001 (2004)
Y. Iwasaki, K. Kanaya, S. Kaya, S. Sakai, T. Yoshie, Phase structure of lattice QCD for general
number of flavors, Phys.Rev.D69, ref.014507 (2004)

1.5.2 Proceedings
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Y. Maezawa, S. Aoki, S. Ejiri, T. Hatsuda, N. Ishii, K. Kanaya and N. Ukita, Thermodynamics of
two-flavor lattice QCD with an improved Wilson quark action at non-zero temperature anddensity, J. Phys. G: Nucl. Part. Phys. 34, 651 (2007)
YUSUKE TANIGUCHI, Schroedinger functional formalism for overlap Dirac operator anddomain-wall fermion, Modern Physics Letters
A22, 499 (2007)
Y. Nakamura, S. Aoki, M. Fukugita, N. Ishizuka, Y. Iwasaki, K. Kanaya, Y. Kuramashi, J. Noaki,
M. Okawa, Y. Taniguchi, A. Ukawa, T. Yoshie, Kaon $B$-parameters for Generic $¥Delta
S=2$ Four-Quark Operators in Quenched Domain Wall QCD, PoS(LAT2006), 089 (2006)
Y. Kuramashi, S. Aoki, K.-I. Ishikawa, T. Ishikawa, N. Ishizuka, K. Kanaya, N. Tsutsui, M.
Okawa, Y. Taniguchi, A. Ukawa, T. Yoshie, 2+1 Flavor Lattice QCD with Luescher's
Domain-Decomposed HMC Algorithm, PoS(LAT2006), 029 (2006)
T. Ishikawa, S. Aoki, M. Fukugita, S. Hashimoto, K.-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K.
Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, Y. Taniguchi, N. Tsutsui, A. Ukawa, N. Yamada,T. Yoshie, 2+1 flavor light hadron spectrum and quark masses with the $O(a)$ improved
Wilson-clover quark formalism, PoS(LAT2006), 181 (2006)
N. Ukita, S. Ejiri, T. Hatsuda, N. Ishii, Y. Maezawa, S. Aoki, K. Kanaya, Finite temperature phasetransition of two-flavor QCD with an improved Wilson quark action, PoS(LAT2006), 150 (2006)
K-I. Ishikawa, S. Aoki, T. Ishikawa, N. Ishizuka, K. Kanaya, Y. Kuramashi, M. Okawa, Y.
Taniguchi, A. Ukawa, T. Yoshie, An application of the UV-filtering preconditioner to the
Polynomial Hybrid Monte Carlo algorithm, PoS(LAT2006), 027 (2006)
T. Kaneko, S. Aoki, H. Fukaya, S. Hashimoto, K-I. Ishikawa, K. Kanaya, H. Matsufuru, M.
Okamoto, M. Okawa, T. Onogi, A. Ukawa, N. Yamada, T. Yoshie, JLQCD's dynamical overlap
project, PoS(LAT2006), 054 (2006)
Hideo Matsufuru, Hidenori Fukaya, Shoji Hashimoto, Kazuyuki Kanaya, Takashi Kaneko, Kenji
Ogawa, Masataka Okamoto, Tetsuya Onogi, Norikazu Yamada, Improvement of algorithms for
dynamical overlap fermions, PoS(LAT2006), 031 (2006)
H. Fukaya, S. Hashimoto, K. Kanaya, T. Kaneko, H. Matsufuru, K. Ogawa, M. Okamoto, T.
Onogi, N. Yamada, Dynamical overlap fermions in the epsilon-regime, PoS(LAT2006), 050(2006)
E. Shintani, S. Aoki, N. Ishizuka, K. Kanaya, Y. Kuramashi, M. Okawa, A. Ukawa, T. Yoshie,
Calculation of Neutron EDM in quenched and full QCD, PoS(LAT2006), 123 (2006)
S. Aoki, M. Fukugita, K.-I. Ishikawa, T. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, Y.
Kuramashi, M. Okawa, Y. Taniguchi, A. Ukawa, N. Yamada, T. Yoshie, An estimate of the eta
and eta-prime meson masses in Nf=2+1 lattice QCD, PoS(LAT2006), 204 (2006)
S. Aoki, M. Fukugita, K.-I. Ishikawa, N. Ishizuka, K. Kanaya, Y. Kuramashi, Y. Namekawa, M.
Okawa, K. Sasaki, A. Ukawa, T. Yoshie, $¥rho$ meson decay from the lattice, PoS(LAT2006),
110 (2006)
Y. Maezawa, S. Ejiri, T. Hatsuda, N. Ishii, N. Ukita, S. Aoki, K. Kanaya, Static quark free

- 13 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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energies at finite temperature with two flavors of improved Wilson quarks, PoS(LAT2006), 141(2006)
S. Hashimoto, S. Aoki, H. Fukaya, K. Kanaya, T. Kaneko, H. Matsufuru, M. Okamoto, T. Onogi,
N. Yamada, Dynamical overlap fermion at fixed topology, PoS(LAT2006), 052 (2006)
S. Ejiri, T. Hatsuda, N. Ishii, Y. Maezawa, N. Ukita, S. Aoki, K. Kanaya, Equation of state for
two-flavor QCD with an improved Wilson quark action at non-zero chemical potential,
PoS(LAT2006), 132 (2006)
N. Yamada, S. Aoki, H. Fukaya, S. Hashimoto, K-I. Ishikawa, K. Kanaya, T. Kaneko, H.
Matsufuru, M. Okamoto, T. Onogi, Mobility edge and locality of the overlap-Dirac operator withand without dynamical overlap fermions, PoS(LAT2006), 060 (2006)
A. Ukawa, S. Aoki, K.-I. Ishikawa, T. Ishikawa, N. Ishizuka, K. Kanaya, Y. Kuramashi, K. Sasaki,
N. Tsutsui, M. Okawa, Y. Taniguchi, T. Yoshie, Status and physics plan of the PACS-CS Project,
PoS(LAT2006), 039 (2006)
Sinya Aoki, Oliver Bar, Automatic O$(a)$ improvement for twisted-mass QCD, PoS(LAT2006),
165 (2006)
Sinya Aoki, Oliver Bar, WChPT analysis of twisted mass lattice data, QNP '06 (2006)
Noriyoshi ISHII, Sinya AOKI, Tetsuo HATSUDA, Nuclear Force from Lattice QCD,PoS(LAT2006), 109 (2006)
Sinya AOKI, QCD Phases in Lattice QCD, Int. J. Mod. Phys.A21, 682 (2006)
T.Boku, M.Sato, A.Ukawa, D.Takahashi, S.Sumimoto, K.Kumon, T.Moriyama, M.Shimizu,
PACS-CS: A large-scale bandwidth-aware PC cluster for scientific computations, Proc.of
CCGrid2006,Singapore (2006)
S.Sumimoto, K.Ooe, K.Kumon, T.Boku, M.Sato, A.Ukawa, Scable Communication Layer for
Multi-Dimensional Crossbar Network Using Multiple Gigabit Ethernet, Proc.of
ICS2006,Cairns,Australia (2006)
Akira Ukawa, Lattice QCD: Status and Prospect, AIP Conference Proceedings 815, 2430250(2006)
Akira Ukawa, Hadron Spectrum from Lattice QCD, Int.J.Mod.Phys. A21, 726 (2006)
CP-PACS Collaboration: Y. Kuramashi, S. Aoki, O. Bar, K.I. Ishikawa, T. Ishikawa, N. Ishizuka,
Y. Iwasaki, K. Kanaya, T. Kaneko, M. Okawa, Y. Taniguchi, N. Tsutsui, A. Ukawa, N. Yamada,T. Yoshie, Quenched scaling study of charm and bottom systems with a relativistic heavy quark
action, PoS(LAT2005), 226 (2005)
Eigo Shintani, S. Aoki, N. Ishizuka, K. Kanaya, Y. Kikukawa, Y. Kuramashi, M. Okawa, A.
Ukawa, T. Yoshie, Neutron electric dipole moment on the lattice, PoS(LAT2005), 128 (2005)
CP-PACS, JLQCD Collaborations: T. Ishikawa, S. Aoki, O. Bar, M. Fukugita, S. Hashimoto, K.-I.
Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, Y.
Taniguchi, N. Tsutsui, A. Ukawa, T. Yoshie, Light hadron spectrum and quark masses in 2+1
flavor QCD, PoS(LAT2005), 057 (2005)
S. Hashimoto, S. Aoki, M. Fukugita, K.-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T.
Kaneko, Y. Kuramashi, M. Okawa, N. Tsutsui, A. Ukawa, N. Yamada, T. Yoshie, Pion form
factors in two-flavor QCD, PoS(LAT2005), 336 (2005)
N. Tsutsui, S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K.
Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, A. Ukawa, N. Yamada, T. Yoshie, Kaon
semileptonic decay form factors in two-flavor QCD, PoS(LAT2005), 357 (2005)
S. Aoki, K.-I. Ishikawa, T. Ishikawa, N. Ishizuka, K. Kanaya, Y. Kuramashi, M. Okawa, K.
Sasaki, Y. Taniguchi, N. Tsutsui, A. Ukawa, T. Yoshie, The PACS-CS Project, PoS(LAT2005),
111 (2005)
T. Ishikawa, S. Aoki, O. B¥""ar, M. Fukugita, S. Hashimoto, K.-I. Ishikawa, N. Ishizuka, Y.
Iwasaki, K. Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, Y. Taniguchi, N. Tsutsui, A. Ukawa,T. Yoshie, Light hadron spectrum and quark masses in 2+1 flavor QCD, PoS(LAT2005), 057(2005)
Sinya Aoki, Oliver Bar, Determining the low energy parameters of Wilson Chiral Perturbation
Theory, PoS(LAT2005), 046 (2005)- 14 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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T. Ishikawa, S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki,
K. Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, T. Onogi, N. Taniguchi, N. Tsutsui, A.
Ukawa, T. Yoshie, Light hadron spectrum in 2+1 flavor full QCD by CP-PACS and JLQCD
Collaborations, Nucl. Phys.B (Proc. Suppl.) 140, 225 (2005)
S. Takeda, S. Aoki, M. Fukugita, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T. Kaneko,
Y. Kuramashi, M. Okawa, Y. Taniguchi, A. Ukawa, T. Yoshie, A scaling study of the step scaling
function of quenched QCD with improved gauge actions, Nucl. Phys. B (Proc. Suppl.) 140, 740(2005)
Y. Kayaba, S. Aoki, M. Fukugita, K-I. Ishikawa, Y. Iwasaki, K. Kanaya, T. Kaneko, Y.
Kuramashi, M. Okawa, A. Ukawa, T. Yoshie, Charmed meson spectra and decay constants with
one-loop $O(a)$ improved relativistic heavy quark action, Nucl. Phys. B (Proc. Suppl.) 140, 479(2005)
S. Aoki, M. Fukugita, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T. Kaneko, Y.
Kuramashi, M. Okawa, A. Ukawa, T. Yamazaki, T. Yoshie, $I=2$ Pion Scattering Length from
Two-Pion Wave Function, Nucl. Phys. B (Proc. Suppl.) 140, 305 (2005)
Y. Namekawa, S. Aoki, M. Fukugita, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya,
T. Kaneko, Y. Kuramashi, V.I. Lesk, M. Okawa, A. Ukawa, T. Umeda, T. Yoshie,
Chiral extrapolations with small sea quark mass data in two-flavor lattice QCD, Nucl. Phys. B(Proc. Suppl.) 140, 314 (2005)
Norikazu Yamada, Sinya Aoki, Yoshinobu Kuramashi, One-loop determination of massdependent $O(a)$ improvement coefficients for the heavy-light vector and axial-vector currents
with relativistic heavy and domain-wall light quarks, Nucl. Phys. B (Proc. Suppl.) 140, 719 (2005)
Yusuke Taniguchi, Schroedinger functional formalism with Ginsparg-Wilson fermion, Nucl. Phys.
B (Proc. Suppl.) 140, 737 (2005)
Akira Ukawa, Status of International Lattice Data Grid -- An Overview --, Nucl. Phys. B (Proc.
Suppl.) 140, 207 (2005)
S.Aoki, K.-I.Ishikawa, Y.Iwasaki, K.Kanaya, T.Kaneko, Y.Kuramashi, N.Tsutsui, A.Ukawa,T.Yoshie, Lattice QCD on Earth Simulator, Nucl. Phys. B (Proc.Suppl.) 129&130, 859 (2004)
Sinya Aoki, Yasuhisa Kayaba, Yoshinobu Kuramashi, One-loop calculation of mass dependent${¥cal O}(a)$ improvement coefficients for the relativistic heavy quarks on the lattice, Nucl. Phys.
B (Proc.Suppl.) 129&130, 352 (2004)
K. Ide, S. Aoki, M. Fukugita, N. Ishizuka, Y. Iwasaki, K. Kanaya, T. Kaneko, Y. Kuramashi, V.
Lesk, M. Okawa, Y. Taniguchi, A. Ukawa, T. Yoshie, Non-perturbative renormalization of vector
and axial vector currents in quenched QCD for a renormalization group improved gauge action,
Nucl. Phys. B (Proc.Suppl.) 129&130, 426 (2004)
R. Sommer, S. Aoki, M. Della Morte, R. Hoffmann, T. Kaneko, F. Knechtli, J. Rolf, I. Wetzorke,
U. Wolff, Large cutoff effects of dynamical Wilson fermions, Nucl. Phys. B (Proc.Suppl.)
129&130, 405 (2004)
Shinji Takeda, Sinya Aoki, Kiyotomo Ide, A perturbative determination of O($a$) boundary
improvement coefficients for the Schr¥""odinger Functional coupling at 1-loop with improved
gauge actions, Nucl. Phys. B (Proc.Suppl.) 129&130, 408 (2004)
T. Yamazaki, S. Aoki, M. Fukugita, K-I. Ishikawa, N. Ishizuka, Y. Iwasaki, K. Kanaya, T.
Kaneko, Y. Kuramashi, V. Lesk, M. Okawa, Y. Taniguchi, A. Ukawa, T. Yoshie, I=2 pion-pion
scattering phase shift in the continuum limit calculated with two-flavor full QCD, Nucl. Phys. B(Proc.Suppl.) 129&130, 191 (2004)
K-I. Ishikawa, S. Aoki, M. Fukugita, S. Hashimoto, N. Ishizuka, Y. Iwasaki, K. Kanaya,
T.Kaneko, Y. Kuramashi, V. Lesk, M. Okawa, N. Tsutsui, A. Ukawa, T. Umeda, N. Yamada, T.
Yoshie, Study of finite volume effects in the non-perturbative determination of $c_{¥rm
SW}$ with the SF method in full three-flavor lattice QCD, Nucl. Phys. B (Proc.Suppl.) 129&130,
444 (2004)
N. Tsutsui, S. Aoki, M. Fukugita, S. Hashimoto, K-I. Ishikawa, T. Ishikawa, N. Ishizuka, Y.
Iwasaki, K. Kanaya, T. Kaneko, Y. Kuramashi, M. Okawa, T. Onogi, N. Taniguchi, A. Ukawa, T.
Yoshie, Continuum limit of proton decay matrix elements in quenched lattice QCD, Nucl. Phys. B- 15 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007•••(Proc.Suppl.) 129&130, 284 (2004)
T.Kaneko, S.Aoki, M.Fukugita, S.Hashimoto, K-I.Ishikawa, T.Ishikawa, N.Ishizuka, Y.Iwasaki,
K.Kanaya, Y.Kuramashi, M.Okawa, N.Taniguchi, N.Tsutsui, A.Ukawa, T.Yoshie, Light hadron
spectrum in three-flavor QCD with O(a)-improved Wilson quark action, Nucl. Phys. B(Proc.Suppl.) 129&130, 188 (2004)
A.C. Irving, R.D. Kenway, C.M. Maynard, T. Yoshie, Progress in building an International
Lattice Data Grid, Nucl. Phys. B (Proc.Suppl.) 129&130, 159 (2004)
JLQCD Collaboration: T. Onogi, S. Aoki, N. Ishizuka, Y. Iwasaki, K. Kanaya, A. Ukawa, T.
Yoshie, K.I. Ishikawa, M. Fukugita, S. Hashimoto, T. Kaneko, Y. Kuramashi, N. Tsutsui, M.
Okawa, N. Yamada, Heavy-light decay constants for B and D mesons in n(f) = 2 unquenched
QCD in Fermilab formalism, Nucl. Phys. B (Proc.Suppl.) 129&130, 373 (2004)- 16 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

2. Division of Particle Physics and Astrophysics: Computational Astrophysics Group
2.1 Research Activity
In the computational astrophysics group, we have explored first generation objects in an
early universe, formation and evolution of galaxies, large-scale structures in the universe,
active galactic nuclei with the formation of supermassive black holes. In particular, we haveconcentrated on the coupling effects of radiation and matter. For the purpose, the methodsof multi-dimensional radiative transfer and radiation hydrodynamics (RHD) have beendeveloped. In addition, ultra-high resolution hydrodynamic simulations on the early
evolution of galaxies through multiple supernovae, and the large-scale simulations of
far-infrared or submillimeter galaxies have been performed, which can be compared withthe future observations with ALMA.
To realize high-resolution RHD simulations, we have urged the FIRST project, anddeveloped a new type of hybrid computer dedicated for astrophysical RHD, called FIRST
simulator, in the collaboration with the Division of High Performance Computing Systems.
This project is funded by a Specially Promoted Research in Grants-in-Aid for Scientific
Research over four years (2004~2007) with the budget of JPY329.5 million (US$2.8
million), approved by The Ministry of Education, Culture, Sports, Science and Technology(MEXT) in Japan. With FIRST simulator, we have performed high-resolution simulations
on the evolution of first generation objects, and obtained new results.
2.2 Research Results
2.2.1 Dedicated Computer and Numerical Methods
1) First Simulator
For the realization of 3D radiation hydrodynamics, we have built up a hybrid PC cluster,called FIRST (Fusional Integrator for Radiation-hydrodynamic Systems in Tsukuba
University) simulator, where a newly-developed board for gravity calculations, called
Blade-GRAPE, is embedded in each node. The Blade-GRAPE is composed of four
GRAPE-6 chips and designed for PCI-X bus in a PC cluster. The theoretical peak
performance of Blade-GRAPE is 136.8GFLOPS. Each board has 16MB memory and cancalculate the self-gravity of 260,000 particles simultaneously at the maximum. The
Blade-GRAPE is directly connected via PCI-X bus, and occupies the space of two PCI-X
bus slots. The electric power supply is from the PCI-X bus (3.3V) as well as from thecluster server board, +12V (54W). Each server PC is equipped with multi-port Gigabit
Ethernet NIC to be connected to a special interconnection network with commodity- 17 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

FIGURE 1. Blade-GRAPE X64

FIGURE 2. FIRST simulator (256 node, 36.1TFLOPS)

Ethernet switches. Using Blade-GRAPEs, we have constructed a 256 node hybrid PC
cluster system, that is, FIRST simulator. The host PC cluster node is a 2U-size of 19-inchrack mountable server PC (HP ProLiant DL380 G4) that has dual Xeon processors in SMP
configuration. The peak performance of FIRST simulator is 36.1TFLOPS, where the hostPC cluster is 3.1 TFLOPS and the Blade-GRAPEs are 33 TFLOPS. All nodes are connected
uniformly with each other via multi-port Gbit ether interconnect switch. The total memoryof FIRST simulator is 1.6TB. Also, the Gfarm Grid file system, which is thecommodity-based distributed file system that federates local disk of each node
(http://datafarm.apgrid.org/index.en.html), is installed. With Gfarm, the storage of 22TB isavailable as a seamless file server. In Figure 2, 256 node FIRST simulator is shown.
2) Numerical Methods for Astrophysical RHD
As for 3D radiative transfer, we have developed a grid-based scheme with
CP-PACS（ 1992-2005 ） . Then, a SPH-based RHD (RSPH) scheme has been developed in"Development of Next Generation Massive Parallel Computer" Project (1997 - 2001),
which is funded by the "Research for the Future Program" of Japan Society for the
Promotion of Science. Also, in this project, HMCS (Heterogeneous Multi-Computer
System) was constructed, where an RSPH scheme is installed. This RSPH scheme has been
improved to optimize FIRST simulator.
3) Hydrodynamic Scheme with SSE
To utilize the potentiality of CPU to the maximum, an SPH scheme with SSE(Streaming SIMD extension), which is equipped in x86 architecture, has been developed.
Also, we are planing to develop a radiative transfer scheme with SSE.
2.2.2 Large-Scale Numerical Simulations
1) RHD Simulations on First-Generation Objects
Using FIRST simulator, we have performed three-dimensional RHD simulations to
scrutinize the feedback by a first star in first generation objects. It has been found that anearby collapsing core is evaporated by a shock if an M-type I-front sweeps the core. But,
- 18 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

in higher density cores, the I-front changes to D-type and an H2 shell forms ahead of theI-front, which effectively shields H2 dissociating radiation from a source star. Then, thecores can collapse owing to H2 cooling. The present numerical study has shown that almost
all density peaks can collapse in first generation objects. Hence, the star formation

FIGURE 3. Time sequence of the propagation of I-front in a collapsing cloud. The colors of particles
denote the H2 fraction. The photodissociating radiation is shielded by an H2 shell, which is produced by
the propgation of ionizing radiation, and eventually the cloud can collapse.

efficiency in first generation objects is expected to be higher by an order of magnitude thanargued so far.

FIGURE 4. Cover page of Nature (March 30, 2006).
Simulation by Mori and Umemura is presented.

- 19 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

2) Origin of Elliptical Galaxies
We have performed an ultra-high-resolution hydrodynamic simulation that follows
evolution from the earliest stages of galaxy formation through the period of dynamicalrelaxation. The bubble structures produced by multiple supernovae at an early evolutionary
stage (< 3×108 years) resemble closely the high-redshift Lyman α emitters (LAEs). After
109 years these bodies are dominated by stellar continuum radiation and look like the
Lyman break galaxies (LBGs) known as the high-redshift star-forming galaxies at which
point the metallicity appears to be solar. After 1.3×1010 years, these galaxies resemble
present-day elliptical galaxies.
3) Far Infrared and Submillimeter Galaxies
The large-scale structure of high redshift galaxies has been simulated, focusing on far
infrared and submillimeter properties. The theoretical prediction can be tested by ALMA innear future.
2.3 Collaboration
In the collaboration with the Division of High Performance Computing Systems,
HMCS (Heterogeneous Multi-Computer System) was constructed under "Development of
Next Generation Massive Parallel Computer" Project (1997 - 2001), which is funded by the"Research for the Future Program" of Japan Society for the Promotion of Science. With thisskill for hybrid computer systems, we have propelled the FIRST project (2004-2007), anddeveloped the FIRST simulator. In this simulator, the Gfarm Grid file system, which has
been developed in the Division of High Performance Computing Systems, was installed. As
a result, the distributed storage has been integrated as a seamless file server.
2.4 Future Plan
We aim to develop a next-generation hybrid computer system that can extract thepotentiality of special purpose processor, SSE, and new-generation graphic board to the
maximum. Using such a next-generation hybrid computer, we would like to perform the 3D
radiation hydrodynamics further. Then, a goal is to construct "Computational Observatory",
which allows the direct comparison of simulation results to multi-wavelength observational
data. Computational Observatory could be the third pillar in astronomy, with Astronomical
Observatory and Virtual Observatory.
2.5 Publications
2.5.1 Journal Papers- 20 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Shimizu, Ikkoh; Umemura, Masayuki; Yonehara, Atsunori, Large-scale structure of short-lived
Lyman ƒ¿ emitters, Monthly Notices of the Royal Astronomical Society:
Letters,380,L49-L53,2007
Mori, Masao; Umemura, Masayuki, Galactic winds from primeval galaxies, Astrophysics andSpace Science,281,,2007
H. Hirashita, H. Shibai, T. T. Takeuchi, Search for high column density systems with gamma ray
bursts, Astronomy & Astrophysics,452,481-485,2006
I. T. Iliev, H. Hirashita, A. Ferrara,Fate of clumps in damped Lyƒ¿ systems, Monthly Notices of
the Royal Astronomical Society,368,1885-1892,2006
Y. Hibi, H. Shibai, M. Kawada, T. Ootsubo, H. Hirashita, Common Correlations between 60, 100,
and 140 ƒÊm Intensities in the Galactic Plane and Magellanic Clouds, Publications of the
Astronomical Society of Japan,58,509-519,2006
Kawakatu, Nozomu; Anabuki, Naohisa; Nagao, Tohru; Umemura, Masayuki; Nakagawa, Takao;
Mori, Masao, Formation of SMBHs and QSO evolution, New Astronomy
Reviews,50,769-771,2006
Yoshida, Makiko; Shimasaku, Kazuhiro; Kashikawa, Nobunari; Ouchi, Masami; Okamura,
Sadanori; Ajiki, Masaru; Akiyama, Masayuki; Ando, Hiroyasu; Aoki, Kentaro; Doi, Mamoru;
Furusawa, Hisanori; Hayashino, Tomoki; Iwamuro, Fumihide; Iye, Masanori; Karoji, Hiroshi;
Kobayashi, Naoto; Kodaira, Keiichi; Kodama, Tadayuki; Komiyama, Yutaka; Malkan, Matthew
A.; Matsuda, Yuichi; Miyazaki, Satoshi; Mizumoto, Yoshihiko; Morokuma, Tomoki; Motohara,
Kentaro; Murayama, Takashi; Nagao, Tohru; Nariai, Kyoji; Ohta, Kouji; Sasaki, Toshiyuki; Sato,
Yasunori; Sekiguchi, Kazuhiro; Shioya, Yasuhiro; Tamura, Hajime; Taniguchi, Yoshiaki;
Umemura, Masayuki; Yamada, Toru; Yasuda, Naoki, Luminosity Functions of Lyman Break
Galaxies at z~4 and z~5 in the Subaru Deep Field, Astrophysical Journal,653,988-1003,2006
Iliev, Ilian T.; Ciardi, Benedetta; Alvarez, Marcelo A.; Maselli, Antonella; Ferrara, Andrea;
Gnedin, Nickolay Y.; Mellema, Garrelt; Nakamoto, Taishi; Norman, Michael L.; Razoumov,Alexei O.; Rijkhorst, Erik-Jan; Ritzerveld, Jelle; Shapiro, Paul R.; Susa, Hajime; Umemura,
Masayuki; Whalen, Daniel J., Cosmological Radiative Transfer Codes Comparison Project I: The
Static Density Field Tests,Mon. Not. Roy. Astron. Soc.,371,1057-1086,2006
Hirose, Yoshiyasu; Umemura, Masayuki; Yonehara, Atsunori; Sato, Jun’chi, Imprint ofGravitational Lensing by Population III Stars in Gamma Ray Burst Light Curves, AstrophysicalJournal,650,252-260,2006
Susa, Hajime; Umemura, Masayuki, Secondary Star Formation in a Population III Object,
Astrophysical Journal Letters,645,L93-L96,2006

2.5.2 Proceedings
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Mori, M.; Umemura, M. , Chemodynamics of Lyman alpha emitters, Lyman break galaxies andelliptical galaxies ,EAS Publications Series,24,221-226,2007
Kawakatu, N.; Umemura, M.; Mori, M. ,The Growth of SMBHs in Optically-Thick Starburst
Galaxies,Growing black holes: accretion in a cosmological context,,466 - 467,2005
Susa, H.; Umemura, M. ,The effects of early reionization on the formation of dwarf galaxies,
Near-fields cosmology with dwarf elliptical galaxies, IAU Colloquium Proceedings of theinternational Astronomical Union 198 ,,147-150,2005
Kawakatu, Nozomu; Umemura, Masayuki ,Radiation-hydrodynamic formation of massive blackhole,Highlights of Astronomy,13,380 - 381,2005
Watabe, Yasuyuki; Umemura, Masayuki ,Obscuration of Active Galactic Nuclei by
Circumnuclear Starburst-Origin Clouds,THE EVOLUTION OF STARBURSTS: The 331stWilhelm and Else Heraeus Seminar. AIP Conference Proceedings,738,245-250,2005
Kawakatu, N.; Umemura, M.; Mori, M. ,A Scenario for the Coevolution of an Elliptical Galaxy
and a QSO,Coevolution of Black Holes and Galaxies,,31,2004
Umemura, M. ,The Growth of Supermassive Black Holes and QSO Formation,Coevolution ofBlack Holes and Galaxies,,61,2004- 21 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Umemura, M.; Kawakatu, N.; Sato, J.; Mori, M. ,A Coevolution Scheme for Supermassive Black
Holes and Galactic Bulges,Progress of Theoretical Physics Supplement,155,198-201,2004
Kawakatu, N.; Umemura, M. ,Formation of Massive Black Holes in Globular Clusters,Progress ofTheoretical Physics Supplement,155,355-356,2004
Umemura, Masayuki; Nakamoto, Taishi; Susa, Hajime,The Epoch of Cosmic
Reionization,Studies of Galaxies in the Young Universe with New Generation
Telescope,,77-82,2004
Susa, Hajime; Umemura, Masayuki ,Galaxy Formation in the Presence of Ultraviolet Background
Radiation Field --- A Simulation by Radiation-SPH ---,Studies of Galaxies in the Young Universe
with New Generation Telescope,,83-86,2004
Ohsuga, Ken; Umemura, Masayuki ,Radiative Effects in the Circumnuclear Region of Active
Galaxies,Studies of Galaxies in the Young Universe with New Generation Telescope,,95-98,2004
Yonehara, A.; Umemura, M.; Susa, H. ,Quasar Mesolensing as a Probe of CDM
Substructures,International Astronomical Union Symposium no. 220,,141,2004
Watabe, Y.; Umemura, M. ,Formation of obscuring clouds by circumnuclear Starbursts, The
Interplay among Black Holes, Stars and ISM in Galactic Nuclei, Proceedings of IAU Symposium,
No. 222 ,,371-372,2004
Kawakatu, N.; Umemura, M.; Mori, M. ,QSO formation under coevolution of SMBH and bulge,
The Interplay among Black Holes, Stars and ISM in Galactic Nuclei, Proceedings of IAU
Symposium, No. 222 ,,493-496,2004- 22 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

3. Division of Materials and Life Sciences: Computational Condensed Matter
Science Group
3.1 Research Activity
In a group of Computational Condensed Matter Science, we try to clarify microscopic
mechanisms for phenomena in condensed matters, predict new phenomena and thenexplore new materials with fascinating properties by theoretical and computational
approaches. In particular, we clarify and predict properties of materials by computationallysolving fundamental equations of quantum mechanics from the first principles sinceelectrons and nuclei which constitute materials are described by quantum theory. We
believe that this first-principle approach is valid for nano-materials and also forbio-materials. Hence Bio-materials are also our targets which are tackled by computational
quantum-theoretical approaches.
Nano-crystal with 10 nm cube, for instance, contains about fifty thousands of atoms. A
typical protein consists of ten thousands of atoms. One of our short-term research targets isthus to develop a method of total-energy electronic structure calculations that is capable oftreating 10 thousands atoms from the first principles of quantum mechanics. By using thescheme, we aim to clarify mechanisms of appearance of functions in nano- andbio-materials where atom-scale reactions induce nano-scale shape variation and then cause
particular functions. More specifically, we are developing real-space density functional
theory (RSDFT) in which all the quantities are computed on lattice in real space. This
scheme has several advantages in large-scale parallel computing.
To overcome multi-scale problems in time is another target. Usual chemical reactions
take place in nano-, micro-, or milli-seconds. Electronic transitions described in quantum
mechanics, on the other hand, take place in femto-seconds. We encounter intrinsic difficulty
to describe phenomena with multi-scale in time. We now combine Car-Parrinello molecular
dynamics method with meta-dynamics and tackle the multi- scale phenomena especially inbiosystems.
We also focus on semiconductor materials that are basis of current technology andcarbon nano-materials that may be boosters in the next-generation technology. A variety of
total-energy electronic-structure calculations and DFT-based molecular-dynamics
calculations are performed for those materials as well as bio-materials.
To develop a new scheme beyond local density approximation and generalized
gradient approximation in DFT is another important task in our group.
Some members in our group are conducting several research projects supported from- 23 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

government or other foundations. They include ``Construction of nano- architecture basedon computational quantum-theoretical science” (JST-CREST; leader = A. Oshiyama),``Quantum design of shapes and functions of nano- and bio-materials” (Grant-in-aid,
MEXT, leader = A. Oshiyama), ``Prediction of properties of nano-scale silicon from firstprinciples of quantum theory” (Grant-in-aid, MEXT, leader = K. Shiraishi), and ``Physicalproperties and material design of complex structures of carbon nanotubes” (Grant-in-aid,
MEXT, leader = S. Okada).
3.2 Research Results
1) Developments and Applications of Large-scale Real-space Quantum Mechanical
Methodology
We are developing a RSDFT method that is capable of describing phenomena in realmaterials with large number of atoms from the first principles of quantum theory. The
RSDFT in which lattice is introduced in real space and all the quantities such as electron
wave-functions are calculated on each lattice point has several advantages in thenext-generation supercomputing: The advantages include that heavy all- to-all
communications such as FFT are unnecessary and that flexible boundary conditions on
wave-functions are able to be set at the boundaries of the computational cell, thereby
expanding its applicability to various materials.
A newly developed code is now being tuned on PACS-CS, and a net performance of
10-20% to ideal peak performance has been achieved on 512-node computations. In
particular, (a) the algorithm for Gram-Schmidt orthonormalization which is an order N cube
part and becomes a bottleneck in large-scale computations has been changed so that it isreduced to the (matrix x matrix) form and the net performance becomes 60 % of the peak
performance; (b) A Divide-and-Conquer method is introduced in the diagonalization ofsubspace and the net performance of 71 % has been achieved. Fig.1 shows calculated stablestructure of the divacancy in Si. Calculations of ionization energies and electron affinitiesof 10,000-atom clusters are being processed with an aim to pave an unified approach formolecules, clusters and bulk materials.

- 24 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Fig. 1: Electron clouds around the divacancy in Si. When two Si atoms are missing in crystal(divacancy), a new electron states appear in the band-gap and thereby affects on electgronic and opticalproperies of Si. [Iwata, Shiraishi & Oshiyama: Physical Review B (2007) to appear]2) Developments of Multi-scale Molecular Dynamics Technique and its Application to
Biomaterials
We have been developing Car-Parrrinello molecular dynamics methods combined withmeta-dynamics technique to tackle an important issue with multi scale in time where
coupling between electron and ion degrees of freedom (femto seconds for electrons andmicro seconds for ions) is important. In the meta-dynamics scheme, reaction coordinates
are introduced in lagrangean and details of reaction processes and corresponding freeenergy barriers are obtained. Fig. 2 shows calculated free-energy barrier for the protontransfer process in cytochrome c oxidase in the relevant reaction coordinate space.

Fig.2: Cytochrome c oxidase is located in inner membrane of mytchondria and responsible for protontransfer which is a principal process in synthesizing ATP. Our calculations have clarified a new- 25 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

mechanism of proton transfer through peptide bonds [Kamiya, Boero, Tateno, Shiraishi & Oshiyama:
Journal of American Chemical Society (2007)]

Currently, a new code is being developed with real-space technique, considering
efficient computations on the next-generation computers.
3) Atomic Structures and Electron States at Nanometer-scale Interfaces
It has been recognized that Schottky barriers at metal/semiconductor or metal/insulator
interfaces are primarily determined by the workfunction of the metal and the electron
affinity of the semiconductor (insulator), and they are modified by electric double layer
generated at the interfaces. In recent experiments for metal/high-k insulator/semiconductor
MOS structures, however, observed Schottky barriers are unable to be explained by theconventional concept above. We have shown that the observed barriers are beautifully
explained by a new idea that electron states of the metal are hybridized selectively withparticular atomic orbitals in the insulator. [Shiraishi et al: Thin Solid Films (2006) ]4) Properties of Carbon Nanotubes and their Hybrid Structures
One of the applications of Carbon Nanotubes (CNTs) may be electron devices in
nano-electronics. From such viewpoints, clarification of electronic and physical properties
of hybrid structures of CNTs and metal electrodes or semiconductor substrates becomes
extremely important.
Fig. 3 shows calculated electron states of CNT adsorbed on surfaces of metal electrodes.
Al and Ca are considered. It is found that CNT is bound to Ca loosely with the binding
energy of 0.5 eV [Fig. 3(a)], whereas CNT on Al forms a covalent bonding with the binding
energy of 3.2 eV [Fig. 3(b)]. It is also found that electrons of 5.2 x 106 cm-1 are injectedfrom Ca to CNT, thereby inducing n-type conduction.

Fig. 3: Contour Plots of electron density of (10,0) CNT on (a) Ca(100) and (b) Al(100) surfaces. In (a)and (b), each left panel shows increase (black lines) and decrease (red lines) of electron density upon

- 26 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

adsorption. Each right panel shows total electron density [Okada & Oshiyama: Physical Review Letters(2005)].

We have also explored a possibility of placing CNTs regularly on semiconductor
surfaces (Fig. 4). We considered Si(001) surface. For a thin (5,5) CNT, it has been foundthat the site on the terrace is most stable with the binding energy 2.77 eV and that the next
most stable is the site along step edges with the binding energy 1.88 eV. The binding
energies should depend on tube radii and thicker tubes favor step edges. In the Si(001)vicinal surfaces, double-layer step edges are known to align regularly. The present
calculations show a possibility to align CNTs using step edges as templates.

Fig 4: Various sites of CNTs adsorbed on Si(001) surface. A, B, C and D are the sites on terraces,
whereas E, F, G and H are the sites near double-layer step edges ( lower part of the figure is the upperterrace)[Berber & Oshiyama: Physical Review Letters (2007)].

CNT is expected to be used channels in next-generation transistors. In the case,quantitative determination of capacitance of tubular structures is imperative in device
design. We have recently calculated capacitance of double-wall CNT which may be an
ultimate cylindrical structure. It is found that quantum effects cause drastic variation of
capacitance with changing bias voltage [Uchida, Okada, Shiraishi and Oshiyama: PhysicalReview B (2007) ].
In application to medical engineering, waters or solutions in CNT may be important.
Waters confined in nano-space have not been studied, however. We have recently calculated
structures of ice in CNT and found that polygonal-shaped ice is stable in CNT. CNT works
as templates for new polymorphs of materials [Kurita, Okada and Oshiyama: PhysicalReview B (2007)].

- 27 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

3.3 Collaboration
1) Alliance with Division of High Performance Computing System
Tuning of RSDFT code on PACS-CS has become possible in collaboration with people
at division of High Performance Computing System. In addition to examination ofalgorithms as described above, detailed discussion on general aspects as well as particularcoding has been done regularly and contributes a lot to promotion of research.
2) Collaboration with Computational Life Science Group
Our stance is to recognize common features in nano- and bio-materials, perform
calculations based on quantum theory, and clarify and predict various phenomena in bothmaterials. Collaboration with computational life science group is therefore essential. This ismanifested as several publications which include the clarifications of microscopic
mechanisms of (A) self-cleaving of ribozymes [Boero et al, Int J. of Theory andComputation (2005)] and (B) proton transfer in Cytochrome c Oxidase [Kamiya et al,
JACS (2007)], using Car-Parrinelo Molecular Dynamics and Metadynamics.
3) Collaboration with Quantum Many Body Group
Time-dependent density functional theory is an important methodology in quantum
many body group. The scheme has common aspects with our RSDFT code. Collaboration
on efficient computations is now in progress.
3.4 Future Plan
In our research activity, there are several different phases: developments of newcomputational methodology, sophistication of current methodology , and the applications toreal materials. It is important to make those different activities proceed interactively. By
focusing all those phases, we try to contribute to materials science by computational
approach and to the progress in theoretical physics and chemistry as well as computational
science.
In the phases of developments and sophistication of methodologies, schemes which arecapable of accurate and large-scale calculations are required. The DFT scheme is now
capable of treating 10,000 atoms on 10-TFLOPS machine where 1,000 nodes (CPUs) atmost are used. Yet to clarify stability and electronic properties of 10-nanometer-scale
structures, including proteins, calculations for 100,000 atoms by using 10,000 or 100,000
nodes may be necessary. We are planning to optimize RSDFT scheme and introduce a
hybrid QM/MM scheme to tackle this issue. The plat form we consider is thenext-generation peta-flops supercomputers consisting of several hundred thousands nodes.
- 28 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Improvement of accuracy is also important. That is a development of a new scheme
which is capable of treating phenomena inaccessible by the current DFT. Our main target inthis phase will be van der Waals forces which play important roles in carbon nanomaterials
and biomaterials. It would be beneficial when a new scheme can be combined withlarge-scale DFT-based scheme.
In addition to total-energy electronic-structure calculations and molecular dynamics
calculations, simulations or predictions of response functions of materials are important.
We have already developed several computational schemes to calculate conductance andcapacitance and applied them to real materials. We plan to continue those calculations forvarious materials and structures.
3.5 Publications
3.5.1 Journal Papers
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S. Okano and A. Oshiyama, ``A New Identification of C-Type Defects on Si(100) Surfaces" Surf.
Sci. 554, 272-279 (2004).
S. Okano, K. Shiraishi and A. Oshiyama, ``Density Functional Calculations and Eigenchannel
Analyses for Electron Transport in Al and Si Atomic Wires" Phys. Rev. B 69, 045401 (2004).
M. Usuda, N. Hamada, K. Shiraishi and A. Oshiyama, ``Band Structures of Wurtzite InN andGa1-xInxN by All-Electron GW Calculation", Jpn. J. Appl. Phys. 43, L407-L410 (2004).
M. Boero, A. Oshiyama and P. L. Silvestrelli, ``E’ Centers in Silicon Dioxide: First Principles
Molecular Dynamics Studies" Mod. Phys. Lett. B 18, 707 (2004).
K. Kamiya, K. Shiraishi, and A. Oshiyama, ``Electronic Structure of Polyglycine and Active sitesof Cytochrome c Oxidase" J. Phys. Soc. Jpn. 73, 3198-3208 (2004).
S. Okada, R. Arita, Y. Matsuo, E. Nakamura, A. Oshiyama and H. Aoki, ``Electronic Structures of
Stacked C60 Shuttlecocks", Chem. Phys. Lett. 399, 157-161 (2004).
M. Uematsu, H. Kageshima, Y. Takahashi, S. Fukatsu, KM. Itoh, K. Shiraishi, “Simulation ofcorrelated diffusion of Si and B in thermally grown SiO2” J. Appl. Phys., 96, 5513-5519(2004).
A. Taguchi and K. Shiraishi, “First-principles investigations of GaAs(311)A surface reconstruction- failure of the electron counting model” Appl. Surf. Sci., 237 189-193 (2004).
T. Ito, K. Tsutsumida, K. Nakamura, Y. Kangawa, K. Shiraishi, A. Taguchi, and H. Kageshima,“Systematic theoretical investigations of adsorption behavior on the GaAs(001)-c(4 x 4) surfaces”
Appl. Surf. Sci., 237 194-199 (2004).
K. Shiraishi, H. Tamura, and H. Takayanagi, “Theoretical design of a semiconductor ferromagnet
based on quantum dot superlattices” Physica E, 24 107-110 (2004).
M. Uematsu, H. Kageshima, Y. Takahashi, S. Fukatsu, KM. Itoh, and K. Shiraishi, “Correlated
diffusion of silicon and boron in thermally grown SiO2” Appl. Phys. Lett., 85, 221-223 (2004).
H. Tamura, K. Shiraishi, and H. Takayanagi, “Tunable exchange interaction in quantum dot
devices” Jap. J. Appl. Phys. PART 2-Express Letters, 43, L691-L693 (2004).
M. Uematsu, H. Kageshima, K. Shiraishi, M. Nagase, S. Horiguchi, Y. Takahashi,“Two-dimensional simulation of pattern-dependent oxidation of Si nanostructures on
Si-on-insulator substrates” Solid State Electronics, 48, 1073-1078 (2004)
S. Fukatsu, K.M. Itoh, M. Uematsu, H. Kageshima, Y. Takahashi and K. Shiraishi, “Effect of
Si/SiO2 Interface on Si and B diffusion in Thermally Grown SiO2” Jpn. J. Appl. Phys. 43,
7837-7842 (2004).
A. Uedono, M. Goto, K. Higuchi, K. Shiraishi, K. Yamabe, H. Kitajima, R. Mitsuhashi, A.

- 29 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Horiuchi, K. Torii, T. Arikado, R. Suzuki, T. Ohdaira and K. Yamada, “Characterization of
Hf0.3Al0.7Ox Fabricated by Atomic-Layer-Deposition Technique Using Monoenergetic Positron
Beams” Jap. J. Appl. Physs. Part 1 43, 7848-7852 (2004).
H. Kageshima, M. Uematsu, K. Akagi, S. Tsuneyuki, T. Akiyama and K. Shiraishi , “Theoretical
Study of Excess Si Emitted from Si-oxide/Si Interfaces” Jap. J. Appl. Phys. Part1 43, 8223-8226(2004).
K. Shiraishi, K. Yamada, K.Torii, Y. Akasaka, K. Nakajima, M. Konno, T. Chikyow, H. Kitajima
and T. Arikado, “Oxygen Vacancy Induced Substantial Threshold Voltage Shifts in the Hf-based
High-K MISFET with p+poly-Si Gates -A Theoretical Approach” Jpn. J. Appl. Phys. PART
2-Express Letters, 43, L1413-L1415 (2004).
K. Shiraishi, K. Yamada, K. Torii, Y. Akasaka, K. Nakajima, M. Konno, T. Chikyow, H. Kitajima
and T. Arikado, “Physics in Fermi Level Pinning at the PolySi/Hf-based High-k Oxide Interface”
Tech. Digest of 2004 Symposium on VLSI Technology, Honolulu, USA, p.108-109 (2004).
K. Torii, K. Shiraishi, S. Miyazaki, K. Yamabe, M. Boero, T. Chikyow, K. Yamada, H. Kitajima
and T. Arikado, “Physical Model of BTI, TDDB, and SILC in HfO2 based high-k gate dielectrics”
Tech. Digest of 2004 IEEE Int. Electron Device Meeting, San Francisco, p.129-133 (2004).
M. Boero, T. Ikeshoji, C. C. Liew, K. Terakura and M. Parrinello, Hydrogen Bond Driven
Chemical Reactions: Beckmann rearrangement of cyclohexanone oxime into ε-caprolactam insupercritical water, J. Am. Chem. Soc. 126, 6280 (2004).
L. M. Ramaniah, M. Boero and M. Laghate, Tantalum-Ffullerene Clusters: A First-Principles
Study of Static Properties and Dynamical Behavior, Phys. Rev. B 70, 035411 (2004).
H. Kino, M. Tateno, M. Boero, J. A. Torres, T. Ohno, K. Terakura, H. Fukuyama, A Possible Origin
of Carrier Doping into DNA Polymer and Effects of Anderson Localization, J. Phys. Soc. Japan 73,
2089 (2004).
M. Boero, A. Oshiyama, P. L. Silvestrelli and K. Murakami, ``Free Energy Molecular Dynamics
Simulations of Pulsed-Laser-Irradiated SiO2: Si-Si Bond Formation in a Matrix of SiO2", Appl.
Phys. Lett. 86 201910 (2005).
T. Kawai, S. Okada, Y. Miyamoto and A. Oshiyama, ``Carbon three-dimensional architecture
formed by intersectional collision of graphite patches", Phys. Rev. B 72, 035428 (2005).
S. Okada, Y. Enomoto, K. Shiraishi and A. Oshiyama, ``New Electron States that Float on
semiconductor and Metal Surfaces", Surf. Sci. 585 L177-L182 (2005).
M. Boero, M. Tateno, K. Terakura and A. Oshiyama, ``Double-Metal-Ion/Single-Metal-Ion
Mechanisms of the Cleavage Reaction of Rybozymes: First-Principles Molecular Dynamics
Simulations of a Fully Hydrated Model System" J. Chem. Theory and Computation 1 925 (2005).
S. Okada and A. Oshiyama, ``Electronic Structure of Semiconducting Nanotubes Adsorbed on
Metal Surfaces", Phys. Rev. Lett. 95 206804 (2005).
K. Kamiya, M. Boero, K. Shiraishi and A. Oshiyama, ``Enol-to-Keto Tautomerism of Peptide
Groups", J. Phys. Chem. B 110 4443 (2006).
M. Uematsu, H. Kageshima, and K. Shiraishi, “Effect of nitrogen on diffusion in silicon
oxynitride” Jap. J. Appl. Phys. PART 1, 44, 7756 (2005).
H. Watanabe, S. Kamiyama, N. Umezawa, K. Shiraishi, S. Yoshida, Y. Watanabe, T. Arikado, T.
Chikyow, K. Yamada and K. Yasutake, “Role of nitrogen incorporation into Hf-based high-k gate
dielectrics for termination of local current leakage paths” Jap. J. Appl. Phys. PART 2, 44, L1333(2005).
K. Torii, T. Kawahara, and K. Shiraishi, “Improvement of interfacial layer reliability byincorporation of deuterium into HfAlOx formed by D2O-ALD” IEEE Electron Device Lett., 26,
722 (2005).
N. Umezawa, S. Tsuneyuki, T. Ohno, K. Shiraishi, and T. Chikyow, “A practical treatment for thethree-body interactions in the transcorrelated variational Monte Carlo method: Application toatoms from lithium to neon” J. Chem. Phys., 122, 224101 (2005).
T. Ito, K. Asano, T. Akiyama, K. Nakamura, K. Shiraishi and A. Taguchi, “An ab initio-based
approach to Ga adatom migration on GaAs(n 1 1)A-(001) non-planar surfaces” Appl. Surf. Sci,
244, 178 (2005).

- 30 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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H. Ishizaki, T. Akiyama, K. Nakamura, K. Shiraishi, A. Taguchi and T. Ito, “Theoreticalinvestigation of phase transition on GaAs(001)-c(4 x 4) surface” Appl. Surf. Sci, 244, 186 (2005).
N. Umezawa, K. Shiraishi, T. Ohno, H. Watanabe, T. Chikyow, K. Torii, K. Yamabe, K. Yamada,H. Kitajima and T. Arikado, “First-principles studies of the intrinsic effect of nitrogen atoms on
reduction in gate leakage current through Hf-based high-k dielectrics” Appl. Phys. Lett. 86,
143507 (2005).
F. L. Gervasio, A. Laio, M. Parrinello and M. Boero, Charge Localization in DNA Fibers, Phys.
Rev. Lett. 94, 158103 (2005).
M. Boero, T. Ikeshoji and K. Terakura, Density and Temperature Dependence of Proton Diffusion
in Water: a First Principles Molecular Dynamics Study, Chem. Phys. Chem. 6, 1775 (2005).
P. L. Silvestrelli, F. Ancilotto, F. Toigo, C. Sbraccia, T. Ikeda and M. Boero,
Hydrophobic/hydrophilic Interactions of Water with Alkanethiolate Chains from First Principles
Calculations, Chem. Phys. Chem. 6, 1889 (2005)
Y. Rikiishi, Y. Kashino, H. Kusai, Y. Takabayashi, E. Kuwahara,Y. Kubozono, T. Kambe, T.
Tkenobu, Y. Iwasa, N. Mizorogi, S. Nagase, and S. Okada, ``Metallic phase in themetal-intercalated higher fullerene Rb8.8(7)C84" Physical Review B, 71, 224118 (2005).
S. Okada, ``Energetics and Electronic Structures of Potassium Intercalated C60-Peapods''
Physical Review B, 72, 153409 (2005).
S. Berber and A. Oshiyama, ``Atomic and Electronic Structures of Carbon Nanotubes on Si(001)
Stepped Surfaces", Phys. Rev. Lett. 96 105505 (2006).
M. Uematsu, H. Kageshima, S. Fukatsu, K. M. Itoh, K. Shiraishi, M. Otani and A. Oshiyama,``Enhanced Si and B diffusion in Semiconductir-Grade SiO2 and the Effect of Strain on
Diffusion", Thin Solid Films 508 (2006) 270.
Y. Akasaka, G. Nakamura, K. Shiraishi, N. Umezawa, K. Yamabe, O. Ogawa, M. Lee, T. Amiaka, T.
Kasuya, H. Watanabe, T. Chikyow, F. Ootsuka, Y. Nara, and K. Nakamura, “Modified Oxygen
Vacancy Induced Fermi Level Pinning Model Extendable to P-Metal Pinning”, Jpn. J. Appl. Phys.
Part 2, 45, L1289-L1292, (2006).
Uedono, T. Naito, T. Otsuka, K. Shiraishi, K. Yamabe, S. Miyazaki, H. Watanabe, N. Umezawa, T.
Chikyow, Y. Akasaka, S. Kamiyama, Y. Nara, and Yamada, “Introduction of defects into HfO2
gate dielectrics by metal-gate deposition studied using x-ray photoelectron spectroscopy andpositron annihilation”, J. Appl. Phys. 100, Art. No. 064501 (2006).
K. Shiraishi, K. Yamada, K. Torii, Y. Akasaka, K. Nakajima, M. Konno, T. Chikyow, H. Kitajima,
T. Arikado and Y. Nara, “Oxygen-vacancy-induced threshold voltage shifts in Hf-related high-kgate stacks”, Thin Solid Films, 508, 305-310 (2006).
M. Uematsu, H. Kageshima, S. Fukatsu, KM. Itoh, K. Shiraishi, M. Otani and A. Oshiyama,“Enhanced Si and B diffusion in semiconductor-grade SiO2 and the effect of strain on diffusion”,
Thin Solid Films, 508, 270-275 (2006)
N. Umezawa, K. Shiraishi, T. Ohno, M. Boero, H. Watanabe, T. Chikyow, K. Torii, K. Yamabe, K.
Yamada, and Y. Nara, “Unique behavior of F-centers in high-k Hf-based oxides”, PHYSICA
B-CONDENSED MATTER, 376, 392-394 (2006)
H. Kageshima, M. Uematsu, K. Akagi, S. Tsuneyuki, T. Akiyama and K. Shiraishi, “Mechanism ofoxide deformation during silicon thermal oxidation”, PHYSICA B-CONDENSED MATTER, 376,
407-410 (2006)
M. Oshikiri and M. Boero, Water Molecule Adsorption Properties on the BiVO4 (100) Surface, J.
Phys. Chem. B 110, 9188 (2006).
F. L. Gervasio, M. Boero and M. Parrinello, Double Proton Coupled Charge Transfer in DNA,
Angew. Chem. Int. Ed. 45, 5606 (2006).
L. M. Ramaniah and M. Boero, Structural, Electronic, and Optical Properties of theDiindenoperylene Molecule from First-Principles Density Functional Theory, Phys. Rev. A 74,
042505 (2006)
M, Boero, T. Ikeda, E. Ito and K. Terakura, Hsc70 ATPase: An Insight into Water Dissociation and
Joint Catalytic Role of K+ and Mg2+ Metal Cations in the Hyrolysis Reaction J. Am. Chem. Soc.
128, 16798 (2006).

- 31 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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S. Okada, K. Nakada, K. Kuwabara, K. Daigoku, and T. Kawai, ``Ferromagnetic Spin Ordering on
Carbon Nanotubes with Topological Line Defects" Phys. Rev. B 74, art. no. 121412(R) (2006).
M. Boero, F. L. Gervasio and M. Parrinello, Charge Localisation and Hopping in DNA, Mol.
Simul. 33, 57 (2007).
T. Ikeda, M. Boero and K. Terakura, Hydration of Alkali Ions from First Principles Molecular
Dynamics Revisited, J. Chem. Phys. 127, 074503 (2007).
T. Kurita, S. Okada, A. Oshiyama: ``Energetics of Ice Nanotubes and their Encapsulation in
Carbon Nanotubes from Density-Functional Theory", Physical Review B 75, art no 205424(2007).
K. Kamiya, M. Boero, M. Tateno, K. Shiraishi and A. Oshiyama: ``Possible Mechanism of Proton
Transfer through Peptide Groups in the H-pathway of the Bovine Cytochrome c Oxidase" Journalof American Chemical Society, 129, 9663-9673 (2007).
Ming Z, Nakajima K, Suzuki M, Kimura K, Uematsu M, Torii K, Kamiyama S, Nara Y, Watanabe
H, Shiraishi K, Chikyow T, Yamada K: ``Isotopic labeling study of the oxygen diffusion in
HfO2/SiO2/Si", Applied Physics Letters, 90, Art. No. 133510 (2007).
Kangawa Y, Matsuo Y, Akiyama T, Ito T, Shiraishi K, Kakimoto K: ``Ab initio-based approach on
initial growth kinetics of GaN on GaN (001)", Journal of Crystal Growth, 301, 75-78 (2007).
Ohmori K, Ahmet P, Yoshitake M, Chikyow T, Shiraishi K, Yamabe K, Watanabe H, Akasaka Y,
Nara Y, Chang KS, Green ML, Yamada K: ``Influences of annealing in reducing and oxidizing
ambients on flatband voltage properties of HfO2 gate stack structures", Journal of Applied Physics,
101, Art. No. 084118 (2007).
N. Umezawa, K. Shiraishi, S. Miyazaki, A. Uedono, Y. Akasaka, S. Inumiya, R. Hasunuma, K.
Yamabe, H. Momida, T. Ohno, K. Ohmori, T. Chikyow, Y. Nara, and K. Yamada: ``Guiding
Principle of Energy Level Controllability of Silicon Dangling Bonds in HfSiON", Japanese
Journal of Applied Physics, 46,. 1891-1894 (2007).
A. Uedono, T. Naito, T. Otsuka, K. Ito, K. Shiraishi, K. Yamabe, S. Miyazaki, H. Watanabe, N.
Umezawa, T. Chikyow, T. Ohdaira, R. Suzuki, Y. Akasaka, S.Kamiyama, Y. Nara, and K.Yamada:``Characterization of Metal/High-k Structures Using Monoenergetic Positron Beams", Japanese
Journal of Applied Physics, 46, 3214-3218 (2007).
N. Umezawa, K. Shiraishi, S. Miyazaki, T. Ohno, T. Chikyow, K. Yamada, and Y. Nara: ``Hafnium
4f Core-level Shifts Caused by Nitrogen Incorporation in Hf-based High-k Gate Dielectrics",
Japanese Journal of Applied Physics, 46, 3507-3509 (2007).
N. Umezawa, K. Shiraishi, K. Torii, M. Boero, T. Chikyow, H. Watanabe, K. Yamabe, T. Ohno, K.
Yamada, and Y. Nara: ``Role of Nitrogen Atoms in Reduction of Electron Charge Traps in
Hf-Based High-κ Dielectrics", IEEE Electron Device Letters, 28, 363-365 (2007).
T. Endoh, K. Hirose and K. Shiraishi: ``Physical Origin of Stress-Induced Leakage Currents in
Ultra-Thin Silicon Dioxide Films", IEICE TRANSACTIONS on Electronics E90-C, 955-961(2007).
S. Okada, K. Nakada, and T. Kawai: ``Orientation Dependence of Magnetic Moment of Carbon
Nanotubes with Topological Line Defects", Applied Physics Letters, 90, art. no. 103120 (2007).
S. Okada: ``Electronic structures of finite-length carbon nanotubes: Crossover from fullerenes tonanotubes" NANO, 2, pp. 51--57 (2007).
S. Hino, M. Kato, D. Yoshimura, H. Moribe, H. Umemoto, Y. Ito, T. Sugai, H. Shinohara, M. Otani,
Y. Yoshimoto, and S. Okada: ``Effect of encapsulated atoms on the electronicstructure of thefullerene cage: A case study on La2@C78 and Ti2C2@C78 via ultraviolet photoelectron
spectroscopy", Physical Review B, 75, 125418 (2007) .
S. Okada: ``Radial-breathing mode frequencies for nanotubes encapsulating fullerenes", Chemical
Physics Letters, 438, 59-62 (2007).
S. Okada, K. Nakada, and T. Kawai: ``Energetics and Electronic Structure of Armchair Nanotubes
with Topological Line Defect", Journal of Physics: Condensed Matter, 19, 365231 (2007).

- 32 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

3.5.2 Proceedings
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Y. Akasaka, K. Miyagawa, T. Sasaki, K. Shiraishi, S. Kamiyama, O. Ogawa, F. Ootsuka and Y.
Nara, “Impact of Electrode-side Chemical Structures on Electron Mobility in Metal/HfO2
MISFETs with sub-1nm EOT” Technical Digest of 2005 Symposium on VLSI Technology, Kyoto,
Japan, p.228 (2005).
K. Shiraishi, Y. Akasaka, S. Miyazaki, T. Nakayama, T. Nakaoka, G. Nakamura, K. Torii, H.
Furutou, A. Ohta, P. Ahmet, K. Ohmori, H. Watanabe, T. Chikyow, M. L. Green, Y. Nara, and K.
Yamada, “Universal theory of workfunctions at metal/Hf-based high-k dielectrics interfaces—Guiding principles for gate metal selection—“ Technical Digest of IEEE International Electron
Devices Meeting, Washington D.C., USA, p.43 (2004).
T. Nakaoka, K. Shiraishi, Y. Akasaka, T. Chikyow, K. Yamada, and Y. Nara, “First-principles
studies on metal induced gap states (MIGS) at metal/high-k HfO2 interfaces” Extended Abstracts ofthe 2004 Conference on Solid State Device and Materials, Kobe, Japan, p.860, (2005).
H. Momida, T. Hamada, T. Yamamoto, T. Uda, N. Umezawa, K. Shiraishi, T. Chikyow
and T. Ohno, “Microscopic Effect of Nitrogen Doping on Dielectric Constant of
Hf-silicate” Extended Abstracts of the 2004 Conference on Solid State Device andMaterials, Kobe, Japan, p.488, (2005).
N. Umezawa, K. Shiraishi, K. Torii, M. Boero, T. Chikyow, H. Watanabe, K. Yamabe, T. Ohno, K.
Yamada, and Y. Nara, “The Role of Nitrogen Incorporation in Hf-based High-k Dielectrics:
Reduction in Electron Charge Traps” Proceedings of 35th European Solid-State Device Research
Conference (ESSDERC 2005) p.201, 12-16 September 2005, Grenoble, France.
S. Berber and A. Oshiyama, ``Reconstruction of mono-vacancies in carbon nanotubes: atomic
relaxation vs. spin polarization", Physica B 376-377 272-275 (2006).
M. Boero, A. Oshiyama, P. L. Silvestrelli and K. Murakami, ``First-principle molecular dynamics
study of bond disruption and formation in SiO2 upon irradiation", Physica B 376-377 945-949(2006).
J.-I. Iwata, A. Oshiyama and K. Shiraishi, ``Real-space Density-functional Calculations for Si
Divacancies with Large Size Supercell Models", Physica B 376-377 196-199 (2006).
K. Shiraishi, K. Torii, Y. Akasaka, T. Nakayama, T. Nakaoka, S. Miyazaki, T. Chikyow, K.
Yamada, and Yasuo Nara, “THEORETICAL STUDIES ON THE PHYSICAL PROPERTIES OF
POLY-SI AND METAL GATES/HfO2 RELATED HIGH-K DIELECTRICS INTERFACES”,
ECS Transactions, 1 (5) 479-493 (2006).
K. Higuchi, T. Naito, A. Uedono, K.Shiraishi, K.Torii, M.Boero, T.Chikyow, S.Yamasaki,
K.Yamada, R. Hasunuma, and K.Yamabe, “ASYMMETRIC DISTRIBUTION OF CHARGE
TRAP IN HfO2-BASED HIGH-K GATE DIELECTRICS”, ECS Transactions, 1 (5) 777-788(2006).
K. Shiraishi, T. Nakayama, Y. Akasaka, S. Miyazaki, T. Nakaoka, K. Ohmori, P. Ahmet, K. Torii,
H. Watanabe, T. Chikyow, Y. Nara, H. Iwai, and K. Yamada, “New Theory of Effective Work
Functions at Metal/High-k Dielectric Interfaces -Application to Metal/High-k HfO2 And La2O3
Dielectric Interfaces –”, ECS Transactions, 2 (1) 25-40 (2006).
N. Umezawa, K. Shiraishi, H. Watanabe, K. Torii, Y. Akasaka, S. Inumiya, M. Boero, A. Uedono,
S. Miyazaki, T. Ohno, T. Chikyow, K. Yamabe, Y. Nara, and K. Yamada, “Extensive Studies for
Effects of Nitrogen Incorporation into Hf-based High-k Gate Dielectrics”, ECS Transactions, 2 (1)63-78 (2006).
T. Nakayama, K. Shiraishi, S. Miyazaki, Y. Akasaka, T. Nakaoka, K. Torii, A. Ohta, P. Ahmet, K.
Ohmori, N. Umezawa, H. Watanabe, T. Chikyow, Y. Nara, H. Iwai, and K. Yamada, “Physics ofMetal/High-k Interfaces”, ECS Transactions, 3 (3) 129-140 (2006).
K. Ohmori, P. Ahmet, K. Shiraishi, K. Yamabe, H. Watanabe, Y. Akasaka, N. Umezawa, K.
Nakajima, M. Yoshitake, T. Nakayama, K.-S. Chang, K. Kakushima, Y. Nara, M.L. Green, H. Iwai,
K. Yamada, and T. Chikyow, “Wide Controllability of Flatband Voltage in La2O3 Gate Stack
Structures – Remarkable Advantages of La2O3 over HfO2 –”, ECS Transactions, 3 (3) 351-362- 33 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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(2006)
Y. Akasaka, K. Shiraishi, N. Umezawa, O. Ogawa, T. Kasuya, T. Chikyow, F. Ootsuka, Y. Naraand K. Nakamura, “A Novel Remote Reactive Sink Layer Technique for the Control of N and O
Concentrations in Metal/High-k Gate Stacks”, Technical Digest of 2006 Symposium on VLSI
Tech., Honolulu, USA, p.206-207, (2006).
Z. Ming, K. Nakajima, M. Suzuki, K. Kimura, M. Uematsu, K. Torii, S. Kamiyama, Y. Nara, H.
Watanabe, K. Shiraishi, T. Chikyow, K. Yamada, “High-resolution RBS analysis of Si-dielectrics
interfaces”, Extend Abstract of the 2006 International Conference on Solid State Devices andMaterials, Yokohama, Japan, p.380-381, (2006).
K. Kamiya, M. Boero, M. Tateno, K. Shiraishi and A. Oshiyama, Novel Mechanism for Proton
Transfer in Bovine Cytochrome c Oxidase J. Phys. Cond. Mat. 19, 365200 (2007).
K. Uchida, S. Okada, K. Shiraishi and A. Oshiyama: ``Quantum Effects in Cylindrical
Carbon-Nanotube Capacitor", Journal of Physics: Condensed Matter Physics, 19, 365218 (2007).

- 34 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

4. Division of Materials and Life Sciences: Computational Life Science Group
4.1 Research Activity
The Computational Life Science Group is one of the new research sections that plannedand started at the beginning of the activities of the Center for Computational Sciences, justtwo years ago. In this respect, this is a relatively young group. As a general overview, theresearch activities assume, as a starting point, the 3D structures and functions of biologicalmacromolecules such as protein, DNA, and RNA, and aims at the study of the reaction
mechanisms and molecular system formation processes, as the basis of the living organisms.
One of the ultimate goals is to address issues useful and of practical technological interest
to the emerging field of nano-bio engineering.
Because of the complexity involved in these biological systems, various techniques incomputational sciences, theoretical physics and chemistry, structural bioinformatics, andrelated fields are intensively used and integrated, thus allowing for the elucidation of theelectronic, atomic, and molecular mechanisms involved in biological phenomena.
Concretely, in order to apply molecular simulation techniques, such as molecular dynamics,
first principles quantum-mechanics-based calculations, etc., to biological macromoleculeswith both high accuracy and high efficiency, fundamental algorithms are developed andimplemented in computer codes. Specifically, the topics below have been tackled;
1) Development of quantum mechanics / molecular mechanics (QM/MM) hybrid
schemes based on all-electron DFT calculations as a QM driver.
2) Development of an energy functional which accurately describes the electron
correlation responsible for the stacking of aromatic rings in amino acid residues and bases
in nucleotide residues.
3) Development of a molecular docking calculation method for proteins and ligands
including explicitly the solvent water molecules.
4) Development of a protein-protein docking calculation method based on hydrogenbond networks formed around the interface region.
The use of these computational systems is expected to lead to more accurate results thanwhat can be achieved by conventional methodologies, thus allowing for a better elucidationof the basic functional mechanisms of living organisms. As far as the specific problems
targeted by our group, we have focused on the following important topics:
1) Hydrolysis reaction mechanisms of RNA enzymes (ribozymes).
2) Energy conversion mechanisms by the electron transport system in mitochondria.
- 35 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

3) Charge localization and transport in synthetic Z-DNA and native DNA.
4) Reaction mechanisms of the ATP synthase (ATPase) in heat shock cognate proteins(Hsc70).
5) Molecular recognition and enzymatic reaction mechanisms in the protein
biosynthesis system.
6) Gene expression mechanisms through interactions of transcriptional factors andDNA.
7) Dynamical mechanisms occurring in the formation process of three-dimensional
structure of protein (folding).
8) Dynamical behavior of cellular reaction network systems for signal transduction.
In the next section, some research achievements are summarized from the topics listed
above.
4.2 Research Results
1) Mechanisms of self-cleavage reaction of ribozymes
Enzymes include not only proteins, but also RNA; RNA enzymes were discovered in the20th century latter halves, and the discoverers were awarded the Nobel Prize. An RNA
enzyme is called ribozyme, and it led to a new hypothesis on the origin of life, i.e. theprimordial organisms were originated from RNA (ribozyme), and such a phase in theevolution of organisms is called the “RNA world”.

O(R)
O(S)

Fig. 1 (left) The crystal structure of the hammerhead ribozyme. [Boero, M., Tateno, M., Terakura, K., andOshiyama, A., J. Chem. Theo. and Comp., 1 (2005), 925-934] (right) The free energy profile and several
conformations of the ribozyme obtained by performing CPMD coupled to metadynamics.

A ribozyme is able to cleave (hydrolyzes) its own phosphodiester bond or the one of- 36 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

another RNA molecule. If one can tune this mechanism to specifically cleave the mRNA of
oncogene, the ribozyme would work as an anticancer agent and/or can be used as atherapeutic agent in cancer gene therapy. This makes ribozyme an important research target
in fundamental biology and medical sciences, and for this reason it has been the subject ofintense studies by several research groups in the world since more than ten years. In ourstudy, by using first-principles molecular dynamics simulations, the details of themechanism of the ribozyme reaction have been elucidated at an atomic-scale level.
In the ribozyme reaction in vitro, it is well known that cations play the role of catalysts
and help in enhancing the reaction rate. However, the number of the cation(s) involved in
the catalytic activity was, and to a certain extent still is, one of the major open questions on
the ribozyme reaction, i.e. some experimental results concluded that one single cation
participates to the reaction, whereas other experiments claim that two cations are involved.
We investigated this issue, performing first-principles molecular dynamics calculations forseveral models, both in the absence of cations and in the presence of one or two Mg2+ metalions.
As a result, we found that the minimal activation barrier arises in the case in which two
Mg2+ cooperate to the reaction. In contrast, if only one Mg2+ cation, or none, are present,
the activation barrier increases remarkably, and thus, in those cases the reaction is notexpected to occur. Furthermore, we found that the addition of an OH- hydroxyl anion,
along with two Mg2+ decreases further the activation barrier. Moreover, we also elucidated
the active role of each player, namely each Mg2+, OH-, H2O, in the reaction. Thus, we could
address theoretically some of the basic issues about the ribozyme reaction and we provided
a clear atomistic picture of the mechanisms.
2) Mechanisms of biological energy conversion in electron transport system
The role of the electron transport system in a cell (mitochondria) is to operate an energy
conversion from carbohydrates into the chemical high energy bond of the ATP molecule,which is available at various sites in living organisms. One of the ultimate goals of ourresearch is to clarify the entire picture of the mechanisms of the electron- 37 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Fig. 2. (left) The functional subunits of cytochrome c oxidase (CcO) and the site analyzed by performing
CPMD coupled to metadynamics are depicted. [Kamiya, K., Boero, M., Tateno, M., Shiraishi, K., andOshiyama, A., J. Ame. Chem. Soc., 129 (2007), 9663-9673](right) Electronic structure calculated by the

all-electron based QM/MM hybrid calculation.

transport system in organisms. In this respect, a molecular system that deserves special
attention and that has been intensively studied is the cytochrome c oxidase (CcO), since it is
one of the key factors in electron transport and cell respiration process. In particular, aJapanese research group (Tsukihara and Yoshikawa) has been able to determine, with highaccuracy, the three-dimensional structure of the bovine CcO by X-ray crystallography; theresult is certainly recognized as being worldwide unprecedented.
In our group, we have investigated the mechanisms of proton transfer, electron transfer,and catalytic reaction operated by CcO, performing electronic structure calculations basedon the first principles molecular dynamics simulations and QM/MM hybrid calculations. As
far as the proton transfer is concerned, in conventional propagation paths (K-path andD-path) proposed in the literature, it is expected to occur along hydrogen bond networks
inside proteins. However, Tsukihara and Yoshikawa found an alternative pathway that
includes a peptide group within hydrogen bond networks in CcO, which apparently
interrupts the proton transfer. They suggested that the peptide group can transfer protons via
an keto-enol isomerization, and therefore, that the hydrogen bond network would still result
fully connected; this novel pathway is called H-path.
By using Car-Parrinello-based molecular dynamics simulations, coupled to themetadynamics method, we investigated the possibility that the proton transfer reaction canreally occur through the covalent bond (peptide bond). As a result, protons of the amidegroups of the two peptide groups (Y440-S441 and S441-D442), which are located close to- 38 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

each other, could be transferred sequentially, leading to a continuous proton transfer
reaction chain of the H-pathway. This could be a novel mechanism of proton transfer, if it isexperimentally proven. However, for the calculation, crucial interactions of the peptidegroup and the side chain of the other amino acid residue could not be included in the model
system, and this leaves still some open issues about the estimation of the actual activation
barrier.
In order to overcome those difficulties, we pursued the investigation by performing
QM/MM hybrid calculations for structures derived from the original X-ray data, where allof the functional subunits of CcO (i.e. subunits I, II, and III) and solvent water molecules
are included explicitly. Moreover, since heme (which is a complex of a porphyrin ring andan iron) moieties play crucial roles in the enzymatic reaction, in proton/electron transfer
reactions, in free energy transfer, etc., we investigate these relevant functional sites by
QM/MM hybrid calculations. These projects on CcO are presently under execution.
4.3 Collaboration
For research projects on the ribozyme reaction and the proton transfer of CcO, we havecollaborated with the Computational Condensed Matter Science Group. Furthermore, inorder to improve the performance of CPMD code, in particular, on PACS-CS, we havecollaborated with the High Performance Computing System Group. In particular, fruitful
discussions, benchmarking, and testing of the CPMD code, both in the full quantum and in
the hybrid QM/MM versions, done jointly with the High Performance Computing System
Group, along with their suggestions, allowed to port and tune the code on the PACS-CS
machine and provided a useful background in the development of CPMD.
Other development and functionalities of the code are now being implemented, such as
the handling of different thermostats and thermostat chains for classical and quantum atoms,
handling of ultrasoft pseudopotentials in the hybrid QM/MM code, new collective variables
for the selection of the reaction coordinates in metadynamics and blue moon / umbrellasampling approaches, etc.
Furthermore, also for the QM/MM hybrid calculation system based on all-electron DFT
calculations, similar collaborations with the High Performance Computing System Groupare planned.
4.4 Future Plan
We have been developing and fundamentally improving several crucial calculation
systems described in the above first section, since the former systems developed in thisfield turned out to be insufficient to several extents in analyzing functional mechanisms of- 39 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

biological macromolecules. For the issues on the ribozyme reactions and the electrontransport system, nearest future plans are briefly mentioned in the second section, as
applications of those new systems. Also for the other issues described in the first andsecond sections, we are searching for a possible break-through of each of the fields
summarized below.
1) Protein docking algorithm and its applications to the CcO-Cc complex
It is well known that the reaction of cytochrome c oxidase (CcO) requires the formationof the complex with cytochrome c (Cc), since electrons are transferred from the outside of
CcO. However, despite intensive efforts by crystallographers, the crystal structure of thecomplex of CcO and Cc has not yet been experimentally determined. We have developed anovel protein docking simulation algorithm, based on theoretical identification of hydrogenbond networks at the interface of the two proteins.
This algorithm allows for the exploration and detection of specific interactions ofproteins, which can decrease the large amount of both false positive and false negative
candidate structures of the complex. The implementation of this algorithm enables us toperform the calculations necessary to obtain an accurate docking model of the CcO-Cc
complex. This theoretical model makes now possible to investigate in detail themechanisms of the electron transfer and enzymatic reaction of CcO.
2) Development of an energy functional able to describe the electron correlation effects
responsible for the stacking of aromatic side chains in protein and nucleic acids.
It is well known that the stacking of aromatic side chains (the parallel- and T-types) is
crucial for the stabilization of proteins and nucleic acids. However, this stabilization cannot
be obtained by any of the present-day DFT-level approaches and one has to rely on
computationally more demanding methods, such as MP2 and CCSD.
We have developed an effective energy functional for describing those interactions ofaromatic side chains, allowing for accurate calculations at a small computational cost,which is available not only in the case of static calculations, but also in the case in whichclassical molecular dynamics simulations are performed. We are now applying this scheme
to the protein folding problem, to explore the free energy surface at a level of accuracy not
yet reached.
3) QM/MM hybrid calculation system
Using the all electron-based QM/MM hybrid simulation program, large scalecalculations are scheduled in our group through collaboration with the High Performance- 40 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Computing System Group. For CcO and the CcO-Cc complex, the catalytic center, whichamounts to about 1000-atom, is treated as the QM subsystem, whereas the rest is describedby classical force fields.
These QM/MM calculations would make possible a close inspection of the changes inthe electronic structure occurring in the catalytic reactions involved in the various processes.
Also for aminoacyl-tRNA synthetases, which are crucial for the protein biosynthesis inside
the cell, simulations including 1000 QM-atom, are planned, in order to elucidate the entire
mechanisms of the enzymatic reaction indispensable to convert genetic information intoamino acid sequences.
4.5 Publications
4.5.1 Journal Papers
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T. Tanabe, K. Noda, E. B. Starikov, and M. Tateno: Regular threshold-energy increase with charge
for neutral-particle emission in collisions of electrons with oligonucleotide anions: Phys. Rev. Let.,93, 0432011-0432014 (2004).
M. Odaka, N. Yuki, M. Tatsumoto, M. Tateno, K. Hirata, Ataxic Guillain-Barré syndrome
associated with anti-GM1b and anti-GalNAc-GD1a antibodies: J. Neurology, 251, 24-29 (2004).
H. Kino, M. Tateno, M. Boero, J. A. Torres, T. Ohno, T. Kiyoyuki, H. Fukuyama, A Possible Origin
of Carrier Doping into DNA polymer: J. Phys. Soc. Japan, 73 (2004), 2089-92.
K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, et al., A Novel Zinc-binding Motif Revealed by
Solution Structures of DNA-binding Domains of Arabidopsis SBP-family Transcription Factors: J.
Mol. Biol., 337, 49-63 (2004).
K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, et al., Solution Structure of the B3 DNA-Binding
Domain of the Arabidopsis Cold-Responsive Transcription Factor RAV1: Plant Cell, 16, 3448-3459(2004).
M. Boero, T. Ikeshoji, C. C. Liew, K. Terakura and M. Parrinello, Hydrogen Bond Driven Chemical
Reactions, Beckmann rearrangement of cyclohexanone oxime into ε-caprolactam in supercriticalwater, J. Am. Chem. Soc. 126, 6280 (2004)
舘野 賢，マウロ ボエロ: 第一原理分子動力学シミュレーションによる RNA 酵素（リボザイム）の触媒反応機構の解析, 日本化学会情報化学部会誌, 22, 100-103 (2004).
Boero Mauro, 押山 淳, First principles molecular dynamics calculations for catalytic reactions ofRNA, 個体物理 39, 178 (2004).
相澤 秀昭、寺倉清之、Boero Mauro, Prediction of properties of catalysts by first principles
calculations, 個体物理 39, 120 (2004).
T. Tanabe, K. Noda, E. B. Starikov, and M. Tateno, Neutral-particle emission in collisions withbiomolecular ions in an electrostatic storage ring: J. Phys. Cond. Mat., 4, 239-244 (2005).
F. L. Gervasio, A. Laio, M. Parrinello and M. Boero, Charge Localization in DNA Fibers, Phys. Rev.
Lett. 94, 158103 (2005).
M. Boero, M. Tateno, K. Terakura, and A. Oshiyama, Double-Metal-Ion/Single-Metal-Ion
Mechanisms of the Cleavage Reaction of Ribozymes: First-Principles Molecular Dynamics
Simulations of a Fully Hydrated Model System, J. Chem. Theor. Comput. 1, 925 (2005).
K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, et al., Solution Structure of an Arabidopsis WRKY
DNA-Binding Domain: Plant Cell, 17, 1-13 (2005).
M. Boero, T. Ikeshoji and K. Terakura, Density and Temperature Dependence of Proton Diffusion
in Water: a First Principles Molecular Dynamics Study, ChemPhysChem. 6, 1775 (2005).
P. L. Silvestrelli, F. Ancilotto, F. Toigo, C. Sbraccia, T. Ikeda and M. Boero,- 41 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Hydrophobic/hydrophilic Interactions of Water with Alkanethiolate Chains from First Principles
Calculations, ChemPhysChem. 6, 1889 (2005).
寺倉 清之、池田 隆司、Boero Mauro, First-principles molecular dynamics simulations for physicaland chemical properties of water: supercritical water and high-pressure phases of methane hydrate,
低温科学 64, 57 (2005).
H. Yamaguchi, M. Tateno, and K. Yamasaki, Solution structure and DNA-binding mode of thematrix attachment region-binding domain of the transcription factor SATB1 that regulates the T-cellmaturation: J. Biol. Chem., 281, 5319-5327 (2006).
K. Kamiya, M. Boero, K. Shiraishi and A. Oshiyama, Enol-to-keto tautomerism of peptide groups,
J. Phys. Chem. B 110, 4443 (2006).
F. L. Gervasio, M. Boero and M. Parrinello, Double Proton Coupled Charge Transfer in DNA,
Angew. Chem. Int. Ed. 45, 5606 (2006).
M, Boero, T. Ikeda, E. Ito and K. Terakura, Hsc70 ATPase: An Insight into Water Dissociation and
Joint Catalytic Role of K+ and Mg2+ Metal Cations in the Hyrolysis Reaction, J. Am. Chem. Soc.
128, 16798 (2006).
舘野 賢, ゲノム DNA の塩基配列と遺伝子領域の発見, ナノシミュレーション技術ハンドブック（川添良幸・池庄司民夫編）, 32-33 (2006).
舘野 賢, 相同性（ホモロジ）検索, ナノシミュレーション技術ハンドブック（川添良幸・
池庄司民夫編）, 411-413 (2006).
Mauro Boero, Jung Mee Park, Yohsuke Hagiwara, and Masaru Tateno: First principles molecular
dynamics study of catalytic reactions of biological macromolecular systems: Toward analyses with
QM/MM hybrid molecular simulations, J. Phys. Cond. Mat. 19, 365217 (2007).
K. Kamiya, M. Boero, M. Tateno, K. Shiraishi and A. Oshiyama, First-principles molecular
dynamics study of proton transfer mechanism in bovine cytochrome c oxydase, J. Phys. Cond. Mat.
19, 365220 (2007).
K. Kamiya, M. Boero, M. Tateno, K. Shiraishi and A. Oshiyama, Possible mechanism of protontransfer through peptide groups in the H-pathway of the Bovine cytochrome c oxidase: J. Ame.
Chem. Soc., J. Am. Chem. Soc. 129, 9663 (2007).
T. Ikeda, M. Boero and K. Terakura, Hydration of Alkali Ions from First Principles Molecular
Dynamics Revisited, J. Chem. Phys. 126, 034501 (2007).
M. Boero, F. L. Gervasio and M. Parrinello, Charge Localisation and Hopping in DNA, Mol. Simul.
33, 57 (2007).
M. Boero, Excess electron in water at different thermodynamic conditions, J. Phys.
Chem. A, in press.
舘野 賢，マウロ ボエロ, RNA による酵素反応の機構：量子力学に基づくシミュレーシ
ョンが創る「量子構造生物学」への序, 化学と工業 60-6, 587-589 (2007).

4.5.2 Proceedings•

Mauro Boero and Masaru Tateno, Investigations of Catalytic Reaction Mechanisms of Biological
Macromolecules by Using First Principles and Combined Classical Molecular Dynamics Methods,
in Modelling Molecular Structure and Reactivity in Biological Systems, pp. 206-216, Ed. by J. J.
Naidoo, J. Brady, M. Field, J. Gao, and M. Hann, RSC Publishing, July 2006. ISBN 0 85404 668 2.

- 42 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

5. Division of Materials and Life Sciences: Quantum Many-Body Systems Group
5.1 Research Activity
The members of the research group of quantum many-body systems are Kazuhiro
Yabana, Yukio Hashimoto, Takashi Nakatsukasa, who belong to Institute of Physics, and
Ken-ichi Hino, Hiroyasu Koizumi, Xiao-Min Tong, who belong to Institute of Material
Sciences. Most of the members joined the Center for Computational Sciences when theCenter has started in 2004. Xiao-Min Tong joined this group in October, 2005. Ken-ichi
Hino moved to a position outside the Center in the Univ. of Tsukuba in April of 2007.
Takashi Nakatsukasa moved to RIKEN as Associate Chief Scientist in August, 2007.
Applications of candidates for the position after Ken-ichi Hino are being accepted.
We study a variety of matters in the physical world such as atomic nuclei, atoms, molecules,
and solids. In the world of quantum physics, all the constituent particles of matters behave
as waves. We are developing methods of calculating time evolution of the wave function
based on quantum theory to describe individual motion of particles – protons and neutronsin nuclei, electrons and nuclei in materials – and to investigate a variety of quantum
phenomena taking place in nature. The researches in our group include (1) interaction
between laser-light and materials [Hino, Tong; Yabana, Nakatsukasa], (2) quantum
dynamics of few-body reaction [Hino, Tong; Yabana, Nakatsukasa], (3) transportphenomena of strongly-correlated systems [Koizumi], and (4) quantum dynamics of
excitations, responses, and reactions of atomic nuclei [Yabana, Hashimoto, Nakatsukasa].
○ Interaction between laser and material
Laser sciences are rapidly developing as an interdisciplinary field of various scientificareas. One of the frontiers in laser sciences is the interaction of ultra-short and intense laser
pulse with matter. In this field, there have been observed a variety of electron dynamics
which originates from nonlinear interaction between the laser and matter in a time scale asshort as femto- or even atto-second. Such processes are expected to be useful to control theproperties of materials quantum mechanically. We are developing computational
approaches to understand elementary processes of laser-matter interaction, to predict new
phenomena, and to assess and/or propose possible ways of quantum control with laser.
Atoms and molecules in the intense laser field are ionized through multiphoton andtunneling mechanisms. Emitted electrons in the ionization are accelerated by the laser field
and re-scattered by the parent core. This re-scattering is a characteristic process in intenselaser field, causing such nonlinear processes as high-order harmonic generation and- 43 -CCS Report: PART II, Research Activities, Results
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non-sequential multiple ionization. The ionized molecules are then fragmented bydissociation or by Coulomb explosion. To understand these processes, we are developing
approaches solving the time-dependent Schroedinger or Kohn-Sham equations in real-time.
In the optical interaction between laser and low-dimensional semiconductors, there has
been observed a variety of electronic states reflecting the nanostructure in low-dimension.
Such laser-material interactions are expected to be useful for quantum control of lowdimensional structure. We are developing a new computational method for them, extending
a frameworks developed in atomic and molecular physics.
For the interaction of intense laser pulse with electrons in bulk crystal, we havedeveloped a new framework describing electron dynamics in infinite periodic systems. This
framework has opened a new field, a simulation of nonlinear electron dynamics in bulk
material, and has been applied to investigate such phenomena as optical breakdown andcoherent phonon in dielectrics.
○ Quantum dynamics of few-body reaction
Accelerated particles are the basic probes to investigate microscopic structure ofmatters through scatterings and reactions. Recently, the accelerated particles have come to
be used to synthesize new matters through reaction processes. These studies are now underprogress as big-science projects in several fields of fundamental sciences. We aredeveloping computational approaches for quantum few-body reactions relevant to newmatter syntheses such as an anti-proton helium which is produced by a collision ofanti-proton and matter, and reactions of exotic atomic nucleus produced in the RIBF
(Radioactive Ion Beam Factory project) in RIKEN.
In traditional scattering theory, one solves the time-independent Schroedinger equation
for a fixed energy to obtain scattering wave function. We have developed a newcomputational method solving the time-dependent Schroedinger equation for the scattering
process. This approach is especially useful for scattering processes involving more than
three-particles.
○ Transport phenomena in strongly correlated systems
Compounds containing transition metals are known to show a variety of functions
depending on the transition-metal atom in them and ligands surrounding it. They aresusceptible to interaction between contacted molecules or external fields such as light, heat,pressure, electric and magnetic fields. We have been studying anomalous electronictransport phenomena and superconductivity for these systems of transition metal complex
with strong electronic correlations and strong electron-lattice interactions. In particular,- 44 -CCS Report: PART II, Research Activities, Results
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elucidations of the mechanism of huge magnetoresistance in manganese-oxide and theelucidation of high-temperature superconductivity in copper-oxide have been studied withhigh priority.
○ Quantum dynamics of excitation, responses, and reactions in atomic nuclei
In the history of quantum many-particle theory, electronic many-body systems
composed of electrons and atomic nuclei, and nuclear many-body systems (atomic nuclei)
composed of protons and neutrons are the two major matters where the quantum
many-body theory has been developed. In recent development of computational quantum
sciences, common methods have also been successful in both systems such as thedensity-functional theory. We are developing a time-dependent density-functional approachfor excitation and responses of atomic nuclei. Yabana and Nakatsukasa take part in the
project UNEDF (Universal Nuclear Energy Density Functional) organized as a SciDAC
project in USA.
The number of published papers in this group is as follows:2004 : 28 (refereed journal 20 + conference paper 8 )2005 : 40 (refereed journal 24 + conference paper 16)
2006 : 25 (refereed journal 17 + conference paper 8 )2007 : 19 (refereed journal 12 + conference paper 7 )There are 6 grants from MEXT (4 for Kiban (C), and 2 for Priority Area) for which amember of this group is a representative researcher.
5.2 Research Results○ To describe and understand physical phenomena relevant to a few-body systems with
Coulomb interaction, we have developed a numerical method solving the time-dependent
Schroedinger equation with high accuracy. The method has been applied to phenomena
such as a tunnel ionization of atoms under ultra-short intense pulse laser, a synthesis anddecay dynamics of an anomalously long-lived anti-proton helium system, and reactions of
exotic nuclei with halo structure. These calculations have been useful to describe measured
data accurately and to obtain deep insight of their physical mechanisms. The figure shows
the time evolution of the electron energy distribution re-scattered in the field of intenselaser. [Hino, Tong; Yabana, Nakatsukasa]- 45 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007○ We have made a large-scale calculation for the quasi-energy structure of Floquet state(dynamical Wannier-Stark ladder state) which shows a strong coupling between thesemiconductor Wannier-Stark ladder and the laser field. The right figure shows the band
structure of quasi-energy band of Floquet state by monochromatic laser. Our work clarified
the exciton effects, Zener effects, and the acceleration effect by periodic pulses. In particular,
we have found a new approach of quantum control erasing both static and dynamics Zener
effect coherently by periodic pulse sequence and a curious behavior in the density of states of
Floquet states. [Hino, Tong]○We have succeeded the first-principles calculation of the electron dynamics for laser
induced dielectric breakdown of dielectrics. When an ultra-intense laser field is irradiatedto the dielectrics, a great number of electron-hole pairs are excited even for a visible lightwhich should be transparent in large-gap dielectrics. These excitations make the response of
the dielectrics metallic, and are employed for the purpose of laser machining and surgeries.
We have shown, for the first time, that this process of optical dielectric breakdown can be- 46 -CCS Report: PART II, Research Activities, Results
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Excitation energy [eV atom ]naturally described by solving the time-dependent Kohn-Sham equation. The figure showsthe energy transfer from the laser pulse to the electrons in diamond as a function of the
maximum intensity of the laser pulse. Around 1015 W/cm2, a substantial increase of theenergy transfer is seen where the dielectric breakdown occurs. A part of this calculation isachieved by PACS-CS. [Yabana, Nakatsukasa]
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Irradiance [W/cm ]○We have achieved cluster calculations employing molecular-orbital method for
manganese-oxides and copper-oxides, and have obtained new insights on local electronic
structure and electron-phonon interactions. In the both systems, electron-phonon interaction
is so strong that the doped carriers become small polarons. We have also obtained a newmechanism for electronic current generation in which a fictitious magnetic field that is
induced by spin vortex excitations gives rise to electric current. [Koizumi]○ We have developed a computational code of many-electron dynamics with real-time andreal-space method appropriate for massively parallel computers. To describe electron
dynamics based on the time-dependent density-functional theory, one need to calculate time
- 47 -CCS Report: PART II, Research Activities, Results
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evolution of the orbital functions,φi(x,y,z,t). We have developed two computational codes,
one is parallel in orbitals or k-points, and the other is the code parallel in spatial division,
and we have evaluated the efficiency of the codes in PACS-CS. The k-point parallel code isused in the calculations of optical breakdown at PACS-CS. The parallelization with space
division is expected to show good scalability for massively parallel computation. Further
developments to achieve better communication costs and better computational efficiency
are now under progress. [Yabana, Nakatsukasa, Hashimoto]
5.3 Collaboration
The members in the Institute of Physics who have experiences in nuclear physics(Yabana, Hashimoto, Nakatsukasa) and the members in the Institute of Material Sciences
who have experiences in atomic and molecular physics (Hino, Tong) have common
interests in laser sciences and quantum dynamics, and employ similar computational
methods. We are now considering to promote a close cooperation on large-scalecomputation in quantum dynamics.
The real-time, real-space DFT code as well as the real-space DFT code which runs
efficiently in massive parallel machines have been developed under close cooperation withthe group of computational material sciences and the group of computer system. A regularmonthly meeting has been organized for this purpose. A considerable part of the sourcecode of the real-time calculation is common with a real-space density-functional code
which has been developed in the group of computational material sciences.
Besides present cooperation described above, we hope to initiate the followings infuture. Since the electronic excitation and dynamics are important to understand functionsof biological molecules, real-time DFT calculation may be useful. We hope to cooperatewith computational biology group on this subject. In the group of computational elementary
particles, the lattice QCD calculations of nuclear force and nuclear matter have been rapidly
developing. They may bring a breakthrough and may open a new frontier for the studies ofnuclear structure. Cooperation with them on nuclear DFT study will be expected.
Since the group members have their own offices in two different areas in the campus
outside the Center, there is a problem of insufficient daily interchange among members in
the group and with members in other groups.
5.4 Future Plan
We consider the time-dependent computational approach for quantum dynamics is apromising field. We plan to further develop methods of solving time-dependent
Schroedinger and Kohn-Sham equations and to explore quantum dynamics in a variety of- 48 -CCS Report: PART II, Research Activities, Results
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fields, especially in optical sciences. To extend the areas of application and to investigate
quantitatively for large systems and/or correlated systems, computational codes which work
efficiently in massive parallel computers need to be developed.
In the fields of laser-matter interaction and few-body quantum dynamics calculations,we plan to proceed with the following researches:
1. To explore electron dynamics in atto-second scale, multipole ionization process of
atoms will be explored taking account of the effect of electronic correlations.
2. The interaction of laser with biological molecules is a promising fields. We willdevelop first-principle calculations of electron dynamics, taking into account future
experiments in XFEL (X-ray free electron laser).
3. The optical breakdown and the coherent phonon are typical examples reflecting
nonlinear interaction between intense laser and solid. We explore their basic mechanismwith the first-principle calculation.
4. A new real-time computational method will be explored for the electronic states dressedwith light (Floquet state).
5. A new method of quantum control will be investigated making use of the coupling
between laser and materials.
In the cluster calculations for strongly correlated systems, a large-size cluster
calculation with the molecular orbital method is planned. It will be compared with the bandcalculation in the density functional theory. In the future, we plan to design biosensing
materials by using molecules with strong correlation and electron-lattice interaction; theirunique transport phenomena and high susceptibility to external fields are expected to besuitable for detecting molecular environments. This part of the work will be conducted bycollaboration with Prof. Satoko of Nihon University.
In nuclear physics, we proceed with a study of unstable atomic nuclei which are now
rapidly developing in the RIBF (Radioactive Ion Beam Factory) project. One of theultimate goals is a construction of computational nuclear data for both stable and unstable
nuclei, by developing the density-functional approach for nuclei. We expect simultaneous
research on both systems of Coulombic and strong interactions will be beneficial topromote computational sciences of quantum dynamics with wide scope.

5.5 Publications
5.5.1 Journal Papers•

T. Nakatsukasa, T. Inakura, and K. Yabana, Finite amplitude method for the solution of the- 49 -CCS Report: PART II, Research Activities, Results
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random-phase approximation, Phys.Rev.C76, 024318(2007)
T. Otobe, K. Yabana, Density functional calculation for tunnel ionization rate of hydrocarbon
molecules, Phys. Rev. A75, 062507(2007)
K. Nobusada, K. Yabana, Photoinduced electric currents in ring-shaped molecules bycircularly polarized pulses, Phys. Rev. A75, 032518 (2007)
N. Hinohara, T. Nakatsukasa, M. Matsuo, and K. Matsuyanagi, Gauge-Invariant Formulation of
Adiabatic Self-Consistent Collective Coordinate Method, Prog. Theor. Phys. 117 (2007) 451-478.
Y. Hashimoto and T. Horibata, Wobbling motions in 182Os Expected through the generator
coordinate method based on the three-dimensional cranked HFB, INFORMATION, Vol.10(2007),
199-207.
K. Hino, X. M. Tong, and N. Toshima, Interacting dynamic Wannier-Stark ladder driven by aperiodic pulse train, Phys. Rev. B accepted (2007).
E. Gagnon, P. Ranitovic, X. M. Tong, C. L. Cocke, M. M. Murnane, H. C. Kapteyn, and A. S.
Sandhu, Soft X-ray driven femtosecond molecular dynamics, Science 317, 1374-78 (2007).
X. M. Tong, S. Watahiki, K. Hino and N. Toshima, Numerical observation of the rescattering
wavepacket in laser-atom interactions, Phys. Rev. Lett. 99, 093001:1-4 (2007).
X. M. Tong, T. Shirahama, K. Hino, and N. Toshima, Time-dependent approach to three-bodyrearrangement collisions: application to the capture of heavy negatively charged particles byhydrogen atoms, Phys. Rev. A 75, 052711:1-7 (2007).
X. M. Tong and C. D. Lin, Dynamics of light control of molecular dissociation at the few-cycle
limit, Phys. Rev. Lett. 98, 123002:1-4 (2007).
X. M. Tong and C. D. Lin, Carrier-envelope phase dependence of nonsequential double ionizationof H2 by few-cycle laser pulses, J. Phys. B 40, 641-49 (2007).
H.Koizumi, The origin of the Fermi arc in cuprates. Physica C 460-462 (898-899) 2007.
H. Koizumi, Current flow around small polarons embedded in a Mott insulator., J. Mol. Structur.
838 (2007) 211-215.
矢花一浩 (K. Yabana), 多電子ダイナミクスの量子シミュレーション, 日本物理学会誌 62,406-414 (2007).
K. Yabana, T. Otobe, J.-I. Iwata, First-principles density-functional approach for many-electron
dynamics under intense laser fields, Springer Series in Chemical Physics 84, pp.77-94 (2006)
G.F. Bertsch, K. Yabana, Density functional theory, Introduction to Computational Methods in
Many Body Physics, pp.123-169, Eds. M. Bonitz and D. Semkat, Rinton press Inc. (2006).
K. Yabana, T. Nakatsukasa, J.-I. Iwata, and G.F. Bertsch, Real-time, real-space implementation of
the linear response time-dependent density-functional theory, Phys. Stat. Sol. (b)243, 1121 (18pages) (2006)
M. Ito, K. Yabana, T. Nakatsukasa, and M. Ueda, Suppressed Fusion Cross Section for Neutron Halo
Nuclei, Phys. Lett. B637 (2006) 53-57.
S. Shinohara, H. Ohta, T. Nakatsukasa, and K. Yabana, Configuration mixing calculation forcomplete low-lying spectra with the mean-field Hamiltonian, Phys. Rev. C 74 (2006) 054315 (10pages).
M. Ito, K. Yabana, T. Nakatsukasa, M. Ueda, Suppressed fusion cross section for neutron halo
nuclei, Physics Letters B637 (2006), pp.53-57.
N. Hinohara, T. Nakatsukasa, M. Matsuo, and K. Matsuyanagi, Effects of time-odd components inmean field on large amplitude collective dynamics,Prog. Theor. Phys. 115 (2006) 567.
Y.Hashimoto and T.Horibata, Stability of s-band states in the tilting calculation of 182Os,
Phys.Rev.C74(2006), 017301.
T. Inakura, H. Imagawa, Y. Hashimoto, S. Mizutori, M. Yamagami, K. Matsuyanagi, Mixed
representation RPA calculation for octupole excitations on superdeformed states in the 40Ca andneutron-rich sulfur regions, Nucl. Phys. A768(2006), 61-79.
K. Hino and N. Toshima, Wannier-Stark ladder by means of a pulse train with periodic repetition,
Solid State Communications, 138, 341-346 (2006).
X. M. Tong, K. Hino, and N. Toshima, State-specified protonium formation in low-energy
antiproton-hydrogen-atom collisions, Phys. Rev. Lett. 97, 243202:1-4 (2006).

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Zhangjin Chen, Toru Morishita, Anh-Thu Le, M. Wichenhauser, X. M. Tong, and C. D. Lin,
Analysis of two-dimensional photoelectron momentum spectra and the effect of the long-range
Coulomb potential in single ionization of atoms by intense lasers, Phys. Rev. A. 74 053405:1-11(2006).
M. Wickenhauser, X. M. Tong, D. G. Arbo, J. Burgdorfer, and C. D. Lin, Signatures of tunnelingand multiphoton ionization in the electron-momentum distributions of atoms by intense few-cycle
laser pulses, Phys. Rev. A 74, 041402:1-4(R) (2006).
X. M. Tong, K. Hino and N. Toshima, Phase-dependent atomic ionization in few-cycle intense laser
fields, Phys. Rev. A 74, 031405:1-4(R) (2006).
J. J. Carrera, X. M. Tong and S. I. Chu, Creation and control of a single coherent attoseccond xuv
pulse by few-cycle intense laser pulses, Phys. Rev. A 74, 023404:1-7 (2006).
X. M. Tong, Z. X. Zhao and C. D. Lin, Comment on “Correlation quantum dynamics between an
electron and D2+ molecules with attosecond resolution”, Phys. Rev. Lett. 97, 049301:1-1 (2006).
X. M. Tong and C. D. Lin, Attosecond xuv pulses for complete mapping of the time-dependent
wave packets of D2+,, Phys. Rev. A 73, 042716:1-4 (2006).
T. Le, X. M. Tong and C. D. Lin, Evidence of two-center interference in high-order harmonic
generation from CO2, Phys. Rev. A 73, 041402:1-4(R) (2006).
X. X. Guan, X. M. Tong and S. I. Chu, Effect of electron correlation on high-order-harmonic
generation of helium atoms in intense laser fields: Time-dependent generalized pseudospectral
approach in hyperspherical coordinates, Phys. Rev. A 73, 023403:1-9 (2006).
M. Wickenhauser, X. M. Tong and C. D. Lin, Laser-induced substructures inabove-threshold-ionization spectra from intense few-cycle laser pulses, Phys. Rev. A 73
011401:1-4(R) (2006).
Shiratori, K. Nobusada, K. Yabana, Multiple ionization of a silver diatomic molecule in an
intense laser field, Chem. Phys. Lett. 404 (2005) 365.
T. Nakatsukasa and K. Yabana, Linear response in the continuum for deformed nuclei: Green’s
function vs time-dependent Hartree-Fock with the absorbing-boundary condition, Phys. Rev. C71(2005) 24301.
M. Kobayasi, T. Nakatsukasa, M. Matsuo, and K. Matsuyanagi, Collective paths connecting theoblate and prolate shapes in 68Se and 72Kr suggested by the adiabatic self-consistent collective
coordinate method, Prog. Theor. Phys. 113 (2005) 129.
Y. Hashimoto and T. Horibata, Tilted Axis Rotation in Hartree-Fock Framework,
INFORMATION, Vol.8, No.3 (2005), 347-357.
K. Hino and N. Toshima, Dimensionality transitions of exciton Fano-resonance spectra in asemiconductor Wannier-Stark ladder, Solid State Communications 135, 119-123 (2005).
K. Hino and N. Toshima, Spectral modulation of exciton Fano resonance due to Zener breakdown
in strongly biased superlattices, Phys. Rev. B 71, 205326:1-19 (2005).
K. Hino, K. Yashima and N. Toshima, Zener resonance in a dynamic Wannier-Stark ladder: Two
miniband model, Phys. Rev. B 71, 115325:1-6 (2005).
M. Maharjan, A. S. Alnaser, X. M. Tong, B. Ulrich, P. Ranitovic. S. Ghimire, Z. Chang, I. V.
Litvinyuk and C. L. Cocke, Momentum imaging of doubly charged ions of Ne and Ar in thesequential ionization region, Phys. Rev. A 72, 041403:1-4(R) (2005).
S. Alnaser, M. Zamkov, X. M. Tong, C. M. Maharjan, P. Ranitovic, C. L. Cocke, I.V. Litvinyuk,
Resonant excitation during strong field dissociative ionization, Phys. Rev. A 72 (2005)
041402:1-4(R) (2005).
Anh-Thu Le, Toru Morishita, X. M. Tong, and C. D. Lin, Signature of chaos in high-lying
doubly-excited states of helium atom, Phys. Rev. A 72, 032511:1-14 (2005).
S. Alnaser, B. Ulrich, X. M. Tong, I. V. Litvinyuk, C. M. Maharjan, P. Ranitovic, T. Osipov, R. Ali,
S. Ghimire, Z. Chang, C. D. Lin, and C. L. Cocke, Simultaneous real-time tracking of coherent
wave packets on two different potential curves in H2+ and D2+, Phys. Rev. A 72, 030702:1-4(R)(2005).
XiaoXin Zhou, X. M. Tong, Z. X. Zhao, and C. D. Lin, Alignment dependence of high-orderharmonic generation from N2 and O2 molecules”, Phys. Rev. A 72, 033412:1-7 (2005).

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K. Tokesi, X. M. Tong, C. Lemell, and J. Burgdorfer, Energy loss of charged particles at large
distances from metal surfaces, Phys. Rev. A 72, 022901:1-16 (2005).
X. M. Tong and C. D. Lin, Empirical formula for static field ionization rates of atoms andmolecules by lasers in the barrier-suppression regime, J. Phys. B: 38, 2593-2600 (2005).
Juan J. Carrera, Shih-I Chu, and X. M. Tong, High-order harmonic generation from Argon atoms insuper intense pulsed laser fields: A case study of self-interaction-free time-dependent
density-functional approach, Phys. Rev. A 71, 063813:1-4 (2005).
XiaoXin Zhou, X. M. Tong, Z. X. Zhao, and C. D. Lin, Role of molecular orbital symmetry on thealignment dependence of high-order harmonic generation with molecules, Phys. Rev. A 71,
061801:1-4(R) (2005).
Z. X. Zhao, Zenghu Chang, X. M. Tong and C. D. Lin, Circularly-polarized laser-assisted
photoionization spectra of Argon for attosecond pulse measurements, Optic Express 13, 1966-77(2005).
S. Alnaser, C. M. Maharjan, X. M. Tong, B. Ulrich, P. Ranitovic, B. Shan, Z. Chang, C. D. Lin, C.
L. Cocke, and I.V. Litvinyuk, Effects of orbital symmetries in dissociative ionization of moleculesby few-cycle laser pulses, Phys. Rev. A 71, 031403:1-4(R) (2005).
X. M. Tong and C. D. Lin, Double photoexcitation of He atoms by attosecond XUV pulses in thepresence of intense few-cycle infrared lasers, Phys. Rev. A 71, 033406:1-6 (2005).
X. M. Tong, Z. X. Zhao, A. S. Alnaser, S. Voss, C. L. Cocke, and C. D. Lin, Post ionizationalignment of the fragmentation of molecules in an ultrashort intense laser field, J. Phys. B 38,
333-41 (2005).
S. Miyaki, S. Uzuhara, K. Terada, K. Makoshi, H. Koizumi, Molecular orbital cluster calculation
study of electron correlation and local instability in La2-2xSr1+2xMn2O7, Phys. Rev. B
71(085117-1,10), 2005
Nobusada, K. Yabana. High-order harmonic generation from silver clusters: Laser-frequency
dependence and the screening effect of d electrons, Phys. Rev. A70 (2004) 043411
T. Otobe, K. Yabana, J.I. Iwata. First-principle calculations for the tunnel ionization rate of atoms
and molecules. Phys. Rev. A69 (2004) 053404.
J.-I. Iwata, K. Yabana, G.F. Bertsch, Real-space computational method for linear and nonlinear
polarizabilitiesm, Journal of Computational Methods in Sciences and Engineering 4 (2004) 461.
M. Ueda, K. Yabana, and T. Nakatsukasa, Absorbing Boundary Condition Approach to Breakup
Reactions of One-Neutron Halo Nuclei, Nucl. Phys. A738 (2004) 288.
K. Yabana, M. Ito, M. Kobayashi, M. Ueda, and T. Nakatsukasa, Fusion reaction of halo nuclei: A
time-dependent approach, Nucl. Phys. A738 (2004) 303.
H. Ohta, K. Yabana, and T. Nakatsukasa, Variation after parity projection calculation with Skyrmeinteraction for light nuclei, Phys. Rev. C70 (2004) 014301.
M. Kobayasi, T. Nakatsukasa, M. Matsuo, and K. Matsuyanagi. Collective path connecting theoblate and prolate local minima in 68Se, Prog. Theor. Phys. 112 (2004) 363.
T.Inakura, M.Yamagami, K.Matsuyanagi, S.Mizutori, H.Imagawa and Y.Hashimoto, Static anddynamic non-axial octupole deformations suggested by Skyrme-HF and Selfconsistent RPA
calculations, Int. Journ. Mod. Phys. E13 (2004) 157-163.
K. Hino and N. Toshima, Anomalous variation of the exciton Fano-resonance spectra in strongly
biased Wannier-Stark ladder, Solid State Communications 132, 449-453 (2004).
K. Hino, K. Goto and N. Toshima, symmetric Autler-Townes-like doublets in laser-driven excitonic
Fano resonance in biased superlattices: Roles of many-body Coulomb exchange, Phys. Rev. B 69,
035322:1-16 (2004).
S. Alnaser, X. M. Tong, T. Osipov, S. Voss, C. M. Maharajan, B. Shan, Z. Chang, C. D. Lin, and C.
L. Cocke,Routes to control of H2 Coulomb explosion in few-cycle laser pulses, Phys. Rev. Lett. 93,
183202:1-4 (2004).
S. Voss, A. S. Alnaser, X. M.Tong, C. Maharjan, P. Ranitovic, B. Ulrich, B. Shan, Z. Chang, C. D.
Lin and C. L. Cocke, High resolution kinetic energy release spectra and angular distributions fromdouble ionization of nitrogen and oxygen by short laser pulses, J. Phys. B 37, 4239-58 (2004).
S. Alnaser, S. Voss, , X. M. Tong, C. Maharjan, P. Ranitovic, B. Ulrich, T. Osipov, B. Shan, Z.

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Chang and C. L. Cocke, ffects of molecular structure on ion disintegration patterns in ionization ofO2 and N2 by short laser pulses, Phys. Rev. Lett. 93, 113003:1-4 (2004).
S. Alnaser, X. M. Tong, T. Osipov, S. Voss, C. M. Maharjan, B. Shan, Z. Chang and C. L. Cocke,
aser peak intensity calibration using recoil-ion momentum imaging, Phys. Rev. A 70, 023413:1-6(2004).
E. P. Benis, J. F. Xia, X. M. Tong, M. Faheem, M. Zamkov, B. Shan, P. Richard, and Z. H. Chang,
Ionization suppression of Cl2 molecules in intense laser fields, Phys. Rev. A 70, 025401:1-4 (2004).
X. M. Tong and C. D. Lin, Time-resolved sequential double ionization of D2 molecules in an
intense few-cycle laser pulse, Phys. Rev. A 70, 023406:1-4 (2004).
X. M. Tong and C. D. Lin, How to read a molecular clock with sub-femtosecond accuracy, Int. J.
Modern Physics B 18, 1659-78 (2004).
X. M. Tong and C. D. Lin, Propensity rule for novel selective double photoexcitation of helium
atoms in strong static electric fields, Phys. Rev. Lett. 92, 223003:1-4 (2004).
B O’Rourke, H Kuramoto, Y M Li, S Ohtani, X M Tong, H Watanabe and F J Currell, Dielectronic
recombination in He-like titanium ions, J. Phys. B 37, 2343-53 (2004).
N. Hiraoka, M. Itou, A. Deb, Y. Sakurai, Y. Kakutani, A. Koizumi, N. Sakai, . Uzuhara, S. Miyaki,
H. Koizumi, K. Makoshi, N. Kikugawa, Y. Maeno, Ru-O orbital hybridization and orbital
occupation in SrRuO3: A magnetic Compton-profile study, Phys. Rev. B 70(054420-1,4), 2004.

5.5.2 Proceedings
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T. Nakatsukasa and K. Yabana, Real-time Skyrme TDHF dynamics of giant resonances, Nucl. Phys.
A768(2007), 349-354.
M. Ito, K. Yabana, T. Nakatsukasa, and M. Ueda, Fusion Reaction of Halo Nuclei: A Real-Time
Wave-Packet Method for Three-Body Tunneling Dynamics, Nucl. Phys. A787(2007), 267-274.
K. Hino, X. M. Tong, and N. Toshima , Interacting Dynamic Wannier-Stark Ladder Driven By A
Pulse Train With Periodic Repetition: Removal Of Interminiband Interactions And Negative
Absorption, 28th International Conference on the Physics of Semiconductors, 459 (2007). (24-28
July, Vienna, Austria, 2006).
X. M. Tong, K. Hino, N. Toshima and J. Burgdorfer, Computational methods in the laser-atominteraction, (Invited talk), Journal of Physics: Conference Series (accepted, 2007).
T. Le, X. M. Tong, and C. D. Lin, Alignment dependence of high-order harmonic generation from
CO2, Journal of Modern Optics, 54, 967-80 (2007).
X. M. Tong, S. Watahiki, K, Hino and N. Toshima, Observation of resattering wavepacket byquantum simulation, 25th International Conference on Photonic, Electronic and Atomic Collisions,(Freiburg, Germany 25-31 July 2007) We066 (2007).
X. M. Tong, T. Shirahama, K, Hino and N. Toshima, Theoretical study on capture of antiprotons byhelium atoms, 25th International Conference on Photonic, Electronic and Atomic Collisions,(Freiburg, Germany 25-31 July 2007) Mo055 (2007).
X. M. Tong, T. Shirahama, K, Hino and N. Toshima, Theoretical study on state-specified capture of
massive negatively-charged particles by hydrogen atoms, 25th International Conference on Photonic,
Electronic and Atomic Collisions, (Freiburg, Germany 25-31 July 2007) Mo056 (2007).
T. Nakatsukasa, K. Yabana, M. Ito, and M. Ueda, Fusion Reaction of Halo Nuclei: A Real-Time
Wave-Packet Method for Three-Body Tunneling Dynamics, AIP Conference Proceedings 853 (AIP
Press, 2006) pp. 291-296
T. Nakatsukasa, M. Ito, and K. Yabana, Nuclear dynamics in time-dependent picture, AIP
Conference Proceedings 865 (AIP Press, 2006) pp. 114-119.
Y.Hashimoto and T.Horibata, Possible excitations of the wobbling motion in 182Os based on thethree-dimensional cranked HFB, Proceedings of the fourth international Conference on
information(ed. Lei Li et al., 1-5 Aug., 2006, University College Cork, Cork, Ireland), 118-121.
C.D. Lin, X.M. Tong, Z.X. Zhao, Effects of orbital symmetries on the ionization rates of aligned
molecules by short intense laser pulse, Journal of Modern Optics 53, 21-33 (2006)- 53 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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C.D. Lin, X.M. Tong and T. Morishita , Direct experimental visualization of atomic and electron
dynamics with attosecond pulses, J. Phys. B 39, S419-426 (2006).
C.D. Lin and X.M. Tong, Depednence of tunneling ionization and harmonic generation on the
structure of molecules by short intense laser pulses, J. Photochem. and Photobio. A 182, 213-219(2006).
X. M. Tong, K, Hino and N. Toshima, State Specified Protonium Formation in Antiproton
Hydrogen collisions. 20th International Conference on Atomic Physics, (Innsbruck, Austria 16-21
July 2006) 261 (2006).
８．M. Wickenhauser, J. Burgdorfer, X. M. Tong, and C. D. Lin, 2D Electron-Momentum
Distributions of Atoms Subject to Intense Few-Cycle Laser Pulses, 20th International Conference on
Atomic Physics, (Innsbruck, Austria 16-21 July 2006) 584 (2006).
J. J. Carrera, S. I. Chu, and X. M. Tong, Creation and Control of Single Attosecond XUV Pulse by
Few-Cycle Laser Pulses, 20th International Conference on Atomic Physics, (Innsbruck, Austria
16-21 July 2006) 585 (2006).
X. M. Tong, K. Hino, and N. Toshima, Phase Dependent Atomic Ionization in Few-Cycle Intense
Laser Fields, 20th International Conference on Atomic Physics, (Innsbruck, Austria 16-21 July
2006) 586 (2006).
T. Nakatsukasa and K. Yabana, Unrestricted TDHF studies of nuclear response in the continuum,
Eur. Phys. J. A 25 (2005) 527 .
H. Ohta, K. Yabana, and T. Nakatsukasa, Light exotic nuclei studied with the parity-projected
Hartree-Fock method, Eur. Phys. J. A 25 (2005) 549.
M. Kobayasi, T. Nakatsukasa, M. Matsuo, and K. Matsuyanagi, Collective ｐath ｃonnecting theoblate and prolate local minima in proton-rich N=Z nuclei around 68Se, Eur. Phys. J. A 25 (2005)
547.
T. Nakatsukasa and K. Yabana, Time-dependent density functional theories for finite many-fermion
systems, Proceedings of the XXIX International Workshop on Condensed Matter Theories (Nova
Science Publishers, New York).
D. Ward, R.M. Clark, M. Cromaz, M.A. Deleplanque, R.M. Diamond, P. Fallon, G.J. Lane, I.Y. Lee,
A. Goergen, A.O. Macchiavelli, F.S. Stephens, C.E. Svensson, K. Vetter, D. Cline, A.B. Hayes, R.
Teng, C.-Y. Wu, and T. Nakatsukasa, Aspects of the coriolis interaction in 235U,AIP Conf. Proc. 764(2005) 263.
S. Shinohara, H. Ohta, T. Nakatsukasa, K. Yabana, Nuclear excitations described by the randomly
selected multiple Slater determinants, J. Phys. Conf. Ser. 20 (2005) 193.
H. Ohta, T. Nakatsukasa, K. Yabana, Parity projected Skyrme Hartree-Fock and angular momentum
projection approach to Mg isotopes, J. Phys. G. 20 (2005) 211.
M. Ito, K. Yabana, K. Kato, K. Ikeda, Low energy collisions of α+6He and the continuum
structures in 10Be, Journal of Physics : Conference Series Vol. 20 pp.185-186 (2005).
M. Ito, K. Yabana, K. Kato, K. Ikeda, Description of the single-particle motions around two
inert-cores based on the microscopic cluster model, YITP Report, Soryushron-kennkyuu 112 (2005)
B1
M. Ito, K. Yabana, Absorbing kernels to study resonances based on the generator
coordinate method in the microscopic cluster model, YITP Report, Soryushron-kennkyuu
112 (2005) B1
X. M. Tong, Z. X. Zhao and C. D. Lin, Molecular tunneling ionization and rescattering induced
double ionization of H2 and D2 molecules, Journal of Modern Optics 52, 185-199 (2005).
T. Osipov, A. S. Alnaser, S. Voss, M. H. Prior, T. Weber, O. Jagutzki, L. Schmidt, H.
Schmidt-Bocking, R. Dorner, A. Landers, E. Wells, B. Shan, C. Maharjan, B. Ullrich, P. Ranitovic,
X. M. Tong, C. D. Lin and C. L. Cocke, Photon-ion Collisions and Molecular Clocks, Journal ofModern Optics 52, 439-451 (2005).
K. Hino and N. Toshima, Anomalous Spectral Modulation of Exciton Fano Resonance due to Zener
Breakdown in Strongly Biased Superlattices, The 9th Conference on Optics and Excitons in
Confined System and 2nd Intern'l Conference on Spontaneous Coherence in Excitonic System,(Southampton, UK, 2005) 36 (2005).

- 54 -CCS Report: PART II, Research Activities, Results
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K. Hino, K. Yashima and N. Toshima,Zener resonance in a dynamic Wannier-Stark ladder, Intern'lSeminar on Atomic Processes in Intense Laser Fields and Related Many-Body Phenomena,(Shonan,
Kanagawa, Japan, 2005) 49 (2005).
Nakatsukasa, M. Ueda, and K. Yabana, Continuum response and reaction in neutron-rich be nuclei,
AIP Conference Proceedings 701 (AIP Press, 2004) p.179.
T. Nakatsukasa and K. Yabana, Response in the continuum for light deformed neutron-rich nuclei,
Proc. of Int. Symp. on “A New Era of Nuclear Structure Physics (NENS03)”, (World Scientific,
2004) p.251.
Nakatsukasa, K. Yabana, M. Ito, M. Kobayashi, and M. Ueda, Fusion reaction of halo nuclei:
proton versus neutron Halo, Prog. Theor. Phys. Suppl. 154 (2004) 85.
M. Kobayasi, T. Nakatsukasa, M. Matsuo, and K. Matsuyanagi, Application of the adiabatic
self-consistent collective coordinate method to the prolate-oblate shape coexistence phenomena,
Proc. of Int. Symp. on “A New Era of Nuclear Structure Physics (NENS03)”, (World Scientific,
2004) p.349.
T. Nakatsukasa, M. Ueda, and K. Yabana, Continuum response and reaction in neutron-rich be
nuclei, AIP Conference Proceedings 701 (AIP Press, 2004) p.179.
Y.Hashimoto and T.Horibata,Microscopic Theory of Three-dimensional Nuclear Rotation,
Proceedings of the Third International Conference on Information (Edited by Lei Li and Kang K.
Yen, Nov.29-Dec.2, 2004, Hosei University, Tokyo.)- 55 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

6. Division of Global Environment and Biological Sciences: Global Environmental
Science Group
6.1 Research Activity
In the Group of the Global Environmental Science of the Division of Global Environment
and Biological Sciences, there are two fulltime staffs of Prof. Hiroshi L. Tanaka and Asst.
Prof. Hiroyuki Kusaka (Dept. of Life and Geoenvironmental Science) and one collaborative
staff of Prof. Fujio Kimura (Dept. of Life and Geoenvironmental Science) and one affiliatedstaff of Prof. Akio Kitoh (Meteorological Research Institute, Japan Meteorological
Agency).
6.1.1 Activity in 2005
The main research activity of the group in 2005 was to establish a new collaboration
with the groups of High Performance Computing System and Computational Informatics
because it was the first year for our group as the newly founded division in the Center for
Computational Sciences (CCS). As the first attempt of our group, we started to archive thedaily numerical weather prediction data called grid point values (GPV) provided by theJapan Meteorological Agency (JMA). This activity of archiving initial data and ensemble
prediction data was organized by the world-wild project called THORPEX: The Observing
System Research and Predictability Experiment. The THORPEX project has started in 2003
and will continue to 2012 under the leadership of the WMO: World MeteorologicalOrganization, with a special emphasis of improving the deterministic weather predictability
and developing the advanced observational system.
The aim of the THORPEX is to improve the prediction skill especially for the extreme
events for the range of one day to two weeks by combining the advanced observational
technology and the sophisticated high-performance prediction models based on the recent
technology of the ensemble prediction, four-dimensional data assimilation, targeted optimal
observation, high-tech satellite imageries, etc. Under the THORPEX project, our university
held a research contract with the JMA and started to archive the ensemble prediction data
provided by the JMA. The project is called GPV/JMA project that attempts to establish alarge meteorological database within the CCS facility.
The Group of Global Environmental Science started the collaboration with the High
Performance Computing System and Computational Informatics in CCS, assembling
periodically once a month. First, we bought a data server named gpvjma to archive thevarious kinds of GPV/JMA data, assisted by the Computational Informatics group for the- 56 -CCS Report: PART II, Research Activities, Results
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maintenance and by the High Performance Computing System group for the technicalsupport. The data archive and release to the public began in January 2005. The GPV data
are not only archived but also analyzed to present many kinds of weather maps andanimations of the maps to present for the public.

Figure 1. Weather data called GPV (grid point value) provided by JMA(Japan Meteorological Agency) and the data flow to CCS.
Under the research contract between the University of Tsukuba and JMA, we sent one
graduate student in the doctoral degree program for the project of the Advanced Ensemble
Prediction Technology. We imported the operational weather forecasting model of the JMA
called Global Spectral Model (GSM T63L40) in order to conduct ensemble prediction by
installing the model to the PACS-CS under the construction at CCS. The test run was
performed under the PC cluster system.
Since the GPV/JMA project of archiving real-time weather data became an operational
phase with steady increase of the users, a new plan of archiving and releasing the Japan
Reanalysis Data for 25 years (JRA-25) is proposed. The JRA-25 data are provided by thecollaborative work by the JMA and the Central Research Institute for Power Industry(CRIPI), although the plan was still pending by the restrictions and regulations announced
by the JMA.
As the application studies of the global environment and atmospheric science, Prof.
Tanaka obtained a research fund from the National Science Foundation (NSF) by way ofthe collaboration with International Arctic Research Center (IARC) of the University of
Alaska Fairbanks in USA for the study of the global warming in connection to the Arctic
climate. With this fund the 6th International Conference on Global Change: Connection to
the Arctic (GCCA-6) was held in December 2005 at the Miraikan in Tokyo Japan. The
former GCCA-5 was held at the University of Tsukuba in 2004.
At this time, the fulltime staff in the group was only Prof. Tanaka. An employment of- 57 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

additional young staff was the urgent problem to enhance the group activities. As the future
plan of the group, an expert in the regional weather prediction modeling was proposed tocompensate the research activity in the global ensemble predictions with the generalcirculation model.
6.1.2 Activity in 2006
In 2006, the main activity of our group was devoted to the study of the Arctic
Oscillation, which causes the global scale abnormal weather. The increased occurrence of
the abnormal weather in recent years is accompanied by the geographical distribution
characterized by the Arctic Oscillation which may have a close relation to the global
warming.
For example, an extreme heavy snow along the west side of Japan Island was broken
out in the winter of 2005/06, which was named as Heisei 18 Heavy Snow Event. The
subsequent winter of 2006/07 was, on the contrary, abnormally warm with the extremelylate first snow fall in Tokyo recorded on 16 March 2006. These abnormal winters wereexplained by the manifestation of the Arctic Oscillation phenomenon.

Figure 2. Arctic Oscillation and the abnormal weather in the Northern Hemisphere.
Assisted by the sever weather in recent years, the Grant In Aid research proposal of
Category A to the JSP by Prof. Tanaka was granted. The research title is The dynamical
understanding of the Arctic Oscillation and the low-frequency variability. Additional
research fund has arrived from the IARC/UAF in the USA and from Asahi Brewery
Foundation for the study of the Arctic Oscillation and its prediction. In February 2007, the
7th International Conference on the Global Change: Connection to the Arctic (GCCA-7)
was held in Fairbanks Alaska, USA. University of Tsukuba is one of the organizing- 58 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

members.
The operational global spectral model in JMA was update from GSM T63L40 to GSM
TL159/319 due to the replacement of the new computing system in JMA. We need tore-install the GSM every time whenever updated. Since the operational spectral model will
not fit in the PC cluster scalar machine, using GSM of JMA for the PACS-CS must bereconsidered for the future plan.
In parallel with global weather forecasting model, we wish to install a regional
weather forecasting model for the future plan. Dr. Hiroyuki Kusaka was hired as a new
Assistant Professor in our group who is an expert of the WAR regional model, especiallyfor the urban climate model development nested in the regional and global weather
forecasting model. Combined with the real-time GPV/JMA data and the JRA-25 analysis
data, the regional model experiments of heavy shower and heavy snow events in Japan had
started in our group. Currently, the latest WAR model is version 2.2 released on 23
December 2006 by the National Center for Atmospheric Research (NCAR), where theurban model originally developed by Dr. Kusaka is installed in the official WRF module.
6.1.3 Activity in 2007
In 2007, the operation of the PACS-CS has started. In association with the PACS-CS
project, we established a new research contract with the Center for Climate System
Research (CCSR) of the University of Tokyo in order to collaborate for the development of
the next generation cloud resolving non-hydrostatic icosahedral general circulation model(NICAM), which was developed by the group in CCSR and the Frontier Research Center
for Global Change (FRCGC) in JAMSTEC. The NICAM of CCSR/FRCGC is superior to
the GSM of JMA in that the dynamical core of the model is formulated specifically for themassively parallel processing using MPI which fits perfectly with the PACS-CS. The
traditional spectral model like the GSM needs all to all data transfer. Therefore, the spectral
dynamical core would reach to the dead end in the future development.
In contrast, the NICAM can extend the model resolution to 3.5 km global mesh withcloud resolving physical process. The testing phase with an aqua planet model (notopography) has completed successfully, and full terrain has just installed in the model.
Using the latest version of the NICAM with topography, a near real-time prediction
experiments are conducted attached with the realtime GPV/JMA data archive under the
PACS-CS facility.
The GPV/JMA data is free to the public. Yet, the data resolution released to the public
is quite coarse and not sufficient for the accurate weather prediction as the initial data. The
JMA and the Meteorological Society of Japan (MSJ) established a comprehensive research- 59 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

contract in July 2007 as the Weather Research Consortium. Prof. Tanaka is elected as oneof the first board member of the consortium. Under this contract, the accurate initial datawith full resolution of the operational weather forecasting model by JMA are released to themember of the consortium. Our group in CCS is expected to serve as the data mirror site of
the consortium data. We purchased 8.25TB raid server and started to archive the consortium
data in addition to the GPV/JMA data.

Figure 3. Simulation of surface temperature by the regional model called WRF. A record
high temperature of 40.9 deg C was observed on this day.
The WRF regional model was progressively developed under the PACS-CS project.
Coupled with the real-time GPV/JMA data, the real-time regional weather prediction
system was constructed experimentally. A test run was demonstrated for the explosive
cyclogenesis event occurred on 7 January 2007 to confirm that the system is useful for
educational purpose as well as research. Since the real-time weather prediction is restricted
to release for the public without the permission by the JMA, the prediction is used onlyinternally within the group.
As the product of the collaboration with the Computational Informatics group, a
research project of the advanced utility of weather information based on the weather
ontology leaded by Prof. Kitagawa was promoted to show a real time weather maps
superimposed on the Google Earth. Various weather maps of GSM (global spectral model),RSM (regional spectral model), and MSM (meso-scale non-hydrostatic model) are
combined with Google Earth in terms of the KML files. The product was released to the- 60 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

public in conjunction with the GPV/JMA products by the effort of Asst. Prof. Amagasa. The
real time monitoring is displayed at the entrance of the CCS using large screen TV since theOpening Ceremony of the PACS-CS System in September 2007.
6.2 Research Contributions
Contributions by Dr. Hiroshi L. Tanaka for 2005-2007(1) Articles, Papers and Reports: total of 38 papers
Books: 3, Papers with peer review 19, other 16(2) Arctic Oscillation in connection to the global warming(3) Arctic Oscillation and abnormal weather(4) Singular eigenmode theory of the Arctic Oscillation(5) Changes in tropical circulations under the global warming(6) Theory of energy saturation by Rossby wave breaking(7) Energy spectrum of E=mc^2 observed in general circulation
Contributions by Dr. Hiroyuki Kusaka for 2005-2007(1) Articles and papers reviews for regional and urban model(2) Review paper on meso model in Japan Wind Engineering(3) Review paper on urban model in Tenki MSJ(4) Review paper on urban climate in Regional Geography Japan(5) Research fund by Japan Weather Association (PI)(6) Research fund by Weather Engineering Institute (PI)(7) Research fund by Ministry of the Environment (Co-PI)(8) Forecast experiment for the record hot on 16 August(9) Educational application of the forecasting system

6.3 Collaboration
Our Group of Global Environmental Science has a close collaboration with High
Performance Computing System and Computational Informatics under the common
subject of constructing the large database of real time weather data, named GPV/JMA
project. This project is to archive real time weather data of the global spectral model(GSM), regional spectral model (RSM), meso scale non-hydrostatic model (MSM)
provided by the JMA. In addition to those model data, weekly ensemble forecast data andmonthly ensemble forecast data are also archived, and released to the public using the
CCS homepage. The archive started in January 2005 and stably maintained up to now:
- 61 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

September 2007. Those data are useful for the study of developing ensemble Kalman filter,
which is the state-of the-art four dimensional assimilation system. The knowledge of thestaff in Computational Informatics is helpful to construct the safe distribution of the data
to the public. The technical support by High Performance Computing System wasessential to install and maintain the system. The weather map presented on the Google
Earth is the product by the staff in Computational Informatics.
A unique general circulation model, called barotropic S-model, has been developed byour group in the university of Tsukuba, which predict the vertical average status of theatmosphere. The model is useful to predict the low-frequency variability such as blocking
phenomenon and the Arctic Oscillation. An ensemble prediction system has beendeveloped using the barotropic S-model on the platform of the PACS-CS. Although it is
EP application of a number of simple predictions, we can extend the ensemble size up to
256 members. This ensemble prediction is applied to construct the four dimensional
assimilation by means of the ensemble Kalman filter. Since the solution by the true
Kalman filter is possible to compare with the approximation of the ensemble Kalman filter
for this model, the research subject is important for the study of the four dimensional
assimilation. The research is supported by the knowledge of the High Performance
Computing System.

Figure 4. Real time weather prediction system by the regional model WRF.
6.4 Future Plan
The most important subject of the future plan in CCS is how to collaborate with othergroups of computer science and other application sciences in astrophysics, particle physics,- 62 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

materials and life sciences, biology, etc; without it the success in the research by CCS
would be questioned. We expect further support by those groups in CCS. Following is thelist of the future research subjects:(1) Prediction model for the Arctic Oscillation(2) Ensemble Kalman filter using the barotropic S-model(3) Numerical experiments with the next generation model NICAM(4) Urban climate simulation with the regional model WRF.
(5) Organize a regular session in Earth and Planet Conventions(6) Organize a special session in Meteorological Society of Japan(7) Organize an International Symposium on the Arctic Regions(8) Collaboration with IARC/UAF USA(9) Organize the Meteorological Research Consortium(10) Collaboration with National Institutes: NIRP, JAMSTEC, MRI, NIES
(11) Collaboration with Commercial Industries: JWA, JAL, TEPCO

6.5 Publications
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Tanaka, H.L., D. Nohara, and H.-R. Byun 2006: Numerical simulation of wind hole circulation at
Ice Valey in Korea using a simple 2Dmodel. J. Metor. Soc. Japan, 83, 1073-1084.
Tanaka, H. L. and Koji Terasaki, 2006: Blocking Formation by an Accumulation of Barotropic
Energy Exceeding the Rossby Wave Saturation Level at the Spherical Rhines Scale. J. Meteor.Soc.
Japan, 83, 319-332.
Tanaka, H. L. and M. Matsueda, 2005:Arctic Oscillation analyzed as a singular eigenmode of the
globalatmosphere. J. Meteor. Soc. Japan, 83, 611-619.
Tanaka, H. L. and Koji Terasaki, 2005: Energy Spectrum and Energy Flow of the Arctic Oscillationin the Phase Speed Domain. SOLA, 1, 65--68.
Tanaka, H.L., N. Ishizaki, and D. Nohara, 2005: Intercomparison of the intensities and trends ofHadley, Walker and monsoon circulations in the global warming projections, SOLA, 1, 77-80.
Tanaka, H.L., and M. Kanetaka, 2005: Realtime prediction system of forest-fire smoke using
satellite data and PUFF model. A case study for May 2003. SOLA, 1, 9-12.
Tanaka, H.L., Y. Watarai, and T. Kanda, 2004: Energy spectrum proportional to the squared phasespeed of Rossby modes in the general circulation of the atmosphre. Geophysial Research Letters,
31(13), 13109, doi: 10.1029/2004GL019826.
Tanaka, H.L. and M. Matsueda, 2004: Analysis of recent extreme events measured by thebarotropic component of the atmosphere. Journal of the Meteorological Society of Japan, 82,
1281-1299 .
Tanaka, H. L., N. Ishizaki, and A. Kitoh, 2004: Trend and interannual variations of Walker,
monsoon, and Hadley circulations defined by velocity potential in the upper troposphere. Tallus,
56A, 250-269.
Tanaka, H.L., 2003:Analysis and modeling the Arctic Oscillation using a simple barotropic modelwith baroclinic eddy forcing. J. Atmos. Sci., 60, 1359-1379.
Tanaka, H.L., and K. Yamamoto, 2002: Numerical Simulations of volcanic plume dispersal fromUsu volcano in Japan on 31 March 2000. Earth, Planets and Space, 54, 743--752.

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Tanaka, H.L. and H. Tokinaga, 2002: Baroclinic instability in high latitudes induced by polarvortex:
A connection to the Arctic oscillation. J. Atmos. Sci., 59, 69--82.
Kusaka, H. and H. Hayami (2006) Numerical simulation of local weather for a highphotochemical Oxidant event using the WRF model. JSME International Journal, Ser. B, vol. 49,
p72-77.
Kusaka, H., A. Crook, J. Knievel, and J. Dudhia (2005) Sensitivity of WRF model to advection
and diffusion schemes on simulation of heavy rainfall event along the Baiu front. SOLA, vol.1,
p177-180.
Kusaka, H., A. Crook, J. Dudhia, and K. Wada (2005) Comparison of the WRF and MM5 models
for simulation of heavy rainfall along the Baiu front. SOLA, vol.1, p197-200.
Kusaka, H. and F. Kimura (2004) Coupling a single-layer urban canopy model with a simple
atmosphericmodel: Impact on urban heat island simulation for an idealized case. Journal of the MeteorologicalSociety of Japan, vol.82, p.67-80.
Kusaka, H. and F. Kimura (2004) Thermal effects of urban canyon structure on the nocturnal heatisland: Numerical experiment using mesoscale model coupled with urban canopy model. Journal ofApplied Meteorology, vol.43, p.1899-1910.
Kawase, H., F. Kimura, and Y. Takeuchi (2006) Precipitable water vapor around orographicallyinduced convergence line. SOLA, 2, 25-28.
Tsunematsu, N., F. Kimura, T. Sato, K. Kai, Y. Kurosaki, T. Nagai, H. Zhou, and H. Mikami (2006)
Extensive dust outbreaks following the morning inversion breakup in the Taklamakan Desert. J.
Geophys. Research. 110, D2120720.1029/2005JD005994.
Kusaka, H., S. Kataniwa, and H. L. Tanaka, F. Kimura (2006) Numerical simulation of polar low
development over the Japan sea. Proceedings of 2006, Joint WRF Users Workshop, in CD-ROM.
Kawase, H., F. Kimura, and T. Sato (2005) Diurnal cycle of convective instability around theCentral Mountains in Japan during the warm season. J. Atmos. Sci. 62, 1626-1636.

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7. Division of Global Environment and Biological Sciences: Biological ScienceGroup
7.1 Research Activity.
All organisms on earth are classified into three “domains,” such as eubacteria,
archaebacteria, and eukaryotes. Recent progress in evolutionary biology suggests thateukaryotes are comprised of 6 “supergroups” below (Fig. 1).
1) Opisthokonta; includes
multicellular animals, fungi,
and their closely related
unicellular cells.
2) Planta; photosynthetic cellswith the “primary” plastids
that are direct descendents ofan endosymbiotic
cyanobacterium.
3) Chromalveolata; unicellular
eukaryotes presumably
evolved from photosynthetic ancestral cells that captured their “secondary” plastids
from an endosymbiotic red alga. This group includes non-photosynthetic lineages thatprobably experienced secondary losses of plastids.
4) Rhizaria; comprised of Cercozoa, Foraminifera, and Radiolaria.
5) Excavata; diverged unicellular eukaryotes commonly possess a set of uniquemorphological/ultrastructural features. Many amitochondriate eukaryotes are includedin this supergroup.
6) Amoebozoa; an assemblage of amoeboid-like eukaryotes.
Among the six supergroups, only monophyly of Opisthokonta has been concreted
by molecular phylogenetic analyses, it remains controversial whether the rest of the fivesupergroups are natural groups. Furthermore, there are several eukaryotes that bear no clear
evolutionary affinity to any of the 6 supergroups. By using molecular phylogenetic analyses,
we aim (i) to resolve global relationships amongst the major eukaryotic groups, and (ii) toinvestigate the origin and evolution of organelles in eukaryotic cells (mitochondria andplastids).
To investigate global eukaryotic phylogeny, it is essential to assemble large scale sequence
data from phylogenetically diverged lineages. Although genome sequencing projects have
- 65 -CCS Report: PART II, Research Activities, Results
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rapidly progressed, the currently available sequence data are not sufficient for robust global
phylogeny of eukaryotes for the reasons below: The lineages that are beneficial/pathogenic
to human have been mainly subjected to genome-scale analyses, while few sequence data
are available for the lineages of which evolutionary affinities are uncertain. Furthermore, it
is almost certain that massive number of eukaryotes that can hold the keys to understandeukaryotic evolution remain unidentified in natural environments. Considering the bias intaxonomic sampling for sequence data, we firstly need to grow the key organisms andsequence multiple marker genes to achieve our research goals for eukaryotic evolution. By
combining our original sequence data and those in public genome databases, we can assess
global relationship among major eukaryotic groups by large-scale phylogenetic analyses(Fig. 2).
Phylogenetic analyses basedon single-gene data sets(single-gene analyses) havebeen extensively conducted todate, while we just recently
start analyzing multiple genes(multi-gene analyses). Thus,
we need to accumulate theknowledge regarding multi-gene analyses. So far, multi-gene data sets have been assessed
mainly by maximum-likelihood (ML) and/or Bayesian analyses under the “concatenate” (or“linked”) model, in which a single set of parameters was enforced on the genes that arepotentially evolving under different substitution patterns in a multi-gene data set. Under
such model conditions, the actual sequence evolution in the multi-gene data may not be
sufficiently described, since the concatenate model ignores the heterogeneity of substitution
processes across genes. Importantly, studies of both empirical and simulation data indicatethat such “model misspecification” can introduce significant artifacts in tree reconstruction.
On the other hand, the model misspecification in concatenate analyses can be overcome by
the analyses under the “separate” model: Under this model, the heterogeneity of sequence
evolution across genes can be taken into account. Thus, the multi-gene estimates under the
separate model may be much less biased than that under the concatenate model.
ML analyses under the separate model are indispensable to achieve robust phylogenetic
estimates from multi-gene data sets. Nevertheless, separate analyses are computationallymuch more intensive than concatenate analyses in general, and no phylogenetic program
allows estimation of ML trees from multi-gene data using efficient heuristic tree search
procedures. Under the separate model conditions, ML trees are now exhaustively searched- 66 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

for, but the number of test trees quickly becomes very large. For instance, log-likelihood(lnL) scores of more than 2.0 x 106 trees are required to select the ML tree from a data set
including only 10 sequences/groups. In order to facilitate large calculation of lnL scores, we
modified sequential lnL calculation in a widely used phylogenetic program Tree-Puzzle into
parallel with MPI.
7.2 Research Results
We analyzed the following multi-gene data sets.
7.2.1 Testing the monophyly of red algae and green plants
We prepared a multi-gene data set comprised of 26 nucleus-encoded genes to assess theevolutionary relationship between red algae and green plants. Translation elongation factor
2 (EF2) phylogenies strongly support the monophyly of red algae and green plants. The
sisterhood between red algae and green plants recovered by EF2 analyses has been widely
accepted since this tree topology agreed with the single origin of the primary plastids in red
algae and green plants. However, the robust sisterhood between red algae and green plants
recovered in EF2 phylogenies has been suspected as a gene-specific artifact, since theestimates from a multi-gene data set with EF2 and that without EF2 were sometimes
conflict with one another regarding the relationship between red algae and green plants. We
separately investigated and compared phylogenetic signals in the 26 genes, and found that
EF2 and α-tubulin signals are largely different from the signals in the rest of the genes.
Importantly, the monophyly between red algae and green plants was successfully recoveredby the analyses excluding EF2, suggesting that the particular tree topology is also
supported by other genes. The multi-gene analyses under the separate model conditions
described above were conducted by using the MPI version of Tree-Puzzle (“MPI-Puzzle”).
7.2.2 Monophyly between cryptophytes and haptophytes
Cryptophytes acquired their plastids by the secondary endosymbiotic uptake of a red alga.
Several other algal lineages acquired plastids through such an event, but cryptophytes are
distinguished by the retention of a relic red algal nucleus, the nucleomorph. The
nucleomorph (and its absence in other lineages) can reveal a great deal about the process
and history of endosymbiosis, but only if we know the relationship between cryptophytes
and other algae, and this has been controversial. Several recent analyses have suggested a
relationship between plastids of cryptophytes and some or all other red alga-containing
lineages, but we must also know whether host nuclear genes mirror this relationship to
determine the number of endosymbiotic events, and this has not been demonstrated. We- 67 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

have carried out an expressed sequence tag (EST) survey of the cryptophyte Guillardia
theta. Phylogenetic analyses of 102 orthologous nucleus-encoded proteins (18,425 aminoacid alignment positions) show a robust sisterhood between cryptophytes and haptophytes(Pavlova lutheri and Isochrysis galbana) which also have a red alga-derived plastid. This
relationship demonstrates that loss of nucleomorphs must have taken place in haptophytes
independently of any other red alga-containing lineages and that the ancestor of bothalready contained a red algal endosymbiont.
7.2.3 Phylogenetic position of Centrohelida
Centrohelida, one of major heliozoan groups, are eukaryotes of which evolutionary affinity
remains uncertain. In this study, we newly determined the genes encoding EF2, cytosolicheat shock protein 70 (HSP70), and cytosolic heat shock protein 90 (HSP90) from thecentroheliozoan Raphidiophrys contractilis. The three Raphidiophrys genes were then
combined with previously determined actin, α-tubulin, β-tubulin, and SSU rRNA sequences
to phylogenetically analyze the position of Centrohelida in global eukaryotic phylogeny.
Although the multi-gene data sets examined in this study are the largest ones including thecentroheliozoan sequences, the relationships between Centrohelida and the eukaryotic
groups considered were unresolved. Our careful investigation revealed that thephylogenetic estimates were highly sensitive to genes included in the multi-gene alignment.
The signal of SSU rRNA and that of α-tubulin appeared to conflict with one another: theformer strongly prefers a monophyly of diplomonads (e.g., Giardia), parabasalids (e.g.,
Trichomonas), heteroloboseans (e.g., Naegleria), and euglenozoans (e.g., Trypanosoma),while the latter unites diplomonads, parabasalids, metazoans, and fungi. In addition, EF2
robustly unites red algae and green plants, while the remaining genes considered in thisstudy do not positively support the particular relationship. Thus, it is difficult to identify thephylogenetic relatives of Centrohelida in the present study, since strong (and some areconflicting) gene-specific “signals” are predominant in the current multi-gene data. We
concluded that larger scale multi-gene phylogenies are necessary to elucidate the origin andevolution of Centrohelida. We constructed a cDNA library of R. contractilis and recently
started the expressed sequence tag (EST) analysis.
7.2.4 Origin of chlorophyll-c containing plastids
Recent multi-gene phylogenetic analyses of plastid-encoded genes have recovered arobust monophyly of chlorophyll-c containing plastids (Chl-c palstids) in cryptophytes,
haptophytes, photosynthetic stramenopiles, and dinoflagellates. However, all the plastid
multi-gene phylogenies published to date utilized the concatenate model, which ignores the- 68 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

heterogeneity of sequence evolution across genes in alignments. Both empirical andsimulation studies show that, compared to the concatenate model, the separate model,
which accounts for gene-specific evolution, can greatly improve multi-gene estimations.
Here we newly sequenced 46 genes of Chl-c plastids, and examined the Chl-c plastid
evolution by multi-gene analyses under the separate model. Unexpectedly, Chl-c plastid
monophyly received only low to medium support in our analyses based on multi-gene data
sets including up to 4829 alignment positions. Although we systematically surveyed andexcluded the genes that could mislead estimation, the (inconclusive) support for Chl-c
plastid monophyly was not significantly altered. We conclude that the estimates from thecurrent plastid-encoded gene data are insufficient to resolve Chl-c plastid evolution withconfidence, and are highly affected by genes subjected to the analyses, and methods for tree
reconstruction applied.
7.2.5 Sisterhood between Cercozoa and Foraminifera
Recently, there has been increasing molecular evidence of phylogenetic affinity between
Cercozoa and Foraminifera in the eukaryotic lineage. We performed phylogenetic analyses
based on the combined (concatenated) amino acid sequence data of actin, α-tubulin, andβ-tubulin from a wide variety of eukaryotes, including the foraminifers Planoglabratella
opercularis and Reticulomyxa filosa, as well as cercomonad and chlorarachniophyte
members of Cercozoa. A monophyletic lineage composed of two foraminiferan species
branched with the centroheliozoan species Raphidiophrys contractilis was reconstructed inboth Bayesian and maximum-likelihood (ML) analyses under concatenate models,
enforcing a single set of the parameters (the parameters for among-site rate variation andbranch lengths) on the entire combined alignment. Considering the extremely divergent
nature of Foraminifera and Raphidiophyrs tubulins, the union of these lineages recovered ismost probably a long-branch attraction artifact due to ignoring gene-specific evolutionary
processes. On the other hand, the foraminiferan lineage was within the radiation of
Cercozoa in Bayesian analyses under the separate model conditions, accommodating
differences in evolutionary processes across the three genes in the combined alignment.
The Foraminifera + Cercozoa affinity recovered in the latter multi-gene analyses is most
likely genuine, and thus our data presented here provide further support for the close
relationship between these two protist lineages.
7.2.6 New excavate flagellates
In addition to the multi-gene analyses described above, we isolated and analyze previously
undescribed eukaryotes. Dysnectes brevis n. gen., n. sp., a- 69 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

free-living heterotrophic excavate flagellate was isolated from microaerophilic sediment(Fig. 3). Our detailed microscopic observations revealed that D. brevis possesses all the key
ultrastructural characters considered typical of Excavata. Among the 10 excavate groups
previously recognized, D. brevis displays an evolutionary affinity to members of theFornicata (i.e. Carpediemonas, retortamonads, and diplomonads), while the internalbranching pattern of the D. brevis–Fornicata clade was not resolved with confidence.
We also isolated another excavate flagellate NY176 fromoxygen-depleted sediment from a deep-sea methane cold seep ofSagami Bay, Japan (Fig. 4). The morphological characteristics ofthis flagellate appeared to be similar to those of D. brevis andCarpediemonas. In a SSU rRNA phylogeny, the flagellate
NY176 grouped with the members of the Fornicata, but did notshow strong affinity to any member of the Fornicata previously described. We constructed
a cDNA library of the flagellate NY176 and randomly sequenced 3,000 clones. Based on
those sequence information, we plan a multi-gene phylogenetic analysis to resolve theinternal relationship amongst the member of the Fornicata.
7.3 Collaboration
The MPI version of Tree-Puzzle was developed in co-operation with Dr. M. Sato in the
HPC group. As described in section 2.1 this program has been utilized for multi-gene
analyses under the separate model conditions.
7.4 Future Plan
We will utilize the MPI version of Tree-Puzzle (MPI-Puzzle) for various multi-gene data
sets. As described in 2.3 and 2.6, we are currently conducting the EST analyses on thecentrohelid R. contractilis and the excavate flagellate NY176. The sequence data generated
from these analyses will be subjected to multi-gene analyses using the MPI-Puzzle. In
addition, we are now investigating the impact of a heuristic tree search method on ML
bootstrap analyses. In this study, it is critical to compare the trees heuristically searched forwith the exact ML tree. We will prepare 100 bootstrap replicates including 9 sequences (thepossible trees for 9 sequences are 135,135). By using MPI-Puzzle, the exact ML trees will
be exhaustively selected from all the possible trees, and subsequently compare with thetrees that are heuristically searched for. We will also start exploring the possibility for aheuristic tree search method under the separate model conditions.

- 70 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

7.5 Publications
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Takishita K, Yubuki N, Kakizoe N, Inagaki Y, Maruyama T. Diversity of microbial eukaryotes in
sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment
samples and two enrichment cultures. Extremophiles 11:563-576 2007
Patron NJ, Inagaki Y, Keeling PJ. Multiple gene phylogenies support the monophyly of
cryptomonad and haptophyte host lineages. Current Biology 17:887-891 2007
Maki Y, Hashimoto T, Zhou M, Naganuma T, Ohta J, Nomura T, Robinson C.V, Uchiumi T. Threebinding sites for stalk protein dimers are generally present in ribosomes from archaeal organism.
Journal of Biological Chemistry in press 2007
Tanabe K, Escalante A, Sakihama N, Honda M, Arisue N, Horii T, Culleton R, Hayakawa T,
Hashimoto T, Longacre S, Pathirana S, Handunnetti S, Kishino H. Recent independent evolution of
msp1 polymorphism in Plasmodium vivax and related simian malaria parasites. Molecular andBiochemical Parasitology 156:74-79 2007
Makiuchi T, Nara T, Annoura T, Hashimoto T, Aoki T. Occurrence of multiple, independent genefusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic
groups. Gene 394:78-86 2007
Yoshikawa H, Wu Z, Howe J, Hashimoto T, Geok-Choo NG, Tan KSW. Ultrastructural andphylogenetic studies on Blastocystis isolates from cockroaches. Journal of Eukaryotic Microbiology
54:33-37 2007
Sakaguchi M, Inagaki Y, Hashimoto T. Centrohelida is still searching for phylogenetic home:analyses of seven Raphidiophrys contractilis genes. Gene in press 2007
Iida K, Takishita K, Ohshima K, Inagaki Y. Assessing the monophyly of chlorophyll-c containing
plastids by multi-gene phylogenies under the unlinked model conditions. Molecular Phylogenetics
and Evolution 45:227-238 2007
Yubuki N, Inagaki Y, Nakayama T, Inouye I. Ultrastructure and ribosomal RNA phylogeny of thefree-living heterotrophic flagellate Dysnectis brevis n. gen., n. sp., a new member of the Fornicata.
Journal of Eukaryotic Microbiology 54:191-200 2007
Kamikawa R, Inagaki Y, Sako Y. Fragmentation of mitochondrial large subuint rRNA in adinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria.
Protist 158:239-245 2007
Hosoi-Tanabe S, Honda D, Fukaya S, Otake I, Inagaki Y, Sako Y. Proposal of Pseudochattonella
verruculosa gen. nov., comb. nov. (Dictyochophyceae) for a former raphidophycean Chattonella
verruculosa, based on 18S rDNA phylogeny and ultrastructural characteristics. PhycologicalResearch 55:185-192 2007
Nambu T, Inagaki Y, Kutsukake K. Plasticity of the domain structure in FlgJ, a bacterial protein
involved in flagellar rod formation. Genes & Genetic Systems 81:381-389 2006
Inagaki Y, Roger AJ. Phylogenetic estimation under codon models can be biased by codon usage
heterogeneity. Molecular Phylogenetics and Evolution 40:428-434 2006
Inagaki Y, Susko E, Roger AJ. Recombination between elongation factor 1α genes from distantly
related archaeal lineages. Proceeding of National Academy of Science USA 103:4528-4533 2006
Simpson AGB, Inagaki Y, Roger AJ. Comprehensive multigene phylogeneties of excavate protists
reveal the evolutionary positions of “primitive” eukaryotes. Molecular Biology and Evolution
23:614-625 2006
Arisue N, Hasegawa M, Hashimoto T. Root of the Eukaryota tree as inferred from combined
maximum likelihood analyses of multiple molecular sequence data Molecular Biology and
Evolution 22:409-420 2005
Annoura T, Nara T, Makiuchi T, Hashimoto T, Aoki T. "The origin of dihydroorotate dehydrogenase
genes of kinetoplastids, with special reference to their biological significance and adaptation toanaerobic, parasitic conditions. Journal of Molecular Evolution 60:113-127 2005
Suzuki T, Hashimoto T, Yabu Y, Majiwa PAO, Ohshima S, Suzuki M, Lu S, Hato M, Kido Y,
Sakamoto K, Nakamura K, Kita K, Ohta N. Alternative oxidase (AOX) genes of African- 71 -CCS Report: PART II, Research Activities, Results
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trypanosomes: phylogeny and evolution of AOX and plastid terminal oxidase families. Journal of
Eukaryotic Microbiology 52:374-381 2005
Sakaguchi M, Nakayama T, Hashimoto T,Inouye, I Phylogeny of the Centrohelida inferred from
SSUrRNA, tubulins, and actin genes. Journal of Molecular Evolution 61:765-775 2005
Takishita K, Inagaki Y, Tsuchiya M, Sakaguchi M, Maruyama T. A close relationship between
Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acidsequences of three cytoskeletal proteins (actin, α-tubulin, and β-tubulin). Gene 362:153-160 2005
Dantrakool A, Somboon P, Hashimoto T, Saito-Ito A. Identification of a new type of Babesia
species in wild rats (Bandicota indica) in Chiang Mai Province, Thailand. Journal of ClinicalMicrobiology 42:850-854 2004
Suzuki T, Hashimoto T, Yabu Y, Kido Y, Sakamoto K, Nihei C, Hato M, Suzuki S, Amano Y, Nagai
K, Hosokawa T, Minagawa N, Ohta N, Kita K. Direct evidence for cyanide-insensitive quinoloxidase (alternative oxidase) in apicomplexan parasite Cryptosporidium parvum: Phylogenetic andtherapeutic implications. Biochemical and Biophysical Research Communications 313:1044-1052
2004
Suzuki T, Nihei C, Yabu Y, Hashimot, T, Suzuki M, Yoshida A, Nagai K, Hosokawa T, Minagawa N,
Suzuki S, Kita K, Ohta N. Molecular cloning and characterization of Trypanosoma vivax alternativeoxidase (AOX) gene, a target of the trypanocide ascofuranone. Parasitology International
53:235-245 2004
Saito-Ito A, Yano Y, Dantrakool A, Hashimoto T, Tanaka N. Survey of rodents and ticks in humanbabesiosis emergence area in Japan: first detection of Babesia microti-like parasites in Ixodes
ovatus. Journal of Clinical Microbiology 42:2268-2270 2004
Ali V, Hashimoto T, Shigeta Y, Nozaki T. Molecular and biochemical characterization of
D-phosphoglycerate dehydrogenase from Entamoeba histolytica: a unique enteric protozoan
parasite that possesses both phosphorylated and non-phosphorylated serine metabolic pathways.
European Journal of Biochemistry 271:1-12 2004
Yoshikawa H, Morimoto K, Wu Z, Singh M, Hashimoto T. Problems in speciation in the genus
Blastocystis. Trends in Parasitology 20 251-255 2004
Arisue N, Maki Y, Yoshida H, Wada A, Sanchez LB, Muller M, Hashimoto T. Comparative analysisof the ribosomal components of the hydrogenosome-containing protist, Trichomonas vaginalis.
Journal of Molecular Evolution 59:59-71 2004
Ruiz-Trillo I, Inagaki Y, Davis LA, Sperstad S, Landfald B, Roger AJ. Capsaspora owczarzaki is anindependent opisthokont lineage. Current Biology 14:R946-R947 2004
Keeling PJ, Inagaki Y. A class of eukaryotic GTPase with a punctuate distribution suggesting
multiple functional replacements of translation elongation factor 1α. Proceeding of National
Academy of Science USA 101:15380-15385 2004
Inagaki Y, Simpson AGB, Dacks JB, Roger AJ. Phylogenetic artifacts can be caused by leucine,
serine and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study.
Systematic Biology 53:582-593 2004
Susko E, Inagaki Y, Roger AJ. On inconsistency of the neighbor-joining, least-squares, andminimum evolution estimation when substitution processes are incorrectly modeled. Molecular
Biology and Evolution 21:1629-1642 2004
Inagaki Y, Susko E, Fast NM, Roger AJ. Covarion shifts cause a long-branch attraction artifact thatunites microsporidia and archaebacteria in EF-1α phylogenies. Molecular Biology and Evolution
21:1340-1349 2004

- 72 -CCS Report: PART II, Research Activities, Results
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8. Division of High Performance Computing Systems
8.1 Research Activity
In this division, high performance computing systems as the basic technology forcomputational sciences and grid computing technologies on wide area network are studied.
The primary research facility in our center is a massively parallel cluster system PACS-CS
with 2560 nodes which has been developed in this research division. PACS-CS started its
operation from July 2006 and we have been supporting the development of various
application programs with researchers in these fields as well as the basic performance
evaluation of the system. The division also contributed to develop the FIRST cluster system,a large scale hybrid PC cluster by Astrophysics Research Department.
For the research on next generation computing system, all the members of the divisionjoined to a project of “Mega-scale Computing” (leaded by Prof. Hiroshi Nakashima, Kyoto
University) as a JST-CREST program. In the project, Prof. Sato and Prof. Boku contributed
to the low-power computing technology for high-performance parallel computing andhigh-reliability and high-performance communication, respectively. This research project
was on fundamental technologies for next generation large scale parallel processing system
for high performance computing. The project finished successfully on November 2006, andthe research theme was continued to another JST-CREST project of “Low-Power and
Dependable Parallel Processing Platform with Embedded Technology” leaded by Prof. Sato,
which started from October 2006 for five years. In this project we will develop a new
low-power and highly reliable embedded system for next generation parallel processing.
The division also proceeds a research of “Low-Power and High-Speed Device, Circuit and
Logic for Next Generation Supercomputer Systems” as a collaborative research with
Hitachi Ltd. and University of Tokyo. The research group of University of Tsukuba and
Hitachi is contributing the subtheme “Research and Development on Fundamental Logic on
Processor Architecture and Memory Hierarchy”. In the division, we have been studying theon-chip memory architecture and computing acceleration mechanism for low-power andhigh-performance systems. Besides this activity, we have also proposed our original
solution for “Next Generation Supercomputer System Development” project managed by
the supercomputer development division of RIKEN. After the proposal, the researchcontract on the next generation supercomputer between University of Tsukuba and RIKEN
was established, and currently Prof. Ukawa, Sato and Boku joined to the abstract designingteam of RIKEN as visiting researchers.
As a research on development of high-performance numerical library, we studied “Fast- 73 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Fourier Transform Algorithm on Heterogeneous Environment” for cluster systems.
For the practical grid research, we have been studying ILDG (International Lattice Data
Grid) with the research group on particle physics for data sharing of computational resultsby them. We also developed the JLDG (Japan Lattice Data Grid) system to share the Lattice
QCD computational results with nation wide researchers, under support of CSI (Cyber
Science Infrastructure) by NII (National Informatics Institute).
As the grid environment research, we have been developing the OmniRPC grid
programming system as well as “the Research on Scalable P2P Grid Environment for Large
Scale Distributed Computing” supported by Grant-in-Aid of MEXT for future grid anddistributed environment. On these research themes, we have also performed theJapanese-French collaborative research with INRIA on P2P grid environment.
From April 2006, Prof. Tatebe from AIST (Advanced Institute on Science andTechnology) joined as an Associate Professor to the division, and new projects based on his
developed system Gfarm, a file system on distributed environment.
8.2 Research Results
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We have completed a massively cluster system PACS-CS with 2560 nodes.
We joined to JST-CREST project “Mega-Scale Computing” (leaded by Prof. Hiroshi
Nakashima, Kyoto University) and Prof. Sato and Prof. Boku contributed a low-powerhigh-performance parallel processing technology and high-performance highly-reliableinterconnection network, respectively. Especially in the research exhibition on SC06,
we demonstrated the prototype system “MegaProto” and fault-tolerant interconnection
network system and they are highly evaluated.
We have been constructing the ILDG (International Lattice Data Grid) environment fordata sharing among world-wide particle physics researchers, and developed the JLDG
(Japan Lattice Data Grid) environment for nation-wide data sharing in this year.
We performed a collaborative research with KEK (High Energy Accelerator Research
Organization) on Gfarm distributed file system, and got the prize of the winner in
Large System division on HPC Storage Challenge at SC06.

- 74 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Low-Power and High-Performance Cluster Unit “MegaProto”

JLDG:
JLDG:infrastructure
infrastructureof
ofQCD
QCD
collaboration
insideJapan
collaboration inside JapanA part of data can be exported throughwww.jldg.org

KEK

CCS, Tsukuba
Kanazawa university

Kyoto University

U. HIroshima

Data in each site is shared by“Gfarm” global file systemover the grid.

JLDG (Japan Lattice Data Grid) to share nation-wide data sharingof Lattice QCD computational results
8.3 Collaboration• On the PACS-CS system, we developed the high-performance Gram-Shmidt- 75 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Orthogonalization Algorithm for accelerating the computation of RS-DFT (Real Space
Density Function Theory) with Nano-Bio research group. We are also developing thehigh-speed communication library for the nearest neighboring communication
especially required for Lattice QCD simulation.
On the Molecular Evolution Tree Program in Biological Science research group, we aresupporting the parallelization and speed-up of the program.
We have been supporting the development of a large scale hybrid PC cluster FIRST for
Computational Astrophysics research group. In this year, we supported the deploymentof Gfarm system on FIRST cluster for convenience for users.
We are collaborating with Particle Physics research group for construction of ILDG
and JLDG environments for data sharing among international and nation-wide particle
physics researchers.
In the research project of Next Generation Supercomputer System by RIKEN, Lattice
QCD and RS-DFT applications were listed as the most important large scale target
applications, and our division and other related divisions will develop the practicalcodes for them.

8.4 Future Plan
The most important issue is to enhance the performance of PACS-CS on real applicationsin the center with supporting research groups to improve the parallelization andeffectiveness of the codes. In addition, the University of Tsukuba will introduce the next
supercomputer system, and the center will operate it from 2008. It is an important missionof us to support the operation not only within the university but also among otheruniversities and institutes based on grid technology. The basic system architecture andspecification are shared by three universities; University of Tsukuba, University of Tokyoand Kyoto University, and they will introduce their own systems based on the samearchitecture at the same time. We are considering to apply our grid technology currently
under development on the collaborative operation of these supercomputer systems. Anotherproject to develop new system software and compiler is also under going.
The national project on the development of Next Generation Supercomputer is now on thestage of detailed designing, and our division will contribute not only to the designing of thesystem but also to the evaluation and performance improvement of real target application
codes. We consider that such a contribution becomes possible by the unique center like ours
where the researchers of computer science and computational science are collaborating as
daily works.
There are two important issues on the future high performance computing systems;- 76 -CCS Report: PART II, Research Activities, Results
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low-power technology and effective accelerating mechanism for high-performancecomputation. For the former research topic, we will proceed based on current JST-CREST
research project. For the latter one, there are several ways including the starting offollow-up project of FIRST.
Grid technology is now on the practical stage, and it is required to apply to the realapplications and systems as well as the study on highly scalable systems reaching to theexa-scale data sharing.

8.5 Publications
8.5.1 Journal Papers
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岡田真幸，櫻井鉄也，寺西慶太：近似係数行列に対する疎行列用直接解法を用いた前処理，
日本応用数理学会論文誌, Vol. 17, No. 3, pp. 319--329,(2007).
岡本高幸，三浦信一，朴泰祐，佐藤三久，高橋大介：EthernetマルチリンクによるPCクラ
スタ向け高バンド幅・耐故障ネットワークRI2N/UDP，情報処理学会論文誌：コンピューティングシステム, Vol. 48, No. SIG 8(ACS 18),pp. 153--164, (2007).
木原崇智，小瀧義久，多田野寛人，櫻井鉄也：GridRPC/MPIハイブリッドによる修正多重
リスタート付きArnoldi法，情報処理学会論文誌：コンピューティングシステム, Vol. 48, No.
SIG 8(ACS 18), pp. 94--103, (2007).
Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma, Moritoshi Yasunagaand Akihiko
Konagaya: Mesoscopic-level Simulation of Dynamics andInteractions of Biological Molecules
Using Monte Carlo Simulation,Journal of VLSI Signal Processing, Vol. 48, pp. 287--299, (2007).
H. D. Nguyen, Ikuo Yoshihara, Kunihito Yamamori and MoritoshiYasunaga: Implementation of an
Effective Hybrid GA for Large-Scale Traveling Salesman Problems, IEEE Transactions on Systems,
Man and Cybernetics, Part B, Vol. 37, pp. 92--99, (2007).
Yoshiki Yamaguchi, Moritoshi Yasunaga, Kazuya Hayashi, Noriyuki Aibe, Yorihisa Yamamotoand Ikuo Yoshihara: A bio-inspired tracking camera system, Artificial Life and Robotics, Vol. 11,
No. 1, pp. 128--134, (2007).
三浦信一，岡本高幸，朴泰祐，佐藤三久，高橋大介：VFREC-Net：ドライバ制御によるtagged-VLANを用いたPCクラスタ向けマルチパスネットワーク，情報処理学会論文誌：コンピューティングシステム, Vol. 47, No. SIG 12(ACS15), pp. 35--45, (2006).
住元真司，大江和一，久門耕一，朴泰祐，佐藤三久，宇川彰：複数GigabitEthernetを用いた
PACS-CSのための高性能通信機構の設計と評価，情報処理学会論文誌：コンピューティン
グシステム, Vol. 47, No. SIG 12(ACS 15),pp. 25--34, (2006).
堀田義彦，佐藤三久，木村英明，松岡聡，朴泰祐，高橋大介：PCクラスタにおける電力実
行プロファイル情報を用いたDVS制御による電力性能の最適化，情報処理学会論文誌：コンピューティングシステム, Vol. 47, No. SIG 12(ACS15), pp. 272--284, (2006).
木村英明，佐藤三久，堀田義彦，朴泰祐，高橋大介：DVS制御による負荷不均衡のある並列プログラムの電力量削減手法，情報処理学会論文誌：コンピューティングシステム, Vol.
47, No. SIG 12(ACS 15), pp. 285--295, (2006).
中島佳宏，佐藤三久，相田祥昭，高橋大介，朴泰祐，Franck Cappello：複数グリッドジョ
ブ実行システムの計算資源を統合・利用するGrid RPCシステムの設計と実装，情報処理学会論文誌：コンピューティングシステム, Vol. 47,No. SIG 7(ACS 14), pp. 207--218, (2006).
Taisuke Boku, Hajime Susa, Kenji Onuma, Masayuki Umemura, Mitsuhisa Sato and Daisuke
Takahashi: Formation of Dwarf Galaxies Reionized Universe with Heterogeneous Multicomputer
System, International Journal for Multiscale Computational Engineering, Vol. 4, No. 2, pp.
281--289, (2006).
呂毅斌，伊東拓，櫻井鉄也：多重連結領域数値等角写像のPade近似を用いた電荷点配置法，- 77 -CCS Report: PART II, Research Activities, Results
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日本応用数理学会論文誌, Vol. 16, No. 3, pp. 149--164, (2006).
岡田真幸，多田野寛人，櫻井鉄也：複素対称行列に対する前処理の評価方法について，日本応用数理学会論文誌, Vol. 16, No. 4, pp. 497--505, (2006).
X. Niu, T. Sakurai and H. Sugiura: A verified method for bounding clusters of zeros of analytic
functions, J. Comput. Appl. Math.,Vol. 199, No. 2, pp. 263--270, (2006).
中島浩，中村宏，佐藤三久，朴泰祐，松岡聡，高橋大介，堀田義彦：高性能計算のための低電力・高密度クラスタMegaProto，情報処理学会論文誌：コンピューティングシステム, Vol.
46, No. SIG 12(ACS 11), pp. 46--61, (2005).
Daisuke Takahashi: An algorithm for multiple-precision floating-point multiplication, Applied
Mathematics and Computation, Vol. 166, No. 2,pp. 291--298, (2005).
櫻井鉄也，多田野寛人，早川賢太郎，佐藤三久，高橋大介，長島雲兵，稲富雄梅田宏明，
渡邊寿雄：大規模固有値問題のmaster-worker型並列解法，情報処理学会論文誌：コンピューティングシステム, Vol. 46, No. SIG 7(ACS10), pp. 44--51, (2005).
小島好紀，佐藤三久，朴泰祐，高橋大介：MPIを通信レイヤに用いるソフトウェア分散共
有メモリシステム，情報処理学会論文誌：コンピューティングシステム, Vol. 46, No. SIG
7(ACS 10), pp. 63--73, (2005).
大濱潤二，櫻井鉄也，奈良高明：双極子推定客問題に対する直接解法の誤差評価，日本応用数理学会論文誌, Vol. 15, No. 4, pp. 483--494, (2005).
中西崇文，岸本貞弥，村方衛，大塚透，櫻井鉄也，北川高嗣：数式データを対象とした複合連想検索システムの実現，日本データベース学会 Letters,Vol. 4, No. 1, pp. 29--32, (2005).
多田野寛人，櫻井鉄也：LanczosプロセスのリスタートによるCGS法の安定化，日本応用数理学会論文誌, Vol. 15, No. 2, pp. 85--99, (2005).
稲富雄一，梅田宏明，渡邊寿雄，櫻井鉄也，長嶋雲兵：FMO-MO法における大規模分子軌
道計算 -- 固有値分布の特徴 --，日本応用数理学会論文誌，Vol. 15, No. 2, pp. 125--135,(2005).
稲富雄一，梅田宏明，渡邊寿雄，櫻井鉄也，長嶋雲兵：FMO-MO法による大規模分子軌道
計算，情報処理学会論文誌：コンピューティングシステム, Vol. 46,No. SIG 7(ACS 10), pp.
1--8, (2005).
櫻井鉄也，多田野寛人，早川賢太郎，佐藤三久，高橋大介，長嶋雲兵，稲富雄梅田宏明，
渡邊寿雄：大規模固有値問題のmaster-worker型並列解法，情報処理学会論文誌：コンピューティングシステム, Vol. 46, No. SIG 7(ACS10), pp. 44--51, (2005).
中西崇文，岸本貞弥，櫻井鉄也，北川高嗣：特定分野を対象とした連想検索のための書籍の索引部を用いたメタデータ空間生成方式，電子情報通信学会論文誌, Vol. J88, No. 44, pp.
840--851, (2005).
Y. Lu, T. Itoh, S. Itoh, T. Sakurai: Improving the accuracy of numerical conformal mapping by
Pade approximation using the Arnoldi method, J. Inform. Comput. Sci., Vol. 2, No. 2, pp. 289--294,(2005).
Hiroto Tadano and Tetsuya Sakurai: A method for avoiding breakdown in product-type iterative
methods and its behavior for Toeplitz linear systems, Appl. Num. Anal. Comp. Math., Vol. 2, No. 2,
pp. 245--261,(2005).
安永守利，吉原郁夫：セグメント分割伝送線とその設計手法―VLSI実装基板のための高品
質信号配線の提案―，電子情報通信学会論文誌, Vol. J88-D-I,No. 5, pp. 915--929, (2005).
堀田義彦，佐藤三久，朴泰祐，高橋大介，中島佳宏，高橋睦史，中村宏：プロセッサの消費電力測定と低消費電力プロセッサによるクラスタの検討，情報処理学会論文誌：コンピューティングシステム, Vol. 45, No. SIG 11(ACS7), pp. 207--218, (2004).
高橋大介，朴泰祐，佐藤三久：Short Vector SIMD命令を用いた並列FFTの実現と評価，情報処理学会論文誌：コンピューティングシステム, Vol. 45, SIG11(ACS 7), pp. 50--61, (2004).
中島佳宏，佐藤三久，後藤仁志，朴泰祐，高橋大介：CONFLEX-G：OmniRPCによるグリッド環境上での分子立体配座探索プログラムの実装と性能評価，情報処理学会論文誌：コンピューティングシステム,Vol. 45, No. SIG 6(ACS 6), pp. 254--264, (2004).
大滝雄介，高橋大介，朴泰祐，佐藤三久：ヘテロなクラスタ環境におけるStrassenの行列積
アルゴリズムの並列化，情報処理学会論文誌：コンピューティングシステム, Vol. 45, SIG
6(ACS 6), pp. 122--133, (2004).

- 78 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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清水 敏行，建部 修見，工藤 知宏：ファンの振動が計算機内のハードディスクに与える影響について，情報処理学会論文誌：コンピューティングシステム,Vol. 45, No. SIG 6(ACS 6),
pp. 23--34, (2004).
工藤 知宏，松田 元彦，手塚 宏史，清水 敏行，児玉 祐悦，建部 修見，関口智嗣：VLANを用いた複数パスを持つクラスタ向きL2 Ethernetネットワーク，情報処理学会論文誌：コンピューティングシステム, Vol. 45, No. SIG 6(ACS6), pp. 35--44, (2004).
Tetsuya Sakurai, Hiroto Tadano, Yuichi Inadomi and Umpei Nagashima: A moment-based method
for large-scale generalized eigenvalue problems, Appl. Num. Anal. Comp. Math., Vol. 1, No. 3, pp.
516--523, (2004).
中西崇文，岸本貞弥，櫻井鉄也，北川高嗣：複数の書籍の索引部を用いたメタデータ空間
拡張統合方式，日本データベース学会Letters, Vol. 3, No. 1,pp. 141--144, (2004).
小笠原匡，多田野寛人，櫻井鉄也，伊藤祥司：Shifted Linear Systemsに対するKrylov部分空間反復法と固有値問題への応用，応用数理学会論文誌,Vol. 14, No. 3, pp. 193--205, (2004).
牛暁明，櫻井鉄也，杉浦洋：解析関数の多項式因子を求める精度保証付き解法，応用数理学会論文誌，Vol. 14, No. 1, pp. 59--73, (2004).
M. S. Petkovic, Tetsuya Sakurai and L. Rancic: Family of simultaneous methods ofHansen-Patrick's type, Applied Numerical Mathematics,Vol. 50, pp. 489--510, (2004).
Noriyuki Aibe, Ryosuke Mizuno, Masanori Nakamura, Moritoshi Yasunaga and Ikuo Yoshihara:
Performance evaluation system for probabilistic neural network hardware, Artificial Life andRobotics, Vol. 8, No. 2,pp. 208--213, (2004).
Hanxi Zhu, Ikuo Yoshihara, Kunihito Yamamori and Moritoshi Yasunaga: A multimodal neuralnetwork with single-state predictions for protein secondary structure, Artificial Life and Robotics,
Vol. 8, No. 2, pp. 168--173, (2004).
Hanxi Zhu, Ikuo Yoshihara, Kunihito Yamamori and Moritoshi Yasunaga:Multi-Modal Neural
Networks for Symbolic Sequence Pattern Classification, IEICE Transaction on Information and
Systems,Vol. E87-D, No. 7, pp. 1943--1952, (2004).

8.5.2 Proceedings
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Daisuke Takahashi: An Implementation of Parallel 1-D FFT Using SSE3 Instructions on Dual-Core
Processors, Proc. Workshop on State-of-the-Art in Scientific and Parallel Computing (PARA
2006),Lecture Notes in Computer Science, No. 4699, pp. 1178--1187, (2007).
Akira Nukada, Daisuke Takahashi, Reiji Suda and Akira Nishida: High Performance FFT on SGI
Altix 3700, Proc. 3rd International Conference on High Performance Computing andCommunications (HPCC 2007), Lecture Notes in Computer Science, No. 4782, pp. 396--407,(2007).
Jinpil Lee, Mitsuhisa Sato and Taisuke Boku: Design and Implementation of OpenMPD: An
OpenMP-like Programming Language for Distributed Memory Systems, Proc. of Int. Workshop on
OpenMP, pp. 132--135, (2007).
Takayuki Okamoto, Shinichi Miura, Taisuke Boku, Mitsuhisa Sato and Daisuke Takahashi:
RI2N/UDP: High bandwidth and fault-tolerant network for PC-cluster based on multi-link Ehternet,
Proc. 21st IEEE International Parallel and Distributed Processing Symposium (IPDPS'07),
CD-ROM, (2007).
Takayuki Imada, Mitsuhisa Sato, Yoshihiko Hotta, Hideaki Kimura, Taisuke Boku and Daisuke
Takahashi: Power-performance Evaluation on Ultra-Low Power High-performance Cluster System:
MegaProto/E, Proc. IEEE Symposium on Low-Power and High-Speed Chips (COOL Chips X), pp.
117--129, (2007).
Moritoshi Yasunaga, Noriyuki Aibe, Yoshiki Yamaguchi, Yorihisa Yamamoto, Takaaki Awano andIkuo Yoshihara: A Reconfigurable-VLSI-based Double-lens Tracking-camera, Proc. The 12th Int'l
Symp. on Artificial Life and Robotics 2007 (AROB 12th’07), CD-ROM, (2007).
Naoki Koizumi, Kazuya Hayashi, Moritoshi Yasunaga, Kunihito Yamamori and Ikuo Yoshihara:
Variable-Length-Segmental-Transmission-Line and its Design Guidelines, Proc. The 12th Int'l- 79 -CCS Report: PART II, Research Activities, Results
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Symp. on Artificial Life and Robotics 2007 (AROB12th'07), CD-ROM, (2007).
K. Glette, J. Torresen and M. Yasunaga: An Online EHW Pattern Recognition System Applied toFace Image Recognition, EvoWorkshops2007, Lecture Notes in Computer Science, No. 4448, pp.
271--280, (2007).
Takuya Yokozawa, Daisuke Takahashi, Taisuke Boku and Mitsuhisa Sato: Efficient Parallel
Implementation of Classical Gram-Schmidt Orthogonalization Using Matrix Multiplication, Proc.
4th International Workshop on Parallel Matrix Algorithms and Applications (PMAA'06), pp. 37--38,(2006).
Hideaki Kimura, Mitsuhisa Sato, Yoshihiko Hotta, Taisuke Boku and Daisuke Takahashi: Empirical
Study on Reducing Energy of Parallel Programs using Slack Reclamation by DVFS, Proc. 8th IEEE
International Conference on Cluster Computing (Cluster 2006), CD-ROM, (2006).
Yoshiaki Aida, Yoshihiro Nakajima, Mitsuhisa Sato, Tetsuya Sakurai, Daisuke Takahashi and
Taisuke Boku: Performance Improvement by Data Management Layer in a Grid RPC System, Proc.
First International Conference on Grid and Pervasive Computing (GPC 2006), Lecture Notes in
Computer Science, No. 3947, pp. 324--335, (2006).
Daisuke Takahashi: A Hybrid MPI/OpenMP Implementation of a Parallel 3-D FFT on SMP Clusters,
Proc. 6th International Conference on Parallel Processing and Applied Mathematics (PPAM 2005),
Lecture Notes in Computer Science, No. 3911, pp. 970--977, (2006).
Taisuke Boku, Mitsuhisa Sato, Akira Ukawa, Daisuke Takahashi, Shinji Sumimoto, Kouichi
Kumon, Takashi Moriyama and Masaaki Shimizu: PACS-CS: A large-scale bandwidth-aware PC
cluster for scientific computations, Proc. Sixth IEEE International Symposium on Cluster
Computing and the Grid (CCGRID'06), pp. 233--240, (2006).
Yoshihiko Hotta, Mitsuhisa Sato, Hideaki Kimura, Satoshi Matsuoka, Taisuke Boku and Daisuke
Takahashi: Profile-based Optimization of Power Performance by using Dynamic Voltage Scaling on
a PC cluster, Proc. 20th IEEE International Parallel and Distributed Processing Symposium(IPDPS'06), CD-ROM, (2006).
Taisuke Boku, Mitsuhisa Sato, Daisuke Takahashi, Hiroshi Nakashima, Hiroshi Nakamura, Satoshi
Matsuoka and Yoshihiko Hotta: MegaProto/E: Power-Aware High-Performance Cluster with
Commodity Technology,Proc. 20th IEEE International Parallel and Distributed Processing
Symposium (IPDPS'06), CD-ROM, (2006).
Daisuke Takahashi, Mitsuhisa Sato and Taisuke Boku: Computation of High-Precision
Mathematical Constants in a Combined Cluster and Grid
Environment, Proc. 5th International Conference on Large-Scale Scientific Computations(LSSC'05), Lecture Notes in Computer Science, No. 3743, pp. 454--461, (2006).
Tetsuya Sakurai, Kentaro Hayakawa, Mitsuhisa Sato and Daisuke Takahashi: A Parallel Method forLarge Sparse Generalized Eigenvalue Problems by OmniRPC in a Grid Environment, Proc. 7thInternational Workshop on Applied Parallel Computing (PARA 2004), Lecture Notes in Computer
Science, No. 3732, pp. 1151--1158, (2006).
Daisuke Takahashi, Taisuke Boku and Mitsuhisa Sato: An Implementation of Parallel 3-D FFTUsing Short Vector SIMD Instructions on Clusters of PCs, Proc. 7th International Workshop on
Applied Parallel Computing (PARA 2004), Lecture Notes in Computer Science, No. 3732, pp.
1159--1167, (2006).
Tetsuya Sakurai, Yoshihisa Kodaki, Hiroaki Umeda, Yuichi Inadomi, Toshio Watanabe and Umpei
Nagashima: A hybrid parallel method for large sparse eigenvalue problems on a grid computing
environment using Ninf-G/MPI, Proc. 5th International Conference on Large-Scale Scientific
Computations (LSSC'05), Lecture Notes in Computer Science, No. 3743, pp. 438--445, (2006).
Sadaya Kishimoto, Takafumi Nakanishi, Mamoru Murakata, Toru Otsuka, Tetsuya Sakurai, Takashi
Kitagawa: An implementation method of an integrated associative search for mathematicalexpressions, The IASTED International Conference on Databases and Applications, pp.
160--167,(2006).
Takayuki Okamoto, Taisuke Boku, Mitsuhisa Sato, Osamu Tatebe: P2P Overlay Network for TCP
Programming with UDP Hole Punching, Proc. IFIP International Conference on Network andParallel Computing (NPC 2006), (2006).

- 80 -CCS Report: PART II, Research Activities, Results
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Z. Ding, Y. Luo, X. Wei, C. Misleh, W. W. Li, P. W. Arzberger, O. Tatebe: My WorkSphere:
Integrative Work Environment for Grid-unaware Biomedical Researchers and Applications, Proc.
2nd Grid Computing Environment Workshop, (2006).
X. Wei, Z. Ding, W. W. Li, O. Tatebe, J. Jiang, L. Hu, P. W. Arzberger: GDIA: A Scalable Grid
Infrastructure for Data Intensive Applications, Proc. IEEE International Conference on Hybrid
Information Technology (ICHIT 2006), (2006).
Cindy Zheng, David Abramson, Peter W. Arzberger, Shahaan Ayyub, Colin Enticott, Slavisa Garic,
Mason J. Katz, Jae-Hyuck Kwak, Bu-Sung Lee, Philip M. Papadopoulos, Sugree Phatanapherom,
Somsak Sriprayoonsakul, Yoshio Tanaka, Yusuke Tanimura, Osamu Tatebe: The PRAGMA Testbed- Building a Multi-Application International Grid, Proc. International Workshop on Grid Testbeds(Grid Testbeds), (2006).
Wilfred W. Li, Sriram Krishnan, Kurt Mueller, Kohei Ichikawa, Susumu Date, Sargis Dallakyan,
Michel Sanner, Chris Misleh, Zhaohui Ding, Xiaohui Wei, Osamu Tatebe, Peter W. Arzberger:
Building Cyberinfrastructure for Bioinformatics Using Service Oriented Architecture, Proc. FourthInternational Workshop on Biomedical Computations on the Grid (BioGrid), (2006).
Hiroyuki Kawai, Yoshiki Yamaguchi and Moritoshi Yasunaga: Realization of the sound spaceenvironment for the radiation-tolerant space craft, the 3rd International Conference on
ReConFigurable Computing and FPGAs (ReConFig2006), pp. 198--205, (2006).
H. D. Nguyen, Ikuo Yoshihara, Kunihito Yamamori and Moritoshi Yasunaga: A New Three-Level
Tree Data Structure for Optimizing the Traveling Salesman Problem by Lin-Kernighan Heuristic,
International Symposium on Nonlinear Theory and its Applications (NOLTA2006), pp. 871--874,(2006).
Naoki Koizumi, Ikuo Yoshihara, Kunihito Yamamori and Moritoshi Yasunaga: Enhancement of the
Variable-Length- Transmission-Line design method for multi-point optimization, Proc. 2006 IEEE
Congress on Evolutionary Computation (CEC2006), CD-ROM, (2006).
Kyrre Glette, Jim Torresen, Yoshiki Yamaguchi and Moritoshi Yasunaga: On-Chip Evolution Usinga Soft Processor Core Applied to Image Recognition, First NASA/ESA Conference on Adaptive
Hardware and Systems (AHS 2006), pp. 373--380, (2006).
Hiroyuki Kawai, Yoshiki Yamaguchi and Moritoshi Yasunaga: Improvement of module redundancy
using FPGA, 6th European Workshop on Microelectronics Education (EWME2006), pp. 67--70,(2006).
Kazuya Hayashi, Noriyuki Aibe, Yoshiki Yamaguchi, Yorihisa Yamamoto, Moritoshi Yasunaga andIkuo Yoshihara: A Bio-inspired Tracking-camera System, International Symposium on Artificial
Life and Robotics (AROB 11th '06), pp. 755--758, (2006).Shinji Sumimoto, Kazuichi Ooe, Koichi
Kumon, Taisuke Boku, Mitsuhisa Sato, Akira Ukawa: Scalable Communication Layer for
Multi-Dimensional Crossbar Network Using Multiple Gigabit Ethernet, Proc. of Int. Conf. on
Supercomputing 2006, CD-ROM, (2006).
Shinichi Miura, Takayuki Okamoto, Taisuke Boku, Mitsuhisa Sato and Daisuke Takahashi:
Low-cost High-bandwidth Tree Network for PC Clusters based on Tagged-VLAN Technology, Proc.
8th International Symposium on Parallel Architectures, Algorithms, and Networks (I-SPAN 2005),
pp. 84--93, (2005).
Yoshinori Ojima, Mitsuhisa Sato, Taisuke Boku and Daisuke Takahashi: Design of a Software
Distributed Shared Memory System using an MPI communication layer, Proc. 8th International
Symposium on Parallel Architectures, Algorithms, and Networks (I-SPAN 2005), pp. 220--229,(2005).
Hiroshi Nakashima, Hiroshi Nakamura, Mitsuhisa Sato, Taisuke Boku, Satoshi Matsuoka, Daisuke
Takahashi and Yoshihiko Hotta: MegaProto: 1TFlops/10kW Rack Is Feasible Even with Only
Commodity Technology, Proc. ACM/IEEE International Conference on High Performance
Computing, Networking and Storage (SC|05), CD-ROM, (2005).
Mitsuhisa Sato, Yoshihiro Nakajima, Tetsuya Sakurai, Taisuke Boku and Daisuke Takahashi:
OmniRPC Grid Parallel Programming Environment for a Large Scale Numerical Computation,
Proc. 17th IMACS World Congress Scientific Computation, Applied Mathematics and Simulation,
CD-ROM,(2005).

- 81 -CCS Report: PART II, Research Activities, Results
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Taisuke Boku, Kenji Onuma, Mitsuhisa Sato, Yoshihiro Nakajima and Daisuke Takahashi: Grid
environment for computational astrophysics driven by GRAPE-6 with HMCS-G and OmniRPC,
Proc. 19th IEEEInternational Parallel and Distributed Processing, Symposium (IPDPS'05),
CD-ROM, (2005).
Hiroshi Nakashima, Hiroshi Nakamura, Mitsuhisa Sato, Taisuke Boku, Satoshi Matsuoka, Daisuke
Takahashi and Yoshihiko Hotta: MegaProto: A Low-Power and Compact Cluster for
High-Performance Computing, Proc. 19th IEEE International Parallel and Distributed Processing
Symposium (IPDPS'05), CD-ROM, (2005).
Takafumi Nakanishi, Sadaya Kishimoto, Tetsuya Sakurai and H. Kitagawa: A construction methodof a metadata space based on relations between words from an index of a book, Proc. IEEE Pacific
Rim Conference on Communications, Computers and Signal Processing, pp. 438--441, (2005).
Wei Xiaohui, Wilfred W. Li, Osamu Tatebe, Xu Gaochao, Hu Liang, Ju Jiubin: Integrating Local
Job Scheduler - LSF with Gfarm, Lecture Notes in Computer Science, No. 3758, pp. 196--204,(2005).
Wei Xiaohui, Wilfred W. Li, Osamu Tatebe, Xu Gaochao, Hu Liang, Ju Jiubin: Implementing dataaware scheduling in Gfarm using LSF scheduler plugin mechanism, Proc. 2005 International
Conference on Grid Computing and Applications (GCA'05), (2005).
Wilfred W. Li, Peter W. Arzberger, Chang Lim Yeo, Larry Arg, Osamu Tatebe, Satoshi Sekiguchi,
Karpjoo Jeong, Suntae Hwang, Susumu Date,Jae-Hyuck Kwak: Proteome Analysis using iGAP in
Gfarm, Proc. 2nd International Workshop on Life Science Grid (LSGRID 2005), (2005).
Naoki Koizumi, Ikuo Yoshihara, Kunihito Yamamori, and Moritoshi Yasunaga: Variable Length
Segmental-Transmission-Line and Its Parameter Optimization based on GA, Proc. IEEE Congress
on Evolutionary Computation (CEC), CD-ROM, (2005).
Taisuke Boku, Mitsuhisa Sato, Masazumi Matsubara and Daisuke Takahashi: OpenMPI --OpenMP like tool for easy programming in MPI, Proc. 6th European Workshop on OpenMP(EWOMP 2004), pp. 83--88, (2004).
Osamu Tatebe, Noriyuki Soda, Youhei Morita, Satoshi Matsuoka, Satoshi Sekiguchi: Gfarm v2: A
Grid file system that supports high-performance distributed and parallel data computing, Proc. 2004
Computing in High Energy and Nuclear Physics (CHEP04), (2004).
Taisuke Boku, Hajime Susa, Kenji Onuma, Masayuki Umemura, Mitsuhisa Sato and Daisuke
Takahashi: Formation of Dwarf Galaxies in Reionized Universe with HeterogeneousMulti-Computer System, Proc. International Conference on Computational Science 2004 (ICCS
2004), Lecture Notes in Computer Science, No. 3039, pp. 629--636, (2004).
Chikafumi Takahashi, Masaaki Kondo, Taisuke Boku, Daisuke Takahashi, Hiroshi Nakamura and
Mitsuhisa Sato: SCIMA-SMP: on-chip memory processor architecture for SMP, Proc. 3rdWorkshop on Memory Performance Issues (WMPI'04), pp. 121--128, (2004).
Yoshihiro Nakajima, Mitsuhisa Sato, Hitoshi Goto, Taisuke Boku and Daisuke Takahashi:
Implementation and Performance Evaluation of CONFLEX-G: Grid-enabled Molecular
Conformational Space Search Program with OmniRPC, Proc. 18th International Conference on
Supercomputing (ICS'04), pp. 154--163, (2004).
Keiichi Aoki, Shinichi Yamagiwa, Kevin Ferreira, Luis Miguel Campos, Masaaki Ono, Koichi
Wada and Leonel Sousa: Maestro2: High Speed Network Technology for High Performance
Computing, Proc. of the IEEE International Conference on Communications, (2004).
Yoshihiko Hotta, Mitsuhisa Sato, Taisuke Boku, Daisuke Takahashi and Chikafumi Takahashi:
Measurement and Characterization for Power Consumption of Microprocessors for Power-aware
Cluster, Proc. An International Symposium on Low-Power and High-Speed Chips (COOL Chips
VII), pp. 293--303, (2004).
Yuhsuke Ohtaki, Daisuke Takahashi, Taisuke Boku and Mitsuhisa Sato: Parallel Implementation ofStrassen's Matrix Multiplication Algorithm for Heterogeneous Clusters, Proc. 18th International
Parallel and Distributed Processing Symposium (IPDPS'04), CD-ROM, (2004).
Shinichi Yamagiwa, Kevin Ferreira, Luis Miguel Campos, Keiichi Aoki, Masaaki Ono, Koichi
Wada, Munehiro Fukuda and Leonel Sousa: On the Performance of Maestro2 High Performance
Network Equipment, Using New Improvement Techniques, Proc. of the 23rd IEEE International- 82 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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•

Performance Computing and Communications Conference, pp. 103--110, (2004).
Hiroto Tadano and Tetsuya Sakurai: A method for avoiding breakdown in product-type iterative
methods and its behavior for Toeplitz linear systems, Proc. ICNAAM, (2004).
Tetsuya Sakurai, Hiroto Tadano, Yuichi Inadomi and Umpei Nagashima: A moment-based method
for large scale eigenvalue problems, Proc. ICNAAM, pp. 333--336, (2004).
Yuetsu Kodama, Tomohiro Kudoh, R. Takano, H. Sato, Osamu Tatebe, Satoshi Sekiguchi: GNET-1:
gigabit Ethernet network testbed, Proc. 2004 IEEE International Conference on Cluster Computing(CLUSTER'04), pp. 185--192, (2004).
Naotaka Yamamoto, Osamu Tatebe, Satoshi Sekiguchi: Parallel and Distributed Astronomical Data
Analysis on Grid Datafarm, Proc. 5th IEEE/ACM International Workshop on Grid Computing(Grid 2004), pp. 461--466, (2004).
Noriyuki Aibe and Moritoshi Yasunaga: Reconfigurable I/O Interface for Mobile Equipments, Proc.
Int'l Conf. Field-Programmable Technology,pp. 359--362, (2004).
Hung Dinh, Ikuo Yoshihara, Kunihito Yamamori and Moritoshi Yasunaga: A Parallel Hybrid
Genetic Algorithm for Large Scale TSPs, Proc. The 5th Int'l Conf. Simulated Evolution And
Learning, CD-ROM, (2004).
Kouji Ohta, Ikuo Yoshihara, Kunihito Yamamori and Moritoshi Yasunaga: GMDH-based Model
Optimized by GA for Extracting EXON Regions From DNA Sequences, Proc. The 5th Int'l Conf.
Simulated Evolution And Learning, CD-ROM, (2004).
Yoshiyuki Sakaguchi, Ikuo Yoshihara, Naoki Koizumi, Kunihito Yamamori and Moritoshi
Yasunaga: GA-based Timetabling for Satisfying Professors' and Students' Requirements, Proc. The
5th Int'l Conf. Simulated Evolution And Learning, CD-ROM, (2004).
Toshiro Onitani, Ikuo Yoshihara, Kunihito Yamamori and Moritoshi Yasunaga: Extraction of
Feature Patterns Embedded in Non-Transcribed Region of Dictyostelium Discoideum, Proc. The
5th Int'l Conf. Simulated Evolution And Learning, CD-ROM, (2004).
Masakazu Sato, Ikuo Yoshihara, H. D. Nguyen, Kunihito Yamamori and Moritoshi Yasunaga:
Hybrid GA Using Edge Assembly Crossover and Lin-Kernighan Heuristic, Proc. The 5th Int'l Conf.
Simulated Evolution And Learning, CD-ROM, (2004).
Noriyuki Aibe and Moritoshi Yasunaga: Meta-I/O Interface Using Reconfigurable LSIs, IEEE
International Midwest Symposium on Circuits and Systems (MWSCAS2004), pp. 25--28, (2004).
Daekwan Seo, Moritoshi Yasunaga and Jung H. Kim: A Computational Approach to Detect
Transcription Regulatory Elements in Dictyostelium Discoideum, Proc. IEEE Congress on
Evolutionary Computation (CEC), (2004).
Kenji Onuma, Taisuke Boku, Mitsuhisa Sato, Daisuke Takahashi, Hajime Susa and Masayuki
Umemura: Heterogeneous Remote Computing System for Computational Astrophysics with
OmniRPC, Proc. Int. Workshop on High Performance Grid Computing and Network (in 2004 Int.
Symp. on Applications and Internet), pp. 623--629, (2004).
Yoshihiro Nakajima, Mitsuhisa Sato, Taisuke Boku, Daisuke Takahashi and Hitoshi Gotoh:
Performance Evaluation of OmniRPC in a Grid Environment, Proc. Int. Workshop on
HighPerformance Grid Computing andNetwork (in 2004 Int. Symp. on Applications and Internet),
pp. 658--664, (2004).

- 83 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

9. Division of Computational Informatics: Computational Intelligence Group
9.1 Research Activity
In the field of computational sciences, management and utilization of massive data are
extremely important issues. The computational intelligence group in the computational
informatics division is in charge of research and development in the field of dataengineering. In particular, we have been engaging in the following research topics:
infrastructure for integrating heterogeneous databases and various information sources, data
mining and knowledge discovery technologies to discover knowledge and rules frommassive data, XML-related technologies to deal with various data uniformly in the Internet
environment. Additionally, we also have engaged in application studies, such as
development and maintenance of meteorological databases and knowledge discovery fromthe database, in cooperation with Global Environment and Biological Sciences division.
9.1.1 Infrastructure for Information Integration(Research funds: Grant-in-Aid for Scientific Research (A), Grant-in-Aid for Scientific
Research on Priority Areas, Grant-in-Aid for Young Scientists (B), JST CREST)(1-1) System for Information Integration
We have been investigating infrastructures, systems, and applications which enable us to
integrate heterogeneous and distributed databases and information sources. In particular,
we have been developing StreamSpinner, which allows us to integrate not only
conventional data sources, such as relational databases and Web data, but also stream data,such as sensor data and location information. The model of StreamSpinner is based on therelational model, and StreamSpinner has a basic functionality for information integration
based on the model. However, it can also deal with continuous media, such as video andaudio, due to its extensible features. Specifically, it allows us to plug-in programs for
specific applications as external functions, and it can then integrate diverse information by
invoking external functions. Examples are similarity search on time-series data and analysis
of video data streams captured by severance cameras.
Moreover, we have been addressing the problem of stream processing in distributed
environments where StreamSpinners are distributed on multiple nodes. We also havebeen studying the sustainable stream processing system, which is dependable even whensome nodes fail.

- 84 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Infra. for Info.
情報統合基盤
Integration
システム

アプリケーション
Applications
プログラム

メディエータMediator
メディエータAssoc.Rule
相関ルール
Mining
マイニング

External
外部関数
外部関数
Function
呼び出し
呼び出し
機構
Caller機構

Wrapper ラッパー
Wrapper ラッパー
Wrapper ラッパー
Wrapper
ラッパー
ラッパー ラッパー ラッパー ラッパー
Web
Web

Sensors& Tags Cameras
センサー，タグ
カメラ

Modules

API
API
API

Parser
問合せ解析器
問合せ解析器Wrapper
ラッパー
ラッパー

Demonstrations
MDM(2006.5) andMDM （2006.5on）やイノベーション
Innovation
2006.9Japan(2006.9)
ジャパン（）にてデモ展示公開

Results
問合せ結果

Queries
問合せ要求記述

Events
イベント通知Wrapper
ラッパー
ラッパー

マイニング
Miningモジュール

Knowledge
知識発見
DiscoveryVideo
Stream Monitoring
映像ストリームモニタリング

Infra. for Info.
情報統合基盤
Integration
システム

Face
Recog.
顔認識技術

Cameraカメラ

RDBMS

DBの統合利用
センサーデータとIntegrating Sensor
Data and DB

Locationbased Info.
位置に応じた情報提供

Infra
for Info.
情報統合基盤
Integration
システム

Data
データ
Cleaning
クリーニングRDBMSRDBMS XMLDB
XMLDB

RDBMS
RDBMS
Tags
位置タグ

メール
Mails

Fig. 1 StreamSpinner and its applications.

(1-2) Sensing Database Infrastructure
Demands on DBMS for time-series data obtained by real-world monitoring areincreasing. To cope with it, a DBMS should have super fast data insertion function, data
analysis function, and continual query function. We have developed a sensing databaseinfrastructure KRAFT to realize such functions. The features of KRAFT are: fast data
insertion utilizing UPS attached memories, similar
Outlier
Detection
外れ値検出
sequence retrieval functions, and signal processing
Examplebased Outlier Detection
・例示オブジェクトに基づく外れ値検出
functions.
Outlier
Detection for High Dimensional Datasets
・高次元データ中の外れ値検出

9.1.2 Data Mining and Knowledge Discovery(Research funds: Grant-in-Aid for Scientific Research
on Priority Areas, Grant-in-Aid for Scientific
Research (A), Grant-in-Aid for Young Scientists (B),JST CREST)
We have been studying various data mining andRatio-Rule Mining
比率規則マイニングknowledge discovery techniques, such as outlier
Method Outline
提案手法の概略
detection, ratio-rule mining, information extraction
最適
類似した
候補
Support/Clustering
Candidate
サポート
比率規則
パラメータ 確信度
/ConfiParameterfrom documents, time-series document clustering,
をクラスタ
を絞り込む
dence
Selection
区間の
比率規則
Ratio
Input
入力
リング
抽出
データ
Data
Rules
集合
document topic analysis, topic-structure mining, and×
mobility histogram construction for mobile objects. Parameters
パラメータ×
In the following, we explain some topics out of theResults (Wine Database)
実験結果（ワインデータベース）
above main activities.
(2-1) Outlier Detection
2種類の線形関係を
2 Individual
Relationships
個別に捉えている
Outliers are data objects that are greatly different
from other objects, and they are useful for detecting
malfunctions and discovering interesting data objects. Fig. 2 Outlier detection and ratio-rulemining.

- 85 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

Distance-based and density-based methods are the major outlier detection methods today.
When applying those methods, it has been pointed out that there are several problems. Thatis, it is difficult to find an appropriate set of parameters for a given dataset, and it is difficult
to characterize objects in high-dimensional data spaces.
To tackle these problems, we have studied several approaches in which user-provided
examples are used to find outliers. Also, we attempt to find low-dimensional subspaces
which characterize sample outliers the most, instead of dealing with all dimensions.
In the meantime, so far, few papers have addressed the problem of outlier detection for
discrete values, whereas most conventional methods mainly deal with numerical data. For
this reason, we attempt to apply association-rule mining to the problem of outlier detection
in data records and/or transaction data which are mainly consisting of discrete values.
(2-2) Ratio-Rule Mining
Extraction of ratio rules from numerical dataset is an important research issue due to thefact that ratio rules can be used for interpolation, prediction, and outlier detection. However,the principle component analysis (PCA), which is a basic technique to extract ratio rules, is
not able to detect individual linear relationships when multiple linear relationships are
mixed. It is not able to deal with such linear relationships that hold for limited ranges ofaxes, either.
In our novel method, we define the concept of support and confidence of ratio rules in asimilar spirit of association-rule mining, and extract ratio-rules by following the definition.
The technique enables us to obtain ratio rules which reflect users’ intentions.
(2-3) Information Extraction from Documents
Although massive information is available on the Web, we have not yet been able to
make the best use of it because of the heterogeneity of information resources. So far, many
researchers have devoted their efforts to extracting useful information from the Web and/or
documents, and noticed that it is quite important to choose appropriate information sources
out of numerous information sources. In this research, we have developed a system forextracting information from document databases, in which user specified records (seeds)
are used to retrieve related records. Our idea is to select document sources by evaluating
quality of extracted records, which improves accuracy as well as efficiency in terms of thenumber of extracted records.
(2-4) Time-Series Document Clustering
Currently, a large number of documents are circulated in the Internet, and it is therefore
important to be able to summarize their information outline. This research focuses onclustering time-series documents, each of which is assigned temporal information like theissue date of a news article. Specifically, we investigate clustering techniques which takes- 86 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

into account of novelty of documents. For news articles, articles with fresh information
usually have more values compared to those with older information, and old articles will beforgotten in time. Our algorithm takes into account such real-life features, and achieves
efficient clustering over temporal documents.
9.1.3 XML and Web Programming(Research funds: Grant-in-Aid for Scientific Research on Priority Areas，Grant-in-Aid forYoung Scientists (B), JST CREST)XML is a meta-language for data representation, and has been widely used as astandardized data format for data interoperability in network environments. As aconsequence, the amount of data generated and/or stored in the form of XML is explosively
increasing, and this seems to be the trend for the foreseeable future. For this reason, we
have been addressing diverse issues, as described in the following, aiming at developing
efficient and effective means for the management of massive XML resources.
(3-1) OLAP for XML Data
In general, searching is one of the most common ways to find out necessary informationfrom XML data. However, more complicated ways to make analysis of XML data, whichallow us to discover valuable information out of large XML data collections, are becoming
important due to the recent diffusion of XML. In this work we attempt to develop
XML-OLAP (Online Analytical Processing), which enables us to perform analyticalprocessing of XML data.
In OLAP systems, the target data being analyzed is regarded as a multidimensional cube
consisting of several attributes, and we make analysis of the cube by applying operations
dedicated to OLAP analysis. However, when dealing with XML data, it is not a trivial
task to apply (existing) OLAP techniques to them due to the nature of XML, in which XML
data is modeled as trees, and the data model is flexible enough to accommodate structurally
heterogeneous instances. This gives rise to the need of novel (formal) definitions of XML
data cube and related operators, efficient algorithms and indexing structures dedicated tothe model and operators to achieve interactive analysis of large XML datasets. We havebeen addressing these problems, and developing a system based on the scheme.
(3-2) Parallel XML Data Processing
The diversification of XML use-cases causes the emergence of large-scale XML data
ranging from Giga-bytes to Tera-bytes. As a consequence, it is important for us to be able
to deal with such large-scale XML data efficiently. However, the fact that XML data havetree-structures makes it difficult to query large XML data efficiently. To cope with thisproblem, we have been trying to incorporate parallel processing in querying XML data

- 87 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

using PC-cluster systems. The technical challenges are partitioning XML data forsubsequent distribution to cluster nodes, optimal load-aware distribution of XML data,
parallel query processing algorithm, etc. In this research, we attempt to make the best useof the techniques of relational XML databases, which have been well-studied for the past
several years.
s
b
t

m

m
p

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t

t

p

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/s/b

σpexp=‘//b’/s/b/tσpexp=‘//b/t’“DB” “Aoki” “100” “PC” “10” “CAR” “15”Path-approach

XPath://b[t=“PC”]/pPathpathidpathexp

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Queryplan

Relationaltables

PC-cluster

Fig. 3.

Parallel XML data processing.

(3-3) Searching XML Data in P2P Networks
The recent dissemination of the Internet is making the global data interoperability cometrue. In the meantime, there is a growing demand for constructing networks over theInternet exclusively dedicated for particular groups or organizations. This is due to therecent trends in which security preserved efficient information distribution has attracted
much public attentions. Peer-to-peer networks, which allow us to construct such networks
that are dedicated for specific applications, have been widely used as the bases of overlay
networks, and there have been several research projects which aim at sharing scientific datausing overlay networks. In such applications, XML is used as a standardized data format.
From these observations, we have been studying a scheme for storing and querying XML
data using P2P networks.
9.1.4 Meteolorogical Databases(Research funds: Grant-in-Aid for Exploratory Research)(4-1) GPV/JMA Archive
As a collaborative work with the global environmental science group in CCS, we havebeen
developing,
maintaining,andmanaging
GPV/JMA
Archive- 88 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007(http://gpvjma.ccs.hpcc.jp). Its objective is to store meteorological data provided by
theJapan Meteorological Agency (JMA), and make the stored data publicly available toexternal users. The archive stores 6 kinds of JMA/GPV data, i.e., global spectral model
data (GSM), regional spectral model data (RSM), meso-scale non-hydrostatic model data
(MSM), weekly ensemble forecast data, monthly ensemble forecast data, and seasonalensemble forecast data. In addition, it provides weather maps rendered from the grid data
and KML (Keyhole Markup Language) data, which allow users to view the weather maps
by GoogleEarth.

Fig. 4. Viewing a weather map by GoogleEarth.

(4-2) Information Integration using Web Services
At this moment, GPV/JMA Archive only provides simple form-based query interfaces tosearch for stored data. We have been developing a Web service system for GPV/JMA
Archive for aiming at improving the usability, as well as promoting interoperation of
meteorological data across related databases in other countries. Specifically, we attempt to
implement major functionalities concerning meteorological data, such as metadata
extraction, query retrieval, format conversion, and rendering, as Web services. We also
provide BPEL-based workflow engines for allowing users to combine those functionalities
to support their research activities.
9.2 Research Results1) Infrastructure for Information Integration- We have developed a stream-processing engine, StreamSpinner, and have constructedvarious demonstration systems for empirical study. We demonstrated them in many
exhibitions, such as Innovation Japan 2005, 2006, and 2007.
- We have developed a stream database system, KRAFT, and released it as OSS.

- 89 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

2）Data Mining and Knowledge Discovery- We have developed several example-based methods for outlier detection in highdimensional spaces, and confirmed its effectiveness by experiments. Furthermore, we havedeveloped basic algorithms for detecting outliers in discrete data, and investigated someapproaches to make the processing more efficient.
- We have developed a basic method for mining ratio-rules, and confirmed its effectivenessby experimental data. In addition, we made related software as a package for data analysis.
- We have developed a basic method for extracting information from document collections
and several variations as extensions. We confirmed its feasibility by experiments using a
news article archive.
- We have developed a clustering method for time-series documents as an extension of
k-means algorithm, and realized incremental update of clusters.
3) XML and Web Programming- We gave a formal definition of multidimensional datacube of XML data based on XPathexpressions. Based on the definitions, we have developed a prototype system using
relational databases, and evaluated its performance.
- We have developed a basic approach for parallel XML query processing, and confirmed
its feasibility by a prototype system.
- We have developed a prototype system for storage and retrieval of XML data in P2P
networks based on DHT (Distributed Hash Table), and tested its performance by
experimental evaluations.
4) Meteorological Databases- We have constructed GPV/JMA Archive, which stores GPV data provided by JMA, and it
works in a stable manner. As of the end of August, 2007, the amount of stored data is
700GB and there are 174 registered users. We have implemented several Web services on
top of the archive, and confirmed its feasibility using the prototype.
5) Numbers of Refereed Papers
2004: 17 (Journal papers 10, Refereed conference papers 7)
2005: 14 (Journal papers 7, Refereed conference papers 7)
2006: 18 (Journal papers 7, Refereed conference papers 11)
2007: 20 (Journal papers 9, Refereed conference papers 11)(As of August, 2007)- 90 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

6) Relating to the above research activities, we have received two paper awards, one award
for young researchers, and two fellowships from domestic academic societies. In addition,
students in our laboratory have received 15 awards in total.
9.3 Collaboration
We are having regular meetings with the computational media group for discussing
computational informatics in the real-world. In addition, we have been developing,
maintaining, and managing GPV/JMA Archive in cooperation with the global
environmental science group. Recently, we have started a new project in which we apply
data mining techniques to meteorological data.
9.4 Future Plan
1）Research and Development of Technologies for Data Engineering Infrastructure
Owing to the recognition that information integration, data mining, knowledge discovery,
XML and Web programming are all important as technologies for data engineering
infrastructure, we continue to intensively perform research and development in those areas.
We also attempt to make our research activities practical as much as possible in cooperation
with other groups in CCS. As for the topic of infrastructure for information integration, we
attempt to integrate functionalities such as data mining and knowledge processing methods,
and also attempt to make further development on the topics of distributed query processing
and sustainable processing. As for data mining and knowledge processing techniques, we
try to speed up the processing and apply it to large-scale real datasets. We also plan toaddress novel information sources, such as Blogs and SNSs. As for techniques related to
XML and Web programming, we plan to make further development on the current methods.
From the viewpoint of trust, we plan to address the problem of data traceability.

2) Scientific Databases
We continue to develop and maintain GPV/JMA Archive in cooperation with the global
environmental science group. In addition, we plan to construct a new database for JRA-25(Japanese Re-Analysis 25 years). As for Web service systems, we continue thedevelopment, and try to improve the usability of the system. Another topic is related to
gfdnavi, which is a tool for analyzing geophysical fluid data, and we try to cooperate withits developers. We do not limit the research domain to meteorology, and try to address
data engineering problems in other scientific domains.

- 91 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

3) Reinforcement of Cooperation with Other Divisions and Challenge of New Research
Issues
We will further strengthen collaboration with the computational media group, and jointly
develop the infrastructure of sensing, data processing, high performance computation as aframework of real-world computational informatics.
We also promote research on data mining applications for meteorological data (withGlobal Environment and Biological Sciences division), data infrastructure and knowledge
discovery technology (with High Performance Computing Systems division and AIST), anddatabase processing over grid file systems (with High Performance Computing Systems
division).
9.5 Publications
9.5.1 Journal Papers
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Cui Zhu, Hiroyuki Kitagawa, Spiros Papadimitriou, and Christos Faloutsos, "A Method ofDetecting Outliers Matching Users' Intentions", 日本データベース学会 Letters, Vol. 3, No. 1, u
Ishikawa, and Hiroyuki Kitagawa,. 93-96, 2004 年 6 月.
崔春花, 北川博之, 「到着頻度と関連性を考慮した時系列文書のトピック分析」, 日本デー
タベース学会 Letters, Vol. 3, No. 2, pp. 37-40, 2004 年 9 月.
Cui Zhu, Hiroyuki Kitagawa, Spiros Papadimitriou, and Christos Faloutsos, "Example-based
Outlier Detection with Relevance Feedback", 日本データベース学会 Letters, Vol. 3, No. 2, pp.
5-8, 2004 年 9 月.
石川佳治，宮坂集策，北川博之，「RDB 上の XSLT 実体化ビュー のインクリメンタルな更新手法」，日本データベース学会 Letters, Vol. 3, No. 3, pp. 25-28, 2004 年 9 月.
渡辺陽介, 北川博之, 「連続的問合せに対する複数問合せ最適化手法」, 電子情報通信学会
論文誌, Vol. J-87-D-I, No. 10, ld Wide Web Journal. (to appear). 873-886, 2004 年 10 月.
中溝昌佳，森嶋厚行，杉本重雄，北川博之, 「WWW リンク一貫性維持支援システムにおけるリンク切れ自動修復」日本データベース学会 Letters, Vol. 3, No. 3, pp. 5-8, 2004 年 12 月.
張建偉，石川佳治，北川博之，「空間情報ハブ抽出のためのウェブリンク解析手法」，日本
データベース学会 Letters, Vol. 3, No. 3, pp. 9-12, 2004 年 12 月.
Said Mirza Pahlevi and Hiroyuki Kitagawa, "Conveying Taxonomy Context for Topic-Focused
Web Search", Journal of the American Society for Information Science and Technology, Vol. 56, No.
2, pp. 173-188, 2005.
品川徳秀, 北川博之, 「バイナリデータに対する XML ビューの実現」電子情報通信学会論文誌, Vol. J88-D-I, No. 3, pp. 604-616, 2005 年 3 月.
毛利隆軌, 北川博之, 「Hidden Web サイトからの新規トピック文書の抽出」情報処理学会
論文誌：データベース, Vol. 46, No. SIG5 (TOD25), pp. 56-69, 2005 年 3 月.
Cui Zhu, Hiroyuki Kitagawa, and Christos Faloutsos, "Example-Based Outlier Detection for High
Dimensional Datasets", 情報処理学会論文誌：データベース, Vol. 46, No. SIG8 (TOD26), pp.
120-129, 2005 年 6 月.
山田真一，渡辺陽介，北川博之, 「実世界情報ストリーム高度利用のための統合環境」，日本データベース学会 Letters, Vol. 4, No. 1, pp. 105-108, 2005 年 6 月.
品川徳秀，北川博之, 「セキュリティを考慮した RDB の XML 出版の提案」, 日本デー
タベース学会 Letters, Vol. 4, No. 1, pp. 109-112, 2005 年 6 月.
成田 和世，北川博之, 「ノイズを含むデータに対する FP 木を用いた頻出飽和アイテム集
合マイニング」, 日本データベース学会 Letters, Vol. 4, No. 1, pp. 157-160, 2005 年 6 月.
飯田敏成, 澤菜津美, 森嶋厚行, 杉本重雄, 北川博之, 「Web ページ移動先発見のための公- 92 -CCS Report: PART II, Research Activities, Results
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開実験システム」, 日本データベース学会 Letters, Vol. 4, No. 2, pp. 21-24, 2005 年 9 月.
町田陽二, 石川佳治, 北川博之, 「移動軌跡ストリームデータのためのインクリメンタルなヒストグラムの管理手法」, 日本データベース学会 Letters, Vol. 4, No. 2, pp. 45-48, 2005 年 9月.
Sophoin Khy， Yoshiharu Ishikawa, and Hiroyuki Kitagawa, "Incremental Clustering Based on
Novelty of On-line Documents", 日本データベース学会 Letters, Vol. 5, No. 1, pp. 57-60, 2006 年
6 月.
町田陽二, 石川佳治, 北川博之, 「マルコフ連鎖モデルに基づく動的な移動ヒストグラム構
築手法」, 日本データベース学会 Letters, Vol. 5, No. 1, pp. 89-92, 2006 年 6 月.
外間智子, 北川博之,「Web データを用いた人物の呼称抽出」, 日本データベース学会 Letters,Vol. 5, No. 2, pp. 49-52, 2006 年 9 月.
城戸健太郎, 天笠俊之, 北川博之「PC クラスタを用いた XML データ並列処理方式の評価」,
日本データベース学会 Letters, Vol. 5, No. 2, pp. 85-88, 2006 年 9 月.
濱本雅史, 北川博之, 「サポートと確信度をもとにした比率規則による線形関係抽出」情報処理学会論文誌：データベース, Vol. 47, No. ownie: カメラ上に指定された過去のランドマ
ーク情報に基づく実世界探し物検索システム」19 (TOD32), pp. 54-71, 2006 年 12 月.
石川佳治, 町田陽二, 北川博之, 「マルコフ連鎖モデルに基づく移動ヒストグラムの動的構
築法」電子情報通信学会論文誌, Vol. J90-D, No. 2, pp. 311-324, 2007 年 2 月.
戸田浩之, 北川博之, 藤村考, 片岡良治, 奥雅博, 「グラフ分析を利用した文書集合からの話題構造マイニンング」電子情報通信学会論文誌, Vol. J90-D, No. 2, pp. 292-310, 2007 年 2月.
Sophoin Khy, Yoshiharu Ishikawa, and Hiroyuki Kitagawa, "A Novelty-based Clustering Method
for On-line Documents", World Wide Web Journal, 2007.
澤菜津美, 森嶋厚行, 飯田敏成, 杉本重雄, 北川博之, 「Web ページ移動先発見のための効率的なクローリング手法」情報処理学会論文誌：データベース, 2007.
辻良繁, 川島英之, 「CC-Optimizer: キャッシュを考慮した問合せ最適化器」, 日本データベース学会 Letters, Vol. 6, No. 1, pp. 45-48, 2007 年 6 月.
濱本雅史, 北川博之,「対称比率規則の抽出手法」, 日本データベース学会 Letters, Vol. 6, No.
1, pp. 73-76, 2007 年 6 月.
呉俊輝, 天笠俊之，北川博之,「構造型 P2P ネットワークにおける負荷分散を考慮した XML
データ処理」, 日本データベース学会 Letters, Vol. 6, No. 1, pp. 93-96, 2007 年 6 月.
広瀬健志郎, 川島英之, 佐竹聡, 今井倫太, 「異種ロボット間でのジェスチャ情報の共有化」,
日本データベース学会 Letters, Vol. 6, No. 1, pp. 125-128, 2007 年 6 月.
佐竹聡，川島英之，今井倫太，安西祐一郎，「Brownie: カメラ上に指定された過去のランドマーク情報に基づく実世界探し物検索システム」知能と情報(日本知能情報ファジィ学会誌)，2007 年 10 月号．
張建偉, 石川佳治, 北川博之, 「トピックを考慮した大規模文書情報源からのレコード抽出」情報処理学会論文誌：データベース, Vol. 48, No. SIG14 (TOD35), pp. 107-123, 2007 年 9月.
山田真一, 渡辺陽介, 北川博之, 天笠俊之, 「データストリーム管理システム Harmonica の設計と実装」情報処理学会論文誌：データベース, Vol. 48, No. SIG14 (TOD35), pp. 91-106,
2007 年 9 月.
渡辺陽介, 北川博之, 「分散ストリーム処理環境における持続型問合せ処理方式」, 日本データベース学会 Letters, Vol. 6, No. 2, pp. 41-44, 2007 年 9 月.

9.5.2 Proceedings••

Takanori Mouri and Hiroyuki Kitagawa, "Extracting New Topic Contents from Hidden Web Sites",
Proc. IEEE International Conference on Information Technology (ITCC 2004), Las Vegas, pp.
314-319, April 2004.
Cui Zhu, Hiroyuki Kitagawa, Spiros Papadimitriou, and Christos Faloutsos, "OBE: Outlier by
Example", Proc. 8th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD- 93 -CCS Report: PART II, Research Activities, Results
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2004), Sydney, Australia, pp. 222-234,May 2004.
Jia-Yu Pan, Hiroyuki Kitagawa, Christos Faloutsos, and Masafumi Hamamoto, "AutoSplit: Fast andScalable Discovery of Hidden Variables in Stream and Multimedia Databases", Proc. 8thPacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2004), Sydney,
Australia, pp. 519-528, May 2004. PAKDD
Yoshiharu Ishikawa, Yuichi Tsukamoto, and Hiroyuki Kitagawa, "Exracting Mobility Statistics
from Indexed Spatio-Temporal Databases", Proc. 2nd Workshop on Spatio-Temporal Database
Management (STDBM'04), Toronto, Canada, pp. 9-16, August 2004.
Chunhua Cui and Hiroyuki Kitagawa, "Topic Activation Analysis for Document Streams Based on
Document Arrival Rate and Relevance", Proc. 20th Annual ACM Symposium on Applied
Computing (SAC 2005), Vol. 2, pp. 1089-1095, Santa Fe, March 2005.
Biplab Kumer Sarker and Hiroyuki Kitagawa, "A Distributed Algorithm for Outlier Detection in a
Large Database", Proc. 4th International Workshop on Databases in Networked Information
Systems (DNIS 2005), LNCS 3433, pp. 300-309, Aizu-Wakamatsu, Japan, March 2005.
Yousuke Watanabe and Hiroyuki Kitagawa, "Adaptive Query Optimization Method for Multiple
Continuous Queries", Proc. International Special Workshop on Databases for Next Generation
Researchers (SWOD 2005), pp.92-95, Tokyo, Japan, April 2005.
Akiyoshi Nakamizo, Toshinari Iida, Atsuyuki Morishima, Shigeo Sugimoto, and Hiroyuki
Kitagawa, "A Tool to Compute Reliable Web Links and Its Applications", Proc. International
Special Workshop on Databases for Next Generation Researchers (SWOD 2005), pp. 146-149,
Tokyo, Japan, April 2005.
Jianwei Zhang, Yoshiharu Ishikawa and Hiroyuki Kitagawa, "Extended Link Analysis for
Extracting Spatial Information Hubs", Proc. International Workshop on Challenges in Web
Information Retrieval and Integration (WIRI 2005), pp. 17-22, Tokyo, Japan, April 2005.
Masafumi Hamamoto, Hiroyuki Kitagawa, Jia-Yu Pan, and Christos Faloutsos, "A Comparative
Study of Feature Vector-Based Topic Detection Schemes for Text Streams", Proc. International
Workshop on Challenges in Web Information Retrieval and Integration (WIRI 2005), pp. 122-127,
Tokyo, Japan, April 2005.
Kazuyo Narita and Hiroyuki Kitagawa, "Mining Frequent Closed Itemsets from Privacy Preserving
Data", Proc. IADIS International Conference e-Society 2005, pp. 355-362, Qawra, Malta, June
2005.
Jianwei Zhang, Yoshiharu Ishikawa, Sayumi Kurokawa, and Hiroyuki Kitagawa, "LocalRank:
Ranking Web Pages Considering Geographical Locality by Integrating Web and Databases", Proc.
16th International Conference on Database and Expert Systems Applications (DEXA 2005), LNCS
3588, pp. 145-155, Copenhagen, Denmark, August 2005.
Cui Zhu, Hiroyuki Kitagawa, and Christos Faloutsos, "Example-Based Robust Outlier Detection inHigh Dimensional Datasets", Proc. 5th IEEE International Conference on Data Mining (ICDM
2005), Houston, USA, pp. 829-832, November 2005.
Sophoin Khy, Yoshiharu Ishikawa, and Hiroyuki Kitagawa, "Novelty-based Incremental Document
Clustering for On-line Documents", Proc. 2nd International Workshop on Challenges in Web
Information Retrieval and Integration (WIRI 2006), pp. 41-50, Atlanta, USA, April 2006.
Kazuyo Narita and Hiroyuki Kitagawa, "Mining Frequent Itemsets from Noisy Data", Proc. 2nd
International Special Workshop on Databases for Next-Generation Researchers (SWOD 2006),
Atlanta, USA, April 2006.
Kentarou Kido, Toshiyuki Amagasa, and Hiroyuki Kitagawa, "Processing XPath Queries in
PC-Clusters Using XML Data Partitioning", Proc. 2nd International Special Workshop on
Databases for Next-Generation Researchers (SWOD 2006), Atlanta, USA, April 2006.
Yoshiharu Ishikawa, Yoji Machida, and Hiroyuki Kitagawa, "A Dynamic Mobility Histogram
Construction Method Based on Markov Chains", Proc. 18th International Conference on Scientificand Statistical Database Management (SSDBM 2006), pp. 359-368, Vienna, Austria, July 2006.
Masafumi Hamamoto and Hiroyuki Kitagawa, "Ratio Rule Mining with Support and Confidence
Factors", Proc. 3rd IEEE International Conference on Intelligent Systems (IS 2006), pp. 500-505,
London, UK, September 2006.

- 94 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Hiroyuki Toda, Ryoji Kataoka, and Hiroyuki Kitagawa, "Topic Structure Mining for Document Sets
using Graph-Based Analysis", Proc. 17th International Conference on Database and Expert Systems
Applications (DEXA 2006), LNCS 4080, pp. 327-337, Krakow, Poland, September 2006.
Tomoko Hokama and Hiroyuki Kitagawa, "Extracting Mnemonic Names of People from the Web",
Proc. 9th International Conference on Asian Digital Libraries (ICADL 2006), LNCS 4312,
pp.121-130, Kyoto, Japan, November 2006.
Hiroyuki Toda, Ko Fujimura, Ryoji Kataoka, and Hiroyuki Kitagawa, "Topic Structure Mining
using PageRank without Hyperlinks", Proc. 9th International Conference on Asian Digital Libraries(ICADL 2006), LNCS 4312, pp.151-162, Kyoto, Japan, November 2006.
Manabu Nakamura, Hideyuki Kawashima, Satoru Satake, and Michita Imai, "RSV: Sensor Data
Analysis System for Human Robot Interaction", Proc. 2nd IASTED International Conference on
Human-Computer Interaction(IASTED-HCI), Chamonix, France, March 2007.
Chantola Kit, Toshiyuki Amagasa, and Hiroyuki Kitagawa, "OLAP Query Processing for XML
Data in RDBMS", Proc. 3rd IEEE International Workshop on Databases for Next-Generation
Researchers, Istanbul, Turkey, April 2007.
Yuan Li and Hiroyuki Kitagawa, "DB-Outlier Detection by Example in High Dimensional
Datasets", Proc. 3rd IEEE International Workshop on Databases for Next-Generation Researchers,
Istanbul, Turkey, April 2007.
Takeshi Kanda, Yutaka Yanagisawa, Takuya Maekawa, Michita Imai, Hideyuki Kawashima andTakeshi Okadome, "A Distributed Inference System on Sensor Nodes using Neighbor's Context
Data", Proc. 3rd IEEE International Workshop on Databases for Next-Generation Researchers,
Istanbul, Turkey, April 2007.
Manabu Nakamura, Hideyuki Kawashima, Satoru Satake, and Michita Imai, "Mana: A Real World
Oriented Query Processing System Supporting Control of Sensor Characteristics", Proc.
International Workshop on SensorWebs, Databases and Mining in Networked Sensing Systems(SWDMNSS), pp. 23--30, Braunschweig, Germany, June 2007.
Satoru Satake, Hideyuki Kawashima, and Michita Imai, "Brownie: Searching Concealed RealWorld Artifacts", Proc. 4th International Conference on Networked Sensing Systems (INSS'07), pp.
159--162, Braunschweig, Germany, June 2007.
Hideyuki Kawashima, "KRAFT: A Real-Time Active DBMS for Signal Streams", Proc. 4thInternational Conference on Networked Sensing Systems (INSS'07), pp. 163--166, Braunschweig,
Germany, June 2007.
Jianwei Zhang, Yoshiharu Ishikawa, and Hiroyuki Kitagawa, "Record Extraction Based on User
Feedback and Document Selection", Proc. Joint Conference of 9th Asia-Pacific Web Conference
and 8th International Conference on Web-Age Information Management (APWeb/WAIM 2007),
LNCS 4505, pp. 574-585, HuangShan (Yellow Mountains), China, June 2007.
Toshiyuki Amagasa, Chunhui Wu, and Hiroyuki Kitagawa, "Retrieving Arbitrary XML Fragmentsfrom Structured Peer-to-Peer Networks", Proc. Joint Conference of 9th Asia-Pacific Web
Conference and 8th International Conference on Web-Age Information Management(APWeb/WAIM 2007), LNCS 4505, pp. 317-328, HuangShan (Yellow Mountains), China, June2007.
Masafumi Hamamoto and Hiroyuki Kitagawa, "Locality-aware Ratio Rule Mining", Proc. 4thInternational Conference on Fuzzy Systems and Knowledge Discovery (FSKD 2007), Vol. 2, pp.
693-698, Haikou, China, August 2007.
Yousuke Watanabe, Shinichi Yamada, Hiroyuki Kitagawa, and Toshiyuki Amagasa, "Integrating a
Stream Processing Engine and Databases for Persistent Streaming Data Management", 18th Int'l
Conference on Database and Expert Systems Applications (DEXA2007), LNCS 4653, pp. 414-423,
Regensburg, Germany, Sept., 2007.
Toshiyuki Amagasa, Lianzi Wen, and Hiroyuki Kitagawa, "Proximity Search of XML Data using
Ontology and XPath Edit Similarity", 18th Int'l Conference on Database and Expert Systems
Applications (DEXA2007), LNCS 4653, pp. 298-307, Regensburg, Germany, Sept., 2007.
Toshiyuki Amagasa, Kentarou Kido, and Hiroyuki Kitagawa, "Querying XML Data using PC
Cluster System", 2nd International Workshop on XML Data Management Tools and Techniques- 95 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007•(XANTEC'07) in conjunction with DEXA 2007, pp. 5-9, Regensburg, Germany, 2007.
Toshiyuki Amagasa, Hiroyuki Kitagawa, and Tatsuya Komano, "Constructing a Web Service
System for Large-scale Meteorological Grid Data", 3rd IEEE Int'l Conf. on e-Science and Grid
Computing (e-Science 2007), Bangalore, India, December 10-13, 2007, (to appear)- 96 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

10. Division of Computational Informatics: Computational Media Group10.1 Research Activity
The Computational Informatics Research Division is a young division founded in 2004.
The medium-term/long-term mission of this division is to investigate novel methods at thefrontier of computational sciences. We are now conducting researches to establish a newframework of computational science whose target is the human society and its
environment.
The new computational science should handle a system including human as a coreelement. This means that the timescale of computational process cannot be changed
arbitrarily depending on the power of computer. A real-time processing is essential. The
new computational science handles enormous amount of sensing data which come from thereal world. It visualizes the data and merges with related simulation results and presents
the output to human eyes in easily understandable manner. We call this new framework as“Real-World Computational Informatics.”
The backbone of real-world computational informatics is a fusion of technologies on
sensing, database, grid computing, and computer network. Researches on cutting-edgecore technologies and development of needs-oriented application systems are conducted inparallel.
The achievements have been published to flagship international journals in the areas ofcomputer vision or virtual reality. We exhibit our booth at Innovation Japan (Tokyo
International Forum) every year since 2005 for public relations. In 2007, our exhibition
titled “Visual Assistance Technologies Using Mixed Reality” received a Microsoft
Innovation Award as the best technology in IT division.
Outline of research activities in the Computational Media Group conducted by major
research funds are listed below.
1) Live 3D video (3D-TV): Multiple audiences can arbitrarily select their viewing
positions of sports events such as soccer games. Our technology enables live transfer
of 3D-TV via network. (Supported by Strategic Information and Communication R&D
Promotion Programme, Ministry of Internal Affairs and Communications).
2) Visual augmentation for pedestrians using surveillance cameras (See-Through Vision):
Citizens can effectively utilize the video data obtained by many surveillance cameras intown. A novel framework is proposed and fundamental technologies are developed.
(Supported by Grant-in-Aid for Scientific Research (A), Japan Society for the
Promotion of Science).
- 97 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

3) Visual augmentation for drivers in ITS (NaviView): Drivers can see the blind spots by
an augmenting visual support utilizing the videos obtained by road surveillance cameras.
(Supported by Special Coordination Funds for Promoting Science and Technology,
Japan Science and Technology Agency).
4) Autonomous Cooperation of Multimedia Sensor Arrays (Massive Sensing): The goal isto establish a novel method in computer vision that can automatically extract a set of
meaningful images expressing what is going on in daily scene. (Supported by
Grant-in-Aid for Young Scientists (A), Japan Society for the Promotion of Science).
5) Privacy Protecting Video Surveillance System: The goal is to develop an advanced
video surveillance system by combining mobile and fixed cameras, and video media
capable to handle privacy information included in the videos. (Supported by
Grant-in-Aid for Young Scientists (A), Japan Society for the Promotion of Science).
10.2 Research Results
10.2.1 Network Transmission and Interactive Display of Live 3D VideoFor 2004-2006, we have conducted a research project “Network Transmission andInteractive Display of Live 3D Video” with Japan Institute of Sports Science (JISS). It
was supported by Strategic Information and Communication R&D Promotion Programme(SCOPE), Ministry of Internal Affairs and Communications. The project leader is Yuichi
Ohta.
The project aims to realize a 3D free-viewpoint video system that multiple audiences canwatch a live sports event played in a distant large-scale space such as a soccer stadium withfreely moving their viewpoints as they like. The other purpose is to create an advanced
contents technology by developing an interactive method for 3D video display whichenables an ordinary person, without any special knowledge about video capturing andediting, to enjoy the 3D video.
We have developed the world first live 3D free-viewpoint video system in which all thefollowing processes are executed in real time; capturing multiple videos, constructing 3Dmodels, transmitting data via network, and rendering 3D video. The key technology torealize the system is a novel 3D modeling method “Player Billboard” that represents a
person by a single plane (polygon) and the dynamic texture mapped on the plane.
In order to realize a 3D video system which works in practical environments such assoccer stadiums rather than laboratory rooms or camera studios, we concentrated our effort
on the R&D to improve the reliability, versatility, and robustness of the 3D video system byconducting more than 20 experiments in Tokyo National Olympic Stadium and Yoyogi
National Gymnasium. As the result, an unexemplified system for live 3D video in a
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Collaborations and Plan 2004-2007

large-scale space has been successfully developed.
A paper describing the technology of the live 3D video system has been accepted andpublished by International Journal of Computer Vision (IJCV), the flagship journal incomputer vision. The system has been awarded “2006 Image Electronics Technology
Award” from The Institute of Image Electronics Engineering of Japan.

Experiments in Tokyo National
Olympic Stadium.

Outline of live 3D video system.

A snapshot of 3D Video.

10.2.2 Visual augmentation for pedestrians using surveillance cameras
For 2006-2009, we are conducting a research project whose title is “See-ThroughVision: Visual Augmentation for Pedestrians Using Surveillance Cameras.” It is
supported by the Grant-in-Aid for Scientific Research (A), Japan Society for the Promotionof Science. The project leader is Yuichi Ohta.
The aim of this research is to create a novel framework for the application ofsurveillance cameras under the inevitable tendency toward to increase the number ofcameras in public space. Usually the surveillance cameras provide an invisible service“safety” to citizens. The use of images obtained by surveillance cameras, however, isclosed to the owners of the cameras. In the framework, each pedestrian can enjoy a- 99 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

visible service provided by utilizing the images from surveillance cameras; “See-ThroughVision” is an example. A pedestrian can see-through a blind area occluded by a building,etc. simply by holding up his PDA toward the blind area. The images of a surveillancecamera looking at the blind area are converted by computer-vision technology andpresented on the display of PDA. As the result, he can see-through occluding objects as if
he were the superman.
The research includes highly original elemental technologies; geometric registration
based on outdoor natural landmarks observed from surveillance cameras, overlaying
methods of see-through image to real scene, visual navigation between multiple images
from distant viewing positions, image treatment for protecting the privacy of people in theimages, etc.

See-Through Vision: Visual augmentation for pedestrians.
10.2.3 Visual Augmentation of Drivers by Dynamic Sensing of Environment
For 2004-2006, we have conducted a research project named “Visual Augmentation by
Dynamic Sensing of Environment (Project Leader: Yuichi Ohta)” in “Risk Discovery and
Avoidance based on Scene and Intention Recognition (General Manager: Toshiyuki
Inagaki)” supported by Special Coordination Funds for Promoting Science and Technology,
Japan Science and Technology Agency.
Our goal is to realize a novel vision augmentation technology that can show hazardous
areas, which drivers cannot see normally in intersections. This technology is useful todiminish the possibility of accidents.
As all the proposed methods are based on Mixed Reality technology, we first havedeveloped a prototype Wind Shield Display (WSD) on which drivers can see various visualkeys through a wind shield on driving.

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Collaborations and Plan 2004-2007

Vehicle and Simulator

Virtual Slope

Wind Shield Display

Floating Virtual Mirror

Then, we have proposed and evaluated a number of visualization methods including
virtual slope, virtual corner mirror, floating virtual mirror, etc. For example, “Virtual Slope”
is designed for drivers who are going to make a turn over opposite lanes. If some cars arealso waiting to make a turn on the opposite lane, they cannot see the vehicles approaching
to the intersection at opposite lanes. Virtual Slope can show all the coming vehicles as if
they were coming down a virtual slope.
10.2.4 Autonomous Cooperation of Multimedia Sensor Arrays Tightly Connected over
Network (Massive Sensing)For 2004-2006, we have conducted a research project named “Autonomous Cooperationof Multimedia Sensor Arrays Tightly Connected over Network (Project Leader: Yoshinari
Kameda)” supported by Grant-in-Aid for Young Scientists (A), Japan Society for the
Promotion of Science (JSPS).
Our goal in the project is to establish a novel computer vision method that can
automatically extract a set of meaningful images that expresses what is going on in dailyscenes. The challenge is that all the locations of a number of cameras and microphones(sensors) are not measured in advance; hence the method needs to estimate the spatial
relationship among sensors on the fry. Based on our proposed methods, our preliminary
system that holds 35 cameras and 8 microphones can suggest the best set of video clips thatis closely related with a video sequence that is given by a user.

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Collaborations and Plan 2004-2007

A Video Sequence in Question

35 surveillance cameras
Suggested Video Set

By mixing data from microphones with video

Correlation

data from a number of cameras, our system canestimate a set of video/audio data that expresses

Featuresan action and browse it visually and acoustically.
We exploit correlation matrix to segment theTimevideo/audio data

10.2.5 Privacy Considering Video Surveillance System by Combining the Advantages ofMobile and Environmental Cameras
Since 2006, we are conducting a research project “Privacy Considering Video
Surveillance System by Combining the Advantages of Mobile and Environmental Cameras(Project Leader: Itaru Kitahara)” for three years. This project is supported by Grant-in-Aid
for Young Scientists (A), Japan Society for the Promotion of Science (JSPS).
This project aims to research/develop an advanced video surveillance system bycombining the advantages of mobile and environmental cameras, and video media which
can appropriately capture, record and display the video information with considering about
the privacy information in the videos. We are developing a mobile camera calibration
method by using visual information captured by mobile and multiple environment cameras,
and a video surveillance system which expands field of view of environment cameras bymerging mobile videos. We are going to implement a video surveillance system with- 102 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

privacy protecting capability on these developed platforms.

Video surveillance system by combining
mobile and environmental cameras.

Mixed reality display demonstrating
our camera calibration method.

10.3 Collaboration
We organized and continually held “Computational Informatics Seminar” in order toshare the awareness of the problems involved in the frontier field, Computational
Informatics. The seminar member includes all the faculties of Computational Informatics
Division and active researchers in related fields invited from other departments of theuniversity and from the National Institute of Advanced Industrial Science and Technology(AIST).
The Computational Media Group and the Grid Research Group of High Performance
Computing Division have jointly planned a research proposal with other research groups
from Kyoto University, etc. The theme of the proposal is “Sensing Grid,” and is originallytargeted to the Grant-in-Aid for Scientific Research on Priority Areas. This activity
opened a door of new project “Sensing Web” for 2007-2009 supported by the Special
Coordination Funds for Promoting Science and Technology.
10.4 Future Plan
Mixed Reality is a cutting-edge technology to present a novel visual world to our eyes,
and is regarded as a promising next-generation human-interface technology. It seamlessly
merges the visual data obtained from the real world and the visualized data generated in thecomputer. The Computational Media Group will continue the researches on thestate-of-the-art technologies; technology for acquisition/analysis/recognition of massive
visual data, computer vision technology for recovery of 3D world from 2D images,
real-time sensing technology of human pose and eye expression, computer graphics
technology for processing/generating visual images, and the Mixed Reality as thetechnology fusion of these elemental ones.
- 103 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

The Computational Media Group is an outstanding research group in the area of Mixed
Reality. We are one of a few groups which continually present high-level papers in oral
sessions of ISMAR every year; the ISMAR, International Symposium on Mixed andAugmented Reality, is the flagship symposium in Mixed Reality. We intend to develop
novel methods to apply this technology to the framework of Computational Science
Researches, and to create a new framework of Computational Science, which should becalled “Real-World Computational Informatics.”
10.5 Publications
10.5.1 Journal Papers
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Hansung Kim, Ryuuki Sakamoto, Itaru Kitahara, Tomoji Toriyama, and Kiyoshi Kogure, Robust
Foreground Extraction Technique Using Background Subtraction with Multiple Thresholds, SPIE
Journal on Optical Engeering. Vol. 46, 097004, (on-line publication 12 pages) (2007.9)
北原 格, 橋本浩一郎, 亀田 能成, 大田友一, サッカーの自由視点映像提示における気の利いた視点選択手法; 日本バーチャルリアリティ学会 論文誌（TVRSJ), Vol.12, No.2,
pp.171-180 (2007.6)
竹村雅幸, 北原格, 大田友一, MR Face 映像における光学的不整合に関する視覚特性の評
価; 日本バーチャルリアリティ学会 論文誌（TVRSJ), Vol.12, No.2, pp.181-190 (2007.6)
Yuichi Ohta, Itaru Kitahara, Yoshinari Kameda, Hiroyuki Ishikawa, Takayoshi Koyama, Live 3D
Video in Soccer Stadium; International Journal of Computer Vision, Vol.75, No.1, pp.173-187(2007.3)
向川康博, 柿沼孝行, 大田友一, 非平面へのパターン投影のための相互反射の補償; 情報処
理学会論文誌 コンピュータビジョンとイメージメディア, Vol.48, pp.98-106 (2007.2)
西崎隆志, 尾形 涼, 中村裕一, 大田友一, 会話シーンを対象とした自動撮影・編集システ
ム; 電子情報通信学会論文誌 D, Vol.J89-D, No.7, pp.1557-1567 (2006.7)
Takahiro Tsuda, Haruyoshi Yamamoto, Yoshinari Kameda, Yuichi Ohta, Visualization Methods for
Outdoor See-Through Vision; Transactions of the IEICE D, Vol.E89-D, 6, pp.1781-1789 (2006.6)
塚田正人, 大田友一, 記憶色に基づく色再現とその高画質化応用; 映像情報メディア学会
誌, 60, 3, pp.348-357 (2006.3)
Fumihiro Taya, Kazuhiro Kojima, Akihiko Sato, Yoshinari Kameda, Yuichi Ohta, NaviView:Virtual
Mirrors for Visual Assistance at Blind Intersection; International Journal of ITS Research, vol.3,
No.1, pp.29-38 (2005.11)
立野圭祐, 竹村雅幸, 大田友一, 協調型複合現実空間における視線認知特性を考慮した視線提示; 日本バーチャルリアリティ学会論文誌, vol.10, No.3, pp.353-361 (2005.9)"竹村雅幸, 大田友一, 協調型複合現実空間のための顔映像生成による視線情報の復元; 日
本バーチャルリアリティ学会論文誌, vol.10, No.3, pp.313-321 (2005.9)"
Motoyuki Ozeki, Yuichi Nakamura, Yuichi Ohta, Automated Camerawork for Capturing Desktop
Presentations; IEE Proceedings-Vision, Image,and Signal Processing, vol.152, No.4, pp.437-447(2005.8)
向川康博, 永井悠文, 大田友一, SpaceRelighter:パターン投影による照明環境の再現; 日本バーチャルリアリティ学会論文誌, Vol.10, No.2, pp.155-162 (2005.6)
西口 敏司, 村上 正行, 亀田 能成, 角所 考, 美濃 導彦, 受講者撮影機能を持つ双方向コ
ミュニケーション記録型講義自動アーカイブシステム, 知能と情報（日本知能情報ファジ
ィ学会誌）, Vol.17, No.5, pp.587-598 (2005.5)
尾関基行, 中村裕一, 大田友一, 注目喚起行動に基づいた机上作業映像の編集; 電子情報通信学会論文誌 D-II, Vol.J88-D-II, No.5, pp.844-853 (2005.5)- 104 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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西口 敏司, 亀田 能成, 角所 考, 美濃 導彦, 大学における実運用のための講義自動アーカ
イブシステムの開発, 電子情報通信学会論文誌, Vol.J88-D-II, No.3, pp.530-540 (2005.3)
竹村雅幸, 原口俊吾, 大田友一, 複合現実空間におけるインタラクティブ・アトラクショ
ン：BLADESHIPS; 日本バーチャルリアリティ学会論文誌, Vol.10, No.1, pp.119-127 (2005.3)
尾形涼, 中村裕一, 大田友一, 制約充足と最適化による映像編モデル; 電子情報通信学会論
文誌 D-II, vol.J87-D- , 12, pp.2221-2230 (2004.12)
尾関基行, 中村 裕一, 大田友一, 話者の注目喚起行動による机上作業映像の自動編集-ユー
ザインターフェースの側面からの評価-; 第３回情報科学技術フォーラム(FIT2004)
情報科学技術レターズ, LK-010, pp.269-272 (2004.9)
竹村雅幸, 大田友一, 協調型複合現実空間のためのアイコンタクトの復元〜視線認知実験と顔映像の高精細化〜; 第３回情報科学技術フォーラム(FIT2004)
情報科学技術レター
ズ, LK-003, pp.243-246 (2004.9)
永井悠文, 向川康博, 大田友一, 動的シーンに対する仮想光学パターンの投影; 第３回情報科学技術フォーラム(FIT2004)
情報科学技術レターズ, LI-007, pp.179-182 (2004.9)
Itaru Kitahara, Yuichi Ohta, Scalable 3D Representation for 3D Video in a Large-Scale Space;
Presence, Vol.13, No.2, pp.164-177 (2004.4)

10.5.2 Proceedings
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Yoshinari Kameda, Itaru Kitahara, Yuichi Ohta, Visual Assistance for Drivers by using Mixed
Reality; CDROM Proceedings of 14th World Congress on Intelligent Transport Systems, 8pages(2007.10)"Hansung Kim, Ryuuki Sakamoto, Itaru Kitahara, Tomoji Toriyama, Kiyoshi Kogure,
Reliability-Based 3D Reconstruction in Real Environment, ACM Multimedia 2007 Short Papers,
CDROM 4 pages, (2007. 9)"Hansung Kim, Itaru Kitahara, Ryuuki Sakamoto, Tomoji Toriyama, Kiyoshi Kogure, 3D Video
System for Capturing Unexpected Moments in Daily Life, SPIE Optics East, CD-R publication,(2007. 9)
Hitoshi Furuya, Itaru Kitahara, Yoshinari Kameda, Yuichi Ohta, Viewpoint-Dependent Quality
Control on Microfacet Billboaｒding Model for Sports Video; Proceedings of IEEE International
Conference on Multimedia and Expo (ICME2007), pp.1199-1203 (2007.7)
Naobumi Nomura, Itaru Kitahara, Yoshinari Kameda, Yuichi Ohta, A Background Modeling
Method with Simple Operation for 3D Video; 3DTV CON 2007 (Capture, Transmission and
Display of 3D Video), 4pages (2007.5)
Yuichi Ohta, Itaru Kitahara, Yoshinari Kameda, Hiroyuki Ishikawa, Takayoshi Koyama, A
Perceptually Correct 3D Model for Live 3D TV; 3DTV CON 2007 (Capture, Transmission and
Display of 3D Video), 4pages (2007.5)
Hansung Kim, Ryuuki Sakamoto, Itaru Kitahara, Tomoji Toriyama, Kiyoshi Kogure, "Virtual
Camera Control System for Cinematographic 3D Video Rendering", 3DTV CON 2007 (Capture,
Transmission and Display of 3D Video), 4pages (2007.5)
Masato Tsukada, Yuichi Ohta, Color Reproduction Based on Memory Color and its
Implementation; The Second International Workshop on Image Media Quality and its Applications
2007, pp.47-51 (2007.3)
Keisuke Tateno, Itaru Kitahara, Yuichi Ohta, A Nested Marker for Augmented Reality ; IEEE
Virtual Reality 2007, pp.259-262 (2007.3)
Morio Nakahara, Itaru Kitahara, Yuichi Ohta, Sensory Property in Fusion of Visual/Haptic Cues byUsing Mixed Reality; World Haptics 2007 (Second Joint EuroHaptics Conference and Symposium
on Haptic Interfaces for Virtual Environment and Teleoperator Systems), pp.565-566 (2007.3)
Toru Miyamoto, Itaru Kitahara, Yoshinari Kameda, Yuichi Ohta, Floating Virtual Mirrors:
Visualization of the Scene behind a Vehicle; 16th International Conference on Artificial Reality andTelexistence (ICAT2006), LNCS4282, pp.302-313 (2006.11)
Takashi Nishizaki, Kouji Kanari, Yoshinari Kameda, Yuichi Ohta, Scene Clustering with Multiple- 105 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Non-Calibrated Cameras; First Korea-Japan Workshop on Pattern Recognition (KJPR), pp.97-102(2006.11)
Hansung Kim, Ryuuki Sakamoto, Itaru Kitahara, Tomoji Toriyama, Kiyoshi Kogure, Robust
Foreground Segmentation from Color Video Sequences Using Background Subtraction with
Multiple Thresholds, First Korea-Japan workshop on Pattern Recognition (KJPR), pp.188-193,(2006. 11)
Yasuhiro Mukaigawa, Takayuki Kakinuma, Yuichi Ohta, Analytical Compensation ofInter-reflection for Pattern Projection; ACM Symposium on Virtual Reality Software andTechnology (VRST2006), pp.265-268 (2006.11)
Masayuki Takemura, Itaru Kitahara, Yuichi Ohta, Photometric Inconsistency on a Mixed-Reality
Face; Fifth IEEE and ACM International Symposium on Mixed and Augmented Reality(ISMAR2006), pp.129-138 (2006.10)
Akihiko Sato, Itaru Kitahara, Yoshinari Kameda, Yuichi Ohta, Visual Navigation System on
Windshield Head-Up Display; CDROM Proceedings of 13th World Congress on Intelligent
Transport Systems, Technical Paper, PaperID 1221, 8pages (2006.10)
Hansung Kim, Itaru Kitahara, Kiyoshi Kogure, Kwanghoon Shon, A Real-time 3D Modeling
System Using Multiple Stereo Cameras for Free-view VideoGeneration, International Conference
on Image Analysis and Recognition (ICIAR2006), Part II. LNCS 4142, Springer, pp. 237-249,(2006. 9)
Unsang Park, Itaru Kitahara, Kiyoshi Kogure, Norihiro Hagita, Anil Jain, ViSE: Visual SearchEngine Using Multiple Networked Cameras, 18th IAPR International Conference on Pattern
Recognition (ICPR 2006), pp. 1204 - 1207, (2006. 8)
Takahiro Tsuda, Itaru Kitahara, Yoshinari Kameda, Yuich Ohta, Smooth Video Hopping for
Surveillance Cameras; The 33rd International Conference on Computer Graphics and Interactive
Techniques (SIGGRAPH2006) Sketches, (2006.7)
Keisuke Tateno, Itaru Kitahara, Yuich Ohta, "A Nested Marker for Augmented Reality", The 33rd
International Conference on Computer Graphics and Interactive Techniques (SIGGRAPH2006)
Sketches, (2006.7)
Hansung Kim, Ryuuki Sakamoto, Itaru Kitahara, Kiyoshi Kogur, "From Inside and Outside:
Immersive 3D Video Generation"The 33rd International Conference on Computer Graphics andInteractive Techniques (SIGGRAPH2006) Poster, (2006.7)
Yasuhiro Mukaigawa, Takayuki Kakinuma, Yuichi Ohta, A Fast Compensation Method ofInter-reflection for Pattern Projection onto a Non-planar Surface; IEEE International Workshop on
Projector-Camera Systems (PROCAMS2006), pp.9-10 (2006.6)
Hansung Kim, Ryuuki Sakamoto, Itaru Kitahara, Kiyoshi Kogure, Cinematized Reality:
Cinematographic 3D Video System for Daily Life Using Multiple Outer/Inner Cameras, IEEE
Workshop on Three-Dimensional Cinematography (3DCINE'06), CD-ROM Proceedings 8 pages,(2006. 6)"Hansung Kim, Ryuuki Sakamoto, Itaru Kitahara, Kiyoshi Kogure, An Immersive Free Viewpoint
Video System Using Multiple Outer/Inner Cameras, 3rd International Symposium on 3D Data
Processing, Visualization and Transmission (3DPVT 2006) , CD-ROM Proceedings 8 pages , (2006.
6)
Takashi Nishizaki, Yoshinari Kameda, Yuichi Ohta, Visual Surveillance Using Less ROIs ofMultiple Non-Calibrated Cameras; Proceedings of Asian Conference on Computer Vision 2006
(ACCV 2006), vol.3851, pp.317-327 (2006.1)
Jeremy Bluteau, Itaru Kitahara, Yoshinari Kameda, Haruo Noma, Kiyoshi Kogure, Yuichi Ohta,
Visual Support for Medical Communication by Using Projector-Based Augmented Reality and
Thermal Markers; Proceedings of 15th International Conference on Artificial Reality andTelexistence (ICAT2005), pp.1-8 (2005.12)
Takahiro Tsuda, Haruyoshi Yamamoto, Yoshinari Kameda, Yuichi Ohta, Visualization Methods for
Outdoor See-Through Vision; Proceedings of 15th International Conference on Artificial Reality
and Telexistence (ICAT2005), pp.1-8 (2005.12)
Takahiro Koizumi, Yoshinari Kameda, and Yuichi Nakamura, Retrieval of Personal Experience- 106 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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Records Using Relevance Feedback with a Structuring Filter, CDROM Proceedings of 2nd
European Workshop on the Integration of Knowledge Semantic and Digital Media Technologies(EWIMT), 8 pages (2005.11)
Itaru Kitahara, Ryuuki Sakamoto, Mika Satomi, Kaoru Tanaka, Kiyoshi Kogure, CinematizedReality: Cinematographic Camera Controlling 3D Free-Viewpoint Video, 2nd IEE European
Conference on Visual Media Production (CVMP2005), pp.154-161, (2005. 11)
Fumihiro Taya, Yoshinari Kameda, Yuichi Ohta, NaviView: Virtual Slope Visualization of Blind
Area at an Intersection; Proceedings of 12th World Congress on ITS, Scientific paper, CD-ROM,
pp.1-8 (2005.11)
Akihiko Sato, Yoshinari Kameda, Yuichi Ohta, Adaptive Positioning on Windshield for Information
Display; Proceedings of 12th World Congress on ITS, Technical paper, CD-ROM, pp.1-12(2005.11)
Keisuke Tateno, Masayuki Takemura, Yuichi Ohta, Enhanced Eyes for Better Gaze-Awareness in
Collaborative Mixed Reality; IEEE and ACM International Symposium on Mixed and Augmented
Reality (ISMAR 2005),, pp.100-103 (2005.10)
Kazuhiro Kojima, Akihiko Sato, Fumihiro Taya, Yoshinari Kameda, Yuichi Ohta, NaviView: Visual
Assistance by Virtual Mirrors at Blind Intersection; Proceedings of 8th International IEEE
Conference on Intelligent Transportation Systems (ITSC'05), (2005.9)
Keisuke Tateno, Masayuki Takemura, Yuichi Ohta, Enhanced Eyes for Better Gaze-Awareness in
Mixed Reality; The 32nd International Conference on Computer Graphics and Interactive
Techniques (SIGGRAPH2005), Sketches, DVD, (2005.8)
Ryuuki Sakamoto, Itaru Kitahara, Mika Satomi, Kaoru Tanaka, Kiyoshi Kogure, CinematizedReality: Cinematographic Camera Control in 3D Videos, The 32nd International Conference on
Computer Graphics and Interactive Techniques (SIGGRAPH2005), Sketches, DVD, (2005.8)
Takashi Nishizaki, Ryo Ogata, Yoshinari Kameda, Yuichi Ohta, Yuichi Nakamura, Video Quality
Analysis for an Automated Video Capturing and Editing System for Conversation Scenes; IEEE
International Conference on Multimedia and Expo (ICME2005), pp.1-4 (2005.7)"
Hidenori Tanaka, Itaru Kitahara, Hideo Saito, Hiroshi Murase, Kiyoshi Kogure, Norihiro Hagita,
Dynamic Visual Learning for People Identification with Sparsely Distributed Multiple Surveillance
Cameras, LNCS 3540, Springer, 14th Scandinavian Conference on Image Analysis (SCIA2005),
pp.130-140, (2005. 6)
Masayuki Takemura, Yuichi Ohta, Generating High-Definition Facial Video for Shared Mixed
Reality; Proceedings of IAPR Conference on Machine Vision Applications (MVA2005),
pp.422-425 (2005.5)
Hicham Bouchmaif, Yoshinari Kameda, Yasuhiro Mukaigawa, Yuichi Ohta, Probabilistic
Framework for Intelligent Filming by Switching Temporarily Locked Pan-Tilt Cameras;
Proceedings of IAPR Conference on Machine Vision Applications (MVA2005), pp.108-111(2005.5)
Takayoshi Koyama, Yasuhiro Mukaigawa, Yoshinari Kameda, Yuichi Ohta, Real-TimeTransmission of 3D Video to Multiple Users via Network; Proceedings of IAPR Conference on
Machine Vision Applications (MVA2005), pp.328-331 (2005.5)
Itaru Kitahara, Masami Ito, Haruo Noma, Kiyoshi Kogure, Norihiro Hagita, Thermal-ID: A
Personal Identification Method Using Body Temperature, The 3rd International Conference on
Pervasive Computing (Pervasive 2005) Advances in Pervasive Computing, pp. 69-72, (2005. 5)
Yoshuke Tsubuku, Yuichi Nakamura, Yuichi Ohta, Object Tracking and Object Change Detection in
Desktop Manipulation for Video-Based Interactive Manuals; Pacific-Rim Conference on
Multimedia 2004, pp.104-112 (2004.12)
Hansung Kim, Itaru Kitahara, Kiyoshi Kogure, Norihiro Hagita, Kwanghoon Sohn, Sat-Cam:
Personal Satellite Virtual Camera, LNCS 3333, Springer, Advances in Multimedia Information
Processing, The 5th Pacific-Rim Conference on Multimedia (PCM2004), Part III, pp.87-94, (2004.
12)
Masayuki Takemura, Shogo Haraguchi, Yuichi Ohta, An Interactive Attraction in Mixed Reality- 107 -CCS Report: PART II, Research Activities, Results
Collaborations and Plan 2004-2007

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-BLADESHIPS-; International Conference on Virtual System MultiMedia (VSMM2004) Hybrid
Realities and Digital Partners, pp.1152-1158 (2004.11)
Yoshinari Kameda, Taisuke Takemasa, Yuichi Ohta, Outdoor See-Through Vision Utilizing
Surveillance Cameras; IEEE and ACM International Symposium on Mixed and Augmented Reality(ISMAR04), pp.151-160 (2004.11)
Yasuhiro Mukaigawa, Hirohumi Nagai, Yuichi Ohta, SpaceRelighter -Recording and Reproducing
Illumination in a Real Scene-; International Conference on Virtual Systems and Multimedia(VSMM2004), pp.109-118 (2004.11)
Yoshinari Kameda, Jun Shingu, Satoshi Nishiguchi, and Michihiko Minoh, Active Lighting for
Object Brightness Control
Proceedings of 2004 International Conference on Cyberworlds (CW2004), pp.266-273 (2004.11)
Takashi Nishizaki, Ryo Ogata, Yuichi Nakamura, Yuichi Ohta, Video Contents Acquisition and
Editing for Conversation Scene; Knowledge-Based Intelligent Information and Engineering
Systems (KES'2004), LNAI3213 (Part 1), (2004.9)
Takuya Kosaka, Yuichi Nakamura, Yuichi Ohta, Yoshinari Kameda, Video-Based Interactive Mediafor Gently Giving Instructions; Knowledge-Based Intelligent Information and Engineering Systems(KES'2004), LNAI3213 (Part 1), pp.411-418 (2004.9)
Masayuki Takemura, Shungo Haraguchi, Yuichi Ohta, BLADESHIPS -An Interactive Attraction in
Mixed Reality-; The 31st International Conference on Computer Graphics and Interactive
Techniques (SIGGRAPH2004), (2004.8)
Yoshinari Kameda, Taisuke Takemasa, Yuichi Ohta, Outdoor Mixed Reality Utilizing Surveillance
Cameras; The 31st International Conference on Computer Graphics and Interactive Techniques(SIGGRAPH2004), (2004.8)
Itaru Kitahara, Kiyoshi Kogure, Norihiro Hagita, Stealth Vision for Protecting Privacy, 17th
International Conference on Pattern Recognition (ICPR 2004), Vol.4, pp.404-407, (2004. 8)
Yoshinari Kameda, Takayoshi Koyama, Yasuhiro Mukaigawa, Fumito Yoshikawa, Yuichi Ohta,
Free Viewpoint Browsing of Live Soccer Games; 2004 IEEE International Conference on
Multimedia and Expo(ICME), pp.1-4 (2004.6)
Motoyuki Ozeki, Yuichi Nakamura, Yuichi Ohta, Video Editing Based on
Behaviors-for-Attention-An Approach to Professional Editing Using a Simple Scheme-; 2004
IEEE International Conference on Multimedia and Expo(ICME), pp.1-4 (2004.6)
Motoyuki Ozeki, Yuichi Nakamura, Yuichi Ohta, Automated Camerawork For Capturing
Desktop Presentations-Camerawork Design And Evaluation In Virtual And Real Scenes-; 1stEuropean Conference on Visual Media Production(CVMP), pp.211-220 (2004.3)- 108 -