Welcome to Web site of 3D Active-Site Science

This site provides the information on activity and main results of the 3D Active-Site Science Project.  For further information please follow the links listed in the left menu column.

Information

2018/10/13-14 The 8th Report Meetinge of recent results will be held in Ibaraki Univ.

Special issue of JPSJ related to 3D active-site science was published. It is still on the way. Topics papers will gradually be published. Link to JPSJ Top page Link to SPECIAL TOPICS

Recent Activity

"4th Spring School" was held at Nara Institute of Science and Technology(NAIST).  There were 40 attendees including the lecturers.

The program was as follows,

*1st day : Lectures by Prof. Hayashi (Nagoya Institute of Technology), Prof. Matsui(Institute for Molecular Science), Prof. Wakabayashi(Osaka Univ.),

Prof Yamazaki(Hokkaido Univ.) and Poster Presentations

* 2nd day : Lecture by Prof. Kawasaki(NIMS),Prof. Suzuki(NAIST),Prof. Shibayama(Jichi Medical Univ.),Prof. Hayashi (Nagoya Institute of Technology),Prof. Matsushita(JASRI) and Prof. Wakabayashi(Osaka Univ.)

Mr.Masato Anada and Mr.Kazuki Nagai, both are from Osaka University, received poster award.

2018/6/10 Site Visit of NAIST was held after "Spring School".

Project members visited Prof. Daimon's and Prof. Yamada's laboratory.

2018/5/31  A study of project members has been published in ACS Catalysis .

2018/3/10-11 The 7th Report Meetinge of recent results was held in Hiroshima City Univ.

Date: 2018/3/10-11
Venue: Hiroshima City Univ. (Hiroshima, Japan)
Access; https://www.hiroshima-cu.ac.jp/english/category0029/

2018/1/9-10 A member of this project gave an invited talk

Workshop Name:

ISSP - J-PARC Joint Workshop on Science Frontier by Neutron Scattering
～ The 16th Korea-Japan meeting on Neutron Science ～

Date: 2018/1/9-10

Venue:  The Institute for Solid State Physics, U. Tokyo (Kashiwa)

Speaker:  K. Ohoyama (Ibaraki Univ.)

Title: Novel usage of neutrons:  White neutron holography for investigations of local atomic structures

2017/12/28 A study of project members has been published in Physical Review B

URL： https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.214207
Journal：Physical Review B

Title ： Impurity position and lattice distortion in a Mn-doped Bi2Te3 topological insulator investigated by x-ray fluorescence holography and x-ray absorption fine structure

Authors : S. Hosokawa, J. R. Stellhorn, T. Matsushita, N. Happo, K. Kimura, K. Hayashi, Y. Ebisu, T. Ozaki, H. Ikemoto, H. Setoyama, T. Okajima, Y. Yoda, H. Ishii, Y.-F. Liao, M. Kitaura, and M. Sasaki

Press (Japanese):

Kumamoto Univ.: Link to the Article

JASRI: Link to the Article

2017/12/22-23  The Report Meeting of recent results of the open type research groups was held.

Date ： 2017/12/22-23

Venue：CIVI center, (Osaka, Japan)

2017/12/21 A study of project members has been published in Nano Letters

Journal：Nano Letters, 17, 7533-7538, 2017.
Title：Individual Atomic Imaging of Multiple Dopant Sites in As-Doped Si Using Spectro-Photoelectron Holography
Authours：K. Tsutsui, T. Matsushita, K. Natori, T. Muro, Y. Morikawa, T. Hoshii, K. Kakushima, H. Wakabayashi, K. Hayashi, F. Matsui,
and T. Kinoshita 

URL：http://pubs.acs.org/doi/10.1021/acs.nanolett.7b03467

Press: OPTRONICS, fabcross for エンジニア, 

Tokyo Institute of Technology: Link to the article

SPring-8: Link to the article

Nagoya Institute of Technology: Link to Article

Nara Institute of Science and Technology: Link to Article
Osaka Univ. :Link to Article

2017/12/12 A paper of T. Muro, Y. Kato, and T. Matsushita who are members in this area was published

in Review of Scientific Instruments.

T. Muro of JASRI in “Technique A02”, T. Matsushita of JASRI in “Theory A03”, and their collaborators developed a high-resolution display-type
retarding field analyzer (RFA) for photoelectron holography.

Title: Wide-angle display-type retarding field analyzer with high energy and angular resolutions
Journal: Review of Scientific Instruments 88, 123106 (2017)
Authors: Takayuki Muro, Takuo Ohkochi, Yukako Kato, Yudai Izumi, Shun Fukami, Hidenori Fujiwara, and Tomohiro Matsushita
https://doi.org/10.1063/1.4990769

Conference:Swedish-Japanese Workshop on Nano-Structure Science by Novel Light Sources

Date：　2017/10/2  9:00- 10/3 12:00
Venue：　”Lundmarksalen” (lecture hall in the Astronomy building Lund University) , Lund , Sweden

 

Prof. Ohoyama (Ibaraki Univ) had a lecture about neutron holography to 38 students of Chuo Senior High School in Omitama, Ibaraki.

2017/9/7 Prof. Daimon gave invited talks at NSRRC in Taiwan.

Date:7 September,2017

Place:NSRRC, Hsinchu, Taiwan

Title:：“Imaging 3D Atomic Structure Around Specific Atoms Using Atomic-resolution Holography” 

2017-9/1 Prof. Daimon gave invited talks at Keihanna.

Date:7 September,2017 15:50-17:00

Place:National Diet Library

Title:Viewing atoms by holography -New science on active-site atoms which govern function of materials-

2017/8/19 A paper of members of this project was published in Science Advances.

The authors reports novel technique, multiple-wavelength neutron holography developed in J-PARC (Tokai, Ibaraki, Japan), which have drastically enhanced accurasy of reconstracted atomic images, in particular, light elements, such as B, H, Li, F.

Journal ： Science Advances
Title： Multiple-wavelength neutron holography with pulsed neutrons

Authors: Kouichi Hayashi, Kenji Ohoyama, Naohisa Happo, Tomohiro Matsushita, Shinya Hosokawa, Masahide Harada, Yasuhiro Inamura, Hiroaki Nitani, Toetsu Shishido, Kunio Yubuta

HP: http://advances.sciencemag.org/content/3/8/e1700294

2017/7/22-23 A public experiment for children was conducted at the Himeji Science Museum

At the Himeji Science Museum's "Science stall village" event, a public experiment "Let's see the shape of voice" was conducted. It is an experiment that shows a beautiful interference pattern of waves in the resonance state when placing powder on the board and applying vibration. We held for 2 days at 9: 30-16: 00. There were about 500 people in attendance.

TItle： Correlation Between High Gas Sensitivity and Dopant Structure in W-doped ZnO Authors：Shun Fukami, Munetaka Taguchi, Yutaka Adachi, Isao Sakaguchi, Ken Watanabe, Toyohiko Kinoshita, Takayuki Muro, Tomohiro Matsushita, Fumihiko Matsui, Hiroshi Daimon and Taku T. Suzuki Journal：PHYS. REV. APPLIED 7, 064029 (2017) pp1-6 HP：https://doi.org/10.1103/PhysRevApplied.7.064029 (abstract) Zinc oxide is a representative material which widely used as solid-state gas sensors. However, the local atomic structure around dopant site and these segregation mechanism is not fully understood. The authors find clear evidence for substitution of segregated W atoms into Zn sites in the subsurface layer by photoelectron diffraction techniques, which drastically improves the sensing response. This surface’s structure-function relationship could tell us about how best to prepare these films for this important gas sensing application.

2017/6/28 A paper of a member of this project was published in ACS Catalysis.

2017/6/9 Prof. Daimon gave keynote speech at EMNANO 2017 at Fukui.

Date: 2017/6/9
Place: AOSSA, Fukui, Japan

Title:3D Local structure Science of Active-site by Atomic-Resolution Stereography and Holography. 

2017/6/7 A paper of a member of this project was published in Physical Review B.

The study on the local atomic arrangement in beta titanium alloys by the research group consisting of Associate Prof. Yamamoto (Open Type Research Member), 
Prof. Hayashi, Prof. Hosokawa (A05 Planned Research Members) and Associate Prof. Happo (A12 Planned Research Member) is published in ACTA MATERIALIA. 
The study is also introduced in newspapers, CHUGOKU SHIMBUN newspaper on April 29 and NIKKEI SANGYO SHIMBUN newspaper on May 15. 
The local atomic arrangement near a rare metal atom, Nb, in a beta titanium binary alloy was examined by using X-ray fluorescence holography. 

16 members of Open type Researches discussed with the members of this projects about the research plans.

Date：2017/5/1  13:30-5/2 12:00
Venue：SPring-8 (hyogo)
　　（http://www.spring8.or.jp/ja/about_us/access/）

2017/4/21　A member had a lecture to 26 high school students about holography method.

2017/4/19 A paper of a member of this project was published in Nano Letters

2017/4/3　16 Proposals have been accepted as Open-type Researches in 2017-19

2017/3/29 A paper of our members was published in ACS Nano.

2017/3/19 A paper of a member of this project won a paper award of Physical Society of Japan 2017

2017/3/18　Two Members of this project gave invited talks in 72th Annual Meeting of

Physical Society of Japan

2017/3/15   A paper of our members was published in Chemistry A European Journal

2017/3/14　A student of this project won a poster award of Quantum Beam Science Festa at Tsukuba

2017/3/13-15 The users meeting of MAX IV was held in Lund, Sweden. Some of the members attended to the meeting. After the meeting, the members visited MAX IV and discussed with Dr. Christoph Quitmann (Director of MAX IV) and other beamline staff members, especially about the future collaboration and organization of joint workshop held in October.

One of the target of “3D-active site project” is to promote international collaborations. We consider that MAX IV, most brilliant synchrotron light source, in Sweden can be a candidate of the oversea basement of our project. For future collaboration between European scientists and Japanese members, we plan to organize the joint workshop in October. 

On March 13-15, the users meeting of MAX IV was held. Some members of our project attended to the meeting in order to obtain the detailed information and status of MAX IV. The emittance smaller than 1nm・rad is designed, and the facility was opened from June in 2016. Some user’s activities seem to be started. There are two storage rings, with acceleration energy of 1.5 and 3GeV. About 300 participants attended and the satellite workshops for industrial use etc were held. 

The commissioning of storage rings seems to be well. In the 3GeV ring, storage current up to 200mA was achieved. 24 hours topping up injection is also successful at the storage current of 160mA. The emittance of 340pm・rad was also achieved when the storage current is a few mA. 5 insertion devises has been installed. Single bunch operation of 2.8mA (maximum 8.5mA) was succeeded. For 1.5GeV ring, 135mA topping up operation is possible (maximum 150mA). 

Two beamlines (nanoMAX and BioMAX) which are hard-x-ray beamlines has started their first user’s beam time. Next proposal will soon be accepted. In the soft-x-ray region, ambient pressure photoemission and RIX beamlines are now in under commissioning. 
 
In MAX IV, ~3000 users/ year will visit and ~500 publication is expected. Further ~100 PhD papers will be produced. In the initial stage, the budget for 14 beamlines is approved. Plans of up to 22 beamlines are discussed. 
 
The guesthouse with 21rooms will be available in September 2017. 

The neutron beam facility so called ESS is under construction nearby MAX IV. ESS will start their beamtime in 2023 and the construction will be completed in 2025.

After the users meeting, some members of “3D active-site” project (Daimon, Hayashi, Matsui and Kinoshita) visited MAX IV. Members obtained detailed information of some related beamlines at MAX IV and presented status and activities of the project. Especially, the proposal to NanoMAX beamline was discussed. Further, the detailed discussion of the joint workshop held in October was discussed.

2017/3/4-5 5th Report Meeting of Recent Results was held at Atami

Date: 2017/3/4 - 3/5 Venue：Izuyama Kenshu Center （http://www.uniho.co.jp/hoyojyo/atami.html ） Details ↓ https://sites.google.com/a/3d-activesite.jp/170304/

2017/1/30 A paper of our members about a collaboration work in this project was published on Organometallics.

Journal： Organometallics Title ： Synthesis of (Adamantylimido)vanadium(V) Dimethyl Complex Containing (2-Anilidomethyl)pyridine Ligand and Selected Reactions: Exploring the Oxidation State of the Catalytically Active Species in Ethylene Dimerization Authors： K. Nomura, T. Mitsudome, A. Igarashi, G. Nagai, K. Tsutsumi, T. Ina, T. Omiya, H. Takaya, and S. Yamazoe URL ： http://pubs.acs.org/doi/abs/10.1021/acs.organomet.6b00727

2017/1/11-15 Symposium on Surface and Nano Science 2017(SSNS'17) was held at Furano

2016/12/20-21 Local Functional Properties Emerging at Active Sites on Atomic Layers was held at ISSP.

Date :2016/12/20(Tue)-2016/12/21       Time : 1:00 PM - 3:30 PM        Place : Lecture Room (A632), 6th Floor, ISSP          Committee Chair : Hiroshi Daimon (NAIST)      Details Page : http://osada.issp.u-tokyo.ac.jp/SATL3D/home.html

Name: Chaimongkolkunasin Sapanna Conference：International Symposium on Catalysis and Fine Chemicals 2016 (C&FC2016) Date：2016年11月11－14日 Venue：Howard Civil Service International House, Taipei, Taiwan Title: Synthesis and Reaction Chemistry of (Imido)Vanadium(V)-Alkylidene Complexes: Highly-Active Olefin Metathesis Catalysts URL: http://www.cfc2016.org/index.php

2016/8/16 Our member,  Ken Motokura, won the Challenging Research Award 2016, Tokyo Institute of Technology

Research Project : Multi-Active Site Surface for Novel Molecular Transformation http://www.rso.titech.ac.jp/cat7/detail_32.html

2016/08/01 Our member, Takato Mitsudome, was promoted from Assistant Professor to Associte Professor of Department of Materials Engineering  Science, Graduate School of Engineering Science, Osaka University.

2016/7/26 Our member's paper was published in Journal of Computational Chemistry and its figure was selected as Front Cover.

Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile Yusuke Kanematsu, Masanori Tachikawa, and Yu Takano Journal of Computational Chemistry 37, 2140-2145 (2016). http://onlinelibrary.wiley.com/doi/10.1002/jcc.24438/abstract Cover Page : http://onlinelibrary.wiley.com/doi/10.1002/jcc.24458/full The short hydrogen bond between tyrosine Yz and D1-His190 of photosystem II (PSII) is involved in the oxidation of water at the Mn cluster. We investigated the short hydrogen bond, using multicomponent quantum mechanics, where the quantum fluctuation of a hydrogen nucleus was incorporated into electronic structure calculation. Our computation demonstrated that the deuteration for hydrogen in the short hydrogen bond of PSII led to the reduction of the O…N distance. It indicated an inverse Ubbelohde effect typically recognized in strong and symmetric hydrogen-bonding clusters such as FHF– and H­­­­­­3O­2–.

2016/7/16 Our member's paper was published in PHYSICAL REVIEW LETTERS

Nonvortical Rashba Spin Structure on a Surface with C1h Symmetry  Emilia Annese,Takuya Kuzumaki,Beate Müller,Yuta Yamamoto,Hiroto Nakano,Haruki Kato,Atsushi Araki,Minoru Ohtaka,Takashi Aoki,Hirotaka Ishikawa,Takashi Hayashida,Jacek R. Osiecki,Koji Miyamoto,Yasuo Takeichi,Ayumi Harasawa,Koichiro Yaji,Tetsuroh Shirasawa,Koh-ichi Nittoh,Wooil Yang,Kazushi Miki,Tatsuki Oda,Han Woong Yeom, and Kazuyuki Sakamoto PHYSICAL REVIEW LETTERS  117, 016803 (2016)  The Rashba-Bychkov (RB) effect generates spin-polarized electronic states even in non-magnetic materials, and shows a great potential towards practical application of spintronics. This paper reports the observation of a peculiar RB band, which was not expected so far, originating from the C1h symmetry of the surface.

2016/7/06 Our member's paper was published in Japanese Journal of Applied Physics

2016/7/1 VUVX 2016 satellite workshop "Local 3D atomic and electronic structure imaging"

2016/4 Proceedings of "Element Specific Structure Determination in Materials on Nanometer and Sub-Nanometer Scales using modern X-Ray and Neutron Techniques" are published on ZEITSCHRIFT FÜR PHYSIKALISCHE CHEME.  

Special Issue: Element Specific Structure Determination Using Modern X-ray and Neutron Techniques / Wolf-Christian Pilgrim, Koichi Hayashi, Shinya Hosokawa, Pawel Korecki

2016/3/28 Our member's paper was issued from Journal of Applied Physics.

Large As sublattice distortion in sphalerite ZnSnAs2 thin films revealed by x-ray fluorescence holography Kouichi Hayashi, Naotaka Uchitomi, Keitaro Yamagami, Akiko Suzuki, Hayato Yoshizawa, Joel T. Asubar, Naohisa Happo and Shinya Hosokawa J. Appl. Phys. 119, 125703 (2016) http://dx.doi.org/10.1063/1.4945004

2016/3/21 Our member's paper was issued from Applied Physics Letters.

A divalent rare earth oxide semiconductor: Yttrium monoxide Kenichi Kaminaga, Ryosuke Sei, Kouichi Hayashi, Naohisa Happo, Hiroo Tajiri, Daichi Oka, Tomoteru Fukumura, Tetsuya Hasegawa Appl. Phys. Lett. 108, 122102 (2016) http://dx.doi.org/10.1063/1.4944330

2016/3/1-3/2 Our supported event "Seminar at Insutitute for Protein Research" was held. 

Date ： 2016/3/1 9:30 - 2016/3/2 16:30 Place ： Research Center for Advanced Science and Technology Access  http://www.rcast.u-tokyo.ac.jp/home/access/index_en.html HP ： http://www.protein.rcast.u-tokyo.ac.jp/tanpakuken2016/ Please click here to see the poster.

2016/02/15 Our news letter was issued.

【Contens】  * Event reports  * Achievements      * Schedule of events

2016/2/9 A paper of the collaborative research between our planned research groups was published from Chem. Eur. J.

A result of collaborative research between Nano Catalysts Group (Prof. Motokura) and Surface/Interface Holography (Prof. Wakabayashi and Dr. Tajiri) was issued from Chem. Eur. J.  Authors : H. Noda, K. Motokura, Y. Wakabayashi, K. Sasaki, H. Tajiri, A. Miyaji, S. Yamaguchi, T. Baba Title : Direct Estimation of the Surface Location of Immobilized Functional Groups for Concerted Catalysis Using a Probe Molecule Journal : Chem. Eur. J., Accepted manuscript DOI: 10.1002/chem.201600263 web: http://onlinelibrary.wiley.com/doi/10.1002/chem.201600263/full

2016/1/23 Site Visit in Tokyo Metropolitan University and Tokyo Institute of Technology and Coordination Committee Meeting

Site Visit of laboratories of Tokyo Metropolitan University and Tokyo Institute of Technology was held.  After presentations of recent results of groups of the two university, we visit laboratories of Prof. Nomura, Prof. Tsutsui, Pro. Wakabayashi and Prof. Motokura.  We also had a Coordination Committee Meeting to discuss the project plans including the 3rd anual report meeting, organization of the next international conference and so on.

2015/12/22 A paper of the collaborative research between our planned research groups was published from ACS Catalysis.

Journal：ACS Catal., Just Accepted Manuscript  Tittle：Design of Core-Pd/Shell-Ag Nanocomposite Catalyst for Selective Semihydrogenation of Alkynes Authors ：T. Mitsudome, T. Urayama, K. Yamazaki, Y. Maehara, J. Yamasaki, K. Gohara, Z. Maeno, T. Mizugaki, K. Jitsukawa, K. Kaneda   DOI: 10.1021/acscatal.5b02518  http://pubs.acs.org/doi/abs/10.1021/acscatal.5b02518

2015/12/14 Our member's paper was published and its press release was issued.

Journal ：Scientific Reports (Electric Journal of Nature Publishing Group) Tittle：Time-resolved X-ray Tracking of Expansion and Compression Dynamics in Supersaturating Ion-Networks Authors ：Y. Matsushita, H. Sekiguchi, K. Ichiyanagi, N. Ohta K. Ikezaki, Y. Goto, Y. C. Sasaki DOI No.：10.1038/srep17647 URL:www.nature.com/articles/srep17647     Press Release Unirersity of Tokyo : http://www.k.u-tokyo.ac.jp/info/entry/22_entry441/ SPring-8 :  http://www.spring8.or.jp/ja/news_publications/press_release/2015/151214/ Nikkei web :  http://release.nikkei.co.jp/detail.cfm?relID=402479&lindID=5

2015/12/5 Site Visit and Coordination Committee Meeting in Okayama University

2015/11/28 The lectures at "Spring School" was released at Youtube.

Click here to watch the lectures

2015/11/27-28 Our supported workshop "The present and future of organic photovoltaics" was held. 

Date ： 2015/11/27 （Fri）-28(Sat) Place ： Graduate School of Materials Science, Nara Institute of Science and Technology Click here for the detailed information. Organized by Nara Institute of Science and Technology Supported by "3D-active Site Science"

2015/11/14-15 A supported program was attended to the event "Science Agora".

2015/11/13-15 9th Joint Symposium of the MEXT Projects on Condensed Matter Science was held. 

Date ：2015/11/13(Fri)-15(Sun) Place：University of Tokyo            ・Lecture Hall on 5th Floor of Science Chemistry Bldg. on Nov.13 http://www.topological-qp.jp/ryoikioudan2015/index.html The members gave lectures. Date & time ：15:20-16:50 on 2015/11/13(Fri) ● Hiroshi Daimon （Nara Institute of Science and Technology） ● Kouichi Hayashi（Nagoya Institute of Technology） ● Yuji Sasaki （University of Tokyo）

2015/11/12  A member of this project delivered a lecture on holography in Graduate School of Ibaraki University.

Prof. Ohoyama (Ibaraki Univ) gave a lecture on neutron holography in graduated school of science and engineering, Ibaraki Univ (Hitachi, Japan).  Importance of understanding of local structures, principle of holography and resent results of holography were explained to students of the master course.

2015/09/16 Head Investigator, Prof. Hiroshi Daimon has given a special lecture at the 116th Meeting of Calysis Society of Japan

Date ： 2015/9/16（Wed） Venue ： Mie University Title ： Challenge to visualize the atomic rearrangement in chemical reaction by “3D active-site science” Speaker ： Prof. Hiroshi Daimon （NAIST） http://www.shokubai.org/116/

2015/09/13 The cosponsored symposium has been held at the 53rd Annual Meeting of Biophysical Society of Japan and the members of 3D Active-Site Science have given their speech

Date ： 2015/9/13(Sun) Venue ： Kakuma Campus of Kanazawa University Symposium Title ： Novel 3D imaging of active sites in biomolecular systems to understand the biochemical functions 1) Direct 3D atomic structure analysis project for active-site of bio-molecules by atomic-resolution holography(Hiroshi Daimon /NAIST) 2) Single Molecule Observations by Quantum Beams and Analysis of Functional Active-sites(Yuji Sasaki /The University of Tokyo) 3)Toward understanding ligand-gated ion channels -Potential of diffracted X-ray tracking and atomic resolution holography- (Yuri Nishino/Univ. Hyogo) 4) A QM/MM study of catalytic mechanism of nitrile hydratase (Megumi Kayanuma/Univ. Tsukuba) 5) Challenge of X-ray fluorescence hologaphy toward biomaterials (Koichi Hayashi/Nagoya Inst.of Tech.) 6) Structural dynamics measurements of the intermediate states in the ligand-photolysis of hemoglobin (Ayana Sato/ch. Med., Univ. Jichi) 7) Theoretical study of the relationship between heme distortion and redox potential(Yu Takano/Hiroshima City Univ.) http://www.aeplan.co.jp/jbp2015/index.html

2015/09/07    "International Workshop for Green Photonics" has been held as a cosponsorship event