Organized and Sponsored by - CCL-CMUanscse23.ccl-cmu.com/wp-content/uploads/2019/06/Abstract-Book-f… · • Dr. Uracha Ruktanonchai Deputy Executive Director, National Nanotechnology

The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)

Organized and Sponsored by

55th Anniversary of the Faculty of Science, Chiang Mai University


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WELCOME MESSAGE

Associate Professor Dr. Vudhichai Parasuk

President of Computational Science and Engineering Association

(CSEA),

Thailand

Dear Friends and Colleagues,

It is a great pleasure and an honor to extend to you a warm invitation to attend the ANSCSE23, the 23rd

International Annual Symposium on Computational Science and Engineering, to be held on June 27-29, 2019.

This year the symposium is organized by Faculty of Science, Chiang Mai University, Computational Science

and Engineering Association (CSEA) and National e-Science Infrastructure Consortium, National

Nanotechnology Center (NANOTEC), and National Electronics and Computer Technology Center (NECTEC).

ANSCSE23 has always been one of the greatest gatherings of computational scientists, computer science, and

engineering researchers. After 23 years, we have seen many signs of progress and so many interesting researches

being conducted in this area. In this digital age, rapid progress has been driven by artificial intelligence, big

data, and much higher computing power enabled by new technology such as GPU, FPGA. Thus, the vital role

that computational science plays in human social development becomes clearer and clearer every day.

One of the great spirits of ANSCSE is the live discussion among fellow international researchers. After a few

days of intense discussion on our works, the organizer kindly arranges an excursion to the Doi Inthanon National

Park, the highest mountain in Thailand. I am certain that everyone will enjoy the talk along with the beauty of

Chiang Mai.

Finally, I look forward to meeting all of you. Thank you for sharing your thoughts and ideas in ANSCSE23.

Best Wishes,

Associate Professor Dr. Vudhichai Parasuk

Chulalongkorn University

President of Computational Science and Engineering Association (Thailand)

1




WELCOME MESSAGE

Professor Dr. Suthep Suantai

Department of Mathematics, Faculty of Science,Chiang Mai University,

Thailand

Dear Colleagues,

On behalf of the organizing committee, I am honored and delighted to welcome you to the 23rd International

Annual Symposium on Computational Science and Engineering (ANSCSE23). It is a great honor for Faculty of

Science, Chiang Mai University to be the host of ANSCSE23 and this conference is one of many conferences

to celebrate 55th year of Faculty of Science, Chiang Mai University. Our co-hosts are Computer Science and

Engineering Association (CSEA), National e-Science Infrastructure Consortium, Materials Science Research

Center (MRS), Chiang Mai University, National Nanotechnology Center (NANOTEC) and National Electronics

and Computer Technology Center (NECTEC).

Over twenty-two years, ANSCSE has a long history of gathering researchers who are in the field of

computational science and engineering to cross-fertilize ideas and to strengthen both local and international

networks. The theme of this year is “Expand Your Mind”. Under this theme, ANSCSE23 covers not only various

disciplines of computational science and engineering including fields of Biology, Chemistry, Physics, Fluid

Dynamics, Solid Mechanics, High Performance Computing, Cloud Computing, and Computer Science and

Engineering but also experimental studies particularly material sciences.

There are 2 plenary lectures, 3 special talks, 68 invited talks and about 69 oral and poster presentations. This

year, the scientific programs are accompanied with the “Workshop on e-Science and HighPerformance

Computing: eHPC2019” workshop. This conference aims to provide an exciting venue for scientists to present

and exchange ideas, as well as to strengthen existing collaborations and developing new ones.

As a conference chair of ANSCSE23, I would like to express my sincere appreciation to the steering committee,

the honorary chairs, the international advisory board, the scientific committee chair, the program chairs, the

scientific committee, the reviewers, our sponsors and the organizing team. Last but not the least; recognition

and thank should also go to the local organizing committee team who has really worked hard in organizing the

technical programs and supporting social arrangements.

Finally, ANSCSE23 truly serves the venue for networking and knowledge sharing among the participants which

is an outcome of the comprehensive presentations as well as high-level plenary and panel sessions. We hope

you will take the utmost advantage of this event to start your future collaborations.

Sincerely yours,

Professor Dr. Suthep Suantai

Conference Chair

Department of Mathematics, Faculty of Science, Chiang Mai University, Thailand

2




Map of Faculty of Science, Chiang Mai University

3


Floor plan for ANSCSE23

4


Committees

Steering Committee

• Asst. Prof. Putchong Uthayopas Kasetsart University and Acting President of CSEA, Thailand

• Assoc. Prof. Vudhichai Parasuk Chulalongkorn University and President-Elect of CSEA, Thailand

• Prof. Supa Hannongbua Kasetsart University, Thailand

• Assoc. Prof. Waraporn Parasuk Kasetsart University, Thailand

• Dr. Piyawut Srichaikul National Electronics and Computer Technology Center

(NECTEC), NSTDA, Thailand

Honorary Chair

• Prof. Torranin Chairuangsri Dean of Faculty of Science, Chiang Mai University, Thailand

• Asst. Prof. Schradh Saenton Associate Dean for Academic Affairs, Faculty of Science,

Chiang Mai University, Thailand

• Assoc. Prof. Prasit Wangpakapattanawong Associate Dean for Research and International Relations,

Faculty of Science, Chiang Mai University, Thailand

• Asst. Prof. Sittichai Wirojanupatump Head of Chemistry Department, Faculty of Science,


• Asst. Prof. Winita Punyodom Head of Materials Science Research Center, Faculty of Science,


• Dr. Uracha Ruktanonchai Deputy Executive Director, National Nanotechnology Center

(NANOTEC), NSTDA, Thailand

• Dr. Kajornsak Faungnawakij Research Unit Director of Nanomaterials and Nanosystems

Engineering Research Unit, National Nanotechnology Center

(NANOTEC), NSTDA, Thailand

Scientific Committee Chair

• Prof. Suthep Suantai Chiang Mai University, Thailand

Computational Chemistry Program Chair

• Dr. Supawadee Namuangruk National Nanotechnology Center (NANOTEC), NSTDA, Thailand

• Asst. Prof. Nawee Kungwan Chiang Mai University, Thailand

Computational Biology and Bioinformatics Program Chair

• Asst. Prof. Thanyada Rungrotmongkol Chulalongkorn University, Thailand

• Assoc. Prof. Panida Surawatanawong Mahidol University, Thailand

Computational Physics, Computational Fluid Dynamics and Solid Mechanics Program Chair

• Assoc. Prof. Yongyut Laosiritaworn Chiang Mai University, Thailand

• Assoc. Prof. Anucha Yangthaisong Ubon Ratchathani University, Thailand

• Asst. Prof. Worasak Sukkabot Ubon Ratchathani University, Thailand

High Performance Computing, Computer Science, and Engineering Program Chair



• Dr. Manaschai Kunaseth, National Electronics and Computer Technology Center


Mathematics and Statistics Program Chair • Prof. Suthep Suantai Chiang Mai University, Thailand

• Asst. Prof. Thanasak Mouktonglang Chiang Mai University, Thailand

Experiment Meets Theory Program Chair

• Assoc. Prof. Siriporn Jungsuttiwong Ubon Ratchathani University, Thailand

• Assoc. Prof. Vuthichai Ervithayasuporn, Mahidol University, Thailand

• Assoc. Prof. Phornphimon Maitarad Shanghai University, China

• Dr. Pinit Kidkhunthod Synchrotron Light Research Institute, Thailand

A Joint Workshop on e-Science and High Performance Computing: eHPC2019



• Dr. Manaschai Kunaseth, National Electronics and Computer Technology Center


5


International Scientific Committee

• Prof. Xin Xu Fudan University, China

• Prof. Koichi Kato Institute of Molecular Sciences, Japan

• Prof. Ras B. Pandey University of Southern Mississippi, USA

• Prof. Steven R. Kirk Hunan Normal University, China

• Dr. Kaito Takahashi Academia Sinica, Taiwan

• Dr. Jer-Lai Kuo Academia Sinica, Taiwan

• Prof. Jun-Ya Hasegawa Hokkaido University, Japan

• Prof. Jianwen Liu Shenzhen University, China

• Prof. Akihito Ishizaki National Institutes of Natural Sciences, Japan

• Prof. Tetsuya Taketsugu Hokkaido University, Japan

• Prof. Yasuteru Shigeta University of Tsukuba, Japan

• Prof. Jen-Shiang K. Yu National Chiao Tung University, Taiwan

• Prof. Seiji Mori Ibaraki University, Japan

• Prof. Deva Priyakumar International Institute of Information Technology, India

• Prof. Jhih-Wei Chu National Chiao Tung University, Taiwan

• Prof. Samantha Jenkins Human Normal University, China

• Prof. Thorsten Dickhaus University of Bremen, Germany

• Prof. Shuai Yuan Shanghai University, China

• Prof. Richard M. Laine University of Michigan, USA

• Prof. Hidehiro Sakurai Osaka University, Japan

• Prof. Lei Huang Shanghai University, China

• Prof. Yong-Hyun Kim Korea Advanced Institute of Science and Technology (KAIST),

Republic of Korea

• Prof. Akira Nakayama University of Tokyo, Japan

• Assoc. Prof. Lam K. Huynh International University-Vietnam National University, Vietnam

• Assoc. Prof. Malgorzata Biczysko Shanghai University, China

• Assoc. Prof. Norio Yoshida Kyushu University, Japan

• Assoc. Prof. Hisashi Okumura Institute for Molecular Science, Japan

• Asst. Prof. Satoru Itoh Institute for Molecular Science, Japan

• Asst. Prof. Min-Yeh Tsai Tamkang University, Taiwan

• Assoc. Prof. Phornphimon Maitarad Shanghai University, China

National Scientific Committee

• Prof. Suthep Suantai Chiang Mai University, Thailand


• Assoc. Prof. Panida Surawatanawong Mahidol University, Thailand

• Assoc. Prof. Yongyut Laosiritaworn Chiang Mai University, Thailand

• Assoc. Prof. Anucha Yangthaisong Ubon Ratchathani University, Thailand

• Assoc. Prof. Vuthichai Ervithayasuporn Mahidol University, Thailand



• Asst. Prof. Worasak Sukkabot Ubon Ratchathani University, Thailand



• Dr. Pussana Hirunsit National Nanotechnology Center (NANOTEC), NSTDA, Thailand

• Dr. Chompoonut Rungnim National Nanotechnology Center (NANOTEC), NSTDA, Thailand



• Dr. Manaschai Kunaseth National Electronics and Computer Technology Center


• Dr. Pinit Kidkhunthod Synchrotron Light Research Institute, Thailand

• Dr. Supareak Praserthdam Chulalongkorn University, Thailand

6


Organizing Committee Chair


Organizing Committee




• Assoc. Prof. Jaroon Jakmunee Chiang Mai University, Thailand


• Asst. Prof. Pitchaya Mungkornasawakul Chiang Mai University, Thailand

• Asst. Prof. Kritsana Jitmanee Chiang Mai University, Thailand

• Asst. Prof. Narin Lawan Chiang Mai University, Thailand

• Asst. Prof. Nuttee Suree Chiang Mai University, Thailand

• Asst. Prof. Burapat Inceesungvorn Chiang Mai University, Thailand

• Assoc. Prof. Piyarat Nimmanpipug Chiang Mai University, Thailand

• Asst. Prof. Pipat Ruankham Chiang Mai University, Thailand

• Assoc. Prof. Chulin Likasiri Chiang Mai University, Thailand

• Asst. Prof. Kanyuta Poochinapan Chiang Mai University, Thailand

• Asst. Prof. Kontad Ounnunkad Chiang Mai University, Thailand


• Asst. Prof. Morrakot Khebchareon Chiang Mai University, Thailand

• Asst. Prof. Somchai Sriyab Chiang Mai University, Thailand

• Asst. Prof. Thaned Rojsiraphisal Chiang Mai University, Thailand

• Asst. Prof. Thongchai Dumrongpokaphan Chiang Mai University, Thailand

• Asst. Prof. Thunwadee Limtharakul Chiang Mai University, Thailand

• Dr. Chanisorn Ngaojampa Chiang Mai University, Thailand

• Dr. Thapanar Suwanmajo Chiang Mai University, Thailand

• Dr. Natthawat Semakul Chiang Mai University, Thailand

• Dr. Wasut Pornpatcharapong Chiang Mai University, Thailand

• Dr. Wan Wiriya Chiang Mai University, Thailand

• Dr. Saranphong Yimklan Chiang Mai University, Thailand

• Dr. Pumis Thuptimdang Chiang Mai University, Thailand

• Dr. Yothin Chimupala Chiang Mai University, Thailand

• Dr. Ben Wongsaijai Chiang Mai University, Thailand

• Dr. Chanida Puangpila Chiang Mai University, Thailand

• Dr. Nattapol Ploymaklam Chiang Mai University, Thailand

• Dr. Nawinda Chutsagulprom Chiang Mai University, Thailand

• Dr. Supanut Chaidee Chiang Mai University, Thailand

• Mr. Thanakorn Suwanprasert Chiang Mai University, Thailand

• Ms. Amporn Tapburee Chiang Mai University, Thailand

• Mr. Apiroj Lekyong Chiang Mai University, Thailand

• Ms. Jarunee Ngeonphacho Chiang Mai University, Thailand

• Mr. Krisanat Nakthong Chiang Mai University, Thailand

• Mr. Pichai Nakpathom Chiang Mai University, Thailand

• Mr. Pichet Thepsuwan Chiang Mai University, Thailand

• Ms. Rachada Wongsuwan Chiang Mai University, Thailand

• Ms. Sirichan Wongkaew Chiang Mai University, Thailand

• Ms. Thanikan Yamano Chiang Mai University, Thailand

7


Session Summary

Plenary Lecture

PL-1 Prof. Xin Xu

Department of Chemistry, Fudan University, China

PL-2 Prof. Koichi Kato

Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Japan

Scientific Session

ANSCSE23 will be held under the theme “Expanding your mind” and will cover topics in the following

area:

CHE Computational Chemistry CSE High Performance Computing,

Computer Science, and Engineering

BIO Computational Biology, Bioinformatics,

Biochemistry, and Biophysics MST Mathematics and Statistics

PFD Computational Physics, Computational

Fluid Dynamics, and Solid Mechanics EMT Experiment Meets Theory

Special Talk

ST1 eHPC: Current Status of Thailand HPC Infrastructure

Dr. Piyawut Srichaikul

NSTDA Supercomputer Center, Thailand

ST2 Applications of Synchrotron-based X-ray Absorption Spectroscopy on Advanced

Functional Materials

Dr. Pinit Kidkhunthod

Synchrotron Light Research Institute (Public Organization), Thailand

S3 Combined Experimental Computational Multi-Scale Studies in Catalysis

Dr. Supareak Praserthdam

Chulalongkorn University, Thailand

Special Workshop

eHPC A Joint Workshop on e-Science and High Performance Computing: eHPC2019

Dr. Piyawut Srichaikul and Dr. Manaschai Kunaseth

National Electronics and Computer Technology Center (NECTEC), NSTDA, Thailand

8


Overall Program

Wednesday, June 26, 2019

Expected all participants arrive in Chiang Mai and check-in at hotels

Thursday, June 27, 2019

08.00 – 09.00 Registration 1st floor of CB1

09.00 – 09.30 Opening Ceremony

Room:

CB1220

Chairman: Supawadee Namuangruk

09.30 – 10.15

The XYG3 Type of Doubly Hybrid Density Functionals: From

Molecular Systems to Extended Solids

Plenary Lecture: Prof. Xu Xin from Fudan University, China

10.15 – 10.35 eHPC: Current Status of Thailand HPC Infrastructure

Special Talk: Dr. Piyawut Srichaikul from NECTEC, Thailand

10.35 – 11.00 Coffee Break

11.00 – 12.00

Six Parallel Sessions

Room:

CB1220

Room:

CB1310

Room:

CB1313

Room:

CB1210

Room:

CB1314

Room:

CB1320

CHE BIO PFD MST EMT eHPC

12.00 – 13.00 Lunch

13.00 – 15.30


Room:

CB1220

Room:

CB1310

Room:

CB1313

Room:

CB1210

Room:

CB1314

Room:

CB1320



15.50 – 17.15


Room:

CB1220

Room:

CB1310

Room:

CB1313

Room:

CB1210

Room:

CB1314 Room: CB1320


17.15 – 18.30 Poster Session

18.45 Welcome Dinner

9


Friday, June 28, 2019

Chairman: Thanyada Rungrotmongkol and Siriporn Jungsuttiwong

Room:

CB1220

09.00 – 09.45

Experimental and Computational Approaches for Elucidating

Glycofunctional Mechanisms

Plenary Lecture: Prof. Koichi Kato from Institute of Molecular

Science, Japan

09.45 – 10.05

Applications of Synchrotron-based X-ray Absorption

Spectroscopy on Advanced Functional Materials

Special Talk: Dr. Pinit Kidkhunthod from Synchrotron Light

Research Institute, Thailand

10.05 – 10.25

Combined Experimental Computational Multi-Scale Studies in

Catalysis

Special Talk: Dr. Supareak Praserthdam from Catalyst Group,



11.00 – 12.00


Room:

CB1220

Room:

CB1320

Room:

CB1313

Room:

CB1210

Room:

CB1314

Room:

CB1310

CHE BIO PFD MST EMT CSE

12.00 – 13.00 Lunch

13.00 – 15.00


Room:

CB1220

Room:

CB1320

Room:

CB1313

Room:

CB1210

Room:

CB1314

Room:

CB1310



15.20 – 16.35


Room:

CB1220

Room:

CB1320

Room:

CB1313

Room:

CB1210

Room:

CB1314

Room:

CB1310


16.35 – 17.00 Closing Conference with Poster and Oral Presentation Award Announcement

Saturday, June 29, 2019

07.15 – 16.00 Excursion: Mountain Tour (optional)

16.00 – 22.00 Saturday walking street market (optional)

Sunday, June 30, 2019

Depart from Chiang Mai Province

10


Scientific Program

11




Session: Computational Chemistry (CHE)


08.00 – 09.00 Registration


09.30 – 10.15 Plenary Lecture 1

10.15 – 10.35 Special Talk 1


Chairman: Supawadee Namuangruk and

Chompoonut Rungnim

11.00 – 11.30 CHE-I-01 Prof. Yong-Hyun

Kim

11.30 – 12.00 CHE-I-02 Prof. Akihito

Ishizaki

12.00 – 13.00 Lunch

Chairman: Akira Nakayama and

Suwit Suthirakun

13.00 – 13.30 CHE-I-03 Prof. Malgorzata

Biczysko

13.30 – 14.00 CHE-I-04 Prof. Jianwen Liu

14.00 – 14.30 CHE-I-05 Dr. Chompoonut

Rungnim

14.30 – 15.00 CHE-I-06 Dr. Supareak

Praserthdam

15.00 – 15.15 CHE-O-01 Mr. Tinnakorn

Saelee

15.15 – 15.30 CHE-O-02 Mr. Yuki Oba


Chairman: Tetsuya Taketsugu and

Jun-Ya Hasegawa

15.50 – 16.20 CHE-I -07 Prof. Woo-Youn

Kim

16.20 – 16.35 CHE-O-03 Mr. Panyakorn

Taweechat

16.35 – 16.50 CHE-O-04 Mr. Tanabat

Mudchimo





09.45 – 10.05 Special Talk 2

10.05 – 10.25 Special Talk 3


Chairman: Jianwen Liu and Supawadee Namuangruk

11.00 – 11.30 CHE-I-08 Prof. Jun-Ya Hasegawa

11.30 – 12.00 CHE-I-09 Dr. Suwit Suthirakun

12.00 – 13.00 Lunch

Chairman: Tim Kowalczyk and Nawee Kungwan

13.00 – 13.30 CHE-I-10 Prof. Tetsuya Taketsugu

13.30 – 14.00 CHE-I-11 Dr. Karan Bobuatong

14.00 – 14.30 CHE-I-12 Prof. Akira Nakayama

14.30 – 14.45 CHE-O-05 Ms. Kiriko Ishii

14.45 – 15.00 CHE-O-06 Mr. Nuttapon Yodsin


Chairman: Malgorzata Biczysko and

Supareak Praserthdam

15.20 – 15.50 CHE-I-13 Dr. Takako Mashiko

15.50 – 16.20 CHE-I-14 Prof. Tim Kowalczyk

16.35 – 17.00 Closing Conference

12


Session: Computational Biology, Bioinformatics, Biochemistry, and Biophysics (BIO)





10.15 – 10.35 Special Talk 1


Chairman: Thanyada Rungrotmongkol

11.00 – 11.30 BIO-I-01 Prof. Lee-Wei Yang

11.30 – 12.00 BIO-I-02 Prof. Hisashi Okumura

12.00 – 13.00 Lunch

Chairman: Seiji Mori and Jitrayut Jitonnom

13.00 – 13.30 BIO-I-03 Prof. Deva Priyakumar

13.30 – 14.00 BIO-I-04 Prof. Jen-Shiang K. Yu

14.00 – 14.30 BIO-I-05 Prof. Norio Yoshida

14.30 – 15.00 BIO-I-06 Prof. Min-Yeh Tsai

15.00 – 15.15 BIO-O-01 Mr. Nikorn Shinsuphan

15.15 – 15.30 BIO-O-02 Mr. Thodsaphon Lunnoo


Chairman: Jen-Shiang K.Yu

15.50 – 16.20 BIO-I-07 Prof. Yasuteru Shigeta

16.20 – 16.35 BIO-O-03 Mr. Pikkanet Suttirat

16.35 – 16.50 BIO-O-04 Mr. Pongsakorn

Kanjanatanin





09.45 – 10.05 Special Talk 2

10.05 – 10.25 Special Talk 3


Chairman: Panida Surawatanawong

11.00 – 11.30 BIO-I-08 Prof. Christian

Schröder

11.30 – 12.00 BIO-I-09 Prof. Jhih-Wei Chu

12.00 – 13.00 Lunch

Chairman: Yasuteru Shigeta and Nuttee Suree

13.00 – 13.30 BIO-I-10 Prof. Seiji Mori

13.30 – 14.00 BIO-I-11 Prof. Satoru Itoh

14.00 – 14.30 BIO-I-12 Prof. Supa

Hannongbua

14.30 – 14.45 BIO-O-05 Mr. Tanawat

Horsirimanon

14.45 – 15.00 BIO-O-06 Ms. Natchayatorn

Keawkla


Chairman: Deva Priyakumar

15.20 – 15.50 BIO-I-13 Prof. Jitrayut

Jitonnom

15.50 – 16.20 BIO-I-14 Prof. Nuttee Suree


13


Session: Computational Physics, Computational Fluid Dynamics

and Solid Mechanics (PFD)





10.15 – 10.35 Special Talk 1


Chairman: Yongyut Laosiritaworn and

Suraphong Yuma

11.00 – 11.30 PFD-I-01 Prof. Samantha

Jenkins

11.30 – 12.00 PFD-I-02 Dr. Tirawut

Wooakitpoonpon

12.00 – 13.00 Lunch

Chairman: Anucha Yangthaisong and

Worasak Sukkabot

13.00 – 13.30 PFD-I-03 Prof. Lam K.Kuynh

13.30 – 14.00 PFD-I-04 Prof. Steven R.Kirk

14.00 – 14.30 PFD-I-05 Prof. Ras B.Pandey

14.30 – 15.00 PFD-I-06 Dr. Suraphong Yuma

15.00 – 15.30 PFD-I-07 Dr. Osamu Kobayashi


Chairman: Udomsilp Pinsook and

Worasak Sukkabot

15.50 – 16.20 PFD-I-08 Prof. Masanori

Tachikawa

16.20 – 16.50 PFD-I-09 Prof. Theerapong

Puangmali

16.50 – 17.05 PFD-O-01 Ms. Saowalak Somjid





09.45 – 10.05 Special Talk 2

10.05 – 10.25 Special Talk 3


Chairman: Theerapong Puangmali and

Tirawut Wooakitpoonpon

11.00 – 11.30 PFD-I-10 Prof. Jer-Lai Kuo

11.30 – 12.00 PFD-I-11 Prof. Udomsilp

Pinsok

12.00 – 13.00 Lunch


Worasak Sukkabot

13.00 – 13.30 PFD-I-12 Prof. Taro Udagawa

13.30 – 14.00 PFD-I-13 Prof. Malliga

Suewattana

14.00 – 14.30 PFD-I-14 Dr. Tsutomu

Kawatsu

14.30 – 14.45 PFD-O-02 Dr. Kanokkorn

Pimcharoen



Worasak Sukkabot

15.20 – 15.50 PFD-I-15 Dr. Nirand Pisutha-

Arnond

15.50 – 16.20 PFD-I-16 Prof. Ryo Maezono

16.20 – 16.35 PFD-I-17 Prof. Kenta Hongo


14


Session: Mathematics and Statistics (MST)





10.15 – 10.35 Special Talk 1

10.35– 11.00 Coffee Break

Chairman: Suthep Suantai and

Thanasak Mouktonglang

11.00 – 11.30 MST-I-01 Prof. Kazuyuki Koizumi

11.30 – 12.00 MST-I-02 Prof. Thorsten Dickhaus

12.00 – 13.00 Lunch

Chairman: Suthep Suantai and

Thanasak Mouktonglang

13.00 – 13.30 MST-I-03 Prof. Chalump Oonariya

13.30 – 14.00 MST-I-04 Prof. Pakinee Aimmanee

14.00 – 14.30 MST-I-05 Prof. Chidchanok

Lursinsap

14.30 – 14.45 MST-O-01 Ms. Wipawinee Chaiwino

14.45 – 15.00 MST-O-02 Mr. Panasun Manorost

15.00 – 15.15 MST-O-03 Mr. Tawatchai Petaratip

15.15 – 15.30 MST-O-04 Ms. Monthiya Ruangnai





No session

15


Session: Experiment Meets Theory (EMT)





10.15 – 10.35 Special Talk 1


Chairman: Siriporn Jungsuttiwong

11.00 – 11.30 EMT-I-01 Prof. Hiroshi M.

Yamamoto

11.30 – 12.00 EMT-I-02 Prof. Vinich

Promarak

12.00 – 13.00 Lunch

Chairman: Hiroshi M. Yamamoto and

Vuthichai Ervithayasuporn

13.00 – 13.30 EMT-I-03 Prof. Nantanit

Wanichacheva

13.30 – 14.00 EMT-I-04 Dr. Duangporn

Polpanich

14.00 – 14.30 EMT-I-05 Dr. Deanpen

Japrung

14.30 – 15.00 EMT-I-06 Prof. Shinji

Nonose

15.00 – 15.30 EMT-I-07 Prof. Richard M.

Laine


Chairman: Nantanit Wanichacheva

15.50 – 16.20 EMT-I-08 Prof. Hidehiro

Sakurai

16.20 – 16.50 EMT-I-09 Dr. Kajornsak

Faungnawakij





09.45 – 10.05 Special Talk 2

10.05 – 10.25 Special Talk 3


Chairman: Phornphimon Maitarad

11.00 – 11.30 EMT-I-10 Prof. Shuai Yuan

11.30 – 12.00 EMT-I-11 Dr. Pinit Kidkhunthod

12.00 – 13.00 Lunch

Chairman: Kajornsak Faungnawakij and

Pinit Kidkhunthod

13.00 – 13.30 EMT-I-12 Prof. Vuthichai

Ervithayasuporn

13.30 – 14.00 EMT-I-13 Prof. Takuji Ohigashi

14.00 – 14.30 EMT-I-14 Prof. Lei Huang

14.30 – 15.00 EMT-I-15 Prof. Theeranun Siritanon


Chairman: Lei Huang

15.20 – 15.50 EMT-I-16 Prof. Kittipong Chainok

15.50 – 16.20 EMT-I-17 Prof.Burapat Inceesungvorn


16


Session: High Performance Computing, Computer Science and Engineering (CSE)


No session

.



09.45 – 10.05 Special Talk 2

10.05 – 10.25 Special Talk 3


Chairman: Manaschai Kunaseth

11.00 – 11.30 CSE-I-01 Dr. Putt

Sakdhnagool

11.30 – 11.45 CSE-O-01 Dr. Arpiruk

Hokpunna

12.00 – 13.00 Lunch

Chairman: Putt Sakdhnagool

13.00 – 13.15 CSE-O-02 Dr. Chidchanok

Choksuchat

13.15 – 13.30 CSE-O-03 Ms. Wassamon

Phusakulkajorn



17


Special Workshop

18




Workshop on e-Science and High Performance Computing: eHPC2019

“A Drive Toward National Computing Platform”

9.00. – 17.00, June 27, 2019, Room: CB1320, Chiang Mai University

Tentative Program

Time Invited Speakers / Topic



09.30 – 10.15 The XYG3 Type of Doubly Hybrid Density Functionals: From


Plenary Lecture: Prof. Xu Xin from Fudan University, China

10.15 – 10.35 eHPC: Current Status of Thailand HPC Infrastructure

Special Talk: Dr. Piyawut Srichaikul from NECTEC, Thailand


11.00 – 11.25 Dawn of TARA: An Early Experience and Lesson Learned from

Developing Large-Scale Generalized HPC Service

Dr. Manaschai Kunaseth

11.25 – 11.50 HPC and AI in KU

Prof. Putchong Uthayopas

12.00 – 13.30 Lunch

13.30 – 13.55 Big data & AI in academic

Prof. Sarana Nutanong

13.55 – 14.20 Early experience of Taiwan Computing Cloud

Chun-Yu LIN, Associate Researcher

14.20 – 14.45 TBA

Dr. Utane Swangwit

14.45 – 15.10 Usability of Four-Factor Authentication in Information Security

Dr. Chalee Vorakulpipat


15.45 – 17.00 Panel discussion: การพฒนา National Computing Platform ใหเหมาะสมกบการใชงานในประเทศไทย (Thai language)

17.15 – 18.30 Poster Session (All Poster Presentation)


19


General Information

1. The ANSCSE23 registration counter will be located in front of the Multifunctional Room

(CB1112), 1st floor of Chemistry Building 1 (CB1), Department of Chemistry, Faculty of

Science, Chiang Mai University. Opening times are as follows:

Thursday, June 27 at 8:00 a.m. – 9:00 a.m.

Friday, June 28 at 8:00 a.m. – 9:00 a.m.

2. Registration will be in alphabet order according to A-Z (List of participants). Please memorize

your status.

3. Upon registration at the counter, you will receive your badge, receipt and conference materials.

To facilitate the process, please bring with you your registration confirmation. You are kindly

requested to wear your name badge during all events of the conference.

4. In case of issuing the new receipt (misspelling name/address or any incorrect information), the

fee of 300 Baht for Thai participants or 10 USD for foreigner participants will be charged per

receipt.

Poster presentation

1. The content of the poster should cover title, objectives, methodology, results, discussion, and

conclusion.

2. The poster size must not exceed 80 cm width x 120 cm height.

Oral presentation

1. Oral presentations are required to be made by PowerPoint 2003 or higher.

2. Standard fonts, such as Arial, Times New Roman or Cordia New are preferable for the

PowerPoint presentation.

3. All speakers are required to load and check the files in slide loading room at least 2 hours

before the presentation.

4. The presentation time for general oral presentation is 15 minutes (12 minutes for presentation

+ 3 minutes for Q&A).

5. The time for invited presentation is 30 minutes (25 minutes for presentation + 5 minutes for

Q&A).

6. A PC computer and an LCD projector will be provided.

20


Plenary Lecture

21




The XYG3 Type of Doubly Hybrid Density Functionals: From


X. Xu*

Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis

and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan

University, Shanghai 200433, China * E-mail: [email protected]; Fax: +86 21 6564 3029; Tel. +86 21 3124 3529

ABSTRACT

Doubly hybrid (DH) functionals have emerged as a new class of density functional approximations (DFAs),

which not only have a non-local orbital-dependent component in the exchange part, but also incorporate the

information of unoccupied orbitals in the correlation part, being at the top rung of Perdew’s view of Jacob’s

ladder in DFAs. In particular, the XYG3 1 type of doubly hybrid (xDH) functionals use a low rung functional

(e.g. B3LYP) to perform the self-consistent-field calculation to generate orbitals and densities, with which a top

rung DH functional is used for final energy evaluation. The xDH functionals have been shown to have

remarkable accuracy for molecular systems. This talk presents the results that the xDH functionals are extended

from molecular systems to extended solids. This is achieved by combining the xDH functionals with the XO

(i.e., eXtended ONIOM 2) method that allows for the overlapping fragmentation. Here the high level is described

with the cluster model at the xDH level, while the low level for the whole system is now described with the

periodic boundary condition (PBC) at the PBE level. The method, thus coined as XO-PBC@XYG3 3, is applied

to the cohesive energy predictions for molecular crystals, which shows promise in discriminating the multiple

crystal packing motifs that have important implications for pharmaceuticals, organic semiconductors, and many

other chemical applications.

Keywords: XYG3, XO, molecular crystal, density functional theory, ONIOM

REFERENCES

1. Zhang, Y., Xu, X., Goddard, W. A. III Proc. Nat. Acad. Sci, USA, 2009, 106, 4963-8.

2. Guo, W., Wu, A., Xu, X. Chem. Phys. Lett., 2010, 498, 203-8.

3. Chen, B., Xu, X. To be submitted.

Ph.D. at Xiamen University (XM), China, in 1991.

Associate professor (1993-1995) and Professor (1995-2010) at Department of

Chemistry, XM, Lu-Jia-Xi chair professor at Department of Chemistry, XM,

(2006-2010).

Distinguished professor at Department of Chemistry, Fudan University (2010-),

Changjiang chair professor (2012-).

22


Experimental and Computational Approaches for Elucidating

Glycofunctional Mechanisms

Koichi Kato1, 2, 3

1 Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki,

Japan

2 Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan 3 Graduate School of Pharmaceutical Sciences, Nagoya City University

* E-mail: [email protected]; Fax: +81 564 59 5225; Tel. +81 564 59 5224

ABSTRACT

Since biomolecules exert versatile functions through interacting with their binding partners, detail structural

characterization of their interaction modes is of importance not only for deeper understanding the functional

mechanisms but also for controlling and improving their functionality. Accumulating crystallographic data of

biomolecular complexes have provided atomic descriptions of their interactions, offering the structural basis

necessary for rational biomolecular engineering and drug design. However, it should be noted that biomolecules

generally possess motional freedoms under physiologically conditions. Oligosaccharides represent one of the

most extreme classes of biomolecules that are characterized by conformational flexibility.

We have developed a method for elucidating dynamic conformations of oligosaccharides in solution by

employing MD simulation in conjunction with our developed NMR technique [1]. This has enabled exploration

of conformational spaces of complicated, branched oligosaccharides. We herein apply this method to design of

unnatural oligosaccharides having higher affinities for a specific target protein. Furthermore, we combined our

structural biology approach with MD simulation for characterizing conformational dynamics of the Fc portion

of immunoglobulin G, thereby providing a mechanistic view of improved functional efficacy of therapeutic

antibodies depending on their glycosylation [2].

Keywords: NMR spectroscopy, MD simulation, Oligosaccharide, glycoprotein, therapeutic antibody

REFERENCES

1. Kato, K., Yagi, H., and Yamaguchi, T. Modern Magnetic Resonance, 2nd Edition (G.A.Webb ed.),

Springer International Publishing, 737-754 (2018)

2. Yagi, H., Yanaka, S., and Kato, K. Glycobiophysics (Y.Yamaguchi and K.Kato ed.), Springer Nature

Singapore, 219-235 (2018)

Ph.D. at the Tokyo University (TU) in 1991, Assistant professor (1991) and

Lecturer (1997) at Graduate School of Pharmaceutical Sciences, TU, Professor

at Graduate School of Pharmaceutical Sciences, Nagoya City University (2000-

), Professor at Okazaki Institute for Integrative Bioscience (Institute for

Molecular Science 2008-) and Director and Professor at Exploratory Research

Center on Life and Living Systems (ExCELLS), National Institutes of Natural

Sciences (2018-).

23


Special Talk

24




eHPC: Current Status of Thailand HPC Infrastructure

P.Srichaikul

NSTDA Supercomputer Center, Thailand * E-mail: [email protected] Tel. +66-2564-6900

ABSTRACT

HPC infrastructure is a critical component for Computational science and Engineering research advancement.

It has been nearly three decades of Thailand HPC journey. While it was a bumpy road, progress were made,

even if far from the dream for fields of gold.

This presentation gives a brief update on Thailand HPC infrastructure and its related activities.

Keywords: High Performance Computing, Computing Infrastructure, Supercomputing

Ph.D. (Solid State Physics) Auburn University, USA. (1995),

NSTDA Supercomputer Center (ThaiSC), NECTEC, NSTDA (2019- )

A nice looking Bangkok native middle age Asian male with dark sense of humor

who had scientific training background knowledge in Solid State Physics. His

work experience over 20 years at National Electronics and Computer Technology

Center, Thailand put him in multi-disciplinary roles of coordination and

management such as Computational Science, High Performance Computing,

Geo-informatics, Assistive Technology, Organization Management, Research

Innovation, Data Analytics, and most recent, Computing Infrastructure Service.

His latest post is senior researcher supervising Computing and Cyber-Physical

Infrastructure of NSTDA.

25

mailto:[email protected]


Applications of Synchrotron-based X-ray Absorption Spectroscopy on

Advanced Functional Materials

Pinit Kidkhunthod*

Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Muang, Nakhon Ratchasima, 30000,

Thailand * E-mail: [email protected]; Fax: +66 44 217 047; Tel. +66 44 217 040

ABSTRACT

The investigation of the local geometric and electronic structure of probing element in bulk samples is the most

extensive field of application in X-ray Absorption Spectroscopy (XAS). XAS consists of two main regions

which are X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure

(EXAFS). The former region is used to explain the local geometry and oxidation states of selected element in a

sample whilst the latter one is used to address the local structure around probing element in samples. Owing to

the high brightness of synchrotron radiation, synchrotron based infrared microspectroscopy provides high

spatial resolution, better signal to noise ratio and shorter data acquisition time than the conventional source. In

my talk, the XAS beamlines and their applications on advanced functional materials will be introduced in order

to obtain the accuracy of their locally structural information which cause that such properties in these materials.

Keywords: Advanced functional materials, Local structure, X-ray absorption spectroscopy, XANES, EXAFS

REFERENCES

[1] P. Kidkhunthod, Structural studies of advanced functional materials by synchrotron-based x-ray absorption

spectroscopy: BL5. 2 at SLRI, Thailand, Advances in Natural Sciences: Nanoscience and Nanotechnology 8,

035007

Dr. Pinit Kidkhunthod is a beamline manager at the SUT-NANOTEC-

SLRI XAS beamline (BL5.2), Synchrotron Light Research Institute

(Public Organization), Nakhon Ratchasima, Thailand. His research of

interest is in the fields of structural studies of advanced functional

materials such as energy materials, carbon-based ferrite composite

materials and amorphous materials and novel glasses using an X-ray

absorption spectroscopy (XAS) technique. Dr. Pinit Kidkhunthod

received his B.Sc. (Physics), first class honors 3.99 from Khon Kaen

University, Thailand in 2008, and Ph.D. (Physics) from Bristol

University, U.K in 2012. He was one of two Thai students representative

for DESY summer program, Germany, in 2007. Recently, Dr.

Kidkhunthod has received research grants for young scientist from

Thailand Research Fund (TRF2013), Ministry of Science and

Technology (2014) and SUT-Center of Excellent on advanced functional

materials (SUT-COE-AFM) from 2015-present. Moreover, he has been

awarded a visiting professor position from SAIT, China during 2018-

2020. He is the author and co-author of over 100 papers in ISI journals for structural studies of advanced functional materials using XAS

technique.

26


Combined Experimental-Computational Multi-Scale Studies

in Catalysis

Supareak Praserthdam

Center of Excellence on Catalysis and Catalytic Reaction Engineering (CECC), Department of Chemical Engineering,

Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand * E-mail: [email protected]; Fax: +66 2 2186761; Tel. +66 8 6101 2244

ABSTRACT

The Center of Excellence on Catalysis and Catalytic Reaction Engineering aims towards the goal to help to

mitigate the global warming issues based on the know-how in catalysis. Therefore, our first research theme

dealing with catalysis in energy comprises (1.1) renewable energy production via catalytic processes, (1.2) fuel

cell technology, and (1.3) Biorefinery. Catalysis for environment, the second theme consists of (2.1) CO2

conversion to high value-added chemicals and (2.2) the reduction of NOx using SCR catalysts. Finally, the last

theme is designated to be the support which is the experimental-computational catalysts screening via a

combined high-throughput, density functional theory (DFT), and machine learning. Categorized by areas in

catalysis, the center focuses on (1) photocatalysis, (2) electrocatalysis, (3) Ziegler Natta and metallocene

catalysts for polymerization, (4) SCR catalysts, (5) computational catalyst screening and design, and (6) process

simulation for catalytic processes.

Center of Excellence on Catalysis and Catalytic Reaction Engineering (CECC),

Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn

University, Bangkok, Thailand was established in 1979 by Prof. Dr. Piyasan

Praserthdam, where in January 2001 , the center has received its international

recognition from hosting the Bangkok International Conference on

Heterogeneous Catalyst, the first international conference in catalysis in

Thailand.

27




Invited Speaker

28




CHE-I-01

Graphene Based Single-Atom Catalysts for Oxygen Reduction and

Evolution Reactions

Yong-Hyun Kim1,*

1Graduate School of Nanoscience and Technology and Department of Physics, KAIST, Daejeon 34141, Rep. Korea * E-mail: [email protected]; Fax: +82 42 350 1110; Tel. +82 42 350 1111

ABSTRACT

The oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) play the important role in many

renewable energy applications such as proton-exchange membrane fuel cells, water splitting electrolysis, and

Li-air battery. Traditional metal catalysts (Pt, Ni, etc.) for ORR and OER, however, suffer from several critical

limitations of high cost, large overpotential loss, and limited long-term reliability. Recently, a concept of

alternative catalysts, namely, single-atom catalysts (SAC) has been actively discussed first in theory and

simulation, and later followed by experiments. In SACs, a single atom stabilized in support materials acts as an

efficient catalytic center particularly for various electrocatalytic reactions such as ORR and OER. Graphene is

a superior support material for such electrocatalytic reactions because of its extraordinary electrical conductivity

and mechanical and chemical stabilities.

Based on first-principles quantum materials simulations, we have proposed or analyzed a series of chemical

functionalization methods of graphene-based SAC materials [1-3]. As an early SAC work, we proposed a

biomimetic SAC catalyst, namely, Fe-porphyrin embedded graphene and carbon nanotube catalysts for high-

performance ORR. The SAC proposal as covalent but seamless incorporation of the porphyrinic Fe-N4 moiety

into the carbon nanotube hexagonal side wall was confirmed by x-ray and ultraviolet photoemission

spectroscopies. Because of the covalent connection between the Fe-N4 SAC and electron-conductive CNT

backbone, the SAC-CNT exhibits an excellent ORR performance in terms of speed, efficiency, and reliability.

Especially, it shows the extreme structural stability over 0.1 × 106 cycles, vastly superior to the commercial Pt-

C catalyst. In this talk, I will review our recent progress in designing graphene based SAC for various

electrocatalytic reactions including ORR and OER [4-6].

Keywords: Graphene, single atom catalysts, first-principles calculations, oxygen reduction reaction

REFERENCES

1. W. I. Choi, S.-H. Jhi, K. Kim, and Y.-H. Kim, Phys. Rev. B 81, 085441 (2010).

2. A. T. Lee, J. Kang, S.-H. Wei, K. J. Chang and Y.-H. Kim, Phys. Rev. B 86, 165403 (2012).

3. D. H. Lee, W. J. Lee, W. J. Lee, S. O. Kim and Y.-H. Kim, Phys. Rev. Lett. 106, 175502 (2011).

4. S. Back, J. Lim, N.-Y. Kim, Y.-H. Kim and Y. Jung, Chem. Sci. 8, 1090 (2017).

5. C. Choi, S. Back, N.-Y. Kim, Y.-H. Kim and Y. Jung, ACS Catal. 8, 7517 (2018).

6. J. Lim et al., submitted (2019).

Ph.D. at Department of Physics, KAIST in 2003; Post-doctoral fellow (2003) and

staff scientist (2006) at National Renewable Energy Laboratory, Golden,

Colorado, USA; Assistant professor (2009), associate professor (2011), and full

professor (2017) at Graduate School of Nanoscience and Technology, KAIST;

Jointly-appointed professor in Department of Physics, KAIST.

29


CHE-I-02

Effects of Dephasing upon Quantum Dynamical Phenomena in

Condensed Phase Molecular Processes

Akihito Ishizaki1*

1Institute for Molecular Science, National Institutes of Natural Sciences, Japan * E-mail: [email protected] l; Fax: +81 564 55 7310; Tel. +81 564 53 4660

ABSTRACT

Essentially, any quantum systems can never be regarded as “isolated systems.” Quantum systems are always in

contact with “the outside world,” and hence their quantum natures are sometimes sustained and sometimes

destroyed. In condensed phase molecular systems, especially, quantum systems are affected by the huge amount

of dynamic degrees of freedom such as solvent molecules, amino acid residues in proteins, and so forth. Balance

between robustness and fragility of the quantum natures may dramatically alter behaviours of chemical

dynamics and spectroscopic signals. In this presentation, I will be talking about two topics related to this subject.

The first topic is regarding natural photosynthetic systems. The energy conversion of oxygenic photosynthesis

is triggered by primary charge separation in proteins at the photosystem II (PSII) reaction centre (RC). Here,

we investigate the impacts of the protein environment and intramolecular vibrations on primary charge

separation at the PSII RC. We report that individual vibrational modes play a minor role in promoting charge

separation, contrary to the discussion in recent publications. Nevertheless, these small contributions accumulate

to considerably influence the charge separation rate, resulting in subpicosecond charge separation almost

independent of the driving force and temperature. We suggest that the intramolecular vibrations complement

the robustness of the charge separation in the PSII RC against the inherently large static disorder of the involved

electronic energies [1].

The second topic is about a model photovoltaic system. In organic photovoltaic materials, the recombination of

the once separated electron and hole is a major loss mechanism. Hence, it is the key to elucidate physical

mechanisms of how the electron and hole escape from the donor/acceptor interface for understanding the crucial

factors determining the energy conversion efficiency of organic solar cells. In this talk, we investigate potential

ratchet mechanism that was made possible via the combination of quantum delocalization and its decoherence

in order to get insight into the inner working of experimentally observed ultrafast long-range charge separation

and protection against the charge recombination at the donor/acceptor interface [2].

Keywords: Quantum dissipative dynamics, light harvesting systems, energy/charge transfer dynamics

REFERENCES

1. Y. Fujihashi, M. Higashi & A. Ishizaki, Journal of Physical Chemistry Letters 9, 4921 (2018).

2. A. Kato & A. Ishizaki, Physical Review Letters 121, 026001 (2018).

Akihito Ishizaki received his D. Sc. degree in theoretical chemical physics at

Kyoto University in 2008. He spent the next four years as a postdoctoral

researcher at University of California Berkeley and Lawrence Berkeley National

Laboratory in the United States. In 2012, he began his independent academic

carreer as a research associate professor at Institute for Molecular Science,

National Institutes of Natural Sciences in Japan, and in 2016 he was made a full

professor.

30


CHE-I-03

Computational Spectroscopy: From Astrochemistry to Biomolecules

M. Biczysko1,*

1International Center for Quantum and Molecular Structures (ICQMS), Shanghai University, Shanghai, P.R. China * E-mail: [email protected]

ABSTRACT

Detection of simplest organic molecules in the interstellar space (ISM), prebiotic molecules evolution toward

more complex species and biomolecules self-assembly and structure-function relations are nowadays studied

by broad range of spectroscopic techniques. Majority of molecular structures have been obtained from X-ray

crystallography or microwave (MW) spectroscopy. On the other hand, structure and properties can be monitored

by different spectroscopic measurements such as infrared (IR), Raman, Resonance Raman, UV-vis absorption

or fluorescence or circular dichroism (CD), electron spin resonance (ESR). However, it is seldom

straightforward to link the rich experimental data to the desired information on the specific structure and

properties of complex molecular systems. Moreover, traditionally, these experimental results have been

analysed separately. Quantum chemistry computations yield direct information on all possible properties of

molecular systems, some of them very difficult to obtain from experiment. That provides a missing link between

different experimental techniques, which could not be integrated and fully explored otherwise.

I will discuss status and perspective of the project aimed at spectroscopy studies for systems of increasing size

and complexity, from small prebiotic molecules to larger bio-molecules, complexes and oligomers. We devise

effective theoretical schemes through step-by-step strategy, starting from comparison with highly accurate

theoretical models and/or state-of-the art experimental data for smaller systems, gradually moving towards

larger and more complex molecular systems featuring dispersion interactions, hydrogen bonding, variable local

stereochemistry-conformation, and chirality.

Keywords: DFT, amino-acids, peptides, proteins, dispersion, spectroscopy, FT-IR, UV-Vis, ESR

REFERENCES

1. Biczysko, M., Bloino, J., Puzzarini, C. Wires Comp. Mol. Sci. 2018, 7, 1349.

2. Jiang, Z., Biczysko, M., Moriarty, N. W. Proteins: Structure, Function, and Bioinformatics, 2018, 86,

273-278.

3. Zheng, M., Moriarty, N.W., Xu, Y., Reimers, J.R., Afonine, P.V., Waller, M.P. Acta Cryst. D, 2017,

73, 1020-1028.

Ph.D. at Wroclaw University (Poland) in 2000, Researcher at Italian Research

Council (2013), Associate Professor at Shanghai University (2015-). Editor of

Journal of Molecular Structure (Elsevier, 2016-), Editorial Board member of

International Journal of Quantum Chemistry (2018-), Member of the international

Ph.D. Board at Scuola Normale Supertiore (Pisa, Italy) Methods and Models for

Molecular Sciences (2018-2019), Astrochemistry (2019-2020).

30


CHE-I-04

DFT Studies on the Structure and Reactivity of Zeolites

Jianwen Liu1*, Xian-zhu Fu1 and Jing-li Luo1

1College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518055, China

* E-mail: [email protected]; Tel: +86 755 2693 3834

ABSTRACT

Zeolites are commonly used catalysts in the petrochemical industry. Their main catalytic sites are Brønsted and

Lewis acidic sites. Systematic study on the interaction between the Brønsted/Lewis sites and the Si/Al ratio,

equilibrium charge particles, framework doping and chemical modification in the pores based on first principles

is very important for studying the catalytic activity by uncovering the relationship between the structure and

reactivity. The further mechanistic studies based on the acid sites can uncover detailed chemical/physical

process at the molecular level, which can provide ideas and basis for the designation of zeolites catalysts for

energy and chemical industry.

Keywords: zeolites, Brønsted acid sites, Lewis acid sites, DFT

REFERENCES

1. Chen Y.F, Zhang L.J., Feng G., Wang X.W., Zhang R.B and Liu J.W., Appl. Surf. Sci. 2018, 433, 627–

638.

2. Feng G., Yang J.M., Wang C.Q., Lu K., Zhou J., Liu J.W., Wang X.W. and Zhang R.B. and Zhang N. , Microporous & Mesoporous Mater., 2018, 260, 227–234.

3. Han L.N., Wen C., Wu Z.P., Wang J.C., Chang L.P., Feng G., Zhang R.B., Kong D.J. and Liu J.W.,

Microporous & Mesoporous Mater. 2017, 237, 132-139.

4. Wen C., Han L.N., Geng L., Wang J.C., Chang L.P., Feng G., Kong D.J. and Liu J.W., Phys. Chem.

Chem. Phys. 2015, 17, 29586-29596.

5. Feng G., Lu Z.H., Yang D., Kong D.J. and Liu J.W., Microporous & Mesoporous Mater. 2014, 199, 83-

92.

6. Liu J.W., Mohamed F. And Sauer J. , J. Catal. 2014, 317, 75-82.

Ph.D. at the Chinese University of Hong Kong in 2008, Postdoctoral Researcher

in Humbold University zu Berlin, Germany (2009) , Chief Engineer in the

National Supercomputing Center in Shenzhen, China (2011), Research professor

at College of Materials Science and Engineering, Shenzhen University, China

(2017).

31


CHE-I-05

Applications of Carbon Nanohorn: Insight from Theoretical Studies

Chompoonut Rungnim*, Kajornsak Faungnawakij1, and Supawadee Namuangruk 1

1National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA),

Pathum Thani, 12120, Thailand * E-mail: [email protected]; Tel: +66 2 117 6705

ABSTRACT

In response to the increase of global environmental pollutions and energy demands, the development of

materials for energy and environmental applications is an urgent research topic. Carbon nanohorn (CNH),

having single-walled horn-shaped tubes, is considered as a possible candidate for both energy and

environmental applications because of its unique physical and chemical properties such as high purity, stability,

high surface area, internal vacancy accessibility, and multi-functionalization. In this work, we present the

potential to modify the CNH for toxic heavy metals adsorption and gas storage by using quantum chemistry

calculations. When Pt nanoparticles (Pt and Pt4) were supported on the CNH, the calculations based on density

functional theory (DFT) revealed that the efficiency of hydrogen gas (H2) storage increases via hydrogen

spillover mechanism. The supported Pt nanoparticles are the active site for hydrogen dissociative adsorption

and the high curvature surface of CNH facilitates the accommodation for the migrated H atoms. Furthermore,

the CNH with nitrogen dopant at the vacancy edge shows strong interaction towards the elementary mercury

(Hg) and mercury-halide. Special focus will be provided for the deep understanding related to CNH

modification for the design of novel adsorbents and catalysts.

Keywords: Carbon Nanohorn, Adsorbent, Catalyst

REFERENCES

1. Rungnim, C., Faungnawakij, K., Sano, N., Kungwan, N., and Namuangruk, S. Int. J. Hydrogen Energy,

2018, 43, 23336-23345.

2. Yodsin, N., Rungnim, C., Promarak, V., Namuangruk, S., Kungwan, N., Rattanawan, R., and

Jungsuttiwong, S. Phys. Chem. Chem. Phys. 2018, 20, 21194-21203.

3. Rungnim, C., Promarak, V., Hannongbua, S., Kungwan, N., and Namuangruk, S. J. Hazardous Mater.

2016, 310, 253-260.

Dr. Chompoonut Rungnim received her Ph. D. in Nanoscience and Technology

Program from Chulalongkorn University, Thailand in 2013. After that, she has

joined the Nanoscale Simulation Laboratory, National Nanotechnology Center

(NANOTEC) of Thailand as a researcher since 2014. Her current research

interests focus on the design and development of nanomaterials for

environmental and energy applications by using theoretical and computational

chemistry calculations.

32


CHE-I-06

A DFT-based Stability Screening for Dry Reforming Catalysts via the

Ratings Concept

Siriwimol Somdee1, Mongkol Lerdpongsiripaisarn1, and Supareak Praserthdam1, *

1High-performance computing unit (CECC-), Center of Excellence on Catalysis and Catalytic Reaction Engineering

(CECC), Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand * E-mail: [email protected]; Fax: +66 2 2186761; Tel. +66 8 6101 2244

ABSTRACT

Apart from the direct use of methane from natural gas for electricity, its conversion via the dry reforming process

(DRR) generating syngas is one of the cost-effective processes. A novel optimization component for an on-line

optimization in the DRR process was proposed in this work. The procedure comprises a two-step procedure:

the identification and optimization of the catalysts. The ratings concept proposed as the DRR computational

catalyst evaluation tool was used for the identification of the catalyst’s reactivity and stability [1,2,3]. For each

catalyst, reactivity and stability ratings defined as (RT-S, RT-R) indexes based on its sets of activation energy

in the DRR obtained from the density functional theory (DFT) is designated. These indexes represent the

catalyst’s abilities: (1) activation of reactants (CH4 and CO2) and (2) formation and removal of coke compared

to the reference catalyst. The indexes are located on the reactivity and stability surfaces (RS and SS) to predict

the DRR and coking rates at selected operating conditions. The crucial component of the concept for the stability

screening is the coking boundary, where for the stable catalysts, their (RT-S, RT-R) indexes must be in the

coke-removal zone which is the region where the rate of coke removal is higher than the formation. Moreover,

the extended ratings concept expanding the application to incorporate the experimental apparent activation

energy into the indexes. For the optimization part, the database for DRR and coke formation/removal rates of a

chosen catalyst at different operating temperatures and CO2/CH4 feed ratios must be constructed and being

incorporated into the on-line optimization component of the DRR process. To reach the conditions where for

given changes in the reformer feed composition due to different sources, the reaction rate in the reactor and

coke-resistance of the catalyst can be sustained is the goal.

Keywords: Computational catalyst screening, dry reforming, the ratings concept

REFERENCES

1. Praserthdam, S. and Balbuena, P.B., Reac Kinet Mech Cat, 2017, 122, 53-68.

2. Praserthdam, S. and Balbuena, P.B., Catalysis Today, 2018, 312, 23-34.

3. Praserthdam, S. (2018). Doctoral dissertation, Texas A & M University.

B.Eng. (Chemical Engineering, 1st class honors), Chulalongkorn University (CU)

in 2014, Ph.D. (Chemical Engineering), Texas A&M University in 2018, Lecturer

(2018-present) Department of Chemical Engineering, CU, Thailand, Principal

Investigator (2018-present), High-performance computing unit (CECC-HCU),

CU, Thailand.

Figure 1. Predicted rate of DRR,

coke formation and coke removal

via the ratings concept.

33


CHE-I-07

Automated Prediction of Chemical Reaction Paths Through Graph-

Theoretic Approach

Yeonjoon Kim, Jin Woo Kim, Kyunghoon Lee, and Woo Youn Kim*

Department of Chemistry, KAIST, Daejeon, Korea * E-mail: [email protected]; Fax: +82 42 350 2810; Tel. +82 42 350 2815

ABSTRACT

Despite remarkable advances in computational chemistry, prediction of chemical reactions is still challenging,

because investigating possible reaction pathways is computationally prohibitive due to the high complexity of

chemical space. For instance, their brute-force sampling is too demanding because of their large degrees of

freedom. A stochastic sampling method inherently requires many trials no matter how effective it is, because it

cannot guarantee 100% probability of finding a designated target structure within a finite number of samplings.

A feasible strategy for efficient prediction is to utilize chemical heuristics and machine learning techniques. We

proposed a novel approach to search reaction paths in a fully automated fashion by combining chemical theory

and heuristics. A key idea of our method is to extract a minimal reaction network composed of only favorable

reaction pathways from the complex chemical space through molecular graph and reaction network analysis.

This can be done very efficiently by exploring the routes connecting reactants and products with minimum

dissociation and formation of bonds. Finally, the resulting minimal network is subjected to quantum chemical

calculations to determine kinetically the most favorable reaction path at the predictable accuracy. To further

accelerate the graph-based method, we introduce state-of-the art machine learning techniques. They can replace

chemical heuristics and expensive calculations with more systematic, unbiased computational rules. In this talk,

we show the recent progress in this project with several examples.

Keywords: reaction mechanism, molecular graph, chemical heuristics

REFERENCES

1. Yeonjoon Kim, Sunghwan Choi, Woo Youn Kim*, J. Chem. Theo. Comput. 10, 2419 (2014).

2. Yeonjoon Kim, Jin Woo Kim, Zeehyo Kim, Woo Youn Kim*, Efficient prediction of reaction paths

through molecular graph and reaction network analysis, Chem. Sci. 9, 825 (2018).

3. Sunghwan Choi, Yeonjoon Kim, Jin Woo Kim, Zeehyo Kim, and Woo Youn Kim*, Feasibility of

activation energy prediction of gas-phase reactions via machine learning, Chem. Eur. J. 24, 12354 (2018).

4. Jin Woo Kim, Yeonjoon Kim, Kyung Yup Baek, Kyunghoon Lee, and Woo Youn Kim*, Performance

of ACE-Reaction on 26 Organic Reactions for Fully Automated Reaction Network Construction and

Microkinetic Analysis, J. Phys. Chem. in revision.

Ph.D. at POSTECH in 2009, Postdoctoral fellow at Max-Planck-Institute of

Microstructure Physics (2009-2010), Assistant professor (2011-2015) and

Associate professor (2015~) at Department of Chemistry, KAIST.

34


CHE-I-08

Methane to Ethane Conversion by Liquid Metal Indium: A DFT

Mechanistic Study

Y. Ohtsuka1, A. Nakayama1, Y. Nishikaw2, H. Ogihara3, I. Yamanaka2 and J. Hasegawa1,*

1Institute for Catalysis, Hokkaido University, Sapporo, Japan 2Department of Chemistry and Material Science, Tokyo Institute of Technology, Tokyo, Japan

3Graduate School of Science and Engineering, Saitama University, Saitama, Japan * E-mail: [email protected] l; Fax: +81 11 706 9145; Tel. +81 11 705 9145

ABSTRACT

Conversion of methane to valuable hydrocarbons is one of the designable alternatives to petrochemical

production of higher hydrocarbons. Recently, Yamanaka et al. reported direct dehydrogenative conversion of

methane to higher hydrocarbons by liquid metal indium1. Indium has the low melting point, 430 K, and is liquid

in the experimental condition of 1173 K. In this study, the mechanism of the reaction was investigated with

density functional theory (DFT) calculation and DFT molecular dynamics calculation (MD).

For the DFT calculation, two kinds of model were adopted. Cluster models were used for investigating potential

energy profile of the reactions with small number of in clusters. For the MD calculations, periodic boundary

condition calculations were used. The NVT ensemble was adopted. Blue moon ensemble calculations were

performed to obtain free energy profile.

Metal indium in liquid state at experimental condition (1173 K) was investigated with the DFT MD simulation.

The gas-liquid interface is completely disordered, and its structure was changing time to time. With this result,

several cluster-model calculations were performed to check how many numbers of indium cluster is activate the

methane C-H bond. The DFT result showed that the C-H dissociation is exothermic in low-coordinated indium

atoms. MD calculations were performed to investigate where the CH3-In species stays in the interface. The

trajectory shows that the CH3-In was on the interface and did not move into the liquid phase, which suggests

that the ethane formation would also occurs on the interface. The C-C bond formation between two CH3-In

species on the interface was also investigated, and the activation free energy was evaluated with the Blue moon

ensemble calculation. In the result, the ethane formation occurs on the gas-liquid interface, namely Langmuir-

Hinshelwood (LH) mechanism, and the calculated energy barrier was much smaller than that for the C-H

activation.

Keywords: Liquid indium catalysis, mechane dehydrogenative coupling, ab initio MD calculation

REFERENCES

1. Nishikawa,Y., Ogihara, H., Yamanaka, I. ChemistrySelect, 2017, 2, 4572-6.

Ph.D. at Kyoto University (KU) in 1998, Assistant professor (1999) and Lecturer

(2008) at Department of Synthetic Chemistry and Biological Chemistry, Graduate

School of Engineering, KU, Associate Professor at Fukui Institute for

Fundamental Chemistry, KU (2011), Professor at Catalysis Research Center

(Institute for Catalysis since 2015) at Hokkaido University (2012-).

35


CHE-I-09

Charge Transport Properties in a V2O5 Cathode of Li-ion Batteries: A

Computational Perspective

Panuwat Watthaisong,1,2 Sirichok Jungthawan,2,3 Pussana Hirunsit,4 Suwit Suthirakun*,1,2

1School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand

2Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima,

Thailand 3School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand

4National Nanotechnology Center, National Science and Technology Development Agency, 111 Thailand Science Park,

Pathum Thani, Thailand * E-mail: [email protected]; Tel. +66 44 224 886

ABSTRACT

Vanadium pentoxide (V2O5) has attracted a lot of attention due to its unique physical and chemical properties

in the context of battery materials. It has been proposed as a promising candidate of alternative cathode materials

for Li-ion batteries. The layered structure of V2O5 easily accommodates atoms of small radius, such as Li,

leading to a high capacity for lithium insertion. Insight into the limitations of ion and electron transport in the

V2O5 cathode is crucial for improvements of Li-ion batteries. In this talk, I will present our recent computational

studies on the charge transport of a Li+ ion and its corresponding polaron in the V2O5 cathode in the limit of

initial discharge by means of density functional theory (DFT) calculations. Polaron migration along different

crystallographic directions in the presence and absence of Li+ ions were systematically examined using linear

interpolation (LE) and nudge elastic band (NEB) methods. Computations reveal anisotropic polaron mobilities

where the in-plane conductivity is higher than that across the layer which is consistence with the experimental

observations. Lithiation dramatically affects the behavior of polaron migration. It significantly increases the

reaction energies and hopping barriers due to the strong polaron-ion interaction. In addition, various scenarios

of polaron-coupled ion diffusion were explored. We demonstrate that inspecting only the Li+ movement leads

to barriers of only half the size, grossly overestimating the diffusion in the cathode.

Keywords: V2O5, Li-ion batteries, Li diffusion, Polaron migration, Density functional theory

REFERENCES

1. Suthirakun, S., Genest, A., Roesch, N., J. Phys. Chem. C, 2018, 122, 150.

2. Suthirakun, S., Jungthawan S., Limpijumnong, S., J. Phys. Chem. C, 2018, 122, 5896.

I am a lecturer at School of Chemistry, Suranaree University of

Technology, Thailand. I define myself as a computational chemist whose

expertise lies in material science and heterogeneous catalysis. I received

my PhD (2013) in Chemical Engineering from University of South

Carolina and spent 2 years as a postdoc with Prof. Notker Roesch at IHPC,

A*STAR, Singapore. Our research group used computational tools, based

on first-principles calculations, to obtain better understanding of structure-

performance relationships of functional materials including energy

materials, such as electrode materials for energy storage devices.

36


CHE-I-10

A New Strategy for Reaction Path Concept and Dynamics Effects

Tetsuya Taketsugu 1,2,3*, Takuro Tsutsumi 3, and Yuriko Ono 1,2

1Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan 2Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan

3Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan * E-mail: [email protected]; Fax: +81 11 706 3535; Tel. +81 11 706 3535

ABSTRACT

In quantum chemistry, the intrinsic reaction coordinate (IRC) has been utilized as a uniquely defined reaction

path for a given elementary reaction [1]. The IRC is defined as a steepest descent pathway which connects

reactant and product minima via a transition state on a 3N - 6 dimensional potential energy surface for an N

atom system. Recent developments of automated reaction path search method lead to a global reaction route

mapping (GRRM) strategy, and it becomes possible to generate the IRC network for a given molecular system.

In this talk, I introduce our recently developed methodology to examine reaction dynamics from first principles

by combining ab initio molecular dynamics (AIMD) and GRRM methods [2]. In this approach, the AIMD

trajectory is mapped on the IRC network based on the distance functions between the AIMD point and reference

structures on the IRC pathways in the configurational space, providing a dynamical picture that the molecular

system goes over several minima and transition

states in the reaction path network. In the

application to structural transformations of Au5

cluster [2-4], a variety of reaction routes are

obtained, and the hopping from one IRC to the

other IRC is analyzed. The branching of AIMD

trajectories over a plenty of minima on the

potential energy surface via valley-ridge

transition points is also discussed.

Keywords: Reaction path, ab initio MD, global

reaction route mapping, bifurcation

REFERENCES

1. Maeda, S., Harabuchi, Y., Ono, Y., Taketsugu, T., and Morokuma, K., IJQC, 2015, 115, 258-269.

2. Tsutsumi, T., Harabuchi, Y., Ono, Y., Maeda, S., and Taketsugu, T., PCCP, 2018, 20, 1364-1372.

3. Harabuchi, Y., Ono, Y., Maeda, S., and Taketsugu, T., JCP, 2015, 143, 014301; ibid, 177102.

4. Tsutsumi, T., Ono, Y., Arai, Z., and Taketsugu, T., JCTC, 2018, 14, 4263-4270.

Tetsuya Taketsugu received his Ph.D. degree in theoretical chemistry from the

University of Tokyo in 1994 and became an assistant professor at the University

of Tokyo in 1995. In 1999, he moved to Ochanomizu University as an associate

professor and in 2005, he has become a professor of quantum chemistry group in

Hokkaido University. His research interests focus on the development of new

methodology to explore potential energy surfaces and reaction dynamics, as well

as theoretical approach to design novel catalyst.

Figure 1. Dynamical reaction route beyond the IRC.

37


CHE-I-11

Hydroamination by a Primary Amine of an Unactivated Alkene on

Gold Nanoclusters: A DFT Study

Karan Bobuatong1, Hidehiro Sakurai4 and Masahiro Ehara2,3*

1Department of Chemistry, Faculty of Science and Technology Rajamangala University of Technology Thanyaburi

Klong 6, Thanyaburi, Pathumthani, Thailand 2Institute for Molecular Science and Research Center for Computational Science, Myodaiji, Okazaki, Japan

3Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, Japan 4Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan

* E-mail: [email protected]; Tel. +66 83050 8575

ABSTRACT

Density functional theory calculations have been used to investigate the mechanism of intramolecular

hydroamination of unactivated alkenes by primary amines on gold nanoclusters (NCs) under aerobic conditions.

By examining the activation modes in the cyclization process, the olefin activation mechanism was calculated

to be the most energetically feasible of the three possible pathways. The amine activation pathway suffered

from a high activation barrier, which means that this pathway is unlikely to take place on gold NCs. The catalytic

cycle comprises five elementary steps: (1) Adsorption of O2 on Au NCs results in superoxo-like species and

provides Lewis acidic sites that allow the nucleophilic substrate, 2,2-diphenyl-4-penten-1-amine, to be adsorbed

effectively. (2) Intramolecular cyclization (C−N bond formation) takes place on the Au NCs through anti-

addition of the amino group. (3) Hydroperoxy moiety formation by hydrogen transfer from cyclic intermediate

to superoxo-like species. The formation of (4) hydrogen peroxide and (5) product involves hydrogen transfer

from a hydrated formic acid. Natural bond orbital analysis of the transition states that arise during C−N bond

formation reveals that anti-addition of the substrate is preferred over the syn-addition mechanism. A possible

side reaction, the formation of 2-methylene-4,4-diphenylpyrrolidine through -hydrogen elimination, is also

discussed.

Keywords: Hydroamination, gold nanocluster, aerobic condition, regioselectivity, DFT

REFERENCES

1. Kitahara, H., Sakurai, H. J. Organomet. Chem, 2011, 696, 442-449.

2. Dhital, R, N., Bobuatong, K., Ehara, M., Sakurai, H. Chem. Asian. J, 2015, 10, 2669-2676.

Ph.D. at Kasetsart University (KU) in 2010, Postdoctoral fellowship at Reseach

Center for Molecular Science, Institute for Molecular Science, Japan (2011-

2014), Lecturer (2015-) at Department of Chemistry, Faculty of Science and

Technology Rajamangala University of Technology Thanyaburi

38


CHE-I-12

Reaction Mechanism of the Direct Synthesis of Dimethyl Carbonate

from CO2 and Methanol over Metal-Oxide Catalysts

Akira Nakayama,1,2,3* Toshiyuki Sugiyama,1 and Jun-ya Hasegawa1

1Institute for Catalysis, Hokkaido University, Sapporo, Japan 2JST, PRESTO, Japan

3Deparment of Chemical System Engineering, Gradute School of Engineering, University of Tokyo, Japan * E-mail: [email protected]; Tel. +81-3-5841-7270

ABSTRACT

The direct conversion of carbon dioxide into variable chemicals has been a long-standing challenge to achieve

green sustainable chemistry. In particular, the nonreductive transformation of carbon dioxide is desirable since

it requires a low energy input and thus leads to safer and greener processes. The direct synthesis of dimethyl

carbonate (DMC) from carbon dioxide and methanol is one of the most important processes in this regard, and

it has been reported that CeO2- or ZrO2-based catalysts are effective for this reaction. In this work, we

theoretically investigate the reaction mechanisms of DMC formation over CeO2 and ZrO2 catalysts and clarify

the role of active sites by employing first-principle calculations. For modeling the complex reactions involving

several adsorbed molecules, we placed one carbon dioxide and several methanol molecules over the metal-oxide

surface to represent the adsorbed methanol monolayer, and the first-principle molecular dynamics simulations

were performed to obtain the free energy profiles. Based on the free energy profiles, we found that the reaction

mechanism via surface carbonate species is preferable over CeO2 catalyst and that intermediate with an oxygen

vacancy is formed during the reaction. The stability of the intermediate accompanying an oxygen vacancy is a

key factor that makes CeO2 an efficient catalyst for the direct synthesis of DMC. Comparison of the reaction

mechanism over ZrO2 catalyst is also provided in the session.

Keywords: dimethyl carbonate, cerium oxide, zirconium oxide, enhanced sampling

2001 Ph.D., Department of Chemical System Engineering, Graduate School of

Engineering, University of Tokyo; 2001-2005 Postdoctoral Research Associate,

Department of Chemistry, University of Illinois at Urbana-Champaign; 2005-

2013 Assistant Professor, Department of Chemistry, Faculty of Science,

Hokkaido Univerisity; 2013-2015 Associate Professor, Catalysis Research

Center, Hokkaido University; 2015-2019 Associate Professor, Institute for

Catalysis, Hokkaido University; 2016-present PRESTO Researcher, JST; 2018-

present Visiting Associate Professor, Institute for Molecular Science; 2019-

present Professor, Department of Chemical System Engineering, Graduate School

of Engineering, University of Tokyo

39


CHE-I-13

Study of Aggregation States and Dynamics of PMPC Using Molecular

Dynamics Simulation

Takako Mashiko1, Shihori Yamane2, Masayuki Kyomoto2

1Keihanna research center, KYOCERA Corp., Kyoto, Japan 2Medical R&D center, KYOCERA Corp., Shiga, Japan


ABSTRACT

According to recent studies, salt addition is acceleration of the polymerization of zwitterionic molecules [1-5].

However, the mechanism of the acceleration is unknown. In order to elucidate this mechanism, we have

calculated the aggregation of poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) in various solvents

using molecular dynamics (MD) simulation. To start the polymerization reaction, the methacrylate groups of

the MPC molecules need to aggregate to form the reaction part. Under low solute concentration and high salt

concentration, the methacrylate groups aggregate in all MD trajectories. The results indicate that both solute/salt

molar concentrations strongly influence aggregation and molecular orientation.

Figure 1. PMPC polymerization in an aqueous solution.

Keywords: molecular dynamics, solvation system, polymerization

REFERENCES

1. Liaw D-J, Huang C-C, Sang H-C, Wu P-L. Polymer, 2000, 41, 6123.

2. Liaw D-J, Lee W-F, Whung Y-C. J Appl. Polym. Sci., 1987, 34, 999.

3. Biegle A, Mathias A, Galin J-C. Macromol Chem. Phys., 2000, 201, 113.

4. Wang H, et al. Eur. Polym. J., 2004, 40, 2287-2290.

5. Shiojima T, et al. Acta Biomater., 2016, 40, 38-45.

I am a theoretical physical chemist and researcher at Keihanna Research Center,

KYOCERA Corporation. I received my PhD in 2017 from Yokohama City

University. Our group aims to solve real problems in the industrial field and

contribute to society by using material simulation. Currently I am trying to adept

quantum computers, D-Wave, in material simulations.

40


CHE-I-14

Computational Perspectives on Metal-mediated

Electronic Structure and Reactivity

Megan Deshaye, Jack D’Amelio, Anna Lamping,

Emily McCracken, Reuben Szabo, Preeyaporn Poldorn, and Tim Kowalczyk

Department of Chemistry, Advanced Materials Science & Engineering Center,

and Institute for Energy Studies, Western Washington University, Bellingham, WA, USA * E-mail: [email protected]; Fax: +1 360 650 6562; Tel. +1 360 650 6622

ABSTRACT

In this talk, we share computational perspectives and insights into electronic structure and reactivity of

organometallic species in three disparate contexts. First, we will discuss the electronic structure of a novel

mononitrosyl diiron complex bearing a redox-active pyridinediimine ligand. The plurality of plausible

electronic configurations necessitates a broken-symmetry or multireference DFT approach to characterize this

complex.1 Then we will examine the tunable influence of ligand electronic structure on the activation energy

for C-H functionalization via palladium acetate-based catalysts. Finally, we will analyze the influence of metal-

metal and π-π intermolecular interactions on the stabilization and 3D aromaticity of stacked Ni(II) norcorrole

species.2 The research questions germane to each of these studies were introduced to us through collaboration

with synthetic chemists, and in each case we focus on how the computational modelling complements and

informs experimental efforts.

Keywords: Broken-symmetry DFT, redox-active ligands, transition states, antiaromaticity

REFERENCES

1. P. M. Cheung, K. T. Burns, Y. M. Kwon, M. Y. Deshaye, K. J. Aguayo, V. F. Oswald, T. Seda, L. N. Zakharov,

T. Kowalczyk, J. D. Gilbertson. Hemilabile proton relays and redox-activity lead to {FeNO}x and significant rate

enhancements in NO2− reduction. J. Am. Chem. Soc. 2018, 140, 17040-17050.

2. R. Nozawa, J. Kim, A. Lamping, Y. Wang, S. Shimizu, I. Hisaki, J. Oh, T. Kowalczyk, H. Fliegl, D. Kim, H.

Shinokubo. Antiaromatic cyclophane: Three-dimensional aromaticity and magnetically induced spatial current

stream. Submitted.

Tim Kowalczyk is an Associate Professor at Western Washington University with

joint appointments in Chemistry, Materials Science, and Energy Studies. His

research focuses on excited-state electronic structure of soft materials for energy

conversion and storage applications. Prof. Kowalczyk is a Cottrell Scholar of the

Research Corporation for Science Advancement. He is a recipient of the 2018

ACS Division for Computers in Chemistry Outstanding Junior Faculty Award and

a CAREER award from the National Science Foundation.

Figure 1. Enhancement of redox

activity and control of reactivity with

metal centers.

41


BIO-I-01

First-Principle-Based and Data-Driven Design of Therapeutics

Kun-Lin Tsai1, Yun-Ru Chen1, Kun-Wei Lin1,2, Hsiu-Chen Yang3, Kai-Di Hu1, Pei-Feng Li3, Chih-Wen Shu3,4 and

Lee-Wei Yang1,5,6,7*

1Institute of Bioinformatics and Structural Biology, Tsing Hua University, Hsinchu, Taiwan

2Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan 3Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan

4School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan 5Physics Division, National Center for Theoretical Sciences, Hsinchu 30013, Taiwan

6Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 7TIGP Bioinformatics and CBMB Programs, Academia Sinica, Taipei, Taiwan

* E-mail: [email protected] l; Fax: +886 3 571 5934; Tel. +886 3 574 2467

ABSTRACT

In this talk, I’ll introduce an in silico drug repurposing platform integrated with docking and MD simulations

techniques which were applied to screen over 1300 FDA-approved drugs for selected cancer targets. Among

the top-ranked drugs, tioconazole shows effective inhibition of ATG4B activity in both biochemical and cellular

reporter assays and can enhance the cytotoxicity of chemotherapeutic agents. Along with the results, the intrinsic

allosteric regulation of ATG4B has been examined by linear response theory (LRT) and MD simulations. The

allosteric regulation is modulated by the substrate of ATG4B, LC3, which has a dual role as both substrate and

regulator suggested by previously reported crystal structure. By leveraging the LC3-mediated allosteric

regulation, the in silico drug screening is applied to LC3, and the identified candidates are further subject to in

vitro immunoblotting assays, NMR and tumor cell lines assays. Through the design and repurposing of FDA-

approved drugs, a few drugs with new indications for cancer treatments are repurposed to suppress autophagy-

promoted tumor progression. A general strategy to search possible allosteric sites in a protein will be introduced

when time allows.

Keywords: Allostery, Enzyme, Autophagy, MD simulations, Linear Response Theory, NMR

REFERENCES

1. Pei-Feng Liu et al. (2018). Drug Repurposing Screening Identifies Compound_1 as an ATG4 Inhibitor

that Suppresses Autophagy and Sensitizes Cancer Cells to Chemotherapy. Theranostics. 8, 830-845.

Obtaining Ph.D. at School of Medicine, University of Pittsburgh (2005) and

having postdoctoral trainings in Univ of Tokyo (2006-2009) and Harvard

University (2010-2011), Dr Lee-Wei Yang joined NTHU as an Assistant

Professor in 2011 and is now a Full Professor at Institute of Bioinformatics and

Structural Biology, National Tsing Hua University. He has published ~40

papers/book chapters in reputed journals and has an H-index of 20 with >2550

citations. He was a visiting Professor in IPR, Osaka University and is currently a

program coordinator in National Center for Theoretical Sciences (Physics

division), as well as serving as the Division Director of international students

(2016-2019), Office of Global Affairs, National Using Hua University to

supervise international students' exchange.

42


BIO-I-02

Molecular Dynamics Simulations of Full-length Amyloid-β Peptides

Hisashi Okumura1,2,3,*

1 Exploratory Research Center on Life and Living Systems, Okazaki, Japan 2 Institute for Molecular Science, Okazaki, Japan

3The Graduate University for Advanced Studies, Okazaki, Japan


ABSTRACT

Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 40 serious

human diseases. For example, amyloid-β fibrils (Aβ) are known to be associated with the Alzheimer’s disease.

We performed molecular dynamics (MD) simulations of Aβ fibrils in explicit water. We discovered that

molecular structure is different between two ends: The two β-sheets β1 and β2 are close to each other. On the

other hand, at the odd end the Aβ peptide fluctuates more and takes an open form, too [1]. Our theoretical

prediction was proved by experiment after our MD simulations.

We also performed nonequilibrium molecular dynamics simulations of an Aβ fibril in explicit water under

supersonic wave to mimic some experimental reports that cavitation disrupts amyloid fibrils [2]. We found that

when the pressure was decreased to a negative value, a bubble formation was observed. When the pressure was

increased to a positive value, water molecules attacked the hydrophilic residues, the bubble collapsed, and the

fibril was disrupted.

Another topic is conformational change of Aβ by binding to monosialotetrahexosylganglioside (GM1)-glycan

cluster. Recent studies showed that GM1 clusters induce the pathological aggregation of Aβ peptide responsible

for the onset and development of the Alzheimer’s disease. However, the effect of GM1-glycan cluster on Aβ

conformations has yet to be clarified. We performed MD simulations of Aβ on a recently developed artificial

GM1-glycan cluster [3].

Keywords: Molecular Dynamics, Amyloid Fibril.

REFERENCES

1. H. Okumura and S. G. Itoh, Sci. Rep. 6 (2016) 38422 (9 pages).

2. H. Okumura and S. G. Itoh, J. Am. Chem. Soc. 136 (2014) 10549-10552.

3. Y. Tachi, Y. Okamoto, and H. Okumura, Sci. Rep. 9 (2019) 6853 (11 pages).

Ph.D. at Keio University in 2002, Postdoctoral fellow of the Japan Society

for the Promotion of Science for Young Scientists at University of Tokyo

(2002), Research Associate at Institute for Molecular Science (2002),

Research Lecturer at Nagoya University (2006), Research Assistant (2008)

and Assistant Research Professor (2009) at Rutgers University in USA,

Associate Professor at Institute for Molecular Science (2009-).

43


BIO-I-03

Machine Learning for Property Prediction and Molecular Design

Siddhartha Laghuvarapu, Yashaswi Pathak, Poonganam Jyotish, Karandeep Singh,

and U. Deva Priyakumar

Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology,

Hyderabad 500 032 India * E-mail: [email protected]; Fax: +91 40 6653 1413; Tel. +91 40 6653 1161

ABSTRACT

Recent advances in deep learning methods seemed to have resulted in resurgence of their applications in natural

sciences during the last few years. Fundamentally, these data driven methods can broadly be classified as

supervised and unsupervised methods. In the first part of the presentation, we will discuss the use of artificial

neural network for predicting energies of small molecules. The ANN model was obtained based on a novel

molecule featurization inspired by additive force fields (BAND: bag of Bonds, Angles, Nonbonds and

Dihedrals). We will show that this model is applicable not only to the class of molecules that were used for the

training, but also to more complex molecules. While there is certainly room for improvement, the apparent

potential energy function can also be used to perform geometry optimization.

In the second part of the talk, we will present the use of unsupervised machine learning along with graph theory

to extract folding pathways from replica exchange molecular trajectories. A suitable vector representation was

chosen for each frame in the macromolecular trajectory and dimensionality reduction was performed using

PCA. The trajectory was then clustered using a density-based clustering algorithm, where each cluster represents

a meta-stable state on the energy surface of the biomolecule. A graph was created with these clusters as nodes.

We hypothesize that the most probable path of (un)folding from a starting to an ending state is the widest path

(path which has maximum minimum edge weight) along the graph. Our method makes the understanding of the

mechanism of unfolding in RNA hairpin molecule more tractable. As this method doesn’t rely on temporal data

it can be used to analyse trajectories from Monte Carlo sampling techniques and replica exchange molecular

dynamics (REMD).

Further examples of de novo molecular design that has relevance in drugs and materials using modern deep

learning approaches such as reinforcement learning and autoencoders will be presented.

Keywords: Machine learning, de novo design, atomization energy, pathways, material design

REFERENCES

1. Chattopadhyay, A.; Zheng, M.; Waller, M.; Priyakumar, U. D. J. Chem. Theory Comput. 2018, 14,

3365.

Ph.D., Pondicherry University (2004), Postdoctoral Fellow, University of

Maryland Baltimore (2004-2008), Assistant Professor at IIIT Hyderabad (2008 to

2012), Associate Professor at IIIT Hyderabad (2012 to now), Head of the Center

for Computational Natural Sciences and Bioinformatics (2013 to now). Awards:

Indian National Science Academy Young Scientist Medal, Young Associate of

Indian Academy of Sciences, JSPS Invitation Fellowship, Distinguished Lecture

Award from the Chemical Society of Japan.

44


BIO-I-04

Theoretical Study on the Singly-bonded Dimanganese Coordination

Complexes and Metalloprotein Analogues

M.-H. Hsieh1,2, G.-T. Huang1, P.-C. Chu2 and J.-S. K. Yu1,2,3*

1Department of Biological Science and Technology, National Chiao Tung University, Hsinchu City, Taiwan 2Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu City, Taiwan

3Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu City,

Taiwan * E-mail: [email protected]; Fax: +886 3 5729288; Tel. +886 3 5729287

ABSTRACT

The electronic structure and potential energy surface of the singly-bonded Mn–Mn and Cd–Cd complexes1 of

which geometrical motifs exactly match the theoretically predicted intermediates,2 are reported. The reduction

mechanisms and antiferromagnetic properties in the Mn–Mn bonding system are investigated and rationalized

by broken-symmetry density functional theories (BS-DFT).

Artificial metallothioneins (MTs) are able to capture heavy metals; their structure with designated metal binding

are potential magnetic biomaterials indicating a high-spin ground state, but their crystal structures that possess

magnetism are yet to be determined. Quantum mechanics combined with molecular mechanics (QM/MM) is

used to locate possible geometries of artificial MTs using the X-ray crystal structure3 as the geometric template,

and to investigate their ferromagnetic or antiferromagnetic natures while binding with different metal ions in

groups 7 and 12. It is observed that conventional DFTs at QM level perform similarly accurate in the geometry

optimization to suggest possible structures of MTs, which is consistent with the model calculations reported in

the literature.4 However, to predict the (anti-)ferromagnetism for further design of MTs, it is advised to

reconfirm the ground state using wavefunction theories with multireference characters in the QM region

Keywords: Metal-metal bond, antiferrimagnetism, metallothionein, QM/MM calculation

REFERENCES

1. Lu D.-Y., Yu J.-S. K., Kuo T.-S., Lee G.-H., Wang Y., Tsai Y.-C. Angew. Chem. Int. Edit. 2011, 50,

7611.

2. Tsai Y.-C., Lu D.-Y., Lin Y.-M., Hwang J.-K., Yu J.-S. K. Chem. Commun. 2007, 4125.

3. Kanyo Z. F., Scolnick, L. R., Ash, D. E., Christianson, D. W. Nature 1996, 10, 554.

4. Luber, S., Reiher, M. J. Phys. Chem. B 2010, 114, 1057.

Ph.D. at National Tsing Hua University (Chemistry) in 2002;

Assistant professor (2007–2012), Associate professor (2012–2016) and Professor

(2016– ) at Department of Biological Science and Technology, and Institute of

Bioinformatics and Systems Biology, National Chiao Tung University.

45


BIO-I-05

Understanding Biological Processes in Solution Based on the Statistical

Mechanics Theory of Liquids

Norio Yoshida1*

1Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan * E-mail: [email protected]; Fax: +81 92 802 4133; Tel. +81 92 802 4133

ABSTRACT

Life phenomena are a series and a network of chemical reactions, which are regulated by genetic information

inherited from generation to generation. The genetic information itself is generated and transmitted by a series

of chemical processes. In each of those reactions, some characteristic process takes place, which distinguishes

biochemical reactions from ordinary chemical reactions in solutions. Such a process is referred to as molecular

recognition (MR). MR is an extremely selective and specific process in the atomic level, and that selectivity as

well as specificity plays a key role for living systems to maintain their life. MR is a molecular process

determined by specific interactions between atoms in host and guest molecules. On the other hand, the process

is a thermodynamic process as well, with which the chemical potential or the Gibbs energy of guest molecules

in the recognition site and in the bulk solution are concerned.

A theoretical approach to MR has been launched based on a three-dimensional reference interaction site model

(3D-RISM) method.[1] By solving 3D-RISM equations, we can obtain the solvation structure around a solute.

The theory has been successfully applied to such MR problems as probing ligand molecules caged in protein,

ion binding by protein, and the ion conduction through the channels.

The electronic structural changes of ligand and receptor molecules are another serious concern in MR processes.

Recently, we proposed an efficient implementation of 3D-RISM to the electronic-structure theory of

macromolecules such as fragment molecular orbital (FMO) and quantum mechanics/molecular mechanics

(QM/MM) methods.[2,3] These methods are referred to as FMO/3D-RISM and QM/MM/RISM, respectively.

They allow us to treat an electronic structure of macromolecules, such as protein, as well as a solvent distribution

around the solute macromolecules.

In the presentation, we review our recent studies on the molecular recognition by protein based on 3D-RISM

and its extensions.

Keywords: 3D-RISM, FMO, CADD

REFERENCES

1. Norio Yoshida, J. Chem. Info. Model, 2017, 57, 2646-2656

2. Norio Yoshida, Yasuomi Kiyota, Fumio Hirata, J. Mol. Liquids, 2011, 159, 83-92.

3. Norio Yoshida, J. Chem. Phys., 2014, 140, 214118(1-13)

Ph.D. at Kyoto University (KU) in 2003, Assistant professor (2007) at

Institute of Molecular Science, Associate Professor at Department of

Chemistry, Graduate School of Science, Kyushu University (2012-)

46


BIO-I-06

Multiple Binding Configurations of Fis Proteins on DNA Underlie their

Dissociation Pathways

Min-Yeh Tsai1,2 and Peter G. Wolynes2,*

1Department of Chemistry, Tamkang University, New Taipei City, Taiwan (R.O.C.) 25137 2Department of Chemistry, and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005,

United States * E-mail: [email protected]

ABSTRACT

Fis protein is a nucleoid-associated protein and meanwhile a master transcription regulator in E-coli. While

being primarily non-specific in binding DNA, the kinetics of Fis dissociating from DNA is largely influenced

by its surroundings. In particular, recent single-molecule studies have shown that the dissociation rate increases

as the concentration of Fis in solution-phase increases. This unusual behavior, called facilitated dissociation,

challenges the standard thermodynamic model of gene regulation. The standard model, based on a first-order

unimolecular reaction scheme, fails under many in vitro and in vivo contexts. However, the detailed molecular

mechanism of facilitated dissociation is still not clear. This is in part due to the limitation of current experimental

techniques in probing the presence of key intermediates. Theoretical models and simulation techniques, in this

regard, are very useful for probing complex intermediates and therefore allow us to explore the structure

configurations that are difficult to achieve via experimental methods alone. In this study, we use a hybrid

computational method, namely AWSEM-3SPN protein-DNA force field, to explore the binding energy

landscape of Fis protein with DNA. The simulations uncover several different pathways for the dissociation of

the protein from DNA. These dissociation pathways involve different protein stoichiometries which correspond

to different functional outcomes for the systems biology of gene regulation by Fis.

Keywords: Protein-DNA Interaction, Coarse-grained Modeling, Molecular Dynamics Simulation, Facilitated

Dissociation, Cooperative Dissociation

REFERENCES

1. Tsai, M.-Y.; Zhang, B.; Zheng, W.; Wolynes, P. G., J. Am. Chem. Soc. 2016, 138 (41), 13497−13500.

I am a theoretical physical chemist and currently an assistant professor at the

Department of Chemistry, Tamkang University. I received my PhD in 2011 from

National Taiwan University. Before I joined Tamkang in 2018, I was a postdoc

at Rice University (with Prof. Peter G. Wolynes). My research employs

physicochemical principles to understand biological processes, such as protein-

protein/protein-DNA interactions using coarse-grained molecular simulation.

The goal of my research aims to understand the significance of functional

binding, self-assembly of bio-molecules associated with neurodegenerative

diseases as well as related gene transcription regulation.

47


BIO-I-07

Theoretical Studies on Reaction Mechanisms of Metalloenzymes:

QM/MM analyses

Yasuteru Shigeta

Center for Computational Sciences, University of Tsukuba, Japan * E-mail: [email protected]; Fax: +81 29-853-6496; Tel. +81 29-853-6496

ABSTRACT Proteins are macromolecular compounds with extremely complex structures and drive various biological

functions in vivo such as molecular recognition, signal transduction, enzymatic reaction, and etc. Since it is

expected that there is a correlation between the structure and the function (structure-function relationship), the

three-dimensional structures of many proteins have been clarified by experimental methods such as X-ray

diffraction experiment and nuclear magnetic resonance method (NMR). Especially, dynamic information of a

protein is recently obtained by state-of-the-art experimental techniques such as X-ray free electron laser, cryo-

electron microscopy, AFM and STM, and etc., which enable ones to elucidate protein functions in detail. Under

such circumstances, theoretical calculations become more important to confirm experimental facts at the

microscopic level and predict its vital role.

With recent progress in both supercomputer architectures and computational methodologies to analyze

biomolecules, the field of chemical reaction analysis occurring in vivo has made remarkable progress. In this

talk, we will introduce QM/MM methods for analyzing enzymatic reactions of metalloenzymes. In particular,

an oxygen-evolving complex in photosystem II [1, 2], a catalytic mechanism of a nitrile hydratase [3, 4], a

multi-copper oxidase [5, 6] done recently by our laboratory are reviewed. Keywords: QM/MM, oxigen evolving complex, non-heme iron, multi-copper oxidase

REFERENCES

1. M. Shoji, H. Isobe, Y. Shigeta, T. Nakajima, K. Yamaguchi, J. Phys Chem. B, 2018, 122 (25), 6491-6502.

2. M. Shoji, H. Isobe, T. Nakajima, Y. Shigeta, M. Suga, F. Akita, J.-R. Shen, K. Yamaguchi, Faraday Discuss. 2017, 198, 83-106.

3. M. Kayanuma, M. Shoji, M. Yoda, M. Odaka, Y. Shigeta, J. Phys Chem. B, 2016, 120 (13), 3259-3266. 4. M. Kayanuma, K. Hanaoka, M. Shoji, Y. Shigeta, Chem. Phys. Lett. 623, 8-13 (2015).

5. T. Tokiwa, M. Shoji, V. Sladek, N. Shibata, Y. Higuchi, K. Kataoka, T. Sakurai, Y. Shigeta, F. Misaizu,

Molecules, 2019, 24, 76.

6. M. Akter, T. Tokiwa, M. Shoji, K. Nishikawa, Y. Shigeta, T. Sakurai, K. Kataoka, Y. Higuchi, N. Shibata,

Chem. Euro. J., 2018, 24, 18052-18058.

Prof. Yasuteru Shigeta, a Theoretical Chemist and Biophysicist, graduated from

Department of Chemistry, Osaka University and obtained a Doctor of Science

degree at there in 2000. He joined University of Tsukuba as a full professor since

2014. He has published more than 200 scientific papers and received the

Presentation award for Young Scientists of the Chemical Society of Japan in

2006, PCCP award of Royal Society of Chemistry (UK) in 2007, Young-chemists

award of the Chemical Society of Japan in 2009, the Young-scientists award of

Ministry of Education, Culture, Sports, Science, and Technology (MEXT) Japan

in 2010, the Young-scientists award of Japan Society for Molecular Science in

2012, and the QSCP Promising Scientist Prize of CMOA in 2017.

48


BIO-I-08

Computational Solvation Analysis of Biomolecules

in Aqueous Ionic Liquid Mixtures

Veronika Zeindlhofer1, Christian Schröder1

1University of Vienna, Department of Computational Biological Chemistry, Austria * E-mail: [email protected]; Tel. +43 1 4277 52711

ABSTRACT

Based on their tuneable properties, ionic liquids attracted significant interest to replace conventional, organic

solvents in biomolecular applications. Following a Gartner Cycle, the expectations on this new class of solvents

dropped after the initial hype due to the high viscosity, hydrolysis and toxicity problems as well as their high

costs.

Since not all possible combinations of cations and anions can be tested experimentally, fundamental knowledge

on the interaction of ionic liquid ions with water and with biomolecules is mandatory to optimize the solvation

behaviour, the biodegradability, and the costs of the ionic liquid. Here, we report on current computational

approaches to characterize the impact of the ionic liquid ions on the structure and dynamics of the biomolecule

and its solvation layer to explore the full potential of ionic liquids.

Keywords: MD simulation, ionic liquids, biomolecular solvation

REFERENCES

1. Honegger, P., Schmollngruber, M., Hagn, G., Baig, O., von Baeckmann, C., Steinhauser, O. and

Schröder, C., J. Mol. Liquids, 2018, DOI: 10.1016/j.molliq.2018.09.110

2. Zeindlhofer, V. and Schröder C., Biophys. Rev., 2018, 10, 825.

3. Zeindlhofer, V., Berger M., Steinhauser, O. and Schröder , C., J. Chem. Phys., 2018, 148, 193819.

4. Platzer, S., Leyma, R., Wolske, S., Kandioller, W., Heid, E., Schröder, C., Schagerl, M., Krachler, R.,

Jirsa, F. and Keppler, B. K., J. Haz. Mat., 2017, 340, 113.

5. Zeindlhofer, V., Khlan, D., Bica K. and Schröder, C., RSC Advances, 2017, 7, 3495

6. Heid, E. and Schröder, C., J. Chem. Phys., 2016, 145, 164507.

7. Schröder, C., Steinhauser, O., Sasisanker, P. and Weingärtner, H., Phys. Rev. Lett., 2015, 114, 128101.

Christian Schröder studied chemistry in Giessen and Göttingen (Germany). He

finished his PhD in 2003 at the Max-Planck-Institute for Biophysical Chemistry

in Göttingen before he moved to the university of Vienna (Austria). Since 2006

he has investigated various ionic liquids and their physico-chemical and

spectroscopic properties by (polarizable) MD simulations. Between 2013 and

2017 he led the international work group “Physico-chemical properties of ionic

liquids and their modelling” of the European COST action CM1206. Since 2017

he has a tenured position at the university of Vienna.

49


BIO-I-09

Decomposition of Mechanical Properties in Biomolecules

Yizao Chen1 and Jhih-Wei Chu1,2,3*

1Institute of Bioinformatics and Systems Biology 2Department of Biological Science and Technology

3Institute of Molecular Medicine and Bioengineering * E-mail: [email protected]

ABSTRACT

Biomolecules such as protein and nucleic acids duplexes are of vital importance in biology. A key question for

such systems is how do subtle differences in the chemical composition cause extended variation in structure and

mechanical properties in the system. In this work, all-atom molecular dynamics simulations and multiscale

coarse grained modeling were conducted to resolve the structures and mechanical couplings in dsDNA, dsRNA,

and an enzyme system. The multiscale computational framework developed here allowed quantitative

comparison of the strengths of mechanical couplings for the different interactions in a molecule as well as across

different systems. It was thus established that dsRNA has significantly higher strengths for mechanical

couplings in backbone and sugar puckering than those of dsDNA. For nucleobase interactions of hydrogen

bonding and stacking, on the other hand, dsDNA exhibited stronger mechanical couplings. Moreover, we

showed that the mechanical couplings in the protein structure can be utilized to capture the patterns of sequence

correlation in a multiple sequence alignment.

Keywords: all-atom MD simulation, nucleic acid, protein, mechanical properties, multiscale modeling

Ph.D. Chemical Engineering, MIT; Professor at the Institute of Bioinfomratics

and Systems Biology, National Chiao Tung University, Taiwan, ROC; Dr Chu’s

research aims to elucidate of the manner by which the composing details of a

complex molecular system determine its functional activities by developing and

applying multiscale computational methods based on physical chemistry

principles.

49


BIO-I-10

Bridges between Experiment and Theory on Catalytic Functions

Seiji Mori1,*

1Institute of Quantum Beam Science, Ibaraki University, Mito 310-8512, Japan * E-mail: [email protected]; Tel: +81 29 228 8703

ABSTRACT

I am going to present our recent mechanistic studies on catalytic reactions as follows. (1) Rh(I)BINAP-catalyzed

isomerization of allylic amines, which was used for L-menthol synthesis, was examined by using DFT and

QM/MM calculations, and the Artificial Force Induced Reaction (AFIR) method, which enables us to perform

automatic reaction pathway search. Graph theory approach for this complicated reaction pathways by using

Prim’s algorithm is very useful to find the most economical reaction pathway. [1] (2) Importance of non-

covalent interaction on second-sphere coordination of indole group on one-electron oxidized Cu(II)-salen

complexes [2] and origin of high enantioselectivity in Cu(I)-catalyzed alkynylation of -ketoester. In this

studies, interactions between a cyclohexyl group of the -ketoester and cyclohexylphosphine were found. [3,4]

(3) In my last part, I am going to talk about QM/MM studies on bilin reductase (PcyA)-biliverdin IX complex,

which results in formation of phycocyanobilin, an open-chain tetrapyrrole pigment [5].

Figure 1. bilin reductase (PcyA)-catalyzed reaction of biliverdin IX

Keywords: DFT calculations, artificial force induced reactions (AFIR), QM/MM calculations, bilin reductase

REFERENCES

1. T. Yoshimura, S. Maeda, T. Taketsugu, M. Sawamura, K. Morokuma, S. Mori, Chem. Sci. 2017, 8, 4475-4488.

2. H. Oshita, T. Yoshimura, S. Mori, F. Tani, Y. Shimazaki, O. Yamauchi, J. Biol. Inorg. Chem. 2018, 23, 51-59.

3. T. Ishii, R. Watanabe, T. Moriya, H. Ohmiya, S. Mori, and M. Sawamura, Chem. Eur. J. 2013, 19(40), 13547-

13553.

4. M. C. Schwarzer, A. Fujioka, T. Ishii, H. Ohmiya, S. Mori, M. Sawamura, Chem. Sci., 2018, 9, 3484-3493.

5. E. Iijima, M. P. Gleeson, M. Unno, and S. Mori, ChemPhysChem., 2018, 19, 1809-1813.

Seiji Mori obtained his Ph.D. degree from the University of Tokyo, Japan, under

guidance of Prof. Eiichi Nakamura in 1998, and worked in Emory University,

USA, as a postdoctoral fellow with late Prof. Keiji Morokuma in 1998-2000.

Currently he has been a professor of chemistry, Ibaraki University, Japan since

2012. He was an assistant vice president of international strategy, Ibaraki

University in 2015-2017 for enhancing international collaborations of academic

and student exchanges.

50


BIO-I-11

Aggregation Process of Amyloid- Peptides by the Coulomb Replica-

Permutation Method

Satoru G. Itoh1,2,3,*

1 Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Japan 2Exploratory Research Center on Life and Living Systems, Okazaki, Japan

3 Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Japan * E-mail: [email protected]; Fax: +81 564 66 7025; Tel. +81 564 55 7465

ABSTRACT

The amyloid- peptide (A) is composed of 39–43 amino-acid residues. A tends to form insoluble amyloid

fibrils, which are associated with the Alzheimer's disease. The Oligomer is formed in the early stage of the

amyloidogenesis process. It has been reported recently that the A oligomer is a more plausible candidate for

synaptic dysfunction than the amyloid fibril. To investigate the oligomer formation process of A, we applied

the Coulomb replica-permutation method [1–4] to A fragments, A(29–42) peptides, in explicit water solvent.

A(29–42) consists of the residues 29 to 42, which correspond to the transmembrane domain of A. The length

of A after residue 29 is a critical determinant of the amyloid formation rate. Moreover, this fragment forms

amyloid fibrils by itself.

The Coulomb replica-permutation method is a form of the Hamiltonian replica-permutation method (HRPM)

[2,3]. HRPM combines the advantages of RPM [1] and the Hamiltonian replica-exchange method (HREM).

RPM is a better alternative to REM. In RPM, temperature permutations among more than two replicas are

performed with the Suwa-Todo algorithm. In HREM, by exchanging the parameters that are related only to

limited degrees of freedom, the number of replicas can be decreased in comparison with REM.

In my presentation, I will give a brief introduction of HRPM, and show the details of the aggregation process

A.

Keywords: Amyloid-beta peptides, Molecular dynamics simulation

REFERENCES

1. S. G. Itoh and H. Okumura, J. Chem. Theory Comput. 2013, 9, 570–581.

2. S G. Itoh and H. Okumura, J. Comput. Chem. 2013, 34, 2493–2497.

3. S. G. Itoh and H. Okumura, J. Phys. Chem. B 2014, 118, 11428–11436.

4. S. G. Itoh and H. Okumura, J. Phys. Chem. B 2016, 120, 6555–6561.

Satoru G. Itoh, Ph.D.

Assistant Professor

Institute for Molecular Science, Japan

Education: 2005 Ph.D. School of Physical Sciences, The Graduate University

for Advanced Studies

Area of research: Computational biophysics

51


BIO-I-12

Cheminformatics as a useful tool to search for novel Anti-Alzheimer

from Thai Natural Products Database

Patchareenart Saparpakorn1,2, Chak Sangma1,2 and Supa Hannongbua1,2*

1Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand

2Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University,

Bangkok, 10900, Thailand * E-mail: [email protected]; Fax: +81 11 706 3535; Tel. +81 11 706 3535

ABSTRACT

Due to advancement in science and technology, computational science and digital technology provide

opportunity to the collection of molecular structures of bioactive compounds from Natural products with the

physico-chemical properties obtained from both experimental and calculated data. This necessitates a

comprehensive database for the Natural Products and the fractional extracts whose biological activities have

been verified. In this work, Chemiebase, which consisted of about 4,000 active compounds, has been

constrcuted in order to search for bioactive compounds from Thai Natural Products and Medicinal Herbs.

Extension of the database has been done by addition of reported bioactive compounds from Thai Mushrooms.

Using data from this database and other computer-aided molecular design methods will be presented and

highlighted by successful screening for potential bioactive compounds against Anti-Alzheimer agent, focusing

on Acetylcholine esterase. The expected outcome is based on Data Science and analytics using this database

which will be benefit to an advancement of Natural Products for future drug discovery.

Keywords: Natural products, molecular databases, bioactive compounds, Alzheimer, molecular modeling

REFERENCES

1. Sangma C, Chuakheaw D, Jonkon N, Gadavanij S., Curr Pharm Des. 2010, 16 (15), 1753-84.

2. Chainukool, S., Goto, M., Hannongbua, S., and Shotipruk, A.*, Sep Sci Technol, 2014, 49, 13.

3. Chen, C. J., Jiang, R., Wang, G., Jiao, R. H., Tancharoen, C., Sudto, K., Vajarothai, S., Hannongbua,

S., Ge, H.M., Tan, R.X., Planta Medica, 2014, 80 (17), 1641-6.

4. Rajachan, O., Kanokmedhakul, K., Sanmanoch, W., Boonlue, S., Hannongbua, S., Saparpakorn, P.,

and Kanokmedhakul, S., Phytochemistry, 2016, 132, 68-75.

5. Maha, A., Rukachaisirikul, V., Saithong, S., Phongpaichit, S., Poonsuwan, W., Sakayaroj, J.,

Saparpakorn, P. and Hannongbua, S., Terezine derivatives from the fungus Phoma herbarum PSU-

H256, Phytochemistry, 2016, 122, 223-229.

Professor Dr. Supa Hannongbua graduated Dr.rer.nat from Innsbruck University,

Austria in 1991. She has been an academic member of Department of Chemistry,

Kasetsart University (KU) in 1989, Assistant Professor (1995), Associate

Professor (2004) and Professor (2010-present). She was the Head of Chemistry

Department (2010-2013), the member of Kasetsart University Council (2010-

2012, 2016-2018) and Dean of Faculty of Science, KU (2014-2018). She is

interested in drug discovery research, covering in three research platforms as a

Computational Drug Discovery platform, Biological-physicochemical

experimental platform and Development of methodology and polymeric

compounds.

52


BIO-I-13

Computational Enzymology: Methods and Applications

Jitrayut Jitonnom*

Division of Chemistry, School of Science, University of Phayao, Phayao, Thailand * E-mail: [email protected]; Fax: +66 0 5446 6664; Tel. +66 0 5446 6666 ext 1834

ABSTRACT

Computational enzymology is the application of computational chemistry methods to the study enzymes. One

of its major goals is to elucidate enzyme's catalytic mechanisms, the role of active site residues, as well as the

surrounding protein/solvent environment. Nowadays, there are a range of computational methods available to

the researcher including molecular dynamics (MD), quantum mechanical (QM)-chemical cluster, quantum

mechanical/molecular mechanic (QM/MM). Since each method has its strengths and limitations, it is common

to complementarily apply several of these methods. As a result, the new users must be trained to adapt at

multiple methodologies. In this talk we will discuss what is computational enzymology, as well as practicalities

of such aspects as chemical model construction, commonly applied computational methods and their application

as well as challenges. These will be illustrated using examples from the literature and research from our group.

Keywords: Computational Enzymology, QM cluster, QM/MM, QM/MM/MD REFERENCES

1. Senn, H. M., Thiel, W. Angewandte Chemie, 2009, 48, 1198–229.

2. Quesne, M. G., Borowski, T., de Visser, S. P. Chem. Eur. J., 2016, 22, 2562-81.

3. Sousa, S. F., Fernandes, P. A., Ramos, M. J. Phys. Chem. Chem. Phys., 2012, 14, 12431-441.

4. Himo, F. J. Am. Chem. Soc. 2017, 139, 6780-86.

5. Tuñón, I., Moliner, V., Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis,

The Royal Society of Chemistry Publishing, UK, 2017.

6. Jitonnom, J., Ketudat-Cairns, J. R., Hannongbua, S. J. Mol. Graph. Model., 2018, 79, 175-84.

7. Jitonnom, J., Mujika, J.I., van der Kamp, M.W., Mulholland, A.J., Biochemistry,2017,56,6377-88.

8. Jitonnom, J., Limb, M. A. L., Mulholland, A. J., J. Phys. Chem. B, 2014, 118(18), 4771–83.

I am a theoretical physical chemist and currently an assistant professor at the

School of Science, University of Phayao. I received my PhD in 2011 from Chiang

Mai University. During my PhD, I was a visiting student at the University of

Bristol (with Prof. Adrian Mulholland). My research interests lie in the area of

multiscale modeling of enzymes, such as carbohydrate-active enzymes and zinc

metalloenzymes. These enzymes have relevance to such areas as biofuel, food,

and drug design. Currently, I am interested in mechanistic studies of biocatalysis

and organometallic catalysis which involve a range of computational techniques,

in particular QM/MM and DFT.

53


BIO-I-14

Towards a Cure for AIDS: An Integrated Drug Discovery Model

Targeting Viral-Host Interactions

Nuttee Suree1,2,3,* and Panchika Prankio1,2,3

1Division of Biochemistry and Biochemical Technology, Department of Chemistry, Faculty of Science,

Chiang Mai University; 2Center for AIDS Drug Discovery, Chiang Mai University; 3Interdisciplinary

Program in Biotechnology, Graduate School, Chiang Mai University, Chiang Mai, Thailand * E-mail: [email protected]; Fax: +66 53 892277; Tel. +66 87 1023383

ABSTRACT

Recent developments of computational methods have been beneficial for the study of protein molecular motions

required for ligand recognition and subsequent activity. One of the ‘Holy-Grail’ goals for the field of

computational biochemistry is to construct a correlation between in silico data and the actual in vitro, or even

in vivo results, with acceptable accuracy, reproducibility and universal applicability. For our application in a

preclinical drug discovery campaign targeting several viral and host proteins, multiple modern techniques have

been implemented, ranging from computational biochemistry, molecular dynamics simulations, machine

learning algorithms for modelling inhibitory dynamics-potency relationship, in vitro and in silico screening on

targeted libraries, dynamics modulating inhibition, cell-based viral challenge, and in vivo models for drug

potency and toxicity evaluations. Our interested drug targets are HIV-1 integrase, human CCR5 co-receptor,

protein kinase C, and epigenetic histone deacetylases. Recent advances include 20 drug candidates, an

accelerated in silico/in vitro platform for the drug development, two improved enzyme-inhibitor

binding/dynamics/potency model predictions, and a humanized mouse model for anti-HIV potency assessment

and immune responses. CD4+ T-cell targeted drug delivery system has also been developed successfully using

antibody-functionalized liposomes. Future ventures will also focus on an early cellular profiling upon drug

treatments.

Keywords: HIV, Simulation, Computational, Inhibitor, Medicine

REFERENCES

1. Thangsunan, P., Wongsaipun, S., Kittiwachana, S., and Suree, N., J Biomol Struct Dyn, 2019, DOI:

10.1080/07391102.2019.1580219.

Dr.Nuttee Suree received his Ph.D. degree in Biochemistry and Molecular

Biology from University of California, Los Angeles (UCLA). His post-doctoral

training at UCLA School of Medicine was on human-mouse immunology and

HIV/AIDS gene therapy. He is currently an assistant professor of Biochemistry at

the Department of Chemistry, Chiang Mai University, Thailand. His research

interest has been focusing on enzymological basis of key viral and host proteins

involved in HIV pathogenesis and the viral control of quiescent infection, as well

as drug delelopment targeting these enzymes. Other research works are also on

drug delivery and biocompatibility evaluation for newly invented biomaterials.

54


PFD-I-01

Directional Chemical Perspective with Next Generation QTAIM

Tian Tian1, Tianlv Xu1, Steven R. Kirk*1, Ian Tay Rongde2, Tan Yong Boon2, Sergei Manzhos2,

Yasuteru Shigeta3 and Samantha Jenkins*

1College of Chemistry and Chemical Engineering, Hunan Normal University,

Changsha, Hunan 410081, China 2Department of Mechanical Engineering, National University of Singapore,

Block EA 07-08, 9 Engineering Drive 1, Singapore 117576 3Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Japan

* E-mail: [email protected]

ABSTRACT

The theoretical chemical physics/bio-chemistry that the BEACON research group undertakes seeks to develop

new theory and explanations for chemical observations whilst also posing questions to be answered by future

experiments. Our (next generation) QTAIM based research pioneers new theoretical tools that provide a new 3-

D vector based perspective to solve what was only until recently considered unsolvable. An example of this was

our explanation of chirality using only chemical measures [1]. By providing new tools based on ignoring

previous assumptions in theoretical chemistry/chemical physics we can currently address new areas such as

isotope separation, excited state dynamics [2], prediction of competitive and non-competitive ring-opening

reactions [3], excited state phenomena [4], physical properties including the application of E-fields [5] and

spectroscopic response.

Keywords: QTAIM, chirality, stereoisomers, stress tensor, excited states

REFERENCE

1. Chirality-Helicity Equivalence in the S and R Stereoisomers: A Theoretical Insight, Journal of the

American Chemical Society, 141(13), 5497–5503 (2019).

2. QTAIM and Stress Tensor Characterization of Intramolecular Interactions Along Dynamics

Trajectories of a Light-Driven Rotary Molecular Motor, J. Phys. Chem. A 121(25), 4778–4792, (2017).

3. A vector-based representation of the chemical bond for predicting competitive and noncompetitive

torquoselectivity of thermal ring-opening reactions, International Journal of Quantum Chemistry

118(20), e25707 (2018).

4. A 3-D Bonding Perspective of the Factors Influencing the Relative Stability of the S1/S0 Conical

Intersections of the Penta-2,4-dieniminium Cation (PSB3), International Journal of Quantum

Chemistry, 119(11), e25903 (2019).

5. The Destabilization of Hydrogen-bonds in an External E-Field for Improved Switch Performance,

Journal of Computational Chemistry, Early View (2019).

Ph.D. at Salford University in 2000, Assoicate Professor (Docent in Chemical

Physics) University West 2006, Professor Chemistry, (2010) College of

Chemistry and Chemical Engineering, Hunan Normal University, Director of

Theoretical and Computational Chemistry.

55


PFD-I-02

Finite-N effect in self-gravitating N-body simulations

T. Worrakitpoonpon1*

1Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Nonthaburi, Thailand * E-mail: [email protected]

ABSTRACT

Self-gravitating N-body system is widely employed as toy model to understand the dynamical process of many

astrophysical objects such as galaxies, which are believed to reside in some forms of dynamical equilibria

nowadays. In such system the finite-N fluctuation is intrinsically present, but the role of their graininess nature

has rarely been mentioned in past literatures. In statistical mechanics context, the embedded microscopic finite-

N fluctuation is found non-negligible for the dynamics of many hypothetical models with long-range

interactions and it has been demonstrated that their presence could affect the macroscopic properties.

In this presentation, I will talk about the study of finite-N effect to the violent relaxation of various collapsing

systems governed by Newtonian gravity, which is a member of long-range interaction. The central interest is

on the obtained final properties in those systems as we vary the particle number.

Keywords: Violent relaxation, N-body simulations, Self-gravitating systems

REFERENCES

1. Lynden-Bell, D. Mon. Not. R. Astron. Soc. 1967, 136, 101.

2. Worrakitpoonpon, T. Mon. Not. R. Astron. Soc. 2015, 446, 1335-1346.

3. Benhaiem, D., Joyce, M., Sylos Labini, F., Worrakitpoonpon, T. Mon. Not. R. Astron. Soc. 2018, 473,

2348-2354.

Ph.D. in Astronomy & Astrophysics at Pierre et Marie Curie University, France,

in 2011, Lecturer (2012) and Assistant Professor (2017-present) at Faculty of

Science and Technology, Rajamangala University of Technology Suvarnabhumi,

Thailand.

56


PFD-I-03

Detailed Ab Initio Dynamics of Thermal Unimolecular Decomposition

of Furan – A Combined Deterministic and Stochastic Model

Tam V.-T. Mai,1,2 Yao-Yuan Chuang,3 Binod Raj Giri4 and Lam K. Huynh5,*

1 University of Science, Vietnam National University – HCMC, 227 Nguyen Van Cu, Ward 4, District 5, Ho Chi Minh

City, Vietnam. 2 Molecular Science and Nano-Materials Lab, Institute for Computational Science and Technology, SBI Building, Quang

Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam. 3 Department of Applied Chemistry, National University of Kaohsiung, Kaohsiung 811, Taiwan, Republic of China 4 Clean Combustion Research Center, Division of Physical Sciences and Engineering, King Abdullah University of

Science and Technology, Thuwal 23955-6900, 5 International University, Vietnam National University System – HCMC, Quarter 6, Linh Trung Ward, Thu Duc District,

Ho Chi Minh City, Vietnam. * E-mail: [email protected] | [email protected]

ABSTRACT

The detailed kinetic mechanism of the pyrolysis reactions of furan was comprehensively investigated in a wide

range of temperatures (800-2000 K) and pressures (0.001-100 atm). The reaction potential energy surface (PES)

was explored using different composite electronic structure methods including W1U, CBS-QB3, CBS-APNO,

G3, G3B3 and G4, and the temperature- and pressure-dependent kinetic behaviors of the furan pyrolysis were

characterized using the integrated deterministic and stochastic Master Equation/Rice–Ramsperger–Kassel–

Marcus (ME/RRKM) rate model which includes corrections for the hindered internal rotation (HIR) and

quantum tunneling treatments. The 298-K heat of formation of furan, calculated using both atomization and

isodesmic approaches, is in good agreement with literature values. It is revealed that the pyrolysis mechanism

proceeds via hydrogen atom shift reactions routed through α-carbene and β-carbene intermediates which further

decompose and/or isomerize and lead to three final product, C2H2 + CH2CO (P1), CH3CCH + CO (P2), and

CH2CCH + HCO (P3). Also, the pathways of direct kicking off hydrogen of furan to form 2-furyl + H (P4) and

3-furyl + H (P5) were considered. The calculated results show that the channels P1 and P2 are the primary

products at temperatures higher than 1300 K while P3, P4 and P5 play an irrelevant role. The unimolecular

decomposition of furan mainly occurs via β-carbene with 85 – 91% at T = 1600 – 2000 K and P = 1 atm which

agrees with the recent measurements of Urness and co-workers (J. Chem. Phys., 2013, 139, 124305). The

calculated rate constants, together with the thermodynamic data of the species involved, are in good agreement

with the experimental results; thus they can be confidently used for further modeling and simulation of furan-

related combustion applications. The rate constants obtained from other electronic structure theories were also

discussed.

Keywords: biofuel, furan pyrolysis, rate constants, RRKM/ME, stochastic, and deterministic.

REFERENCES

1. Multi-Species Multi-Channel (MSMC) code, M. v. Duong, H. T. Nguyen, N. Truong, T. N. M. Le and

L. K. Huynh, Int. J. Chem. Kinet., 2015, 47, 564-575 (https://sites.google.com/site/msmccode/)

Ph.D. at University of Utah in 2007, Assistant Professor (2001) and Associate

Professor (2005) at International University, Vietnam National University System

at Ho Chi Minh City, Vietnam

57



https://sites.google.com/site/msmccode/


PFD-I-04

The AIMPAC2 Software Suite for Next-Generation QTAIM

Steven Robert Kirk

Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource

National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of

Resources, College of Chemistry and Chemical Engineering, Hunan Normal University,

Changsha, Hunan 410081, China * E-mail: [email protected]

ABSTRACT

Recent developments, design perspectives and recent research applications of the next-generation QTAIM

software suite AIMPAC2 will be outlined, before its public release later in 2019.

Keywords: QTAIM, Next-generation QTAIM, Software

Ph.D. at Salford University in 2001, Associate Professor (Docent in Chemical

Physics) University West 2011, Professor of Chemistry, (2010), College of

Chemistry and Chemical Engineering, Hunan Normal University. I am also the

Program Manager and Lead Developer of the AIMPAC2 software suite.

58


PFD-I-05

Multi-scale Dynamics and Structures with Particles, Chains, and Sheets

Ras B. Pandey

School of Mathematics and Natural Sciences

University of Southern Mississippi, Hattiesburg, MS 39406-5046, USA

E-mail: [email protected]; Telephone: +1 601 266 4485

ABSTRACT

Particles (solvent, solute), chains (polymer, peptide, and protein), and sheets (clay platelets, tethered membrane,

graphene sheets) are some of the basic constitutive elements to model a range of physical, chemical, and

biological phenomena using computer simulations. Stochastic motion of a particle leads to a range of multi-

scale dynamics (diffusion, sub-diffusion, drift, etc.) depending on the type of host matrix and driving

mechanism. The dynamics of the tethered particle in a chain is complex and becomes more so in a sheet and

provides valuable insight into local and global multi-scale relaxation mechanism. A multi-component system

such as self-organizing flow of an immiscible fluid, morphing structures of nano-materials, and conformational

response of proteins involves multi-scale relaxations that lead to well-defined structures. The dynamics and

structural relaxations are correlated and have strong bearing on the observables.

Using multi-grained mechanism (e.g. simulated interactions, knowledge based data, and phenomenological

interactions) we have examined organizing structures of a number of model systems over the years. For

example, one may be able to investigate self-organizing flow in a multi-component fluid and gain insight into

linear and non-linear responses with interacting lattice gas [1]. Investigations of bio-functional nano materials

(e.g. Au, Pd, graphene) may help identifying appropriate peptides [2].

Despite enormous effort, protein folding (i.e. conformational relaxation) remains an open question. Using a

multi-grain coarse-grained approach augmented by fine-grained data, we are able to examine unusual structural

response of such proteins as AQP1, hHv1 and CorA in their native and denatured phases in recent years. A

number of local and global physical quantities such as the energy and density profiles, contact and mobility

maps, mean square displacements, radius of gyration, and structure factor are analyzed. Some of these findings

[3] will be presented as time permits.

Keywords: Coarse-grained models, multi-component systems, self-organizing flow, bio-nano materials, protein

folding.

REFERENCES

1. Pandey, R.B. and Gettrust, J. F., Phys. Rev. E 2019, 80, 011130.

2. Pandey, R.B., Heinz, H., Feng, J., Farmer, B.L., Slocik, J.M., Drummy, L.F., and Naik, R.R., Phys. Chem.

Chem. Phys., 2001, 11, 1989-2001.

3. Kitjaruwankul, S., Boonamnaj, P., Paudel, S., Jetsadawisut, W., Sompornpisut, P., and Pandey, R.B., 2018

Physica A, 2018, 506, 987-992.

Prof. Pandey received his Ph.D. from IIT Roorkee in 1981 and worked at the North

Carolina State University (1981-1982) as a visiting assistant professor before his

postdoctoral work at Cologne University (1983), University of Cambridge (1984), and

University of Georgia (1984). He became assistant professor at the Jackson State

University in 1985 and moved to University of Southern Mississippi in 1988 where he

is professor of physics for about 30 years. His research spans over a range of topics in

statistical physics (transport and flow of fluid, porous media, polymer, interface and

roughness, bio- nano-composites, proteins). He was awarded Alexander von

Humboldt fellowship early in his career and became a fellow of the American Physical

Society recently. He is currently serving as an associate editor of the journal AIP

Advances published by the American Institute of Physics.

59



PFD-I-06

Machine/Deep Learning in Extragalactic Astronomy

S. Yuma1,*

1Department of Physics, Faculty of Science, Mahidol University, Thailand * E-mail: [email protected]; Tel. +66 2201 5775

ABSTRACT

In order to study the evolution of the universe, it is necessary to look at astronomical objects at different

distances and subsequently different epochs of the universe. Astronomers conducted blind search for such

distant galaxies by using a spectrograph to observe an individual object. This method is very secure in terms of

distance/epoch determination, but it is time and money consuming process. In 1995, Steidel et al. proposed a

new systematic way to select the large amount of distant galaxies at once. The sample size changes from the

order of ten objects to hundreds. This traditional method has been developed years by years since 1995. We can

currently use this type of algorithms to efficiently select normal star forming galaxies (Ono et al. 2018) or even

unique galaxies that show strong emission of gas (Yuma et al. 2017). This method, however, has a disadvantage

that astronomers need to perform visual inspection at every single object. It is a doable task until the recent

years of large sky surveys with more advanced instruments when the sample size reaches the order of million

objects. Looking at each individual galaxy is an unhealthy task and can lead to unpredictable uncertainty. The

rapid growth of data size requires the new automate way to securely select samples with least false detection.

Machine/Deep learning is considered to be one of the promising answers for the extragalactic astronomers. A

new method to select the distance galaxies involving the supervised learning algorithms will be introduced.

Keywords: galaxy formation; galaxy evolution; color selection methods, galaxies at high redshifts

REFERENCES

1. Steidel, C.C. et al. The Astronomical Journal (AJ), 1995, 110, 2519, 2520.

2. Ono, Y. et al. Publications of Astronomical Society of Japan (PASJ), 2018, 70, S10, 1-29

3. Yuma, S. et al. The Astrophysical Journal (ApJ), 2017, 841, 93, 1-17.

4. Yuma, S. et al. Submitted to ApJ, arXiv:1904.11510.

D.Sc. in Physics and Astronomy at Kyoto University, Japan in 2011; Posdoctoral

researcher (2011) at Kyoto University; Project Researcher (2012) and JSPS

Fellow (2013) at Institute for Cosmic Ray Research, The University of Tokyo,

Japan. Lecturer (2015) and Assistant professor (2017-present) at Department of

Physics, Mahidol University, Thailand.

60


PFD-I-07

Application of Particle-mesh Ewald Summation to ONIOM Theory

and the Excited State Lifetime of the Model Molecule of Retinal

Osamu Kobayashi1, Shinkoh Nanbu2, and Masanori Tachikawa 1,3*

1Graduate Schoool of Nano-Bio Science, Yokohama City University, Yokohama, Japan 2 Faculty of Science & Technology, Sophia University, Tokyo, Japan

3Schoool of Data Science, Yokohama City University, Yokohama, Japan * E-mail: [email protected]; Fax: +81 45 787 2188; Tel. +81 45 787 2188

ABSTRACT

Retinal is the chromophore of rhodopsin, and it de-excites by nonadiabatic transition. El-Sayed and coworkers

reported that the lifetime of model molecules of retinal in electronic excited state become longer in solution

than in vacuo. The computational studies of isomerization of the model molecules of retinal in solution has,

however, failed to describe solvent effect on the lifetime for 25 years; more

accurate model is required to reproduce the experimental results. ONIOM

(our Own N-layered Integrated molecular Orbital and molecular

Mechanics) theory1, proposed by Morokuma and coworkers, is the

sophisticated method which combinds quantum mechanics calculation

(QM) and molecular mechanics calculation (MM). The application of

Particle-Mesh Ewald (PME) summation and minimum-image convention

to ONIOM scheme (PME-ONIOM and MI-ONIOM)2 extend the scope of

QM/MM hybrid calculation from the finite system to the infinite system

such as solution. The central idea of PME-ONIOM scheme is to classify

the system in periodic boundary condition into three layers as illustrated in

Figure 1: Solute, Unit Cell, and Replicas. The potential energy of these

layers are calculated by, MM, and PME, respectively.

The nonadiabatic molecular dynamics (MD) based on Zhu-Nakamura version Trajectory Surface Hopping (ZN-

TSH)3 method is the powerful tool to simulate the nonadiabatic phenomena. Combining ZN-TSH method and

PME-ONIOM scheme enables the nonadiabatic MD simulation in explicit solvent molecules. We applied ZN-

TSH method and PME-ONIOM scheme for the simulation of the photoisomerization of (Z)-penta-2,4-

dieniminium cation, which is the model molecule of retinal, in methanol, and we successfully achieved the

theoretical reproduction of the experimental trends with PME-ONIOM scheme. PME technique should be

essential to reproduce the solution environment.

Keywords: Molecular Dynamics, Excited State, Nonadiabatic Transition, Solution

REFERENCES

1. T. Vreven, et al., J. Chem. Theory Comput., 2006, 2(3), 815.

2. O. Kobayashi and S. Nanbu, Chemical Physics, 2015, 461(1), 47–57

3. H. Nakamura, Nonadiabatic Transitions: Concepts, Basic Theories and Applications, second ed.,

World Scientific, Singapore, 2012.

PhD in Science, Sophia University, Tokyo (2016)

Sophia University, Tokyo, April 2016-Feburary 2017

Yokohama City University, March 2017-Present

Figure 1. Graphical

representation of PME-

ONIOM model

Solute(QM)

Unit Cell(MM/EE)

Replicas(PME)

61


PFD-I-08

Ab Initio Study of the Effect of Molecular Vibrations on the Positron-

binding to Polyatomic Molecules

Kaito Dohi1, Yukiumi Kita1, and Masanori Tachikawa1,2

1Graduate School of NanoBioScience, Yokohama City University, Yokohama, Japan 2School of Data Science, Yokohama City University, Yokohama, Japan


ABSTRACT

The positron, which is the anti-particle of the electron, is now widely used in both scientific and technological areas.

The detail mechanism of such processes, however, is still unclear in the molecular level. A positron affinity (PA)

value, which is a binding energy of a positron to an atom or molecule, has now been experimentally measured by

Surko and co-workers for many molecular species such as acetaldehyde, acetone, and acetonitrile molecules, based

on the vibrational Feshbach resonance by incident low-energy positrons. Thus, in order to elucidate the mechanism

of the positron binding to molecules, the theoretical analysis including the effect of molecular vibrations is

indispensable. In this study, we will show the effect of molecular vibrations on PA values, based on ab initio multi-

component quantum Monte Carlo (QMC) and molecular orbital (MCMO) methods for the electronic and positronic

wave functions simultaneously, and the anharmonic vibrational quantum Monte Carlo (QMC) method.

In order to analyze the PA value including the effect of molecular vibrations, we introduced vibrational averaged PA

(PA𝜈) defined by the following equation:

PA𝜈 ≡∫ PA[𝑋](𝑸)|Ψ𝜈(𝑸)|2d𝑸

∫|Ψ𝜈(𝑸)|2d𝑸 ,

where 𝑸 is a set of vibrational coordinates and Ψ𝜈 is the vibrational wave function of the 𝜈-th vibrational excited

state. The PA[𝑋](𝑸) is the vertical PA value at the molecular geometry 𝑸, defined by the total energy difference of

the parent molecule (𝑋) and its positron attached system ([𝑋; e+]) as PA[𝑋](𝑸) ≡ 𝐸[𝑋](𝑸) − 𝐸[𝑋;e+](𝑸). In this

study, 𝐸[𝑋;e+](𝑸) and Ψ𝜈(𝑸) were calculated with configuration interaction level of MCMO theory and vibrational

QMC method, respectively.

In the case of formaldehyde (CH2O) molecule, the vertical PA value at the equilibrium position is predicted as +25(3)

meV with QMC calculation. Applying the anharmonic vibrational analysis, the vibrational excitation of the C=O

stretching mode enhances the PA value, whereas the excitation of CH2 rocking mode deenhances it. We confirmed

that such PA variations arise from the change in both permanent dipole moment and dipole-polarizability at each

vibrational excited state. We will show some results of other larger molecules.

Keywords: Positron molecular compounds, Positron affinity, Multi-component molecular orbital

Dr. Masanori Tachikawa got Ph.D. in Waseda University in 1995, became a JSPS(PD) in

Emory University, and a Special Postdoctoral Researcher (SPDR) in RIKEN in 2000. In

2003 he moved to Yokohama City University as an associate professor, became a professor

in 2006, and now director of Department of Materials System Science, Graduate School

of NanoBioScience. His research area is “Computational Chemistry” and “Quantum

Chemistry”. He is developing new quantum simulation methods, in which both electrons

and hydrogen nuclei are treated quantum mechanically and applying these methods to the

various systems from material science to biochemistry. He has earned the awards for

“Young Scholar Lectures of the Chemical Society of Japan, 2006”, “The Young Scientists’

Prize, The Commendation for Science and Technology by the Minister of Education,

Culture, Sports, Science and Technology 2007”, and, recently, “Award of Society of

Computational Chemistry, Japan, 2017”.

62


PFD-I-09

Designing Aptasensor Based on AuNPs for Naked Eye Detection of

8-Oxo-dG: Combined in Silico and in Vitro Study

P. Toomjeen1, W. Phanchai1, C. Choodet1, and T. Puangmali1,2*

1Department of Physics, Faculty of Science, Khon Kaen University, Thailand 2Institute of Nanomaterials Research and Innovation for Energy (IN-RIE),

Khon Kaen University, Khon Kaen, Thailand *E-mail: [email protected]

ABSTRACT

The concentration of 8-oxo-7,8-dihydro-2’-deoxyguanosine (8-oxo-dG) in urine or serum is associated with the

degree of oxidative damage of DNA and broadly used as a sensitive biomarker for various diseases. However,

determination of a low concentration of 8-oxo-dG in biosamples is not an easy task owing to the complexity of

coexisting substances. Herein, we design an aptasensor based on aptamer-mediated aggregation of cysteamine-

capped gold nanoparticles (Cyst/AuNPs) for the detection of 8-oxo-dG by molecular dynamics simulation. Our

simulations reveal that a positively charged Cyst modified onto the surfaces of AuNP exists in two conformers

including gauche and trans. The trans conformer was prevalent on the AuNP surfaces and can stabilize AuNPs

in the aqueous solution, even in the presence of 8-oxo-dG. Molecular recognition between 8-oxo-dG and the

aptamer was demonstrated and bonding between these biomolecules was thoroughly elucidated. During the

complex formation, van der Waals stacking interactions between 8-oxo-dG molecules were observed and found

to play a significant role in the binding stability. The sensing mechanism of the colorimetric aptasensor was

studied and the feasibility study of the proposed aptasensor was assessed by experimental validation. The

experimental results are in good agreement with the computational study. Our in silico design can pave the way

for, but is not limited to, a highly sensitive aptasensor for the naked-eye detection of 8-oxo-dG.

Keywords: Aptasensor, Gold nanoparticle, 8-Oxo-dG, Molecular dynamics

REFERENCES

1. Phanchai, W., Srikulwong, U., Chompoosor, A., Sakonsinsiri, C., Puangmali, T. Langmuir, 2018, 34,

6161-6169.

2. Toomjeen, P., Phanchai, W., Choodet, C., Chompoosor, A., Thanan, R., Sakonsinsiri, C., Puangmali,

T. J. Phys. Chem. B. 2019, 123(5), 1129-1138.

3. Choodet, C., Toomjeen, P., Phanchai, W., Matulakul, P., Thanan, R., Sakonsinsiri, C., Puangmali, T.

RSC Adv. 2019. (Accepted)

He is an assistant professor at the Department of Physics, Khon Kaen University,

Thailand. He received his M.Sc. and Ph.D. from University of Leeds, UK, in

2007, 2011, respectively. His current research interests cover the in silico design

of nanoparticles for the applications in nanomedicine, espacially for biosensor and

drug delivery.

63


PFD-I-10

Ab-initio Anharmonic Algorithms and Their Applications to

Understand Vibrational Coupling

Jer-Lai Kuo1,*

1 Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica


ABSTRACT

Vibrational motions of molecules are intrinsically “anharmonic”, for example vibrational spectra of protonated

species often consist of complex vibrational features that can not be accounted for by normal modes of the target

molecule due to the vibrational coupling between proton modes and other dark states. Since proton stretch

modes in protonated molecules often carry large oscillator strength which in term gives rise to a great chance to

understand the vibrational coupling in these molecular systems via their vibrational spectra. We have recently

developed two ab initio anharmonic algorithms1,2. These algorithms have been applied to a range of protonated

species to reveal simple pictures behind their complex vibrational feature. Some of the selected systems are

solvated hydronium2,3 and a few proton-bound dimers4-6. Complex vibrational feature of functional group

containing N-H7 and C-H8 due to Fermi Resonance has also been resolved with the assistance of our ab initio

anharmonic schemes.

Keywords: Ab-initio anharmonic algorithm, Vibrational coupling

REFERENCES

1. K-L Ho, L-Y Lee, M. Katada, A Fujii, and J Kuo, Chem. Chem. Phys. 2016, 18, 30498.

2. Q Huang, T. Nishigori, M. Katada, A. Fujii, and J Kuo, Phys. Chem. Chem. Phys. 2018, 20,13836.

3. J Tan, JW Li, C-c Chiu, H. Huynh, HY Liao, and J Kuo, Phys. Chem. Chem. Phys., 2016, 18, 30721.

4. J. A. Tan and J-L Kuo, Phys. Chem. Chem. Phys. 2016, 18, 14531. Shaw, W. H., Business Ethics, 3rd

ed., Wadsworth, Belmont, 1999, 221. 5. D. C. McDonald, D. T. Mauney, D. Leicht, J. H. Marks, J. A. Tan, J-L Kuo, and M. A. Duncan, J. Chem. Phys.

2016, 145, 231101.

6. H-Y Liao, M. Tsuge, J. A. Tan, J-L Kuo, and Y-P Lee, Phys. Chem. Chem. Phys. 2017, 19, 20484.

7. M. Saurabh, J-L Kuo, and N. Patwari Phys. Chem. Chem. Phys., 2018, 20, 21557.

8. QR Huang, YC Li, KL Ho, and J-L Kuo, Phys. Chem. Chem. Phys., 2018, 20, 7653

Dr. Jer-Lai Kuo was born in Quemoy, Taiwan. He received B.Sc and M.Sc in

Physics from National Taiwan University and Ph.D in Chemical Physics from

Ohio State University. He is currently the Dean of Graduate Studies in Academia

Sinica (AS) and a Research Fellow in the Institute of Atomic and Molecular

Sciences (IAMS), AS. Before joining IAMS in 2009, Dr. Kuo taught in Nanyang

Technological University in Singapore. Dr. Kuo’s research interests focus on the

application and development of theoretical and computational tools to study a

wide range of topics in Molecular and Material Research.

64


PFD-I-11

Computer Simulations of Materials under Extreme Conditions

Udomsilp Pinsook1,*

1Department of Physics, Faculty of Science, Chulalongkorn University, Bangkok, THAILAND * E-mail: [email protected]; Fax: +66 2253 1150; Tel. +66 2218 5109

ABSTRACT

In this talk, I will present my research group’s achievement on the computer simulations of materials under

extreme conditions. Our computational tools are the density functional theory and other related methods. The

extreme conditions are the combinations of high pressure and high temperature, which are very important

thermodynamic parameters. At extreme conditions, most materials will have some changes in their physical

properties, sometimes associating with phase transitions. I will start with simple physics and what could be

expected under extreme conditions. Then, I will give several examples from the current researches of my group,

ranging from simple metals like Ca and Na which become not-so-simple under high pressure, some compounds

like GaAs, CIS and CIGS, and solar-related perovskite materials, hydrogen-rich and superconducting materials.

These findings can be applied to the field of geophysics, planetary science, and also advance material design.

Keywords: Density Functional Theory, High Pressure, Phase Transition

REFERENCES

1. L. Koci, R. Ahuja, L. Vitos and U. Pinsook, “Melting of Na at high pressure from ab initio

calculations”, Phys. Rev. B 77, 132101 (2008).

2. P. Pluengphon, T. Bovornratanaraks, S. Vannarat, K. Yoodee, D. Ruffolo and U. Pinsook, “Ab initio

calculation of high pressure phases and electronic properties of CuInSe2”, Solid State Communications

152, 775-778 (2012).

3. T. Pakornchote, U. Pinsook and T. Bovornratanaraks, “The hcp to fcc Transformation path of scandium

trihydride under high pressure”, J. Phys.: Condens. Matter 26, 025405 (2014).

• 1995 B.Sc. (Physics) Chulalongkorn University

• 1999 Ph.D. (Physics) The University of Edinburgh

• 2000-present Associate Professor, Chulalongkorn University

65


PFD-I-12

Multicomponent QM-climbing Image-nudged Elastic Band Method to

Analyze Chemical Reactions Including Nuclear Quantum Nature

Taro Udagawa1,*, Kimichi Suzuki2, and Masanori Tachikawa3,4

1Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan 2Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan

3Graduate School of NanobioScience, Yokohama City University, Yokohama, Japan 4Data Science Center, Yokohama City University, Yokohama, Japan

* E-mail:[email protected]; Fax: +81 45 787 2188; Tel. +81 58 293 2575

ABSTRACT

Nuclear quantum nature (NQE) of light nuclei, such as proton and deuteron, have attracted a lot of attention in

recent years. To directly reflect NQE of hydrogen nucleus on electronic structure, we have recently proposed

multicomponent QM (MC_QM) methods [1-2]. We can analyze H/D isotope effect on geometries (H/D

geometrical isotope effect) conveniently by using MC_QM method. Quite recently, we have proposed

MC_QM-climbing image-nudged elastic band (CI-NEB) method [3] by combining our MC_QM method with

CI-NEB method [4]. We obtain not only transition state structures but also minimum‐energy paths (MEPs) on

the MC_QM effective potential energy surface by using MC_QM-CI-NEB method. We have successfully

analyzed H/D isotope effect in several hydrogen-transfer reactions and have found that NQE affects not only

stationary‐point geometries but also MEPs and electronic structures in the reactions. We clearly demonstrate

the importance of including NQEs for H/D isotope effect on rate constants (kH/kD).

Keywords: Nuclear quantum effect, H/D isotope effect, nudged elastic band method

REFERENCES

1. Udagawa, T., Tachikawa, M., J. Chem. Phys., 2006, 125, 244105.

2. Udagawa, T., Tsuneda, T., Tachikawa, M., Phys. Rev. A, 2014, 89, 052519.

3. Udagawa, T., Suzuki, K., Tachikawa, M., ChemPhysChem, 2015, 16, 3156-3160.

4. Henkelman, G., Jonsson, H., J. Chem. Phys., 2000, 113, 9978.

Taro Udagawa was born in 1980 in Chiba, Japan. He received his B. Sc. (2003) and M.

Sc. (2005) degrees from Rikkyo University under the supervision of Prof. Hiroaki

Tokiwa, and obtained his Ph. D. degree from Yokohama City University under the

supervision of Prof. Masanori Tachikawa in 2008. Then he started an academic career

as an Assistant Professor at Gifu University.

Figure 1. Optimized geometrical

parameters in transition state

structure of OHCHCHCHO ↔

OCHCHCHOH and minimum

energy paths of H- and D-species

obtained by MC_QM calculations.

66


PFD-I-13

Ab initio Calculations of the Exchange Interaction of the Heisenberg

model in Cu-based oxides: AFM 𝜶-Cu2V2O7 and FM Y2Cu2O5

M. Suewattana1, S. Zhang3,4, G. Gitgeatpong1,2,5, A. Miyake6, M. Tokunaga6, P. Chanlert7, N. Kurita7, H.

Tanaka7, T. J. Sato8, Y. Zhao9,10, and K. Matan1,2

1Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400 Thailand

2ThEP, Commission of Higher Education, Bangkok, 10400, Thailand 3 Center for Computational Quantum Physics, Flatiron Institute, 162 5th Avenue, New York, New York 10010 USA

4 Department of Physics, College of William and Mary, Williamsburg, VA 23185 USA 5Department of Physics, Faculty of Science and Technology, Phranakhon Rajabhat University, Bangkok 10220, Thailand

6The Institute for Solid State Physics, University of Tokyo, Kashiwa 277-8581, Japan 7Department of Physics, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan

8IMRAM, Tohoku University, Sendai, Miyagi 980-8577, Japan

9Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA 10NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899,

USA * E-mail: [email protected]; Fax: +66 2 354 7159; Tel. +66 2 201 5783

ABSTRACT

We employ the density functional theory calculation using the generalized gradient approximation GGA+U

method to unravel the magnetic exchange interaction of the antiferromagnet 𝛼-Cu2V2O7 and the ferromagnet

Y2Cu2O5. The exchange coupling constant Ji (the interaction between the two nearest-neighbour magnetic active

cations) are calculated by analysing the different magnetic ground states based on the Heisenberg spin model.

The coupling constants are then extracted by the least-square fitting method.

In the spin ½ antiferromagnet 𝛼-Cu2V2O7, we present a full magnetic model consisting of three dominant spin

coupling constants, J1, J2 and J3. J1 represents the Cu-Cu intrachain bond in the spin chain pathway with the

bond length 3.138 Å while the other two coupling constants J2 and J3 originate from the interchain network of

the intertwining spin chain of short (3.982 Å) and long bonds (5.264 Å). The total energy calculations verify

that the magnetic ground state of 𝛼-Cu2V2O7 is the antiferromagnetic structure which is consistent with the

experimental findings. In addition, we compute the density of state and electronic charge density. Our calculated

bang gap showed that 𝛼-Cu2V2O7 is an insulator with bandgap of 1.8 eV. The majority of state close to the

Fermi level consists of (eg)3 i.e. 3𝑧2 − 𝑟2 and 𝑥2 − 𝑦2 indicating that these orbitals are magnetically active. The

obtained values of the exchange interaction are then used to construct a spin network for the quantum Monte

Carlo simulation to calculate the magnetic susceptibility for comparison with the experimental data.

Additionally, we will present the study of the ferromagnet Y2Cu2O5 under the similar framework. Results will

be discussed in term of the dominant coupling constant and electronic structure.

Keywords: exchange stiction, ab initio calculation, Heisenberg model, frustrated magnet

Ph.D at the College of William and Mary in 2005, Research associate at

Oak Ridge national Laboratory and University of Tennessee in 2005-2007,

Lecturer (2007-2011) and Assistant professor of physics since 2011 at the

Department of Physics, Faculty of Science, Mahidol university.

67


PFD-I-14

Kinetic Energy of the Hydrogen bonds: An Application of the Path

Integral Molecular Dynamics

Tsutomu Kawatsu*

Computational engineering applications unit, R&D group, Head office for information system and cybersecurity,

RIKEN, Wako, Saitama, Japan

Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, Japan * E-mail: [email protected]; Fax: +81 48 467 7502; Tel. +48 467 7503

ABSTRACT Hydrogen bonding systems often have a phase transition behaviour in high-pressured condition as shown

overview in Figure 1. In low pressure, it is the hydrogen bond usually we imagine: the potential of the hydrogen

is double well shape on the hydrogen-bonding axis and the hydrogen atom locates at one of these well. In high

pressure, the barrier between two wells becomes enough low for hydrogen’s moving between wells frequently.

In very high pressure, potential wells merges and the potential shape becomes a single well. Between these

phases, the free energy of the hydrogen differs because the zero-point vibrational energy is large when the

particle is localized and vice versa while the term is not included in normal molecular dynamics or ab initio

structure optimizations. I have investigated the models of the high-pressured ice (VII, VIII, X) [1] and hydrous

alumina (δ-AlOOH) [2,3] using the ab initio path integral molecular dynamics method [4] with the plane-wave

electronic structure calculation. The quantum kinetic energy is investigated that is dominated by the zero-point

vibrational energy at 300 K. The zero-point vibrational energy of the hydrogen atoms varies depending on the

shape of the hydrogen bond as above prediction.

Figure 1. Overview of hydrogen atom distribution on high-pressured hydrogen bonds.

Keywords: hydrogen bond, zero-point vibration, quantum fluctuation, high pressure, Ice.

REFERENCES

1. E. Sugimura et al., Phys. Rev. B, 2008, 77, 214103.

2. T. Kuribayashi, et al., Phys. Chem. Minerals., 2014, 41, 303.

3. A. Sano, et al., Geophys. Res. Letts., 2008, 35, L03303.

4. M. E. Tuckerman, et al., J. Chem. Phys., 1993, 99, 2796.

Doctor of Science, from Nagoya university. Former positions were in Duke,

Georgia tech., Kyoto, Kanazawa, and Yokohama-City (YCU) universities.

Current positions are a postdoctorial resercher of Riken, and visiting associate

proffesor of YCU. The research field is in the theoretical and computational

biophysics, chemistry, and material science. The major forcus is the quantum

effects such as the electron transfer, excitation energy transfer, proton tunneling,

and structural quantum fluctuations in the molecular and material systems.

68


PFD-I-15

The Phase-Field Crystal Method: An Overview,

Development, and Applications

Nirand Pisutha-Arnond1,*

1Department of Industrial Engineering, Faculty of Engineering, King Mongkut's Institute of Technology Ladkrabang,

Bangkok, Thailand * E-mail: [email protected]; Fax: +66 2 329 8340; Tel; +66 2 329 8339

ABSTRACT

The phase-field crystal (PFC) method is a promising continuum modeling approach because of its ability to

simulate complex material phenomena with atomic spatial resolution and at diffusive time scales. The atomic

spatial resolution of the model allows it to naturally include elastic, plastic, and crystalline symmetry effects in

one consistent formulation. Simulation at the diffusive time scale allows the model to examine time scales

commonly involved in material processes that are not easily accessible via molecular dynamics. This

presentation attempts to summarize the past decade of development and applications of the PFC method

subsequent to its introduction in 2002. Two different developments of the PFC method are first presented; one

is the phenomenological development arising from the Ginzburg-Landau model, the phase-field model, and the

Swift-Hohenberg equation, while the other development can be traced back to static and evolution equations of

classical density functional theory (CDFT). Examination of these different developments not only gives

historical perspective on the PFC model but also illuminates the motivation for various extensions and

improvements to the PFC model. The applications of the PFC model are then reviewed to exhibit the promising

capability of the approach; these applications include a variety of material phenomena such as the growth of

crystalline phases from a liquid melt, epitaxial growth, grain boundary pre-melting, dislocation dynamics, and

glass formation.

Keywords: Computational materials science, condensed matter physics, continuum modelling

REFERENCES

1. Elder, K. and Grant, M., Phys. Rev. E, 2004, 70, 051605(1-18).

2. Chan, V.W.L., Pisutha-Arnond, N., and Thornton, K., Comput. Mater. Sci., 2017, 135, 205-213.

Dr. Nirand Pisutha-Arnond graduated from the University of Michigan

(Michigan, USA) in 2013 with the Ph.D. in Materials Science and Engineering.

He has served as a faculty member at the Department of Industrial Engineering,

King Mongkut's Institute of Technology Ladkrabang (Bangkok, Thailand) since

2013. His research interest is the computational materials science at continuum

level. The research focuses on model developement and validation as well as

numerical implementation.

69


PFD-I-16

Machine Learning Clustering Technique Applied to X-ray Diffraction

Patterns to Distinguish Alloy Substitutions

Ryo Maezono1,*

1School of Information Science, JAIST, Ishikawa, Japan * E-mail: [email protected]; Tel: +81 76 151 1240

ABSTRACT

SmFe12 is one of the candidates of the main phase in rare-earth permanent magnets [1]. The origin of intrinsic

properties emerging at high temperature as well as that of the phase stability has not yet been clarified well.

Introducing Ti and Zr to substitute Fe and Sm is found to improve the magnetic properties and the phase

stability. To clarify the mechanism how the substitutions improve the properties, it is desired to identify

substituted sites and its amount quantitatively, preferably with high throughput efficiency for accelerating the

'materials tuning'. Motivated by the above, we have developed [2] a machine learning clustering technique to

distinguish powder XRD patterns to get such microscopic identifications about the atomic substitutions. Ab

initio calculations are used to generate supervising references for the machine learning of XRD patterns: We

prepared several possible model structures with substituents located on each different sites over a range of

substitution fractions. Geometrical optimizations for each model give slight different structures each other. Then

we generated many XRD patterns calculated from each structure. We found that the DTW (dynamic time

wrapping) analysis can capture slight shifts in XRD peak positions corresponding to the differences of each

relaxed structure, distinguishing the fractions and positions of substituents. We have established such a

clustering technique using Ward's analysis on top of the DTW, being capable to sort out simulated XRD patterns

based on the distinction. The established technique can hence learn the correspondence between XRD peak

shifts and microscopic structures with substitutions over many supervising simulated data. Since the ab initio

simulation can also give several properties such as magnetization for each structure, the correspondence in the

machine learning can further predict functional properties of materials when it is applied to the experimental

XRD patterns, not only being capable to distinguish the atomic substitutions. The 'machine learning technique

for XRD patterns' developed here has therefore the wider range of applications not limited only on magnets, but

further on those materials which properties are tuned by the atomic substitutions.

Keywords: Materials Informatics, XRD, Machine learning, Ab initio

REFERENCES

1. K. Kobayashi et al., J. Magn. Magn. Mater. 426, 273 (2017).

2. K. Utimula, R. Hunkao, M. Yano, H. Kimoto, K. Hongo, S. Kawaguchi, S.Suwanna, R. Maezono,

arXiv:1810.03972.

Ph.D. at Tokyo University in 2000, EPSRC fellow at Cavendish Laboratory,

Cambridge University (2000-2002), Tenure researcher at NIMS, Japan (2001-

2007). Lecturer at School of Information Science, JAIST (2007), Associate

Professor (2011), and Professor at School of Information Science, JAIST (2017).

70


PFD-I-17

Ab Initio Materials Informatics for Computational Materials Design

Kenta Hongo1,2,3,4*

1Recearch Center for Advanced Computing Infrastructure (RCACI), JAIST, Nomi, Ishikawa, Japan 2PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan

3CMi2, Research ad Service Division of Materials Data and Integrated System, NIMS, Tsukuba, Ibaraki, Japan 4Computational Engineering Applications Unit, RIKEN, Wako, Saitama, Japan


ABSTRACT

Materials Informatics (MI) [1] has recently emerged as a new approach to computational materials design.

Before its advent, computational material design was performed using materials simulations, though their search

space was limited to tens to hundreds of compounds. Machine learning models expands its search space into

hundred thousands of compounds, and then high throughput virtual screening approaches have demonstrated

success in exploring new materials. In MI, first-principles/ab initio simulations based on density functional

theory (DFT) have been widely used to generate various materials properties. Despite its success in most

property predictions, DFT sometimes fails to reproduce magnetism, molecular interactions, etc. To overcome

the DFT failures, quantum Monte Carlo (QMC), especially diffusion Monte Carlo (DMC), is one of the most

practical approaches used in materials science from the viewpoint of computational cost and accuracy. In

particular, QMC is quite suitable for recent massively parallel computers because of its high parallel efficiency.

In the era of the next-generation exascale supercomputers, QMC can be thought of as one of the next generation

"data generation engines" in the "ab initio MI".

In this talk, I will start with a brief introduction to MI from the viewpoint of materials simulations, including

our achievements [2]. Next, I will demonstrate our recent achievements on first-principles simulations based on

DFT [3-5] and DMC [6,7], followed by a brief introduction to materials simulations.

Keywords: Materials Informatics, Machine learning, Bayesian inferance, ab initio simulations, DFT, QMC

REFERENCES

1. Gomez-Bombarelli, R.; et al., Nat. Mater. 2016, 15, 1120-1127.

2. Ikebata, H.; Hongo, K.; Isomura, T.; Maezono, R.; Yoshida, R. J. Comput. Aided Mol. Des. 2017, 31,

379-391.

3. Nakano, K.; Hongo, K.; Maezono, R. Sci. Rep. 2016, 6, 29661:1-10,; Inorg. Chem. 2017, 56, 13732-

13740.

4. Kato, D.; Hongo, K.; et al., J. Am. Chem. Soc. 2017, 139, 18725-18731.

5. Kuriki, R.; Ichibha, T.; Hongo, K.; et al. J. Am. Chem. Soc. 2018, 140, 6648-6655.

6. Hongo, K.; et al., J. Phys. Chem. Lett. 2010, 1, 1789-1794.

7. Hongo, K.; Maezono, R. J. Chem. Theory Comput. 2017, 13, 5217-5230.

Ph.D. at Tohoku University (TU) in 2005, Postdoctoral researchers at TU (2005),

JAIST (2007), and Harvard University (2009). Research Assistant Professor at

The Institute of Statistical Mathematics (2011). Assistant Professor at School of

Information Science, JAIST (2012), and Associate Professor at RCACI , JAIST

(2017).

71


MST-I-01

On Recent Statistical Modeling

Kazuyuki Koizumi1,* and Rui Ue2

1School of Data Science, Yokohama City University, Yokohama, Japan 2Graduate School of International Management, Yokohama City University, Yokohama, Japan

* E-mail: [email protected]; Tel: +81 45 787 2263

ABSTRACT

The statistical modeling is a versatile way to build flexible models from data. It started with something like a

linear regression model. In the linear regression model, since the estimator of the regression coefficient which

is a parameter is explicitly obtained by the least squares method, it has become widely used. For a non-linear

regression model, a unified parameter estimator has not been obtained, and it is necessary to consider an

appropriate estimation method depending on each situation. Also, in recently, a method for handling high

dimensional data is required, and a sparse estimation method is often used. In this study, we introduce several

sparse estimation methods including LASSO.

Keywords: regression model, high dimensional data, sparse estimation, LASSO

2009 Ph. D, Graduate School of Science, Tokyo University of Science. 2009 Assistant Professor in Mathematical Information Sciences Tokyo University of Science, Tokyo, JAPAN. 2012 Assistant Professor in International Collage of Arts and Sciences Yokohama City University, Yokohama, JAPAN 2017 Assosiate professor in Data Science

Yokohama City University, Yokohama, JAPAN.

72


MST-I-02

Efficient Calculation of the Joint Distribution of Order Statistics

J. von Schroeder1 and T. Dickhaus1,*

1Institute for Statistics, University of Bremen, Bremen, Germany * E-mail: [email protected]; Tel. +49 421 218 63651

ABSTRACT

We consider the problem of computing the joint distribution of order statistics of stochastically independent

random variables in one- and two-group models. While recursive formulas for evaluating the joint cumulative

distribution function of such order statistics exist in the literature for a longer time, their numerical

implementation remains a challenging task. We tackle this task by presenting novel generalizations of known

recursions which we utilize to obtain exact results (calculated in rational arithmetic) as well as faithfully rounded

results. Finally, some applications in stepwise multiple hypothesis testing are discussed, and applications to

real-life datasets are presented.

Keywords: Bolshev's recursion, faithful rounding, multiple testing, Noe's recursion, rational arithmetic, Steck's

recursion

REFERENCES

1. von Schroeder, J., Dickhaus, T. Preprint, available at: arXiv.org > stat > arXiv:1812.09063

Ph.D. at Heinrich Heine University Düsseldorf in 2008, Junior professor at

Department of Mathematics, Humboldt University of Berlin (2010-2013), Senior

researcher at Weierstrass Institute for Applied Analysis and Stochastics Berlin

(2013-2015), Full professor at Faculty 3 - Mathematics and Computer Science,

University of Bremen (2015-).

73


MST-I-03

Influence of across tropical Pacific El Niño to Indochina Peninsula

under climate change

C. Oonariya1,*

1Climate Center, Thai Meteorological Department, Thailand

* E-mail: [email protected] l; Fax: +662 383 8827; Tel. +662 399 1423

ABSTRACT

The El Niño-Southern Oscillation (ENSO) is a major impact to Asian monsoon regions in term of rainfall

anomalies and rainfall extreme. The ENSO is manifestations of the physical phenomena resulting from unstable

interactions between the ocean and atmosphere. Under global warming, most of the exceeded energy has been

stored in the ocean from 1970. Climate is rapidly changing in recent decade. The Sea Surface Temperature

(SST) anomalies is a main driver of the oceanic and atmospheric phenomena. Recently, the ENSO patterns tend

to be transformed from one flavor to the others and the corresponding impacts are also changing. The east

Pacific El Niño is a dominant flavor which defined by SST anomalies pattern positioned over the central and

eastern Pacific. The central Pacific El Niño is defined by SST anomalies pattern with a warming centred over

the central Pacific and confined by both sides of SST cooling. The basin-wide warming El Niño is defined by a

warming SST anomaly across the equatorial Pacific.

The EOF analysis reveals the a few leading modes captured about 72% of the total, the first EOF mode depicts

warming east Pacific SST anomalies, the second EOF mode depicts basin wide warming Pacific SST anomalies

and the third mode depicts a warming central Pacific SST anomalies together with cooling Pacific SST

anomalies on both sides. Corresponding zonal winds anomalies during June-September shown winds anomalies

by influence of El Niño patterns lead to winds shifted. The Niño regions reveal a signal of western Pacific SST

anomalies trigging across Pacific El Niño type under global warming. Both tropical basins as well as extra-

tropical teleconnections have contributed to producing drought/deficit rains over the Indochina Peninsula

regions. The SST anomalies over tropical Pacific have modulated Walker cell and impact to Asian monsoon

season. The convection anomalies caused by the each El Niño types and evident the rainfall anomalies over

Indochina Peninsula. The canonical El Niño gives a strong impact to the western Pacific basin under the

equatorial 5S to 5N by producing dry signals over the Maritime continent during JJAS monsoon season. The

Basin-wide warming El Niño over tropical Pacific may have produced dry signals over upper Indochina

Peninsula during JJAS monsoon season, emerged since 1995. The El Niño Modoki has a specific SST anomalies

pattern with the warming in central tropical pacific, confined by cooling on both sides. It impacts to central

Southeast Asia by producing enhance rainfall over the regions.

Keywords: ENSO types, Zonal winds anomalies, drought, Indochina Peninsula, Global warming

Ph.D. at Suranaree Univerity (SUT) in 2008, Meteorologist (1991-present) at Thai

Meteorological Department (TMD) and Scientist (2010-2015) at Climate

Prediction Center (CPC), NOAA Center for Weather and Climate Prediction, MD,

USA.

74


MST-I-04

A Semi-Fragile Speech Watermarking Scheme based on CNN based

Singular-Spectrum Analysis

K.Galajit1,2,3 , J Karnjana3, M. Unoki1, and P. Aimmanee2

1School of Information Science, Japan Advanced Institute of Science and Technology, Japan

2Sirindhorn Internationl Instiute of Technology, Thmmasat University, Thailand 3NECTEC, National Science and Technology Agency, Thailand

* E-mail: [email protected]; Fax: +66 025013505 Ext 5026 Tel. +66 025013505 Ext 5012

ABSTRACT

The talk is about a semi-fragile watermarking scheme for detecting tampering in speech signals recently

published in a journal of APSIPA Transactions on Signal and Information Processing. The scheme can

effectively identify whether or not original signals have been tampered with by embedding hidden information

into them. It is based on singular-spectrum analysis, where watermark bits are embedded into speech signals by

modifying apart of the singular spectrum of a host signal. The convolutional neural network (CNN)-based

parameter estimation is deployed to quickly and properly select the part of the singular spectrum to be modified

so that it meets inaudibility and robustness requirements. Evaluation results show that CNN-based parameter

estimation reduces the computational time of the scheme and also makes the scheme blind, i.e. we require only

a watermarked signal in order to extract a hidden watermark. In addition, a semi-fragility property, which allows

us to detect tampering in speech signals, is achieved. Moreover, due to the time efficiency of the CNN-based

parameter estimation, the proposed scheme can be practically used in real-time applications.

Keywords: Semi-fragility, Differential evolution, Singular-spectrum analysis, Tampering detection,

Convolutional neural network

REFERENCES

1. Kasorn Galajit; Jessada Karnjana; Masashi Unoki; Pakinee Aimmanee (2019). Semi-fragile speech

watermarking based on singular-spectrum analysis with CNN-based parameter estimation for

tampering detection, APSIPA Transactions on Signal and Information Processing, Vol. 8, 16 April

2019, Article No. e11, 13 p.

Ph.D. at Univeristy of Colorado at Boulder in 2005, Associate Professor (2018),

Assistant professor (2011) and Lecturer (2005) at Sirindhorn International

Institute of Technology

75



MST-I-05

Applying Fast Opposite Gradient Search to Travelling

Salesman Problem

Chidchanok Lursinsap

Advanced Virtual and Intelligent Computing Center

Department of Mathematics and Computer Science, Chulalongkorn University, Bangkok 10330, Thailand

*E-mail: [email protected]

ABSTRACT

Most of optimization problems in Science, Engineering and Business belong to non-polynomial (NP) class. This

implies that the computational time complexity to find the best solution cannot be written in a form of a

polynomial function but possibly in an exponential or factorial form with the number of input data as its variable.

One possible strategy to solve these complex time problems is to apply non-deterministic Turing machine to

guess the solutions. Unfortunately, non-deterministic Turing machine cannot be truly built by deploying current

computer technology because of the theoretical guessing module. Hence, other approaches must be invented to

imitate the guessing module. Among these approaches are evolutionary and meta-heuristic algorithms where

the best solution is not the ultimate goal but only an acceptable solution is the main concern. In this talk, the

problem of travelling salesman problem which is in NP class is considered. This is one of the most important

problems in NP class which can be reduced to many other optimization problems such as complex logistics,

task scheduling. The problem is transformed into a cost function by using Hopfield-Tank concept. Unlike other

meta-heuristic algorithms where the cost function is not involved during the randomly generated solutions but

it is just for filtering those unacceptable randomly generated solutions, we view the cost function as a manifold

in a high dimensional space and traverse this manifold by using the proposed method of fast opposite gradient

search. The method was compared with other meta-heuristic algorithms in terms of speed and obtained distance.

Our approach is significantly faster than the other to reach the shorter distance.

Bachelor of Engineering with honors, Chulalongkorn University, 1978. Master

of Science in Computer Science, University Illinois, 1982. Doctor of Philosophy

in Computer Science, University Illinois, 1986. Lecturer, Chulalongkorn U.,

Bangkok, 1978-1979; visiting assistant professor, University of Illinois, Urbana,

1985-1986; associate professor, U. Southwestern Louisiana, Lafayette, 1994-

1995; associate professor, Chulalongkorn U., Bangkok, since 1995; assistant

dean information technical faculty science, Chulalongkorn U., Bangkok, since

1997. Committee member Association of Thai Professionals in American and

Canada, Lubbock, Texas, since 1991.

76


EMT-I-01

Light-driven Molecular Switch for Reconfigurable Spin Filters

M. Suda1,2,3, Y. Thathong4, V. Promarak4,5, H. Kojima6, M. Nakamura1,6, T. Shiraogawa1,3, M. Ehara1,3 and

H. M. Yamamoto1,2,3,*

1Institute for Molecular Science, Okazaki, Japan 2RIKEN, Wako, Japan

3SOKENDAI (Graduate University for Advanced Studies), Okazaki, Japan 4Suranaree University of Technology, Nakhon Ratchasima, Thailand

5Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand 6Nara Institute of Science and Technology, Nara, Japan

* E-mail: [email protected]; Tel. +81 564 55 7334

ABSTRACT

Artificial molecular switches and machines that enable the directional movements of molecular components by

external stimuli have undergone rapid advances over the past several decades. Particularly, overcrowded alkene-

based artificial molecular motors are highly attractive from the viewpoint of chirality switching during rotational

steps. However, the integration of these molecular switches into solid-state devices is still challenging. In this

presentation, an example of a solid-state spin-filtering device that can switch the spin polarization direction by

light irradiation or thermal treatment will be presented. This device utilizes the chirality inversion of molecular

motors as a light-driven reconfigurable spin filter owing to the chiral-induced spin selectivity effect. Through

this device, we found that the flexibility at the molecular scale is essential for the electrodes in solid-state devices

using molecular machines. The present results are beneficial to the development of solid-state functionalities

emerging from nano-sized motions of molecular switches. [1]

Keywords: Molecular motor, Chirality induced spin selectivity, Organic spintronics

REFERENCES

1. Suda, M., et al, Nature Commun. in press.

Ph.D. at Tokyo University in 1998, Assistant professor (1998) at

Department of Physics, Gakusyuin University, Research Scientis

(1999) and Senior Reserach Scientist (2007) at RIKEN, and

Professor at Institute for Molecular Science (2012-).

77


EMT-I-02

Molecular Engineering of Organic Materials for Organic Electronic

Applications

Vinich Promarak

School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC),

Wangchan, Rayong, 21210 Thailand

Email: [email protected]; Fax: +66 33 014445; Tel. +66 33 014150

ABSTRACT

In my talk, firstly I will give a brief introduction of my research team and a summary of our research interests

and results. I will then focus on the three main topics in the field of organic electronics namely dye-sensitized

solar cells (DSSCs), perovskite solar cells (PSCs) and organic light-emitting diodes (OLEDs). In DSSC, an

improvement of the performance of the organic dyes as sensitizers for DSSC by fine tuning the chemical

structures will be presented. A series of organic dipolar compounds forming D-D-π-A type of dyads bearing

carbazole-carbazole and carbazole-diphenylamine as D-D moieties, number of linearly connected arylene

groups as central π-conjugation bridges (π), acrylic acid, a cyanoacrylic acid and a fused cyanoacrylic acid as

anchoring groups (A) will be compared. In OLED, a molecular design of novel light-emitting materials based

on TADF and a combined TADF and ESIPT for efficient OLEDs will be reported. The structure-property

relationships of these materials obtaining from experimental and state-of-the-art theoretical calculations will be

discussed. Finally, the design of dopant-free hole-transporting material (HTM) for PSCs which has recently

been proved to protect the perovskite photoactive layer from exposure to ambient environments, thus enhancing

the resistance to degradation of perovskite and achieving highly stable devices will be presented. The case of

two alternating copolymers comprised of a 4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b′]dithiophene-2,6-diyl

unit linked with two different thiophene -spacers, thieno[3,4-b][1,4]dioxepine unit and 2,5-bis(3-

hexylthiophen-2-yl)-thieno[3,4-b][1,4]dioxepine unit will be described.

Keywords: Organic Materials, Organic Electronic, DSSC, PSC, OLED

D.Phil. (Organic Chemistry), 2002, University of Oxford, UK. Professor

in Chemistry at VISTEC. Research interests involve around "high-tech"

organic materials that can be used in applications such as organic light-

emitting diode, perovskite/dye-sensitized solar cell, bulk heterojunction

solar cell, sensor, optical switch, organic field-effect transistor

78


EMT-I-03

Fluorescent Sensors for Hazardous Heavy Metals and Cyanide Ions

N. Wanichacheva,1,* J. Sirirak,1 A. Charoenpanich,2 and V. Promarak3

1Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand

2Department of Biology, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand 3School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology,

Wangchan, Rayong 21210, Thailand

*E-mail: [email protected]; [email protected]; Tel. +66 82 787 8249

ABSTRACT

Contaminations of hazardous heavy metals and cyanide ions in food, beverage, and environment can lead to

severe health problems of living species including human. Consequently, sensors for heavy metal and cyanide

ions with high selectivity and low detection limit are required to prevent the contamination outbreaks.

Accordingly, designing and developing of fluorescent sensors for the determination of toxic substances have

become a goal in our research group. Herein, several fluorescent sensors were designed and synthesized for

selective detection of heavy metal ions including Hg2+, Cu2+, and anion CN−. The sensing’s of these sensors

illustrated the fluorescent changes in visible and near infrared (NIR) frequencies as well as chromogenic changes

which were easily visualized by naked eye. Molecular modeling was performed using Gaussian 09 to clarify the

geometries of sensors and to explore the bindings of metal ions or anion with sensor molecules.

Importantly, the detection limits of these sensors were lower than the recommended values of the heavy metal

and cyanide contaminants in drinking water and food of the U.S. EPA, WHO and FDA. In addition, the

developed sensors were test in real samples, biological samples, and commercial products.

Keywords: Heavy metals, Cyanide ions, Fluorescent sensors, Gaussian 09

REFERENCES

1. Tachapermpon,Y., Thavornpradit, S., Charoenpanich, A., Sirirak, J., Burgess, K., Wanichacheva, N.

Dalton Trans. 2017, 46, 16251–16256.

2. Petdum, A., Panchan, W., Sirirak, J., Promarak, V., Sooksimuang, T., Wanichacheva, N. New J. Chem.

2018, 42, 1396–1402.

3. Sakunkaewkasem, S., Petdum, A., Panchan, W., Sirirak, J., Charoenpanich, A., Sooksimuang, T.,

Wanichacheva, N. ACS Sens. 2018, 3, 1016−1023.

4. Piyanuch, P., Sirirak, J., Kamkaew, A., Weeranantanapan O., Promarak, V., Burgess, K., Wanichacheva,

N. ChemPlusChem. 2019, 84, 252−259. (Cover Feature)

Nantanit Wanichacheva is an Associate Professor in Department of Chemistry

and the Assistant to the President for Research at Silpakorn University, Thailand.

She received her Ph.D. in Chemistry from Worcester Polytechnic Institute,

Massachusetts, USA. Her current research interests involve design, syntheses and

development of new optical sensors for metal ions and anion such as Hg2+, Cu2+,

Ag+, Zn2+, CN− in solutions and solid support-strip tests, which were operated in

visible, fluorescent, and near IR frequencies.

79


EMT-I-04

Bioinspired Polydopamine Nanoparticles as SPF Booster:

Effect of Particle Size

Duangporn Polpanich1, Goragot Supanakon1, and Yodsathorn Wongngam1,*

1NANOTEC, National Science and Technology Development Agency (NSTDA)

111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand * E-mail: [email protected]

ABSTRACT

Repeated exposure to ultraviolet radiation (UVA and UVB) from sunlight can induce multiple adverse effects

including cutaneous phototoxicity (sunburn), photoaging (skin wrinkle), and carcinogenesis (damage of cell and

DNA). The use of sunscreen with sun protection factor (SPF) 15 or higher is highly recommended. Many

nanoparticles with a desired UV protection have been continuously developed as an active sunscreen ingredient.

According to a concern for human safety, in this study, a bioinspired polydopamine (PDA) nanoparticles were

synthesized by way of autoxidation of dopamine monomer (DA) in NaOH solution. Mole ratio of DA:NaOH

was varied to tune particle size as it has been believed that size of the particles affects sun protection property.

Results from UV-vis measurement showed that the synthesized PDA nanoparticles raised UV absorption over

the whole UVA/UVB range (290-400 nm). At a given wavelength (320 nm), the absorbance increased with

increasing particle size and reached a maximum value at particle size of 150 nm. The nanoparticles exhibited

no toxicity to human keratinocytes (HaCaT) in the investigated concentration (31-500 g/mL). After mixed the

nanoparticles with base cream to formulate sunscreen product, the UV absorption capacity of the formulation

increased with increasing concentration of PDA nanoparticles. An optimum was observed at concentration of

4% by weight which allowed high boosting of SPF by 54% compared to base formulation (control). Size-

dependent skin penetration will be further investigated.

Keywords: Polydopamine, Bioinspired particles, SPF Booster

REFERENCES

1. Huang, Y., Li, Y., Hu, Z., Yue, X., Proetto, M.T., Jones, Y. and Gianneschi, N.C. ACS Central

Science, 2017, 3, 564-569.

2. Ju, K.-Y., Lee, Y., Lee, S., Park, S. B. and Lee, J.-K. Biomacromolecules, 2011, 12, 625-632.

Dr. Duangporn Polpanich has recieved her Ph.D. in Polymer Science and

Technology from Mahidol University, Thailand in 2007. After that, she has

joined a research team at National Nanotechnology (NANOTEC), National

Science and Technology Development Agency (NSTDA), Thailand as a

researcher since 2008. She takes a position of a Nanolife and Cosmecuetical

(NLC) research team leader since 2019. Her current research interests focus

on design and synthesis of polymeric nanoparticles and encapsution of active

compounds to apply in personal healthcare and cosmecueticals.

80


EMT-I-05

Development of glycated albumin aptasensor for diabetes mellitus

diagnosis

W. Chawjiraphan, K. Segkhoonthod, C. Apiwat, P. Pinpradup, K. Treerattrakoon and D. Japrung*

National Science and Technology Development Agency (NSTDA)

111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand

E-mail: [email protected]; Fax: +66 256 6985; Tel. +66 6117 6665

ABSTRACT

Aptamers are short ssDNA or RNA that specifically bind to target molecule using three-dimensional structure.

Their target molecules could be cells, proteins, metal ions, and toxin. Aptamers are more stable and easily to

produce comparing with the antibody and can be selected from the large aptamer library using the method called

"Systematic Evolution of Ligands by Exponential Enrichment" or "SELEX". Our group selected and modified

DNA aptamers specifically bound human serum albumin (HSA) and glycated human serum albumin (GHSA),

which is intermediated biomarker for kidney dysfunction and Diabetes mellitus, respectively. Three sensor

platforms, which are electrochemical, nanopore and graphene-based aptasensor have been developed. The

fluorescent quenching graphene oxide (GO) and Cy5-labeled aptamers could be used for GHSA and HSA

detection in both serum and urine samples. These indicate that our aptasensor has a potential for diagnosis and

monitoring of diabetes mellitus.

Keywords: Glycated albumin, Aptasensor and Diabetes mellitus

REFERENCES

1. Panman W, Japrung D, Pongprayoon P. Exploring the interactions of a DNA aptamer with human

serum albumins: simulation studies. J Biomol Struct Dyn. 2017 Aug;35(11):2328-2336.

2. Apiwat C, Luksirikul P, Kankla P, Pongprayoon P, Treerattrakoon K, Paiboonsukwong K, Fucharoen

S, Dharakul T, Japrung D. Graphene based aptasensor for glycated albumin in diabetes mellitus

diagnosis and monitoring. Biosens Bioelectron. 2016 Aug 15;82:140-5.

3. Awang T, Wiriyatanakorn N, Saparpakorn P, Japrung D, Pongprayoon P. Understanding the effects of

two bound glucose in Sudlow site I on structure and function of human serum albumin: theoretical

studies. J Biomol Struct Dyn. 2017 Mar;35(4):781-790.

Deanpen Japrung received DPhil degree from University of Oxford in 2010 and

postdoctural researcher at Imperial college London in 2012, then got a position

as a researcher in Nano Molecular Target Discovery Target Laboratory at

National Nanotechnology Center (NANOTEC) since 2012, now she is a

researcher and research group director of the Responsive Nanomaterial and

Nanosensor Research (RMNS) group at NANOTEC.

81


EMT-I-06

Proton Transfer Reactions of Bimolecular Ions

Shinji Nonose1,*, Yu Usui1, Hoshiyuri Oji1, Satoko Kanamori1, Yuko Kobayashi1, Takaaki Iyama1, Wataru

Kadota1, Juri Morishita1, and Yuto Yonebayashi1

1Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan * E-mail: [email protected]; Fax: +81 45 787 2218; Tel: +81 45 787 2218

ABSTRACT

Proton transfer reactions of biomolecular ions were examined in the gas phase. A home-made tandem mass

spectrometer was used for the measurements. Based on experimental observations, we discuss conformation

changes of ions which originates in self-solvation to protons by hydrophilic residues in polypeptide chains, and

delocalization of charges with self-solvation.

Figure 1. Absolute reaction rate constants of proton transfer from angiotensin I (2+) ion to 1-butylamine

is plotted as a function of reaction temperature.

Keywords: Biomolecular Ion, Proton Transfer Reaction, Conformation Change

REFERENCES

1. S. Nonose, T. Okamura, K. Yamashita, A. Sudo, Chemical Physics, 2013, 419, 237-245.

2. S. Nonose, K. Yamashita, A. Sudo, M. Kawashima, Chemical Physics, 2013, 423, 182-191.

3. S. Nonose, K. Yamashita, T. Okamura, S. Fukase, M. Kawashima, A. Sudo, H. Isono, J. Phys. Chem.

B, 2014, 118, 9651-9661.

1986 B.S. Department of Chemistry, Keio University. 1990 Research Associate, The University of Tokyo. 1991 Ph. D, Graduate School of Science and Technology, Keio University. 1996 Senior Researcher, National Institute for Advanced Interdisciplinary Research. 1997 Associate Professor, Kobe University. 2004 Associate Professor, Yokohama City University.

0.05

0.5

270 320 370 420 470

k(X

10

-12

mo

le-1

cm

3 s

-1)

Temperature (K)

Angiotensin I 2+ with 1-Bu

k(

10

-12

mo

le-1

cm3

s-1)

82


EMT-I-07

Finding LUMOs in Unusual Places. Silsesquioxane cages and their

polymers appear to offer semiconducting properties

J. Guan, J. R. Arias, K. Tomobe, S. Jungsuttiwong4, N. Yodsin4, Richard M. Laine

Dept. of Materials Science and Engineering,1 Chemistry2 and Macromolecular3 Science and Engineering, University of

Michigan, Ann Arbor, Michigan, U.S.A., Dept of Chemistry,4 Ubon Ratchathani University, Thailand

E-mail: [email protected]

ABSTRACT

We report here the functionalization of a series of phenyl silsesquioxanes including [PhSiO1.5]8,

[PhSiO1.5]7[RSiO1.5] where R = Me, propyl or [PhSiO1.5]7[OSiMe3]3 or the double decker compound

[PhSiO1.5]8[OSiMe3]4. Each of these cages was functionalized by bromination followed by Heck catalytic cross

coupling. Sets of polymers were also prepared from derivatives of [PhSiO1.5]8[OSiMe3]4.

Photophysical characterization of these series of compounds allow one to establish the existence of a LUMO

that interacts with the conjugated moieties linked to the cage presenting red emission shifts indicating 3-D

conjugation in the excited state. This behavior has been reported before as indicative of semiconducting like

behavior.1,2 However, only for [PhSiO1.5]8 and [vinylSiO1.5]8 cages and their derivatives. Here we demonstrate

similar behaviour where only partial cages are used and the first examples of conjugation in the ground state

pointing the potential of these materials as new types of semiconducting polymers.

Keywords: Silsesquioxane cages, Semiconducting polymers

REFERENCES

1. S. Sulaiman, A. Bhaskar, J. Zhang, R. Guda, T. Goodson III, R.M. Laine,Chem Mater. 2008, 20 5563 –

5573.

2. R. M. Laine, S. Sulaiman, C. Brick, M. Roll, R. Tamaki, M. Z. Asuncion, M. Neurock, J-S., Filhol, C-Y.

Lee, J. Zhang, T. Goodson III, M. Ronchi and M. Pizzotti, S. C. Rand, Y. Li, J. Am., Chem. Soc. 2010,

132 3708–3722.

Dr. Laine received a Ph.D. in Chemistry from the University of Southern

California (Prof. Robert Bau). Following postdoctoral study (R.F. Heck,

Delaware; P.C. Ford, UCSB), Dr. Laine worked at Stanford Research Institute

International for 11 years, last as Associate Director of Inorganic and

Organometallic Chemistry Programs. Dr. Laine joined UM in 1990 as Associate

Professor. He is a 2013 recipient of the International Fellow Award of Society of

Polymer Science of Japan. He was awarded a 1000 Foreign Experts Award from

P.R.C. in 2012. He became an ACS fellow in 2015.

83


EMT-I-08

Understanding the Mechanism of C-F Bond Activation by Pt/Pd

Bimetallic Nanoalloy: Interplay of Experiments and Theory

Hidehiro Sakurai,*1 Raghu Nath Dhital,1 Keigo Nomura,1 and Masahiro Ehara2

1Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan.

2Research Center for Computational Science, Institute for Molecular Science, Aichi 444-0867, Japan. * E-mail: [email protected]; Fax: +81 6 6879 4593; Tel. ++81 6 6879 4591

ABSTRACT

Bimetallic nanoclusters exhibit unique catalytic properties, which differ from those of monometallic ones.

Previously we have reported that For gold/palladium bimetallic nanoclusters protected by poly(N-

vinylpyrrolidone) (AuPd:PVP) effectively activate carbon-chlorine bond at low temperature, and can be applied

to the Ullmann coupling of chloroarenes and related reactions.1 The most important process involves the

oxidative addition to C-Cl bond at the Pd site followed by the spill over of the Cl to the neighboring site, which

only occurs on the bimetallic cluster surface. This success motivated us to study carbon-fluorine bond activation

by bimetallic nanoclusters. Carbon-Fluorine (C-F) bonds are considered the most inert organic functionality and

their selective transformation under mild conditions remains challenging. Herein, we report a highly active Pt-

Pd nanoalloy as a robust catalyst for the

transformation of C-F bonds into C-H bonds at low

temperature, a reaction that has hitherto often

required harsh conditions. The alloying of Pt with Pd

is crucial to promote this the overall C-F bond

transformation process. DFT calculations elucidated

that the key step is the selective oxidative addition of

the O-H bond of 2-propanol to a Pd center prior to C-

F bond activation at a Pt site, which crucially reduces

the activation energy of the C-F bond. Therefore,

both Pt and Pd work independently but

synergistically to promote the overall reaction.

Keywords: Pt/Pd alloy clusters, Crbon-Fluorine

bond activation, DFT calculation

REFERENCE

1. R. N. Dhital, C. Kamonsatikul, E. Somsook, K. Bobuatong, M. Ehara, S. Karanjit, H. Sakurai, J. Am.

Chem. Soc. 2012, 134, 20250.

Ph.D. at The University of Tokyo in 1994, Assistant professor (1994-2000) at

Department of Chemistry, Univ. Tokyo, JSPS Post-doc. (1996-1998), at

University of Wisconsin-Madison, Associate Professor (2000-2004) at Osaka U.,

Associate Professor (2004-2014) at Institute for Molecular Science, Professor at

Division of Applied Chemistry, Osaka University at Osaka University (2014-).

84


EMT-I-09

Nanocatalysis for Biorefinery

K. Faungnawakij

National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), 111

Thailand Science Park, Paholyothin Rd., Klong Laung, Pathumthani 12120, Thailand * E-mail: [email protected]; Tel. +66 (0)2 564 7100 ext 6638

ABSTRACT

Nanocatalysts show a great promise in production processes of biofuels and biochemicals in biorefinery

industries. The catalytic conversion of cellulosic biomass, sugars and biolipids to value-added chemicals, such

as, furan compounds, organic acids, esters, alkanes, and their derivatives is one of the key steps in biorefining.

Our research group has developed nanocatalysts for the chemical conversion processes. For example, we have

developed metal phosphate catalysts for production of 5-hydroxymethylfurfural from cellulose, glucose and

fructose. The spinel-typed catalysts have been focused for the conversion of hemicellulose and xylose to furfural

and furfuryl alcohol. In addition, the mesoporous aluminosilicates with a combination of super-strong and

medium strength acid sites have been developed for xylose transformation to levulinic acid in one step under

hot water media. Levulinic acid can be further converted to gamma-valerolactone, by catalytic transfer

hydrogenation using highly-dispersed metal/carbon or metal/SiO2 composites. Biolipids, including palm oil

which compose of triglycerides and fatty acids have been used as the important feedstocks for liquid biofuels,

including biodiesel, green diesel and bio jet fuels. The catalytic deoxygenation and isomerization of biolipids

over different types of catalysts, such as, metal, alloy, metal sulfide, metal phosphide, and metal oxide have

been studied in our research group. Clearly, the nanocatalysts with tailored functions are essential for a broad

value-chain, and lead to new technologies and markets for bioeconomy.

Keywords: Heterogeneous nanocatalysts, Biorefinery, Oleochemicals, Biochemicals, Biofuels, Bioeconomy

Dr.Kajornsak Faungnawakij, a principal researcher and a director of

nanomaterials and nanosystems engineering research unit at NANOTEC, is

working in the field of advanced materials, membrane separation, and

nanocatalysis for biochemicals and biofuels.

85


EMT-I-10

Nanocrystals Promoting Li+ ion transport in Gel Polymer Electrolyte

of Li-metal battery

Shuai Yuan*, Zhengfu Qiu, Zhuyi Wang, Liyi Shi

Research Center of Nanoscience and Nanotechnology, Shanghai University

99 Shangda Road, Shanghai 200444, P.R.China

Email: [email protected]

ABSTRACT

As electrochemical devices for energy storage, lithium ion batteries have attracted more and more attention due

to applications, such as mobile telephones, personal computers, electric vehicles and hybrid electric vehicles.

Li-metal anode is believed to be one potential anode with large theoretical specific capacity and low potential

for high energy density lithium ion batteries. However, cycling stability is one key issue due the uneven

deposition of lithium and formation of dendrites. The dendrites will consume more liquid electrolyte to generate

new SEI films. Using gel polymer electrolytes (GPEs) to replace liquid electrolyte is helpful to improve the

interface stability. However, the gel polymer electrolytes usually show lower ionic conductivity compared with

liquid electrolytes (LEs). It is still challenging to promote both the ionic conductivity of GPEs and cycling

stability of lithium metal anode.

In this work, the gel polymer electrolyte was prepared by in-situ thermal polymerization. We found that the

properties of pore surface of polyethylene separator (PE) is very important for the ionic diffusion behaviours in

gel polymer electrolyte. Compared with pristine separator, the resistance of modified polyethylene separator by

nanocomposite thin layers through layer-by-layer (LBL) methods shows lower resistance, ever after

polymerization. The electrochemical compatibility of lithium metal electrode was evaluated by monitoring the

cycle performance of symmetric Li/Separator-Electrolyte/Li cells. The GPE sample supported by LBL modified

PE shows the longest cycling stability. In order to understand the reason, the ionic transportation behaviours

and interface stability were investigated in detail.

Keywords: Lithium metal battery, gel polymer electrolyte, nanocrystal, ion transport

REFERENCES

1. Qiu Z., Shi L., Wang Z.*, Mindemark J., Zhu J., Edstrom K., Zhao Y., Yuan S.*. Chemical

Engineering Journal, 2019, 368, 321-330.

2. Chi M., Shi L., Wang Z.*, Zhu J., Mao X., Zhao Y., Zhang M., Sun L., Yuan S.* Nano Energy, 2016,

28,1-11.

Ph.D. at East China University of Science and Technology (ECUST) in

2002-2005; Post-doctor at Osaka University in 2005-2006; Assistant

professor (2006-2008), Associate Professor (2008-2013) and Professor

(2013-) at Research Center of Nanoscience and Nanotechnology, Shanghai

University (SHU).

86


EMT-I-11

X-ray Absorption Spectroscopy on Advanced Functional Materials:

Combination of Experiments and Calculations

Pinit Kidkhunthod*

Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Muang, Nakhon Ratchasima, 30000,

Thailand * E-mail: [email protected]; Fax: +66 44 217 047; Tel. +66 44 217 040

ABSTRACT

In order to understand and address a structure-function of advanced functional materials, an X-ray absorption

spectroscopy (XAS) is one of the powerful techniques which can be employed. XAS consists of two main

regions which are X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine

Structure (EXAFS) providing the local structure information including local geometry or valence states of

probing elements in materials. To obtain these such information, a combination of experimental and theoretical

analysis is the most important task of XAS. In my talk, basic XAS theory and also XAS experiments will be

introduced. Moreover, the XANES and EXAFS data analysis using a combination of both experiments and

calculations will be presents with several case studies.

Keywords: advanced functional materials, Local structure, X-ray absorption spectroscopy, XANES, EXAFS

REFERENCES

1. P. Kidkhunthod, Structural studies of advanced functional materials by synchrotron-based x-ray

absorption spectroscopy: BL5. 2 at SLRI, Thailand, Advances in Natural Sciences: Nanoscience and

Nanotechnology 8, 035007

Dr. Pinit Kidkhunthod is a beamline manager at the SUT-NANOTEC-SLRI

XAS beamline (BL5.2), Synchrotron Light Research Institute (Public

Organization), Nakhon Ratchasima, Thailand. His research of interest is in the

fields of structural studies of advanced functional materials such as energy

materials, carbon-based ferrite composite materials and amorphous materials

and novel glasses using an X-ray absorption spectroscopy (XAS) technique. Dr.

Pinit Kidkhunthod received his B.Sc. (Physics), first class honors 3.99 from

Khon Kaen University, Thailand in 2008, and Ph.D. (Physics) from Bristol

University, U.K in 2012. He was one of two Thai students representative for

DESY summer program, Germany, in 2007. Recently, Dr. Kidkhunthod has

received research grants for young scientist from Thailand Research Fund

(TRF2013), Ministry of Science and Technology (2014) and SUT-Center of

Excellent on advanced functional materials (SUT-COE-AFM) from 2015-

present. Moreover, he has been awarded a visiting professor position from

SAIT, China during 2018-2020. He is the author and co-author of over 100

papers in ISI journals for structural studies of advanced functional materials

using XAS technique.

87

http://scholar.google.com/citations?view_op=view_citation&hl=en&user=QUHyFFkAAAAJ&cstart=20&pagesize=80&citation_for_view=QUHyFFkAAAAJ:JV2RwH3_ST0C

http://scholar.google.com/citations?view_op=view_citation&hl=en&user=QUHyFFkAAAAJ&cstart=20&pagesize=80&citation_for_view=QUHyFFkAAAAJ:JV2RwH3_ST0C


EMT-I-12

Lithium inspired the formation of silsesquioxane cages

Nicha Prigyai,1 Supphachok Chanmungkalakul,1 Nuttapon Yodsin,2 Siriporn Jungsuttiwong,2 Suda

Kiatkamjornwong,3 Vuthichai Ervithayasuporn*,1

1 Department of Chemistry, Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science,

Mahidol University, Rama VI road, Ratchathewi, Bangkok 10400, Thailand 2 Center for Organic Electronic and Alternative Energy, Department of Chemistry and Center for Innovation in

Chemistry, Faculty of Science, Ubon Ratchathani University, Warinchumrap, Ubon Ratchathani 34190, Thailand

3 Office of Research Affaurs, Chulalongkorn University, 254 Phayathai Road, Wangmai, Phatumwan, Bangkok 10330,

Thailand. * E-mail: [email protected]; Tel. +66 81 989 5557

ABSTRACT

Since the discovery of using silica, it has been used widely in many applications terms around us from personal

scale, such as silica sand of filters, moisture adsorbent to industrial scale, such as making glass, house wall,

supporting material for catalysis. Although many practical applications for silica has been presented, the

mysterious mechanism of how can silica plays an important role in all of these still unrevealed due to the

property of pure inorganic structure making silica completely undissolved in all kind of solvent. To understand

what is really happening in molecular scale we need a proper representative for microscopic investigation, the

silsesquioxane materials have proven itself to be the key factor for the mystery solver. For example,

silsesquioxane cages are dissolvable in various organic solvents, which can be used as an representative organic-

inorganic hybrid molecules with empirical formula as (RSiO1.5)n when R represents organic groups as

peripherals. Interesthingly, the formation of incompletely condensed silsesquioxane cage or trisilanol hepta(i-

butyl)silsesquioxane (T7) has been found in extremely high yield up to 85-95%, compared to other cage

products. In this work, T7, synthesized under a sol-gel method with lithium hydroxide as catalyst, has been fully

investigated, while their desired intermediates or products can be isolated and charaterized by NMR, IR, MS.

The result in this work may lead to the synthesis method for silsesquioxane in higher yield.

Keywords: Silica, Silsesquioxane, Silanol, Sol-gel, Cages, Lithium,

REFERENCES

1. V. Ervithayasuporn, K. Kwanplod, J. Boonmak, S. Youngme, P. Sangtrirutnugul, J. Catal. 2015, 332,

62.

2. S. Hanprasit, N. Tungkijanansin, A. Prompawilai, S. Eangpayung, V. Ervithayasuporn, Dalton Trans.

2016, 45, 16117.

Dr. Vuthichai Ervithayasuporn received his Ph.D. in Materials Chemistry from

Japan Advanced Institute of Science and Technology (JAIST), Ishikawa, Japan in

2010. After that he joined Department of Chemistry, Faculty of Science, Mahidol

University, Thailand, where he has been promoted to be Associate Professor in

2013. Recently, he received many National awards such as Young Scientist

Award, Young Chemist Award, and TRF-OHEC-SCOPUS Research Awards for

both Young and Mid-career. His current research focuses on the syntheses and

applications of silsesquioxane materials.

88



EMT-I-13

Development of in-situ measurement techniques for a scanning

transmission X-ray microscope

Takuji Ohigashi* and Hayato Yuzawa

UVSOR Synchrotron Facility, Institute for Molecular Science, Okazaki, Japan * E-mail: [email protected]; Fax: +81 564 54 7079; Tel. +81 564 55 7203

ABSTRACT

A scanning transmission X-ray microscopy (STXM) is a synchrotron-based tool to analyse 2-dimensional (2D)

chemical state of a sample. STXM has various remarkable features such as high spatial resolution, high

transmittance of X-rays, lower radiation damage, and contrast by chemical state. Especially, the high

transmittance of X-rays enables to measure bulk samples (e.g. cells) and samples in atmospheric pressure and

in water, which are difficult for the other tools like electron microscopy. In many situations, this feature is

necessary to elucidate physical or chemical property of materials by in-situ/operando measurement techniques.

Therefore, we have been developing special measurement techniques for our STXM beamline, BL4U, in

UVSOR Synchrotron (Okazaki, Japan) to explore a new field of sciences [1]. For example, in-situ

electrochemistry system and in-situ humidity control system were reported [2]. As different approaches of in-

situ measurement technique, we have recently developed computer tomography (CT) and a sample transfer

system for STXM. CT technique enables to observe 3-dimensional (3D) internal structure of the sample without

any destructive process. Furthermore, by changing the energy of the incident X-ray, 3D X-ray absorption

spectroscopy (i.e. 3D chemical state analysis) can be performed (shown in Fig.1) [3]. The sample transfer system

has been developed for in-situ analysis of extraterrestrial materials. In this presentation, newly developed

techniques and their applications in BL4U are shown.

Keywords: in-situ/operando technique, STXM, computer tomography, sample transfer

REFERENCES

1. T. Ohigashi, et al., 2013, J. Phys.: Conf. Ser., 463, 012006.

2. T. Ohigashi, et al., 2016, AIP Conf. Proc., 1741, 050002.

3. T. Ohigashi, et al., 2018, Microsc. Microanal., 24, 400-401.

Ph. D at University of Tsukuba in 2003 and lecturer until 2004. Assistant

researcher at Tohoku University from 2004 to 2005. Assistant researcher at Japan

Synchrotron Radiation Institute (JASRI) from 2005 to 2008. Post-Doctoral

Researcher at Ritsumeikan University. From 2011, assistant professor at Institute

for Molecular Science.

Figure 1. (a) 3D distribution image

(volume projection) and (b) cross

sectional image of DNA of an

isolated cell nucleus of HeLa S3 cell.

Scale bar is 2 µm

(a) (b)

89


EMT-I-14

Photo-mediated fabrication of nano-catalysts for environmental

application

L. Huang *

Research Center of Nano Science and Technology, Shanghai University, Shanghai, China * E-mail: [email protected]; Fax: +86 66134726; Tel. + +86 66134726

ABSTRACT

Photocatalysis has already triggered enormous researches in the areas of solar energy transfer and environmental

purification since the discovery of hydrogen evolution through electrochemical photolysis of H2O on TiO2 by

Fujishima and Honda in 1972. Therefore, the exploration of photocatalytic reactions in different applications is

interesting and meaningful. In our recent work, we have demonstrated that the photolysis of KMnO4 could

achieve MnOx and related compounds with unique nanostructures and were effective in the catalytic degradation

of methylene blue (MB) in the presence of H2O2. The developed approach is green, facile and controllable.

Here, the photocatalytic reactions were applied to controllably prepare oxides (MnO2, Co3O4) and noble metals

(Pt) over photocatalytic semiconductors like TiO2 and C3N4. The morphologies, crystallographic structures and

surface properties were thoroughly investigated. The formation mechanism was systematically studied. More

importantly, we demonstrated that the developed hybrid nanostructures were effective in the application of

environmental catalysis like selective catalytic reduction of NO with NH3 (NH3-SCR) and catalytic oxidation

of HCHO. The promoted catalytic performance were benefited from the strong interaction between active

species and the supports, the abundant surface active oxygen, the proper valance states of metals and etc. We

believe the obtained hybrids were also interested in other applications of environmental catalysis and the

developed photocatalytic methods could be applied for preparing other functional nanostructures.

Keywords: Environmental catalysis, deNOx, formaldehyde, noble metals, photocatalysis, TiO2.

REFERENCES

1. Duan, L.J., Liu, H., Muhammad, Y., Shi, L.Y., Wu, H.C., Zhang, J.P., Yu, D.Q., Huang, L. Nanoscale,

2019, 11, 8160-9.

2. Huang, L., Hu, X.N., Yuan, S., Li, H.R., Yan, T.T., Shi, L., Zhang, D.S., Applied Catalysis B-

Environmental, 2017, 203, 778-88.

Ph. D at South China University of Technology in Chemistry and Chemical

Engineering(2009). Visiting Ph.D. student at University of Washington 2007-

2008). Postdoctoral Fellow in Dalian Institute of Chemical Physics, Chinese

Academy of Science (2010). Assistant Professor (2012) and Associate Professor

(2013) at the Research Center of Nano Science and Technology, Shanghai

University.

90


EMT-I-15

Understanding structure, optical, and electrical properties of

doped- In4Sn3O12: Experimental and theoretical study

Arreerat Jiamprasertboon1, Narong Chanlek2, Suwit Suthirakun1,3 and Theeranun Siritanon1,3*

1School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand

2Synchrotron Light Research Institute, Nakhon Ratchasima, 30000, Thailand 3Center of Excellence-Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima,

Thailand

* E-mail: [email protected]; Fax: +66 44224649; Tel. +66 44224665

ABSTRACT Several oxides have been investigated for transparent conducting applications. Recently, In4Sn3O12 related

compounds have gained interests as they exhibit good performance with less indium content, thus reducing the

cost. However, the origin of such interesting properties were not clear. The current research aims to investigate

structure-composition-property relationship in In4Sn3O12 related compounds, by means of experiments and

theory. Undoped and M-doped In4Sn3O12 with the formula In4.5Sn2M0.5O12 (M = Nb0 and Ta) have been

synthesized and characterized by several techniques. Detail structural inormation is obtained from powder X-

ray diffraction, while the oxidation states of all elements were identified by X-ray photoelectron spectroscopy.

The larger optical band gap energies were obtained in doped samples, which agree with the results from DFT

calculations. Although the conductivity of In4Sn3O12 is relatively high, those of In4.5Sn2Nb0.5O12 and

In4.5Sn2Ta0.5O12 are much lower. To investigate the conduction mechanism, the conductivity of the samples after

heat treatment in N2 was studied. The improved conductivity after such annealing along with the results from

X-ray photoelectron spectroscopy suggest that the major charge carriers are electrons created from oxygen

vacancies in the lattice. To understand the difference in conductivity from sample to sample, computational

calculations were employed. The obtained results indicate that doping does not significantly change the band

structure nor the carrier mobility.On the other hand, it does affect the oxygen vacancy formation energy which

lead to different degree of reucibility and consequently diferent electrical conductivity in the studied samples.

Keywords: transparent conducting oxides; optical properties; electrical properties; DFT calculation

REFERENCES

1. Jiamprasertboon, A., Waehayee, A., Chanlek, N., Yong, N., Suthirakun, S., Siritanon, T., J. Alloys

Compd., 2019, 783, 28-36.

2. Minami, T., Takeda, Y., Takata, S., Kakumu, T., Thin Solid Films., 1997, 308, 13–18.

3. Choisnet, J., Bizo, L., Retoux, R., Hébert, S., Raveau, B., J. Solid State Chem., 2004, 177, 3748–3751

I am a lecturer at School of Chemistry, Suranaree University of Technology,

Thailand. I received my PhD in Chemistry from Oregon State University in 2011.

I am a solid state chemist whose interests include the structure-property

relationship in solids and their applications as electronic and photocatalytic

materials. Our group employs many advanced experimental techniques, and often

relies on computational results to understand the fundamental properties and

phenomena in solid materials. Such an insight allows us to rationally design other

functional materials with improved properties.

91


EMT-I-16

Crystal Engineering of Porous Crystalline Materials

Kittipong Chainok

Materials and Textile Technology, Faculty of Science and Technology, Thammasat University,

Pathum Thani, Thailand

E-mail: [email protected]

ABSTRACT

The engineering of porous crystalline materials with porous properties has attracted increasing attention over

the past decades due to their unique crystallinity, tuneable porosity and structural diversity with the promising

candidates in diverse potential applications. Herein, we describe the development on the crystal engineering of

novel metal-organic frameworks and porous molecular crystals with an emphasis on our contribution to the

field. Paid to effectiveness in covalent/noncovalent bonding driven self-assembly of the components leading to

organized structures and properties is particular attention. The factors which prove to be of much importance in

directing the synthetic pathway in these systems and the relationship between solid state crystal structures, CO2

adsorption and metal ions sensing properties are discussed.

Keywords: Adsorption, Crystal Engineering, Metal-Organic Frameworks, Soft Porous Materials, Sensing

REFERENCE

1. Chainok, K.; Ponjan, N.; Theppitak, C.; Khemthong, P.; Kielar, F.; Dungkaew, W.; Zhou, Y.; Batten,

S. R. CrystEngComm. 2018, 20, 7446–7457 (black cover).

Ph.D. at Suranaree University of Technology (2008), Lecturer at Department of

Chemistry, Rangsit University (2009), Postdoctoral Research (2010) at School of

Chemistry, The Hong Kong University of Science and Technology, Lecturer at

Department of Chemistry, Naresuan University (2012), Postdoctoral Research at

ICMCB, University of Borduax I (2013), Assistant Professor at Materials and

Textile Technology, Thammasat University (2015-)

92


EMT-I-17

Heterojunction photocatalysts for selective organic transformation

B. Inceesungvorn1,2*, Saranya Juntrapirom1,3, Amornrat Khampuanbutr1,3, Doldet Tantraviwat2,4 and

Sukon Phanichphant1,2

1Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science,

Chiang Mai University, Chiang Mai 50200, Thailand 2Center of Excellence in Materials Science and Technology, Faculty of Science, Chiang Mai University, Chiang Mai

50200, Thailand 3Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand

4Department of Electrical Engineering, Faculty of Engineering, Chiang Mai University, Chiang Mai 50200, Thailand


ABSTRACT

Semiconductor photocatalysts have been extensively explored over the past several decades for environmental

remediation, water splitting, CO2 reduction and the synthesis of high-value chemicals. However, their practical

usage is often limited by inefficient charge separation, slow charge carrier migration, narrow light absorption

rang and poor selectivity toward desired products. Herein, heterojunction formation has been employed to solve

those problems mentioned. Examples of composite photocatalysts and their applications in selective organic

transformation will be presented and discussed. The work would highlight the importance of surface/interface

engineering in designing efficient and selective photocatalysts and would also intensify further development of

semiconductor photocatalysts for organic fine chemical synthesis.

Keywords: Photocatalysis; Activity Improvement; Visible Light; Heterojunction; Oxygen Vacancy

Burapat Inceesungvorn obtained her PhD in Chemistry from Queen’s University

of Belfast, UK in 2009. She then started her academic career as a lecturer in the

Department of Chemistry, Faculty of Science, Chiang Mai University and was

later promoted to assistant professor in 2014. She received National Young

Scientist Award from the Foundation for the Promotion of Science and

Technology under the Patronage of His Majesty the King in 2017, an outstanding

contribution award from the institute for the promotion of teaching science and

technology, Thailand (in recognition of significant contributions and outstanding

service to IPST) in 2018 and TRF-OHEC-SCOPUS Young Researcher Award

(Physical Sciences) in 2019. Her current research interests focus on the

development of photocatalytic materials especially semiconductor metal oxides

for green organic synthesis, water depollution and photoelectrochemical H2

production.

93


CSE-I-01

GPU-based Dynamic Range-Limited n-Tuple Computation in Many-

body Molecular Dynamics Simulation

Putt Sakdhnagool*, Manaschai Kunaseth

National Electronics and Computer Technology Center (NECTEC), National Science and Technology Development

Agency (NSTDA), Pathum Thani, 12120, Thailand * E-mail:[email protected]; Tel. +66 2564 6900 ext. 2600

ABSTRACT

This work proposes a scalable GPU implementation of dynamic range-limited n-tuple computation in many-

body molecular dynamics simulation. The challenge of such implementation comes from the limited parallelism

due to the range-limited nature of the computation. In contrast, GPUs require thousands of threads to be run

simultaneously to fully utilize the hardware. Thus, increasing parallelism is necessary for the algorithm to run

efficiently on GPUs.

The state-of-the-art approach, called Shift-collapse algorithm (SC-MD)1, increases parallelism by exploiting the

computational patterns presented in the cell-based, n-tuple computation. However, capturing those patterns

increase memory usage. Unlike CPU, GPU has dedicated and limited memory space. Thus, applying SC-MD

approach on GPU is challenging. Moreover, the cost of constructing atom interactions from the patterns become

more significant as n grows.

While 2-tuple SC-MD performs well on GPU, going beyond 2-tuple is challenging. Our n-tuple algorithm (for

n 3) extends Full-shell method2 with a data structure, called neighbor table. Each row of the neighbor table

stores all atoms inside a cell and also atoms from the cell’s neighbor. Such data structure allows atom

interactions of a cell to be reconstructed by taking advantage of GPU thread organization while maintaining

small memory footprint.

The many-body MD simulation is then created by combining 2-tuple SC-MD with our n-tuple algorithm.

Benchmarking results show that our GPU implementation running on four Tesla V100 GPUs have achieved up

to 3.4x speedup over CPU-only SC-MD with 80-core CPU. Moreover, our implementation also exhibits

excellent scalability on 4,096-nodes GPU cluster.

Keywords: MD calculation, GPU computing,

REFERENCES

1. M. Kunaseth, R. K. Kalia, A. Nakano, K. Nomura and P. Vashishta, “A scalable parallel algorithm for

dynamic range-limited n-tuple computation in many-body molecular dynamics simulation,”

Proceedings of Supercomputing, SC13 (2013).

2. D. C. Rapaport, "Large-scale molecular-dynamics simulation using vector and parallel computers,"

Computer Physics Reports, vol. 9, pp. 1-53, Dec 1988.

Putt Sakdhnagool received his Ph.D. from Purdue University under the

supervision of Prof. Rudolf Eigenmann in August 2017. He is currently a

researcher at NSTDA Supercomputer Center (ThaiSC), National Electronics and

Computer Technology Center (NECTEC) in Thailand. His current research

interests include high performance computing, parallel programming, GPU

computing, automatic parallelization, parallel programming language, and

compiler optimization.

94


Oral Presentation

95




CHE-O-01

Improvement of the Selectivity of Propylene Production

and Inhibition of C Deposition during PDH Process by

Au Doping on Ni(111) Catalyst

Tinnakorn Saelee1,2, Supawadee Namuangrak 2, Suwit Suthirakun3,4, Nawee Kungwan1,* and Anchalee

Junkaew 2,*

1Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand 2National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathumthani,

12120, Thailand 3School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand

4Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima

30000, Thailand * E-mail: [email protected]* and [email protected]**; Fax: +66 5 389 2277; Tel. +66 5 394 3341

ABSTRACT

Propylene, the crucial chemical feedstock in several chemical industries, can be produced through propane

dehydrogenation (PDH) process using high effective metal catalysts such as platinum (Pt). However, the

concerning of cost-effective is important to production process in the industry. Hence, exploration of a new

cheaper catalyst for PDH process has gained more attention. Recently, nickel (Ni) has been reported as active

catalysts for hydrogenation and dehydrogenation reactions of small alkanes. [1, 2] However, occurrence of

cracking and deep dehydrogenation leads to low selectivity of propylene production. Therefore, product

selectivity improvement of Ni catalyst for PDH process is needed. Experimental observation suggested that

doping Au to Ni can enhance the selectivity of propylene production. However, the role of Au dopant on

selectivity of propylene production and reactivity change of Ni-Au catalysts have not been well understood yet.

In this work, PDH and side reactions on Ni and Ni-Au catalysts have been investigated using density functional

theory (DFT) implemented in VASP package. Our calculated results show that introduction of Au into Ni(111)

surface has no significant effect for propane adsorption (reactant) but effectively increases desorption ability of

propylene (product). Moreover, doping Au into Ni surface significantly weaken the interaction of C adsorption

reducing coke deposition on catalyst surface. The results indicate that doping the Au to Ni(111) surface possibly

enhance the selectivity of propylene production and inhibit coke formation on catalyst surface.

Keywords: DFT, Metal doping, heterogeneous catalyst, Propane dehydrgenation

REFERENCES

1. Yan, Z. and D.W. Goodman, Catal. Lett., 142(5): p. 517-520 (2012).

2. Yan, Z., Y. Yao, and D.W. Goodman, Catal. Lett. 142(6): p. 714-717 (2012).

96


CHE-O-02 Path Integral Molecular Dynamics Simulations

for Muoniated Radicals (Mu-X)

Yuki Oba1, Osamu Kobayashi 1, and Masanori Tachikawa 2*

1Department of Materials System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama,

Japan 2 Department of Data Science, School of Data Science, Yokohama City University, Yokohama, Japan


ABSTRACT

Muonium (Mu) atom is formed by a positive muon (μ+) and an electron, where the mass of μ+ is much smaller

than that of a proton and Mu atom has larger nuclear quantum effect than hydrogen. Muoniated radicals are

used to muon spin resonance (μSR) by using large magnetic moment of μ+. μSR technique provides the

determination of hyperfine structures of muoniated radicals, which is characterized by the reduced muon

hyperfine coupling constant (Aμ´) on a radical. The experimentally measured Aμ´ value of muoniated acetone

radical (Mu-ACE, Figure 1) is found to be 8.56 MHz at 300 K [1], and to be smaller as the temperature decreases

[2]. However, theoretical Aμ´ value for Mu-ACE is calculated to be -5.8 MHz by static optimization calculation

[2] and it does not reproduce experimental Aμ´ values because it ignored the nuclear quantum and thermal

effects. We therefore performed ab initio path integral molecular dynamics (PIMD) simulation, which can

include these effects, to reproduce Aμ´ value of Mu-ACE and explain the temperature dependence.

We performed on-the-fly ab initio PIMD simulation with O3LYP/6-31+G level. We used the massive Nosé-

Hoover chain thermostat to control the system temperature. We also calculated hydrogenated acetone radical

(H-ACE) to compare with Mu-ACE. The numbers of beads for Mu-ACE and H-ACE are 64 and 16,

respectively. Imaginary-time step sizes for these simulations are 40 asec/step and 0.1 fsec/step, respectively.

The number of total time steps is 95,000 steps for both simulations.

Table 1 shows experimental and theoretical Aμ´ values. Our Aμ´ values at 300 K are computed as 32.1 MHz and

3.97 MHz for Mu-ACE and H-ACE, respectively, and

our results qualitatively reproduced the relationship

between Aμ´ of Mu-ACE and H-ACE for corresponding

experimental values. This is caused by increase of spin

density on Mu atom due to both “neutral dissociation of

Mu atom from acetone molecule” and “rotation of Mu

atom around carbonyl group” using large nuclear

quantum and thermal effects [3]. Temperature

dependence and structural discussion will be reported in

oral presentation.

Keywords: Computational Chemistry muon compound,

Hyperfine coupling constant, Path integral

simulation, nuclear quantum effect

REFERENCES

1. D. Buttar et al., Hyperfine Interact., 1990, 65, 927.

2. R. M. Macrae et al., Physica B, 2003, 326, 81.

3. Y. Oba et al., J. Chem. Phys., 2016, 145, 064301.

Figure 1. summarized Aμ´ values for Mu-ACE.

97


CHE-O-03

Structure and Hydration Property of Low Molecular

Weight Hyaluronic Acid by Molecular Dynamics

Simulations

Panyakorn Taweechat1 and Pornthep Sompornpisut 1,*

1Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand


ABSTRACT

Hyaluronic acid (HA) is a linear polysaccharide with repeating disaccharide units, each of which is composed

of glucuronic acid and N-acetyl glucosamine. HA is one of the major matrix substances in extracellular tissue

of vertebrates. One of important properties of HA is high water affinity which makes it to become a moisturizer.

Most of skin-care products have HA being a main ingredient. Many researches reported that low-molecular

weight HA (LMW HA, MW < 50 kDa) have high permeability through skin. The aim of this work is to evaluate

the effect of size of LMW HA on the hydration properties and their conformations by all-atom molecular

dynamics (MD) simulations. Straight-chain structures of HA of various sizes including 5, 10, 20, 30, 40 and 50

units were constructed based on the conformational geometry of the crystal structure (PDB code 2BVK), and

subsequently subjected for 50 ns MD simulations in the gas phase to examine conformational states at different

chain lengths. MD results showed structures with various radius of gyrations (Rg) for all the HA models. 100

ns MD simulations of HA in aqueous solution illustrate the significant decreases of Rg in long chains of HA.

Structures of the first hydration shell of HA extracted from the radial pair distribution functions (RDF) indicates

that the larger molecules of HA have the lower amount of water per disaccharide unit. In addition, HA has major

intramolecular H-bonds at β(1,3)-glycosidic bond with occupancy about 60% while those of β(1,4)-glycosidic

bond have occupancy about 40%, corresponding to results from DFT optimization of HA 1 unit in aqueos state.

Figure 1. (a) Radial pair distribution functions between HA and water (b) Numbers of the first-shell

water of HA per disaccharide unit

Keywords: Hyaluronic acid, Molecular dynamics simulation, Conformation, Hydration

REFERENCES

1. Farwick, M.; Lersch, P.; Strutz, G. SOFW-Journal, 2008, 134(11).

2. Almond, A.; DeAngelis, P. L.; Blundell, C. D. J. Mol. Biol., 2006, 358, 1256-1269.

3. Kaufmann, J.; Möhle, K.; Hofman, H.; Arnold, K. J. Mol. Struc-Theochem., 1998, 422, 109-121. 4.

98


CHE-O-04 Theoretical and Mechanistic Study on H2S Reduction

over The Transition Metal-doped ZSM-12 Clusters

Tanabat Mudchimo1, Yuwanda Injongkol1, Rattanawalee Rattanawan1, and Siriporn Jungsuttiwong1,*

1Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, Thailand

* E-mail: [email protected]; Fax: +66-4535-3048; Tel. +66-4535-3000

ABSTRACT

Nowadays, a fundamental understanding of hydrogen sulfide (H2S) for adsorption and dissociation processes

over the transition metal catalytic materials is potentially important for H2S reduction/removal studies. Because,

sulfur-containing molecules are commonly impurities in natural gas, fossil fuels, and etc. with highly negative

impacts to catalytic processes in various industries, especially for the petrochemical industry. Presently, the

noble metal-based catalytic materials1–3 are commonly used for H2S reduction/removal into less toxic product

with high efficiency and selectivity. However, in term of high cost and limited supply, the exploring of new

catalytic materials that low cost and more abundant also become more interesting for many present researches.

Here, density functional theory (DFT) calculations were used to study the new catalytic materials from the

combination of transition metals and ZSM-12 zeolite cluster (TM-ZSM-12), and also investigate the possible

mechanism for H2S conversion into less toxic product such as carbonyl sulfide (COS) as following: H2S + CO

→ COS + H2. The results showed that H2S molecule adsorption on the top site of TM-ZSM-12 zeolite clusters

are the most stable structures for H2S adsorption with the adsorption energies around -3.00 to -7.00 eV. From

the H2S reduction mechanism, we found that the TM-ZSM-12 can convert CO into less toxic product with high

efficiency, and low activation energy around +0.30 to +1.00 eV. Therefore, we can conclude that the TM-ZSM-

12 clusters are the new candidate catalytic materials that can reduce H2S molecule into less toxic product with

high efficiency, low cost, and no supplying limitation problem as well.

Keywords: Density Functional Theory, Hydrogen Sulfide, H2S Reduction, TM-ZSM-12

REFERENCES

1. H. Luo, J. Cai, X. Tao, M. Tan, Applied Surface Science, 2014, 292, 328–335.

2. Q.-L. Tang, X.-X. Duan, T.-T. Zhang, X. Fan, X. Zhang, J. Phys. Chem. C, 2016, 120, 25351–25360.

3. X. Wen, P. Bai, Z. Han, S. Zheng, B. Luo, T. Fang, W. Song, Applied Surface Science, 2019, 465, 833–

845.

99


CHE-O-05

Development of Anharmonic Vibrational State Theory

Using A Novel Vibrational Coordinate Based on

Backflow Transformation

Kiriko Ishii1, Masanori Tachikawa 1,2*, and Yukiumi Kita 1

1Department of Materials System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama,

Japan 2 Department of Data Science, School of Data Science, Yokohama City University, Yokohama, Japan


ABSTRACT

determine molecular geometries. The anharmonic vibrational state theory based on quantum Monte Carlo

(VQMC) method is one of the most accurate methods to solve a vibrational Schrödinger equation of molecular

systems. In this method, an accurate trial wave function being able to describe molecular vibrations precisely is

indispensable to obtain reliable theoretical predictions for vibrational frequency, molecular geometry, etc.

In this study, we have developed a novel vibrational coordinate based on backflow transformation1 (BF), which

enable us to take correlation effects in quantum many-body systems directly, in order to generate an accurate

vibrational trial wave function. The theoretical accuracy of BF in quantum vibrational problems has been tested

for the vibrational ground states of H2O, HCN, and H2CO molecules. The variational Monte Carlo method2,

which is one of the QMC methods, was used to analyze the molecular properties. The backflow transformation

was applied to vibrational self-consistent field (VSCF) wave function. For comparing, we also employed

Reptation Monte Carlo (RMC) method3, which is able to calculate the exact eigenvalue at the ground state

numerically.

Figure 1 shows the zero-point energy (ZPE) of H2O molecule with several vibrational methods. The ZPE

decreases by the introduction of BF, and ZPE with BF is much lower than that with vibrational configuration

interaction (VCI) wave function. Since ZPE is a variational energy, these results mean that the introduction of

BF is effective for the improvement of vibrational trial wave function. Furthermore, the ZPE result with BF

method is quite consistent with the exact ZPE value with RMC method. We also got similar results for HCN

and H2CO molecules.

Figure 1. The zero-point energy (ZPE) of H2O with several wave functions and methods

Keywords: anharmonic vibrational analysis, quantum Monte Carlo, backflow transformation

REFERENCES

1. P. Lopéz Ríos, et al., Phys. Rev. E, 2006, 74, 066701.

2. R. J. Needs, et al., J. Phys. Condens. Matter., 2010, 22, 023201.

3. S. Baroni and S. Maroni, NIC Series, 2002, 10, 75. 4.

100


CHE-O-06 The Theoretical Study of Catalytic CO2 Hydrogenation

to Formic Acid over a Pt-Decorated Carbon Nanocone

Nuttapon Yodsin1, Chompoonut Rungnim2,*, Supawadee Namuangruk2, and Siriporn Jungsuttiwong1, *

1 Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand

2 National Nanotechnology Center, 130 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand * E-mail: [email protected] and [email protected] (C.R.); Tel. +66 8 1692 2125

ABSTRACT

Carbon dioxide (CO2), a greenhouse gas is one of the most prominent pollutants that must be resolved

immediately. Among the CO2 chemical conversion, formic acid (FA) is an interesting value-added product used

in numerous applications. For the catalytic conversion of CO2, carbon nanocones (CNC) are one of the most

interesting materials for CO2 hydrogenation to FA. In this work, we addressed the potential catalytic role of

platinum decorated on defective CNC (Pt-dCNC) in CO2 hydrogenation reaction to FA following equation; CO2

+ H2 → HCOOH, by density functional theory (DFT) approach. We illustrate that the combination of highly

reactive Pt atoms and defective CNC makes the Pt-dCNC a reactive mono-dispersed atomic catalyst for CO2

hydrogenation reaction. We propose three possible reaction pathways which are i) co-adsorption pathway, ii)

H2-dissociation pathway and iii) H2-dissociation together with H-spillover pathway. The CO2 hydrogenation

reaction via co-adsorption of CO2 and H2 is not a favorable pathway because of a high activation energy (1.49

eV) at the rate determining step. For the H2-dissociation pathway, the H-H dissociation over Pt/dCNC to

generate Pt-H atoms easily undergoes with energy barrier only 0.09 eV and the activation energy for FA

formation via Pt-formate intermediate is lower than the reaction processes through the Pt-carboxylate

intermediate. In the H2-dissociation together with H-spillover pathway, the reaction mechanism starts with H2

dissociation and follow by a spillover of the dissociated H atom to the CNC surface before the CO2 adsorption

and hydrogenation through the formate intermediate. Then, this Pt-formate specie can be converted to FA by

the H2-dissociation of a new H2 molecule. The reaction in this H2-dissociation together with H-spillover pathway

is energetically favorable with a small activation energy (0.76 eV) at the rate determining step. Our results

demonstrated that the rate of FA production is controlled by the H2 amount. The Pt-dCNC would be a promising

candidate catalytic material for the CO2 hydrogenation reaction to FA when the system has high H2

concentration.

Keywords: Density functional theory (DFT); CO2 hydrogenation reaction; Formic acid (FA); Carbon nanocone

(CNC); Platinum (Pt)

REFERENCES

1. J. Sirijaraensre, J. Limtrakul. Applied Surface Science, 2016, 364, 241-248.

2. M.D. Esrafili, F. Sharifi, L. Dinparast. Journal of Molecular Graphics and Modelling, 2017, 77, 143-

152.

101


BIO-O-01

Insight into the Mechanism of the Hydration Structure

and Interaction Energy of Sorbitan Monostearate

(Span60) in the Gas and Aqueous Phases: A QM/MM

Calculations Study

Nikorn Shinsuphan1,2*, Sriprajak Krongsuk1,2

1Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand

2Institute of Nanomaterials Research and Innovation for Energy (IN-RIE), Research Network of NANOTEC- KKU

(RNN), Khon Kaen University, Khon Kaen, 40002, Thailand * E-mail: [email protected]

ABSTRACT

The combined quantum/molecular mechanical (QM/MM) simulations are an extensively popular technique for

investigating the atomistic behaviour of complex bio-molecular systems. In this work, we have studied the

hydration phenomenon of the polar head group of sorbitan monostearate (Span60) in both the gas and aqueous

phases. Firstly, the adaptive region was considered to evaluate a precisely and sufficiently extended the QM/MM

division based on the ONIOM scheme. Next, these conformational models were selected to calculate the

hydration structure and the related properties. The interested region of the system, (active site) was computed

by density functional theory (DFT), while the rest one was treated using molecular mechanical (MM) model.

The QM/MM calculations revealed that the polar head group of span60 interacts with one water molecule,

indicating the mono-hydration effect. More and more adding water molecules, the poly-hydrated phenomena

are clearly observed. Hence, an extended active region indicates both the accuracy and efficiency in the QM

simulation. This work also revealed that a mono-hydrated bonding force formed by the one hydrated molecule

could reciprocate with the hydrophilic region from the several active sites of the sub-region to Span60 molecule,

demonstrating the ability for electrostatic interaction of the largely hydrophilic region.

Keywords: Sorbitan monosterate (Span60), hydration energy, QM/MM calculations, ONIOM scheme

REFERENCES

1. Warshel, A., & Levitt, M. (1976). J. Mol. Biol., 103(2), 227-249.

2. Van Hal, D., Bouwstra, J., Rensen, A., Jeremiasse, E., Vringer, T., & Junginger, H. (1996). J. Colloid

Interface Sci., 178(1), 263-273.

3. Dapprich, S., Komáromi, I., Byun, K., Morokuma, K., & Frisch, M. (1999). J. Mol. Struct.: THEOCHEM,

461–462, 1-21.

102


BIO-O-02 Effect of Surface Functionalization of Aunps on the

Internalization into Mammalian Cell

Thodsaphon Lunnoo1*, Theerapong puangmali1,2


2Institute of Nanomaterials Research and Innovation for Energy (IN-RIE), Khon Kaen University,

Khon Kaen, 40002, Thailand * E-mail: [email protected]

ABSTRACT

The complete understanding of interactions between ligands-coated gold nanoparticles (AuNPs) and cell

membrane is a key step for the development of drug delivery. In the present work, the effect of different surface

charges (anionic, cationic, and zwitterionic) of AuNPs on the internalization in an idealized plasma membrane

was studied by using coarse-grained molecular simulation (CGMD) technique. Our simulation results reveal

that AuNPs (d=2 nm) with different surface charges can be internalized across plasma membrane via direct

diffusion. Based on the potential of mean force calculation, the free energy barriers of anionic, cationic, and

zwitterionic AuNPs are 279.63±3.70, 205.75±3.70, and 416.86±5.93 kJ/mol, respectively. The free energy

barrier during the internalization into the cell membrane is due primarily to a cumulative effect of electrostatic

forces. The highest free energy barrier is found in zwitterionic AuNPs. They demonstrate higher free energy

barrier than positively and negatively charged AuNPs, leading to a lack preference for internalization across the

plasma membrane. Additionally, the aggregation of ligands-coated AuNP results in a slow unfavorable

permeability. Our study indicates that the surface charges play a vital role in the permeability of functionalized

AuNPs into the cell membrane. The understanding of the interactions between ligands-coated AuNPs and the

plasma membrane could provide the novel design of AuNPs in nanomedicine applications.

Keywords: Ligands-coated AuNP, Coarse-grained MD simulation, Plasma membrane, Cellular uptake

REFERENCES

1. Jiang, Y., Huo, S., Mizuhara, T., Das, R., Lee, Y.-W., Hou, S., Moyano, D.F., Duncan, B., Liang, X.-J.,

and Rotello, V.M., ACS Nano, 2015, 9(10), 9986-9993. 2. Arvizo, R.R., Miranda, O.R., Thompson, M.A., Pabelick, C.M., Bhattacharya, R., David Robertson, J.,

Rotello, V.M., Prakash, Y.S., and Mukherjee, P., Nano Letters, 2010, 10(7), 2543-2548.

3. Gupta, R., and Rai, B., Scientific Reports, 2017, 7, 45292.

103


BIO-O-03

Finite Element Modeling of Vaccine Delivery Using

Microneedles: Roles of Microneedle Shape

and Antigen Diffusion Rate

Pikkanet Suttirat1, Jeerapond Leelawattanachai2, Chaiwoot Boonyasiriwat1, and Charin Modchang 1,*

1Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand

2Nano-Molecular Target Discovery Laboratory, National Nanotechnology Center, National Science and Technology

Development Agency, Pathum Thani 12120, Thailand * E-mail: [email protected]; Fax: +66 2354 7159; Tel. +66 2201 5770

ABSTRACT

Microneedle arrays have been developed to deliver various types of biomolecules, including vaccine, into the

skin. It is reported that the skin is a potential target of vaccines due to existence of immune cells with high

density. Microneedle arrays are capable of delivering those molecules without stimulating pain receptors and

reaching or damaging blood vessels that lie beneath. These microneedles are usually designed with a wide range

of geometrical shapes. Recently, a group of researchers had developed a three-dimensional finite element model

describing microneedle‐mediated vaccine delivery. The model describes the diffusion and the kinetics of

delivered antigens via microneedle array. However, some important aspects of microneedle, e.g. shape of

microneedles, have not yet been investigated. In this work, we adapted the established finite element model to

investigate influences of microneedle shape on microneedle‐mediated vaccine delivery. The immune response

is assumed to depend on the number of activated immune cells after antigens are internalized into immune cells.

Moreover, the roles of varying antigen diffusion coefficient within the skin were also investigated. We found

that both microneedle shape and antigen diffusion rate affects to the efficiency of immune cell activation. The

model also shows the important of these parameters in enhancing the immune response of microneedle‐mediated

vaccine delivery into skin.

Keywords: Finite element model, Microneedles, Vaccine delivery

REFERENCES

1. Römgens, A. M., Bader, D. L., Bouwstra, J. A., and Oomens, C. W. J., Comput Methods Biomech

Biomed Engin., 2016, 19(15), 1599-609

2. Al-Qallaf, B., Diganta B. D., and Davidson, A., Asia-Pac. J. Chem. Eng., 2009, 4(6), 845-57

104


BIO-O-04

Computational Design of Bacillus licheniformis RN-01

levansucrase for Control of the Chain Length of Levan-

type Fructooligosaccharides

Pongsakorn Kanjanatanin1,2, Rath Pichyangkura1, Thassanai Sitthiyotha1,2, Thanapon Charoenwongpaiboon1,

Karan Wangpaiboon1 and Surasak Chunsrivirot1,2,*

1Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand

2Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn

University, Pathumwan, Bangkok, Thailand * E-mail: [email protected]; Fax: +66 2 218 5418; Tel. +66 2 218 5425

ABSTRACT

Levansucrase (LS) from Gram-positive bacteria generally produces a large quantity of levan polymer, a polymer

of fructose with one glucose at the end (GFn), but a small quantity of levan-type fructooligosaccharides (LFOs).

The properties and of LFOs depend on their chain lengths, thereby determining their potential applications in

food and pharmaceutical industries such as prebiotics and anti-tumor agents. Therefore, an ability to redesign

levansucrase’s active site for synthesis of products with desired degree of polymerization (DP) is very

beneficial. We employed computational protein design, docking and molecular dynamics to redesign Bacillus

licheniformis RN-01 levansucrase’s active site for production of LFOs with DP around five (GF4), using two

approaches: 1) blocking the oligosaccharide binding track of GF3-LS complex with large aromatic residues and

2) eliminating hydrogen bond interactions between the terminal glucose of GF4 and the side chains of binding

residues of GF4-LS complex. The first approach was successful in designing N251W and N251W/K372Y

mutants that synthesized LFOs with DP up to five. The developed approach may be beneficial for redesigning

other polymerizing enzymes for production of products with desired DP.

Figure 1. computational design scheme of levansucrase for the production of LFOs

Keywords: computational protein design, molecular dynamics simulations, docking, levansucrase, chain length

control

REFERENCES

1. Leaver-Fay, A., Tyka, M., Lewis, S. M., Lange, O. F., Thompson, J., Jacak, R., Kaufman, K., Renfrew,

P. D., Smith, C. A., and Sheffler, W. Meth. Enzymol, 2011, 487, 545.

105


BIO-O-05

Classification and Variable Selection in Large p Small n

with Imbalanced Data Problems using Regularized

AUC

Tanawat Horsirimanon, and Waranyu Wongseree*

Department of Electrical and Computer Engineering, Faculty of Engineering,

King Mongkut's University of Technology North Bangkok, Bangkok, Thailand *E-mail: [email protected]; Fax: +66 2 585 7350; Tel. +66 2 555 x8410

ABSTRACT

Classification and variable selection when the number of variables is much larger than the number of samples

has become increasingly frequent and important in bioinformatics [1]. Regularization methods successfully cope

with this challenge with limitation in imbalanced classification problem [2]. The area under the receiver operating

characteristic curve (AUC) is a measure to evaluate and compare the performance of classifiers especially for

imbalanced class distribution problem. Maximizing AUC in the process of classifier construction can be more

appropriate solution which is however an NP-hard problem due to neither continuous nor concave function of

AUC. Many surrogate functions have been proposed to approximate AUC function [3-5] . Nonetheless, there is

no benchmark experiment to proof that the performance of AUC based classifier is better than accuracy based

classifier when apply to high dimensional imbalanced class data. In this study, We have proposed cross-entropy

function as a surrogate loss function based on pairwise comparisons between positive samples and negative

samples in order to incorporate with lasso logistics regularization. The training data is used to select optimal

regularization parameter via cross-validation and independent testing data is used to compare performance of

the proposed method with lasso logistic regression. The simulation results indicate that the performance of

proposed method is much better than lasso logistic regression in case of skewed class distribution.

Figure 1 The boxplots of AUC in testing sets over 50 runs for simulation cases of log normal mixture data with

difference class distribution ratio.

Keywords: AUC, Lasso, Imbalanced Data, Variable Selection

REFERENCES

1. Ma, S., and Huang, J, Briefings in Bioinformatics, 2008, 9(5), 392-403. 2. Huang, J., and Ling, X., C., IEEE Transactions on Knowledge and Data Engineering, 2005, 17(3), 299-

310. 3. Ma, S., Xiao, S., and Huang, J., BMC Bioinformatics, 2006, 7(253). 4. Zhao, X. G., Dai, W., Li, Y., and Tian, L., Bioinformatics, 2011, 27(21), 3050-5. 5. Yu, W., and Park, T., BMC Genomics, 2014, 15(s10).

106


BIO-O-06

Computational Analysis on the Formation and

Properties of the Dimeric Zirconocene Complex:

The Substituent Effect

Natchayatorn Keawkla1, Worachit Wannasompon1, Jitrayut Jitonnom2 and Wijitra Meelua1,2*

1Demonstration School University of Phayao, Phayao 56000, Thailand

2School of Science, University of Phayao, Phayao 56000, Thailand


ABSTRACT

Density functional theory (DFT) calculations were carried out to determine the stability and geometric

properties for the formation of the dimeric zirconocene complex [Cp2ZrMe(μ-Me)MeZrCp2]+. Such properties

of the dimer were analysed as function of ligand substituent, introducing by methyl, alkyl and phenyl groups.

To analyze this effect, thermodynamic parameters (i.e., Gibb’s free energy, enthalpy, …) and vibrational

frequency were calculated. Calculations showed that the substituent groups produce a steric repulsion between

the two catalysts with a longer Zr-Zr distance, resulting in the lower stability of the dimer. In addition, we found

that the stability can be varied depending on the position of adding phenyl on the Cp ligand. The obtained results

can be used to develop metallocene-based catalyst for biomedical application.

Keywords: metallocene catalyst, dimer zirconocene complex, organometallic compound, DFT

REFERENCES

1. V. A. Karttunen, M. Linnolahti, T. A. Pakkanen, J. R. Severn, E. Kokko, J. Maaranen, and P. Pitkanen,

Organometallics., 2008, 27, 3390-3398.

2. H. H. Brintzinger and D. Fischer, Adv. Polym. Sci., 2013, 258, 29-42.

3. D. H. Al-Amiedy, Z. A. Saleh and R. K. Al-Yasari, IJARPS., 2014, 1(1), 1-9.

4. J. Jitonnom and W. Meelua, J. Organomet. Chem., 2017,841, 48-56.

107


PFD-O-01

Effect of Cholesterol Concentrations on Dynamics and

Interactions of Melatonins in Niosome Bilayer Based on

Using Molecular Dynamics Simulations

Saowalak Somjid1,2*, Sriprajak Krongsuk1,2


2Institute of Nanomaterials Research and Innovation for Energy (IN-RIE), Research Network of NANOTEC-KKU (RNN),

Khon Kaen University, Khon Kaen, 40002, Thailand * E-mail: [email protected]

ABSTRACT

Niosomes are vesicular drug carriers which can entrap both hydrophilic and lipophilic drugs. They are formed

mostly by non-ionic surfactant (e.g. Span60) with cholesterol (Chol) incorporation, leading to high stability and

efficiency of drug encapsulation and release. Melatonin has protective effects in many diseases including

cardiovascular disease, Alzheimer’s disease, and certain types of cancers as well as high antioxidant effect. As

a result, it is widely used for medical and cosmetic proposes. Development of melatonin delivery based on

niosomes has been rapid progress; however, the underlying mechanisms of melatonin formation in lipid

membranes as well as its delivery through cell membranes have yet to be adequately explained. Therefore, in

this study we have investigated on the influence of cholesterols on dynamics and interaction of melatonin in

niosome bilayers using a coarse-grained molecular dynamics (MD) simulation technique. 40 melatonin

molecules were added into the niosome bilayers which correspond to cholesterol concentrations of 0, 10, 20,

30, 40, 50, 60 and 70 mol%, respectively. Each system has been simulated at the constant temperature (298 K)

and pressure (1 bar) using Gromacs program. The results revealed that at the lower cholesterol concentrations,

all of melatonin molecules still remain inside the niosome bilayer, demonstrating the melatonin is strongly

interacted by the head group of span60. As cholesterol concentration increase, some melatonin molecules moved

out from the inside to the outside of the bilayer and some diffused into the water bulk phase. This behavior is

dominant for the higher cholesterol concentrations. This result suggests the role of cholesterol on the lipid

membrane stability in order to control drug release and encapsulation.

Keywords: Span60, Coarse-grained MD simulation, Melatonin, Cholesterol concentration

REFERENCES

1. Marrink, S.J., & Risselada, H.J., & Yefimov, S., & Tieleman, D.P., & de Vries, A.H. (2007). The

MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. The Journal of Physical

Chemistry B, 111, 7812-7824.

2. Kleszczynski, K., & Fischer, T.W. (2012). Melatonin and human skin aging. DermatoEndocrinology,

4(3), 245–252.

3. Khajeh, A., & Modarress, H. (2014). The influence of cholesterol on interactions and dynamics of

ibuprofen in a lipid bilayer. Biochimica et Biophysica Acta (BBA) – Biomembranes, 1838(10), 2431-

2438.

108


PFD-O-02

Modeling of Charge Injection and Transport in Organic

Semiconductors with Electrode Geometry of conducting

Atomic Force Microscopy (c-AFM)

Kanokkorn Pimcharoen1*

1National Nanotechnology Center, National Science and Technology Development Agency, Pathumthani Thailand


ABSTRACT

Conducting atomic force microscopy (c-AFM) is one of the major techniques for investigating the dependence

of electronic properties and nanoscale morphologies. The local current-voltage (I-V) measurement is often

carried out in the space-charge-limited-current (SCLC) regime, yielding the intrinsic properties of organic

semiconductors such as charge carrier mobility, traps and defects [1]. However, the interpretation of the c-AFM

data must be rigorously assisted by reliable theoretical device models, and computational methods capable of

solving these models in multi-dimensions. A continuum device model with a full description of drift (D) and

diffusion (D) transport mechanisms, the so-called DD-SCLC model, is developed for a fundamental study of

charge transport probed by these measurements. The computational algorithms are executed in one-, two- and

three dimensional systems. Particularly, in the fully 3-D system, the DD-SCLC model is able to treat the

inhomogeneity of thin films, including spatially varying trap distributions, nanoscale morphologies, and c-AFM

geometry. The device simulations are performed on the complex 3-D model morphologies that are consistent

with the topography of semiconducting poly(3-hexylthiophene) (P3HT) observed in c-AFM measurements. The

visualization and characterization of hole transport in P3HT thin films will be presented.

Figure 1. Adapted from [1], (a) the on-fiber (A-●) and off-fiber (B-■) I-V responses of the P3HT thin film

are well described by the theoretical I-V characteristics (---) simulated from the 3-D DD-SCLC model using

the morphology of an `edge-on' fiber network; (b) the corresponding on-fiber current flow patterns at

Va=1V are demonstrated.

Keywords: Drift-Diffusion Model, Exponentially Distributed Trap Density, Space Charge Limited Current

(SCLC), Conducting Atomic Force Microscopy (c-AFM), Poly(3-hexylthiophene) (P3HT).

REFERENCES

1. Sun, J., Pimcharoen, K., Wagner, S. R., Duxbury, P. M., and Zhang, P., Organic Electronics, 2014,

15(2):441-448.

109


MST-O-01 A hybrid particle swarm optimization for the pollution

point source identification

Wipaiwnee Chaiwino1, and Thanasak Mouktonglang 1,*

1Master Degree Program in Mathematics, Department of Mathematics, Faculty of Science, Chiang Mai

University Chiang Mai 50200, Thailand 1,*Department of Mathematics, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand


ABSTRACT

In this research, we improved the particle swarm optimization algorithm by using the multidimensional search

with line search, which is without the assistant of derivative, to determine the air pollution point source and its

corresponding emission rate. We started with the measurement of pollutant concentration from the pollution

point source by sensors. Next, the hybrid particle swarm optimization (HPSO) method was used to minimize

square of the difference between measured concentration and theoretical concentration (Gaussian plume inverse

model). All experiments were performed the HPSO testing ability. In addition, the best sensors positioning was

also studied in order to obtain the most effective air pollution point source and the emission rate values [1]. The

comparison of the single-pollutant location detection results of the use of original PSO, original genetic

algorithm (GA), and HPSO were also explained. In the other cases, only the gained results from original PSO

and HPSO was discussed. In the conclusion, the HPSO method verified better performance on the pollutant

locations and emission rate of the air pollution point source than original PSO as well.

Keywords: Particle swarm optimization, Hybrid Particle swarm optimization, atmospheric model.

REFERENCES

1. W. Chaiwino and T. Mouktonglang, “Identication of atmospheric pollution source based on particle

swarm optimization,” Thai Journal of Mathematics, vol. 17, no. 1, pp. 125–140, 2019.

110


MST-O-02 Numerical Simulation for Surface Wave in Shallow

Water Using Boussinesq Paradigm Equation

Panasun Manorost1, Thanasak Mouktonglang1, Ben Wongsaijai1, and Kanyuta Poochinapan1,*

1Department of Mathematics, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand

*E-mail: [email protected]; Fax: +66-4535-3048; Tel.+66-84503-3697

ABSTRACT

Boussinesq paradigm equation (BPE) is the main model representing the behaviour of shallow water wave. The

shallow water simulation also plays import roles in the application of physic and engineering. In this work, we

construct a finite difference method for solving BPE. The finite difference scheme is linear implicit, which has

second order convergence in time and space. Numerical experiments are presented with the aim of two

dimensional realistic simulations. The properties of surface wave are investigated.

Keywords: Finite difference method, Boussinesq equation, Shallow water simulation.

REFERENCES

1. Christov, C. I. "Conservative difference scheme for Boussinesq model of surface waves." Proc. ICFD V

(1995): 343-349.

2. Kolkovska, Natalia, and Milena Dimova. "A new conservative finite difference scheme for Boussinesq

paradigm equation." Open Mathematics 10.3 (2012): 1159-1171.

3. Christov, C. I. "An energy-consistent dispersive shallow-water model." Wave motion 34.2 (2001): 161-

174.

4. Chertock, Alina, Christo I. Christov, and Alexander Kurganov. "Central-Upwind Schemes for

Boussinesq Paradigm Equations." Computational Science and High Performance Computing IV.

Springer, Berlin, Heidelberg, 2011. 267-281.

5. Christov, C. I., and J. Choudhury. "Perturbation solution for the 2D Boussinesq equation." Mechanics

Research Communications 38.3 (2011): 274-281.

6. Christov, Christo I. "Numerical implementation of the asymptotic boundary conditions for steadily

propagating 2D solitons of Boussinesq type equations." Mathematics and Computers in Simulation 82.6

(2012): 1079-1092.

7. Christou, M. A., and C. I. Christov. "Galerkin spectral method for the 2D solitary waves of Boussinesq

paradigm equation." AIP Conference Proceedings. Vol. 1186. No. 1. AIP, 2009.

8. Jordan, P. M., and C. I. Christov. "A simple finite difference scheme for modeling the finite-time blow-

up of acoustic acceleration waves." Journal of sound and vibration 281.3-5 (2005): 1207-1216.

111


MST-O-03 Mathematical Analysis of an Unemployment Model

Tawatchai Petaratip1 and Piyapong Niamsup 1,*

1Department of Mathematics, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand

* E-mail: [email protected]; Tel. +66 8 9558 4947

ABSTRACT

This work presented and analyzed a mathematical model for unemployment by considering three states, namely,

the numbers of unemployed persons, employed persons, and vacancies. In this model, we studied the stability

of the positive equilibrium points and observed the effect of efforts for creating new vacancies made by

government policy. Conditions for the local asymptotic stability and the global asymptotic stability of the

positive equilibrium points are derived. Numerical results have been used to check the theoretical results and

show the effect of creating new vacancies.

Keywords: Unemployment, Vacancy, Mathematical Model, Global Stability.

REFERENCES

1. Misra, A. K. and Singh, A. K., Nonlinear Analysis: Real World Applications, 2011, 12, 128-136.

2. Misra, A. K. and Singh, A. K., Differential Equations and Dynamical Systems, 2013, 21(3), 291-307.

3. Munoli, S.B. and Gani, S., Optimal Control Applications and Methods, 2015, 37, 798-806. 4. Pathan, G. and Bhathawala, P. H., Advances in Dynamical Systems and Applications, 2017, 12, 41-48.

5. Sharma, S. and Samanta, G.P., Differential Equations and Dynamical Systems, 2013, 22(2), 125-145.

6. Korobeinikov, A., Bulletin of Mathematical Biology, 2004, 66, 879–883.

7. Elaiw, A.M., Nonlinear Analysis: Real World Applications, 2010,11(4), 2253–2263.

8. Elaiw, A.M., and Azoz, S.A., Mathematical Methods in the Applied Sciences, 2013, 36, 383–394.

9. LaSalle, J.P., Regional Conference Series in Applied Mathematics Philadelphia, SIAM, 1976, 21,

418-420. 10. Hale, J.K., Ordinary Differential Equations, Wiley, New York, 1969.

11. Khalil, H.K., Nonlinear Systems, 3rd ed., Prentice Hall, New Jersey, 2002.

12. Edelstein Keshet, L., Mathematical Models in Biology, Random House, New York, 1988.

112


MST-O-04 An Upper Bound on the Domination Number of a

Graph Pk ((k1, k2), (k3, k4))

Monthiya Ruangnai 1,* and Sayan Panma 2

1,2Department of Mathematics, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand

* E-mail: [email protected]; Fax: +66 5389 2280; Tel. +66 5394 3326

ABSTRACT

For k, k1, k2, k3, k4 ℕ, let Pk ((k1, k2), (k3, k4)) be a simple graph containing vertices and edges as shown in Figure

1. A graph Pk ((k1, k2), (k3, k4)) has 4 endpoints αk1, β

k2, σk3

, and δk4. Both of vertices 0 and k have degree 3.

Besides these vertices, others have degree 2. Thus the degree sequence of this graph

Pk ((k1, k2), (k3, k4)) is (1,1,1,1,2,2,2, … ,2,3,3). A subset S of vertices of a graph Pk ((k1, k2), (k3, k4)) is a dominating

set of Pk ((k1, k2), (k3, k4)) if every vertex in V(Pk ((k1, k2), (k3, k4))) – S is adjacent to some vertex in S. We

investigate the dominating set of minimum cardinality of a graph Pk ((k1, k2), (k3, k4)) to obtain the domination

number of this graph. Finally, we determine an upper bound on the domination number of a graph Pk ((k1, k2), (k3, k4)).

Figure 1. A graph Pk ((k1, k2), (k3, k4)).

Keywords: Domination Number, A Dominating Set of a Graph, The Domination Number of a Graph

REFERENCES

1. Chartrand, G. and Zhang, P., Introduction to Graph Theory, international ed., McGraw-Hill, 2005, 361-

368.

2. Haynes, T. W., Hedetniemi, S. T., and Slater, P. J., Fundamentals of Dominations in Graphs, Marcel

Dekker, New York, 1998.

3. Wilson, R., Introduction to Graph Theory, 4th ed., Addison Wesley Longman Limited, England, 1996.

113


CSE-O-01 Multi Precision Iterative Poisson Solver on GPU

Arpiruk Hokpunna1*

1Department of Mechanical Engineering, Faculty of Engineering, Chiang Mai University, Chiang Mai, Thailand

* E-mail: corresponding author email; Fax: +66 53 940 146; Tel. +66 940 411

ABSTRACT

Currently, multicore computers are widely available and HPC workstation used in small and medium enterprises

are increasingly more powerful and Reynolds-Averaged Navier-Stokes equations (RANS) has been used

successfully in the industry. Lately GPU has been incorporated to accelerate the solution procedure and allow

CFD to be solved much faster than before. Nevertheless, RANS cannot yet be used to develop new products

where new physical phenomena are unknown. More appropriate approaches are DNS and LES. This work

develops a Poisson solver on GPU which is needed to enforce continuity in the Navier-Stokes equation. In this

project, we aim to develop algorithms for solving Large-Eddy Simulation by computing the momentum

evolution on the main CPU and port the solution of pressure to the GPU. This way, a multi-core workstation

can be accelerated. The bandwidth limit between CPU-GPU is alleviated using mixed precision data transfer

and GPU is tasked to solve only the pressure. The basic performance of the mixed precision Poisson solver will

be presented in the conference using standard one- and two dimensional problems, follows by analysis of

truncated errors and correction procedure. Finally, an application to 3D turbulent flow is presented and the

advantages of the mixed-precision in real flow is discussed.

Keywords: GP-GPU, Naiver-Stokes equation, projection method Poisson equation, iterative solver

114


CSE-O-02 Implementation IoT Rehabilitation Tracking System for

Trigger Finger Patients

Numtip Trakulmaykee, Panupong Kreanual, Khunanya Suksawat, and Chidchanok Choksuchat*

1Information and Communication Technology Programme, Prince of Songkla University,

Hat Yai, Songkla, Thailand * E-mail: [email protected]; Fax: +66 74 288 697; Tel. +66 74 288 674

ABSTRACT

Currently, many patients are suffered with Trigger Finger (TF) which is a symptom that causes stiffness, and a

locking sensation when they bend and straighten their fingers. It really causes pain to patients. The early stage

of trigger finger has not to do a surgery operation. Patient can heal by physical therapy method, slowly repeated

pressing-releasing (paper-rock) manner of palm. The problems of patients and physicians who concerned the

matter that cannot follow up the results of the patients exercise in the proper manner and appropriate time. Our

team related to the Traditional Thai Physician who realized to this problem, hence the solution can be solved

by ICT process. We developed the tracking system as a web application that is used for monitoring the patients.

We focus on displaying the patient's data, which is sent from healthcare Internet-of-Things (IoT) physical

therapy device. Making a convenience to Traditional Thai Medicine (TTMed) staff to track the test results and

patient’s history. The main purpose of this web application that use to track the symptoms of patients especially

under taking care by therapists to efficiency treatment. We will test the performance of web application with

healthy user for parallel improvement,and launch an application to the TTMed staff and TF patient in the further

step.

Figure 1. IoT-Rehabilitation System Architecture (a) and Software Architecture (b).

Keywords: Tracking system, Trigger Finger, Internet of Things, Monitoring Web, Real-time database. REFERENCES

1. Valdes, K. (2012). A retrospective review to determine the long-term efficacy of orthotic devices for

trigger finger. Journal of Hand Therapy, 25(1), 89-96.

2. Langer, D., Maeir, A., Michailevich, M., & Luria, S. (2017). Evaluating hand function in clients with

trigger finger. Occupational therapy international, 2017.

3. Langer, D., et. al. (2014). Occupation‐based Assessments and Treatments of Trigger Finger: A Survey

of Occupational Therapists from Israel and the United States. Occupational therapy international,

21(4), 143-155.

115


CSE-O-03 Corrosion Depth Prediction of an Onshore Gas Pipeline

by Using Artificial Neural Network

Wassamon Phusakulkajorn1,*, Piyamabhorn Uttamung1, Foifon Srisawat1,

Dhritti Tanprayoon1, and Namurata Sathirachinda Palsson1

1National Metal and Materials Technology Center (MTEC), National Science and Technology Development Agency

(NSTDA), 114 Thailand Science Park, Thanon Pahonyothin, Tambon Khlong * E-mail: [email protected]; Fax: +66 2 564 6370; Tel. +66 8 9735 3799

ABSTRACT

Pipelines are well-known as the most reliable means of transporting oil and gas. Since oil and gas pipelines are

subjected to deterioration and degradation during service, their conditions need to be periodically monitored

and assessed. Inspected by means of the widely employed Magnetic Flux Leakage method, external corrosion

was found to be the predominant form of pipeline failure. In order to prevent catastrophic environmental damage

due to oil and gas spillage, inspection data thus need to be accurately interpreted to evaluate corrosion. Poor and

conservative corrosion estimations lead to an unnecessary expenses and production time delay. It is well known

that the linear model gives conservative estimation, surprisingly, it continues being used by many pipeline

inspectors. The reason is that it is simple and practical to predict the corrosion growth rate and depth by

considering only detected metal loss. However, other factors such as environmental and operational conditions

are also responsible for oil and gas pipelines’ deterioration and degradation. Including these external factors

into an external corrosion evaluation, relationship between such factors and the corrosion depth has to be

investigated and defined. Unfortunately, the effect of environments on external corrosion is not straightforward

to factor into a closed mathematical form as it is nonlinear and, sometimes, not well understood. Therefore, in

this work, a nondeterministic artificial intelligent model was employed to predict external corrosion of an

onshore gas pipeline. The pigging data for external corrosion provided by various inspection vendors was used

to develop a model. The result indicated good agreement between the estimation obtained from the model and

the corresponding inspection data.

Keywords: Corrosion depth prediction, Artificial neural network, Onshore gas pipeline, External corrosion

REFERENCES

1. Din, M. M., Ithnin, N., et. al, Journal of Engineering and Applied Science, 2015, 10(2), 512-519.

2. Kamrunnahar, M. and Macdonald, M. U., Journal of Corrosion Science, 2010, 52, 669-677.

3. Birbilis, N., Cavanaugh, M. K., et. al, Journal of Corrosion Science, 2011, 53, 168-176.

4. Senouci, A., El-Abbasy, M. S., Elwakil, E., Abdrabou, B., and Zayed, T., Journal of Structure and

Infrastructure Engineering, 2014, 10(3), 375–387.

5. Cai, J. R., Cottis, A., Lyon, S.B., Journal of Corrosion Science, 1999, 41, 2001-2030.

116




Poster Presentation Program

117




Code Presenter Title

CHE-P-01

Anchalee Junkaew

National Science and Technology

Development Agency, Thailand

Lactic Acid on γ-Alumina: DFT Study

CHE-P-02 Athis Watwiangkham


Theoretical Investigations on Electronic Properties

and Excited State Intramolecular Proton Transfers

of 2-(2′-Hydroxyphenyl) Benzothiazole

Derivatives for Light-Emitting Materials

CHE-P-03

Bundet Boekfa

Kasetsart University Kamphaengsaen

campus, Thailand

The Methanol Formation on Fe, Co and Ni-

porphyrin Catalysts: A DFT Study

CHE-P-04 Chanatkran Prommin


Effects of Substituent, Pi-expansion and Additional

Hydroxyl on the Excited State Single and Double

Proton Transfer of 2-Hydroxybenzaldehyde and its

Relative Compounds: A TD-DFT Static and

Dynamics Study

CHE-P-05

Chanchai Sattayanon


Development Agency (NSTDA), Thailand

Systematic Theoretical Study of Electronic

Structure and Stability of Metal Embedded MoS2

Catalysts for Nitrogen Oxide Electrochemical

Reaction (NOER)

CHE-P-06

Chirawat Chitpakdee


Development Agency (NSTDA), Thailand

Cobalt on Monolayer MoS2 as a Single-atom

Catalyst for Efficient HDO Reaction: A DFT Study

CHE-P-07

Ephrem Gizachew Demissie

City University of Hong Kong,

Hong Kong

Reactivity of Hydrated Monovalent Cobalt (I)

Toward Nitrous Oxide in the Gas Phase

CHE-P-08 Farhan Siddique

Tianjin University, China

The Electronic Transitions of Analogs of Red Wine

Pyranoanthocyanin Pigments

CHE-P-09 Hiroki Sakagami

Yokohama City University, Japan

Development of Combined Plane Wave and

Localized Basis Sets Method to Treat The H/D

Isotope Effect of Adsorption of Atoms/molecules

on Metal Surfaces

CHE-P-10 Khanittha Kerdpol


Effects of Different Number of Replicas on Replica-

Exchange and Replica-Permutation Molecular

Dynamics Simulations of Chignolin

CHE-P-11

Malinee Promkatkaew

Kasetsart University Sriracha Campus,

Thailand

Spectroscopic Properties of Zn2+ Complexes of

1,1'-binaphthyl-based Schiff Bases Calculated

Using DFT and TD-DFT Calculations

118



CHE-P-12 Maya Ozaki


Theoretical Analysis of Positron Affinity and

Pair Annihilation Mechanisms for Amino Acid

Molecules

CHE-P-13 Natcha Chanman

Mahidol University, Thailand

Modelling Effect of Drug Interaction on the

Evolutionary Dynamics of Antibiotic Resistance

CHE-P-14 Natthiti Chiangraeng


Effect of Architectures on Morphologies in Poly

(ethylene oxide)-Poly (methyl methacrylate)

Copolymers: A Theoretical Study

CHE-P-15 Panichakorn Jaiyong

Thammasat University, Thailand

Molecular Interactions of Organic Biomarkers

on the Monolayer Surface of Graphene-based

Models

CHE-P-16

Pussana Hirunsit

National Nanotechnology Center,

Thailand

Acetaldehyde Adsorption on Co13 and Ni13

Clusters Supported on γ-Al2O3

CHE-P-17 Ratchadaree Intayot

Ubon Ratchathani University, Thailand

Theoretical Study of Ti4 Cluster Supported on N-

and B-doped Graphene for Enhancing Hydrogen

Storage Capacity

CHE-P-18 Sakura Okano


Path Integral Molecular Dynamics Simulations

for Muoniated and Hydrogenated Thioacetone

Radicals

CHE-P-19 Sarinya Hadsadee


Theoretical Study of Ni Catalysts for H2

Oxidation and Production via the Minimum

Energy Intersystem Crossing Point

CHE-P-20 Suparada Kamchompoo


Adsorption of Hydrogen (H), Hydroxide (OH-)

and Carbon Monoxide (CO) over Mo/P-

terminated MoP (001,101) Surface: A DFT study

CHE-P-21 Takuya Ikeda


Theoretical Study on the Difference of Volumes

of Self-assembled Nanocube by Encapsulated

Neutral / Anionic Molecules

CHE-P-22 Thanadol Jitwatanasirikul

Ubon Ratchatani University, Thailand

Improvement of MoS2 for Formaldehyde

Removal: A Computational Study

CHE-P-23 Thantip Roongcharoen


Tuning Catalytic Property of Single Fe supported

on Divacancy of Nitrogen Coordinated Graphene

119



CHE-P-24 Tsugutoshi Nashiro


Molecular Dynamics Study of Coil-to-globule

Phase Transition of Thermoresponsive Polymer in

Water Solvent

CHE-P-25 Wachara Benchaphanthawee


Molecular Design of Enhanced Fluorescent

Molecules using Excited State Intramolecular

Proton Transfers of Tetraphenylimidazole-Based

Dyes

CHE-P-26 Warinthon Chansen


Substitution Effect on Photophysical Properties and

Excited-State Intramolecular Proton Transfer of 2’-

Hydroxychalcone Derivatives; Theoretical study

CHE-P-27 Worachit Wannasompon

University of Phayao, Thailand

Theoretical Study on the Formation of Dimeric

Structure in Metallocene-catalyzed Polymerization:

The Effects of Ancillary Ligand and Bridge

CHE-P-28 Yutthana Wongnongwa


Mechanistic Study of Ethylene Aromatization over

GaH2 Embedded ZSM-5 Zeolite

CHE-P-29

Ruangchai Tarsang

Rajamangala University of Technology

Isan Sakonnakhon Campus, Thailand

Theoretical Study of New Carbazole-substituted

Derivatives for Blue TADF Emitters

CHE-P-30 Rusrina Salaeh


The Effect of Protic Solvents on the Excited State

Proton Transfer of 3-Hydroxyflavone: A TD-DFT

Static and Molecular Dynamics Study

BIO-P-01 Amita Sripattaraphan


Binding Affinity Investigation on Anti-viral Agents

Against Enterovirus A71 and Coxsackievirus A16

3C Proteases: MM/PB(GB)SA Calculations

BIO-P-02

Auwal Muhammad

King Mongkut's University of Technology

(KMUTT), Thonburi, Thailand

Characterization and Identifying the Positional

Binding and Ligand Interaction of GH10 Xylanase

via Computational Techniques

BIO-P-03 Pornthep Sompornpisut


Effect of Different Membrane Thickness on The

Closed Conformation of M2 Channel Revealed by

MD Simulation

BIO-P-04 Kanika Verma


Rational Designing of Antimicrobial Peptides

Against Clostridium Difficile Toxin B Protein- A

Computational Strategy

BIO-P-05 Lan Nguyen Ngoc Le


Structure and Dynamics of Spin Label Side Chain

in a Membrane Protein by Molecular Dynamics

Simulations

120



BIO-P-06 Peerapong Wongpituk


Effect of Pyridoxal Phosphate and

Tetrahydrofolate Bound on Human Serine

Hydroxymethyltransferase by Molecular

Dynamics Simulations

BIO-P-07 Pitchayathida Mee-udorn


A Theoretical Study on Redox Potential of

Quinones

BIO-P-08 Thitinan Aiebchun


Molecular Docking Study on Chalcones Acting

Against Ca2+/Calmodulin-Dependent Protein

Kinase Kinase-β

BIO-P-09 Punyaporn Pongsuwan


Computational Approaches for Discovering

Anti-HIV-1 Integrase Compounds Targeting

DNA Strand Transfer Reaction

BIO-P-10 Thanyakarn Choosamai


In Silico Drug Discovery Targeting Histone

Deacetylase 2 as a Potential Cure for HIV

BIO-P-11 Anocha Vongmanee


Discovery of Sirtuin1 (SIRT1) Inhibitors via In

Silico Approaches

BIO-P-12 Kulisara Kittivibul


3D-QSAR Study and Computational Approaches

for Exploring Potent Histone Deacetylase 2

Inhibitors

BIO-P-13 Utid Suriya


Discovery of Inhibitors Targeting HIV-1

Integrase-LEDGF/p75 Interactions via Virtual

Screening, Chemometrics, and Molecular

Dynamics Simulations

BIO-P-14 Suriya Tateing


Enzymatic Activity Modulation Induced by Active

Site Loop Configuration in Histone Deacetylase 2:

An In Silico Dynamics Investigation

PFD-P-01 Jen-Chuan Tung

China Medical University, Taiwan

Structural, Electronic and Magnetic Properties of

Ni2YAl (Y= V, Cr, Mn, Fe and Co) Heusler

Alloys: An Ab Initio Study

PFD-P-02 Patipan Sukpoonprom

Silpakorn University, Thailand

Influence of Pd Doping on Gas Sensing Property

of ZnO Nanofilm: A Theoretical Study

PFD-P-03 Suttikiat Changruenngam

Mahidol University, Thailand

Modelling Impact of Human Movement on the

Transmission of Infectious Disease

121


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Organized and Sponsored by - CCL-CMUanscse23.ccl-cmu.com/wp-content/uploads/2019/06/Abstract-Book-f… · • Dr. Uracha Ruktanonchai Deputy Executive Director, National Nanotechnology