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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Map of Faculty of Science, Chiang Mai University
3
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Floor plan for ANSCSE23
4
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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,
Chiang Mai University, Thailand
• Asst. Prof. Winita Punyodom Head of Materials Science Research Center, Faculty of Science,
Chiang Mai University, Thailand
• 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. Piyawut Srichaikul National Electronics and Computer Technology Center
(NECTEC), NSTDA, Thailand
• Dr. Manaschai Kunaseth, National Electronics and Computer Technology Center
(NECTEC), NSTDA, Thailand
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. Piyawut Srichaikul National Electronics and Computer Technology Center
(NECTEC), NSTDA, Thailand
• Dr. Manaschai Kunaseth, National Electronics and Computer Technology Center
(NECTEC), NSTDA, Thailand
5
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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. Siriporn Jungsuttiwong Ubon Ratchathani 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. Nawee Kungwan Chiang Mai University, Thailand
• Asst. Prof. Thanyada Rungrotmongkol Chulalongkorn University, Thailand
• Asst. Prof. Worasak Sukkabot Ubon Ratchathani University, Thailand
• Asst. Prof. Thanasak Mouktonglang Chiang Mai University, Thailand
• Dr. Supawadee Namuangruk National Nanotechnology Center (NANOTEC), NSTDA, Thailand
• Dr. Pussana Hirunsit National Nanotechnology Center (NANOTEC), NSTDA, Thailand
• Dr. Chompoonut Rungnim National Nanotechnology Center (NANOTEC), NSTDA, Thailand
• Dr. Piyawut Srichaikul National Electronics and Computer Technology Center
(NECTEC), NSTDA, Thailand
• Dr. Manaschai Kunaseth National Electronics and Computer Technology Center
(NECTEC), NSTDA, Thailand
• Dr. Pinit Kidkhunthod Synchrotron Light Research Institute, Thailand
• Dr. Supareak Praserthdam Chulalongkorn University, Thailand
6
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Organizing Committee Chair
• Asst. Prof. Nawee Kungwan Chiang Mai University, Thailand
Organizing Committee
• Dr. Supawadee Namuangruk National Nanotechnology Center (NANOTEC), NSTDA, Thailand
• Assoc. Prof. Siriporn Jungsuttiwong Ubon Ratchathani University, Thailand
• Asst. Prof. Thanyada Rungrotmongkol Chulalongkorn University, Thailand
• Assoc. Prof. Jaroon Jakmunee Chiang Mai University, Thailand
• Asst. Prof. Nawee Kungwan 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. Thanasak Mouktonglang 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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
Six Parallel Sessions
Room:
CB1220
Room:
CB1310
Room:
CB1313
Room:
CB1210
Room:
CB1314
Room:
CB1320
CHE BIO PFD MST EMT eHPC
15.30 – 15.50 Coffee Break
15.50 – 17.15
Six Parallel Sessions
Room:
CB1220
Room:
CB1310
Room:
CB1313
Room:
CB1210
Room:
CB1314 Room: CB1320
CHE BIO PFD MST EMT eHPC
17.15 – 18.30 Poster Session
18.45 Welcome Dinner
9
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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,
Chulalongkorn University, Thailand
10.25 – 11.00 Coffee Break
11.00 – 12.00
Six Parallel Sessions
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
Six Parallel Sessions
Room:
CB1220
Room:
CB1320
Room:
CB1313
Room:
CB1210
Room:
CB1314
Room:
CB1310
CHE BIO PFD MST EMT CSE
15.00 – 15.20 Coffee Break
15.20 – 16.35
Six Parallel Sessions
Room:
CB1220
Room:
CB1320
Room:
CB1313
Room:
CB1210
Room:
CB1314
Room:
CB1310
CHE BIO PFD MST EMT CSE
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Scientific Program
11
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Session: Computational Chemistry (CHE)
Thursday, June 27, 2019
08.00 – 09.00 Registration
09.00 – 09.30 Opening Ceremony
09.30 – 10.15 Plenary Lecture 1
10.15 – 10.35 Special Talk 1
10.35 – 11.00 Coffee Break
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
15.30 – 15.50 Coffee Break
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
17.15 – 18.30 Poster Session
18.45 Welcome Dinner
Friday, June 28, 2019
09.00 – 09.45 Plenary Lecture 2
09.45 – 10.05 Special Talk 2
10.05 – 10.25 Special Talk 3
10.25 – 11.00 Coffee Break
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
15.00 – 15.20 Coffee Break
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Session: Computational Biology, Bioinformatics, Biochemistry, and Biophysics (BIO)
Thursday, June 27, 2019
08.00 – 09.00 Registration
09.00 – 09.30 Opening Ceremony
09.30 – 10.15 Plenary Lecture 1
10.15 – 10.35 Special Talk 1
10.35 – 11.00 Coffee Break
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
15.30 – 15.50 Coffee Break
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
17.15 – 18.30 Poster Session
18.45 Welcome Dinner
Friday, June 28, 2019
09.00 – 09.45 Plenary Lecture 2
09.45 – 10.05 Special Talk 2
10.05 – 10.25 Special Talk 3
10.25 – 11.00 Coffee Break
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
15.00 – 15.20 Coffee Break
Chairman: Deva Priyakumar
15.20 – 15.50 BIO-I-13 Prof. Jitrayut
Jitonnom
15.50 – 16.20 BIO-I-14 Prof. Nuttee Suree
16.35 – 17.00 Closing Conference
13
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Session: Computational Physics, Computational Fluid Dynamics
and Solid Mechanics (PFD)
Thursday, June 27, 2019
08.00 – 09.00 Registration
09.00 – 09.30 Opening Ceremony
09.30 – 10.15 Plenary Lecture 1
10.15 – 10.35 Special Talk 1
10.35 – 11.00 Coffee Break
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
15.30 – 15.50 Coffee Break
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
17.15 – 18.30 Poster Session
18.45 Welcome Dinner
Friday, June 28, 2019
09.00 – 09.45 Plenary Lecture 2
09.45 – 10.05 Special Talk 2
10.05 – 10.25 Special Talk 3
10.25 – 11.00 Coffee Break
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
Chairman: Anucha Yangthaisong and
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
15.00 – 15.20 Coffee Break
Chairman: Anucha Yangthaisong and
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
16.35 – 17.00 Closing Conference
14
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Session: Mathematics and Statistics (MST)
Thursday, June 27, 2019
08.00 – 09.00 Registration
09.00 – 09.30 Opening Ceremony
09.30 – 10.15 Plenary Lecture 1
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
15.30 – 15.50 Coffee Break
17.15 – 18.30 Poster Session
18.45 Welcome Dinner
Friday, June 28, 2019
No session
15
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Session: Experiment Meets Theory (EMT)
Thursday, June 27, 2019
08.00 – 09.00 Registration
09.00 – 09.30 Opening Ceremony
09.30 – 10.15 Plenary Lecture 1
10.15 – 10.35 Special Talk 1
10.35 – 11.00 Coffee Break
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
15.30 – 15.50 Coffee Break
Chairman: Nantanit Wanichacheva
15.50 – 16.20 EMT-I-08 Prof. Hidehiro
Sakurai
16.20 – 16.50 EMT-I-09 Dr. Kajornsak
Faungnawakij
17.15 – 18.30 Poster Session
18.45 Welcome Dinner
Friday, June 28, 2019
09.00 – 09.45 Plenary Lecture 2
09.45 – 10.05 Special Talk 2
10.05 – 10.25 Special Talk 3
10.25 – 11.00 Coffee Break
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
15.00 – 15.20 Coffee Break
Chairman: Lei Huang
15.20 – 15.50 EMT-I-16 Prof. Kittipong Chainok
15.50 – 16.20 EMT-I-17 Prof.Burapat Inceesungvorn
16.35 – 17.00 Closing Conference
16
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Session: High Performance Computing, Computer Science and Engineering (CSE)
Thursday, June 27, 2019
No session
.
Friday, June 28, 2019
09.00 – 09.45 Plenary Lecture 2
09.45 – 10.05 Special Talk 2
10.05 – 10.25 Special Talk 3
10.25 – 11.00 Coffee Break
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
15.00 – 15.20 Coffee Break
16.35 – 17.00 Closing Conference
17
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Special Workshop
18
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
08.00 – 09.00 Registration
09.00 – 09.30 Opening Ceremony
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 – 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
15.15 – 15.45 Coffee Break
15.45 – 17.00 Panel discussion: การพฒนา National Computing Platform ใหเหมาะสมกบการใชงานในประเทศไทย (Thai language)
17.15 – 18.30 Poster Session (All Poster Presentation)
18.45 Welcome Dinner
19
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Plenary Lecture
21
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
The XYG3 Type of Doubly Hybrid Density Functionals: From
Molecular Systems to Extended Solids
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Special Talk
24
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Invited Speaker
28
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]; Fax: +81 0774 95 2121; Tel. +81 0774 95 2120
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]; Fax: +81 564 55 7277; Tel. +81 564 55 7025
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]; Fax: +81 45 787 2188; Tel. +81 45 787 2188
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]; Fax: +81 761 51 1301; Tel. +81 761 51 1296
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
*E-mail: [email protected]
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Oral Presentation
95
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]; Fax: +81 45 787 2188; Tel. +81 45 787 2188
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]; Fax: +66 2 218 7598; Tel. +66 2 218 7604
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]; Fax: +81 45 787 2188; Tel. +81 45 787 2197
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
BIO-O-02 Effect of Surface Functionalization of Aunps on the
Internalization into Mammalian Cell
Thodsaphon Lunnoo1*, Theerapong puangmali1,2
1Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
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
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
* E-mail: [email protected]
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
*E-mail: [email protected]
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Poster Presentation Program
117
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
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
Chiang Mai University, Thailand
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
Chiang Mai University, Thailand
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
National Science and Technology
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
National Science and Technology
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
Chulalongkorn University, Thailand
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Code Presenter Title
CHE-P-12 Maya Ozaki
Yokohama City University, Japan
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
Chiang Mai University, Thailand
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
Yokohama City University, Japan
Path Integral Molecular Dynamics Simulations
for Muoniated and Hydrogenated Thioacetone
Radicals
CHE-P-19 Sarinya Hadsadee
Ubon Ratchathani University, Thailand
Theoretical Study of Ni Catalysts for H2
Oxidation and Production via the Minimum
Energy Intersystem Crossing Point
CHE-P-20 Suparada Kamchompoo
Ubon Ratchathani University, Thailand
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
Yokohama City University, Japan
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
Chiang Mai University, Thailand
Tuning Catalytic Property of Single Fe supported
on Divacancy of Nitrogen Coordinated Graphene
119
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Code Presenter Title
CHE-P-24 Tsugutoshi Nashiro
Yokohama City University, Japan
Molecular Dynamics Study of Coil-to-globule
Phase Transition of Thermoresponsive Polymer in
Water Solvent
CHE-P-25 Wachara Benchaphanthawee
Chiang Mai University, Thailand
Molecular Design of Enhanced Fluorescent
Molecules using Excited State Intramolecular
Proton Transfers of Tetraphenylimidazole-Based
Dyes
CHE-P-26 Warinthon Chansen
Chiang Mai University, Thailand
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
Ubon Ratchathani University, Thailand
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
Chiang Mai University, Thailand
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
Chulalongkorn University, Thailand
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
Chulalongkorn University, Thailand
Effect of Different Membrane Thickness on The
Closed Conformation of M2 Channel Revealed by
MD Simulation
BIO-P-04 Kanika Verma
Chulalongkorn University, Thailand
Rational Designing of Antimicrobial Peptides
Against Clostridium Difficile Toxin B Protein- A
Computational Strategy
BIO-P-05 Lan Nguyen Ngoc Le
Chulalongkorn University, Thailand
Structure and Dynamics of Spin Label Side Chain
in a Membrane Protein by Molecular Dynamics
Simulations
120
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Code Presenter Title
BIO-P-06 Peerapong Wongpituk
Chulalongkorn University, Thailand
Effect of Pyridoxal Phosphate and
Tetrahydrofolate Bound on Human Serine
Hydroxymethyltransferase by Molecular
Dynamics Simulations
BIO-P-07 Pitchayathida Mee-udorn
Chulalongkorn University, Thailand
A Theoretical Study on Redox Potential of
Quinones
BIO-P-08 Thitinan Aiebchun
Chulalongkorn University, Thailand
Molecular Docking Study on Chalcones Acting
Against Ca2+/Calmodulin-Dependent Protein
Kinase Kinase-β
BIO-P-09 Punyaporn Pongsuwan
Chiang Mai University, Thailand
Computational Approaches for Discovering
Anti-HIV-1 Integrase Compounds Targeting
DNA Strand Transfer Reaction
BIO-P-10 Thanyakarn Choosamai
Chiang Mai University, Thailand
In Silico Drug Discovery Targeting Histone
Deacetylase 2 as a Potential Cure for HIV
BIO-P-11 Anocha Vongmanee
Chiang Mai University, Thailand
Discovery of Sirtuin1 (SIRT1) Inhibitors via In
Silico Approaches
BIO-P-12 Kulisara Kittivibul
Chiang Mai University, Thailand
3D-QSAR Study and Computational Approaches
for Exploring Potent Histone Deacetylase 2
Inhibitors
BIO-P-13 Utid Suriya
Chiang Mai University, Thailand
Discovery of Inhibitors Targeting HIV-1
Integrase-LEDGF/p75 Interactions via Virtual
Screening, Chemometrics, and Molecular
Dynamics Simulations
BIO-P-14 Suriya Tateing
Chiang Mai University, Thailand
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
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Note
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Note
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Note
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Note
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Note
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
Note
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.
The 23rd International Annual Symposium on Computational Science and Engineering (ANSCSE23)
This page is intentionally left blank.