Center for Computational Sciences (CCS), University of Tsukuba in Japan, and Big Data for Smart Society Institute (GATE), Sofia University in Bulgaria will conclude a memorandum of understanding (MOU). A signing ceremony and workshop will be held on the following schedule.
Date：26th April, 2024（Fri） 13:00-17:00 Venue：CCS Workshop Room and online
Time
Japan
Bulgaria
12:45 – 13:00
06:45 – 07:00
Registration
13:05 – 13:10
07:05 – 07:10
Welcomed remarks CCS
Prof. Taisuke BOKU
Welcomed remarks GATE
Prof. Sylvia ILIEVA
Welcomed remarks CCS
Prof. Hiroyuki KUSAKA
Welcomed remarks GATE
Prof. Desislava PETROVA-ANTONOVA
13:10 – 13:15
07:10 – 07:15
Ceremony for signing the MoU
Prof. BOKU and Prof. ILIEVA
13:15 – 13:25
07:20 – 07:25
Photo and memorial time
13:25 – 13:30
07:25 – 07:30
Closing the Ceremony
Chair: Asst. Prof. Quang Van DOAN
13:30 – 14:00
07:30 – 08:00
Tour visit of CCS 1
Workshop Part1 Chair: Dr. Vitanova (GATE)
14:00 – 14:05
08:00 – 08:05
Open the workshop
Chair: Asst. Prof. Quang Van DOAN
14:05 – 14:25
08:05 – 08:25
CCS introduction
Prof. Taisuke BOKU
14:25 – 14:45
08:25 – 08:45
Big Data for Smart Society (GATE) Institute: Challenges and achievements
Prof. Sylvia ILIEVA
14:45 – 15:05
08:45 – 09:05
Introduction of Geoenvironment group at CCS
Prof. Hiroyuki KUSAKA
15:05 – 15:15
09:05 – 09:15
Break
Workshop Part2 Chair: Prof. Hiroyuki KUSAKA (CCS)
15:15 – 15:35
09:15 – 09:35
Urban Climate Change Prediction
Asst. Prof. Quang Van DOAN
15:35 – 15:55
09:35 – 09:55
Urban digital twin: Challenges and use cases of Sofia city
Center for Computational Sciences (CCS), University of Tsukuba, invites applications for a full-time (non-tenured) faculty position as described below. We would like to inform all institutes concerning this field, and ask for your cooperation in recommending a suitable candidate for the position. Thank you for your support.
Title: Assistant professor with a fixed-term appointment
Affiliation: Center for Computational Sciences, University of Tsukuba (Division of Particle Physics)
Research field, Content of work: Computational particle physics. In collaboration with Prof. Yoshinobu Kuramashi, the successful candidate will conduct research on lattice field theories using the tensor network approach related to the research project “New development of computational particle physics with tensor network approach” supported by Grant-in-Aid for Scientific Research (A) (Principal Investigator: Yoshinobu Kuramashi). The applicant will be expected to have expertise, skills, and experience on the lattice field theory and related numerical computations.
Starting date: As soon as possible after a hiring decision is made (negotiable).
Terms of employment: Full-time position with possibility of renewal annually, up until March 31, 2028, upon evaluation of the progress. The annual salary will be determined based on the regulations of the University, taking account of the career of the employee.
Qualifications: An applicant needs to have a Doctoral Degree or Ph. D at the start of employment.
Application materials:
Curriculum Vitae (with photograph)
List of research activities including acquired competitive research funds (Separate refereed and non-refereed papers in the list)
Reprints of 5 major papers published within the last 5 years (One paper may be published earlier than 5 years.)
Summary of research activities (up to about 1000 words)
Research plan after the appointment (up to about 1000 words)
Two Reference letters or contact information of the two letter writers
Self-Declaration on Specific Categories (the prescribed form can be downloaded from https://www.ccs.tsukuba.ac.jp/reqdocuments/)
Consent for the handling and extraterritorial transfer of personal data in accordance with the EU-General Data Protection Regulation (GDPR) (*Submit this form only if you are a resident of member countries of the European Economic Area or the United Kingdom, the prescribed form can be downloaded from https://www.ccs.tsukuba.ac.jp/reqdocuments/)
Selection process: After screening the application documents, qualified applicants will be invited to have an online interview in Japanese or English.
Deadline for application: 23:59 (JST), May 31, 2024.
Where to submit: Please write “Application for Assistant Professor Position in Particle Physics” on the subject and send a zip file with a password for the documents 1)-8) in the pdf format via e-mail to application-pp[at]ccs.tsukuba.ac.jp ([at] should be replaced by @). The password is separately sent to kuramasi[at]het.ph.tsukuba.ac.jp ([at] should be replaced by @ as well).
Reference letters should be sent in pdf format via e-mail to application-pp[at]ccs.tsukuba.ac.jp ([at] should be replaced by @). Please write “Letter-XXX” (XXX is the applicant’s name) on the subject.
Who to make contact: Prof. Yoshinobu Kuramashi Chief, Division of Particle Physics Center for Computational Sciences University of Tsukuba Tel: +81-29-853-4469, Email: kuramasi[at]het.ph.tsukuba.ac.jp ([at] should be replaced by @)
Miscellaneous:
The personal information in the application documents will be used solely for the purpose of selection. After the selection all the personal information will be properly deleted.
The Center for Computational Sciences has been approved as a Joint Collaborative Research Center by the Ministry of Education, Culture, Sports, Science and Technology. We promote interdisciplinary computational sciences, including joint use of our supercomputer systems. The University of Tsukuba conducts its personnel selection process in compliance with the Equal Employment Opportunity Act.
The University of Tsukuba has established “University of Tsukuba Security Export Control Regulations” based on “Foreign Exchange and Foreign Trade Act”, and conduct strict examination when employing foreign nationals, persons from foreign universities, companies, government agencies, etc., or persons who fall under a specific category.
The Joint Center for Advanced High Performance Computing (JCAHPC), which is jointly operated under the collaboration between the Center for Computational Sciences, University of Tsukuba, and the Information Technology Center, the University of Tokyo, has named its new supercomputer system “Miyabi,” which is planned to start its entire operation in January 2025.
筑波大学計算科学研究センターと東京大学情報基盤センターが共同運営する、最先端共同HPC基盤施設（JCAHPC：Joint Center for Advanced High Performance Computing、施設長：朴泰祐）は、2025年1月に稼働を開始する次期スーパーコンピュータシステムの名称を “Miyabi”（みやび）に決定しました。
Title: Climate Change Research: Insights from KAUST Speaker: Prof Ibrahim Hoteit（King Abdullah University of Science and Technology） Date: 2 April 2024 Time: 13:30-14:15 Venue: Center for Computational Sciences, Workshop Room Language: English
*After the invited presentation, the following seminar is scheduled.
13:30-14:15 Climate Change Research: Insights from KAUST Prof Ibrahim Hoteit, King Abdullah University of Science and Technology
14:15-14:45 Urban Climate Modeling for urban and district scales: WRF-UCM and City-LES Prof Hiroyuki Kusaka, University of Tsukuba
14:45-15:15 Urban Extreme Weather and Climate Change Asst Prof Quang-Van Doan, University of Tsukuba
講演タイトル:Climate Change Research: Insights from KAUST 講演者: Prof Ibrahim Hoteit（King Abdullah University of Science and Technology） 日時: 2024年4月2日（火） 13:30-14:15 場所: 計算科学研究センター ワークショップ室 言語: English
＊計算科学コロキウムに続けて、セミナーが開催されます。 全体のスケジュールは以下の通りです。
13:30-14:15 Climate Change Research: Insights from KAUST Prof Ibrahim Hoteit, King Abdullah University of Science and Technology
14:15-14:45 Urban Climate Modeling for urban and district scales: WRF-UCM and City-LES Prof Hiroyuki Kusaka, University of Tsukuba
14:45-15:15 Urban Extreme Weather and Climate Change Asst Prof Quang-Van Doan, University of Tsukuba
Researchers led by University of Tsukuba have discovered rdxPolA, a putative DNA polymerase involved in replicating ancestral mitochondrial genomes, in diverse eukaryotic lineages. Based on the phylogenetic distribution of rdxPolA among eukaryotes, they proposed an evolutionary scenario of DNA polymerases for mitochondrial genome maintenance in the early evolution of eukaryotes.
Tsukuba, Japan—Mitochondria are intracellular organelles that evolved from a bacterium belonging to Alpharoteobacteria, which was taken up as an endosymbiont by the common ancestor of eukaryotes. Mitochondria possess their own highly reduced genomes (known as mitochondrial genomes), which are principally the descendants of the genome of the α-proteobacterial symbiont. Phylogenetically diverse eukaryotes use a type of DNA polymerase called “POP” to maintain their mitochondrial genomes.
In this study, the researchers identified 10 novel types of DNA polymerase that are distinct from the previously known types, including POPs, across diverse eukaryotic lineages. The evolutionary origin and subcellular localization of each novel DNA polymerase were investigated. Intriguingly, one of the DNA polymerases identified in this study, rdxPolA, was found to be involved in mitochondrial DNA maintenance and is a direct descendant of the DNA polymerase in the α-proteobacterial symbiont that gave rise to the first mitochondrion. The researchers proposed a scenario for the evolution of DNA polymerases involved in mitochondrial DNA maintenance from primitive to extant eukaryotes.
These findings provide critical insights into the early evolution of the machinery for mitochondrial DNA maintenance and the establishment of mitochondria in primitive eukaryotic cells.
### This research was supported by the Japan Society for Promotion of Sciences projects 18KK0203, 19H03280, 23H02535, and BPI05044 (to Y. Inagaki), 22J11104 (to R. Harada), and 19H03274 (to R. Kamikawa).
Original Paper
Title of original paper:
Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion
Professor INAGAKI Yuji HARADA Ryo (JSPS Research Fellowship for Young Scientists DC2) Center for Computational Sciences (CCS), University of Tsukuba
Senior Researcher YABUKI Akinori Deep-Sea Biodiversity Research Group, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
Resercher YAZAKI Euki Research Center for Advanced Analysis, National Agriculture and Food Research Organization
Associate Professor KAMIKAWA Ryoma Graduate School of Agriculture, Kyoto University
NASA Deep Space Network (DSN)の1つであるオーストラリアのキャンベラ深宇宙通信施設（Canberra Deep Space Communication Complex、CDSCC)とオーストラリアの電波望遠鏡を活用して2015年に小惑星のレーダー観測を開始し、現在までに３０以上もの地球接近小惑星の検出に成功した。小惑星のレーダー観測は、それまでアメリカのGoldstoneやプエルトリコのAreciboなど、主に北半球で行われていた。しかし地球に再接近する小惑星のおよそ５％は南半球からしか観測できないので、ギャップを埋められるようになったことは、小惑星の探査・プラネタリーディフェンス・利用など、多岐にわたる分野で注目されている。講演では、レーダー観測により小惑星の軌道が精度良く決定され、また小惑星の形状や自転、表面物質の素性、表面状態などの情報が得られることを紹介し、またアストロバイオロジーへの応用の可能性についても議論する。
Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion. （オルガネラ局在ファミリーA DNAポリメラーゼ百科：原始ミトコンドリア共生体をふくむ細菌からの進化的貢献について）
Purple sulfur bacteria (PSB) convert light energy into chemical energy through photosynthesis. Interestingly, certain species can photosynthesize even in environments with low-calcium levels. Using cryo-electron microscopy, researchers from University of Tsukuba unveiled the structure of light-harvesting complexes and elucidated the mechanism that facilitates photosynthesis under low-calcium conditions.
Tsukuba, Japan—Photosynthetic bacteria, unlike plants, do not generate oxygen as a photosynthetic byproduct because they use hydrogen sulfide instead of water to convert solar energy into chemical energy (electrons). This process is orchestrated by a protein complex, the light-harvesting 1-reaction center (LH1-RC). Numerous PSB thrive in calcium-rich environments, such as hot springs and seawater. In the three-dimensional LH1-RC structure, the LH1 antenna protein is typically associated with calcium. However, the photosynthetic mechanism remains elusive in Allochromatium vinosum, a model species of autotrophic bacteria capable of thriving in low-calcium or soft-water environments, as hypothetically, calcium is not involved in the photosynthetic process in this model.
Using cryo-electron microscopy, the researchers revealed the LH1-RC structures of this model species at a resolution that enabled individual amino acid visualization. These observations revealed calcium binding only at six specific sites in the LH1 subunit. In contrast, the closely related thermophilic bacterium Thermochromatium tepidum displayed calcium attachment across all 16 LH1 subunits, indicating a calcium binding dependence on the amino acid sequence pattern. These results imply an evolutionary adaptation in this species, enabling it to bind trace amounts of calcium in low-calcium environments, thereby improving its thermal stability for photosynthesis.
These findings would potentially advance the efficient use of solar energy, and contribute to environmental protection, and highlight the capability of certain species to conduct photosynthesis in freshwater while detoxifying hydrogen sulfide, which is toxic to numerous organisms, into sulfur.
### This research was partially supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Numbers JP21am0101118 and JP21am0101116, and JP23ama121004
Original Paper
Title of original paper:
High-Resolution Structure and Biochemical Properties of the LH1-RC Photocomplex from the Model Purple Sulfur Bacterium, Allochromatium vinosum
