Volume 11

iTHEMS Weekly News Letter

Press Release

Yuji Sakai thumbnail

Modeling the functions of condensin in chromosome shaping and segregation

2018-06-22

Former iTHES fellow, Yuji Sakai (Univ. Tokyo) together with Atsushi Mochizuki (iTHEMS), Masashi Tachikawa (iTHEMS), Tetsuya Hirano (RIKEN) and Kazuhisa Kinoshita (RIKEN) have published a paper and a press release.

Immediately before a cell divides, chromosomal DNA in a eukaryotic cell is packaged into a discrete set of rod-shaped chromosomes. This process, known as mitotic chromosome assembly or condensation, secures the faithful segregation of genetic information into daughter cells. Central to this mechanistically complex process is a class of protein complexes known as condensins. However, how condensins support the assembly and segregation of mitotic chromosomes at a mechanistic level remains elusive. Here we construct a coarse-grained physical model of chromosomal DNA fibers and condensin molecules, and study how condensins work in the mitotic chromosome assembly using computer simulations. Our results show that two activities of condensins, formation of consecutive loops in chromosomal DNA fibers and inter-condensin attractions, are necessary for both the shaping and segregation of mitotic chromosomes, and balancing acts of these activities help to coordinate the efficient progress of the processes. Importantly, chromosome shaping and segregation in our results are strongly correlated, implying that they are controlled by the same underlying mechanism mediated by condensins.

Reference

  1. Yuji Sakai, Atsushi Mochizuki, Kazuhisa Kinoshita, Tatsuya Hirano, Masashi Tachikawa, Modeling the functions of condensin in chromosome shaping and segregation, PLoS Comput Biol 14(6): e1006152 (2018), doi: 10.1371/journal.pcbi.1006152

Upcoming Events

Math Lecture

Computational Algebraic Statistics and its Applications

June 26 (Tue) at 10:00 - 16:30, 2018

Satoshi Aoki (Professor, Department of Mathematics, Kobe University)

Lecture 1 (10:00-11:30)
An introduction of Groebner bases of polynomial rings

Lecture 2 (13:00-14:30)
Groebner bases theory in design of experiments

Lecture 3 (15:00-16:30)
Groebner bases theory in sampling problems of contingency tables

This introductory lecture is about statistical theory from the point of view of the computational algebraic statistics, in particular the applications of Groebner bases. The statistical theory is a fundamental tool in natural science, social science and humanities, and the Groebner basis is a topic related to multi-variable polynomials. The Lecture will start from an introduction to the Groebner basis which would have wide applications in mathematics, physics, biology, chemistry, engineering, information science and computer science. Therefore, we welcome scientists in any field who are interested in this subject.

The event official language is Japanese (slides and writing are in English).

Venue: #535-537, 5F, Main Research Building, RIKEN

Event Official Language: Japanese

Seminar

​Denso IT Lab. and RIKEN Joint ​Innovation ​Seminar

June 29 (Fri) at 16:00 - 17:40, 2018

16:00-17:00 Denso IT Laboratory
"About Denso IT lab." H. Iwasaki (Denso)
"Human-Car interface" ​H. Tsukahara​ (Denso)
​"Math in machine leaning and computer vision" K. Ishikawa (Denso)

17:00-17:40 RIKEN
"Math bridging between classical and quantum physics: quantum hall effect in classical system" T. Ozawa (RIKEN)
"Di-Omega: a new particle predicted by K-computer with mathematical science" S. Gongyo (RIKEN)

Venue: Common Room #246-248, 2F Main Research Building, RIKEN

Event Official Language: Japanese

Colloquium

iTHEMS Colloquium

Systems Biology of Cellular Rhythms

July 2 (Mon) at 15:00 - 16:30, 2018

Albert Goldbeter (Professor, Unit of Theoretical Chronobiology, Faculty of Sciences, Université Libre de Bruxelles, Belgium)

Rhythmic phenomena occur at all levels of biological organization, with periods ranging from milliseconds to years. Among biological rhythms, circadian clocks, of a period close to 24h, play a key role as they allow the adaptation of living organisms to the alternation of day and night. Biological rhythms represent a phenomenon of temporal self-organization in the form of sustained oscillations of the limit cycle type. Mathematical models show how the emergent property of oscillatory behavior arises from molecular interactions in cellular regulatory networks, which explains why cellular rhythms represent a major research topic in systems biology. After providing an introduction to biological rhythms and their modeling, I will focus on mathematical models for two major examples of rhythmic behavior at the cellular level : the circadian clock and the cell cycle. The coupling of these rhythms allows for their synchronization and for the occurrence of more complex patterns of oscillatory behavior. I will discuss the reasons why models for cellular rhythms tend to become more complex, upon incorporating new experimental observations. The case of cellular rhythms allows us to compare the merits of simple versus complex models for the dynamics of biological systems.

Venue: Suzuki Umetaro Hall, 1F Bioscience Building, RIKEN

Broadcast: #305-2, Computational Science Research Building, R-CCS, Kobe Campus, RIKEN / SUURI-COOL (Kyoto), #204-205, 2F Maskawa Building for Education and Research, North Campus, Kyoto University / 2F Seminar Room, AIMR Main Building, Advanced Institute for Materials Research (AIMR), Tohoku University

Event Official Language: English

Seminar

Tomoki Ozawa thumbnail
AIMR Main Building venue photo

SUURI-COOL SeminarSUURI-COOL (Sendai)

Topological Photonics and the four-dimensional quantum Hall effect

July 3 (Tue) at 15:00 - 17:00, 2018

Tomoki Ozawa (Senior Research Scientist, iTHEMS)

In this seminar, I will give an introduction to topological photonics, that is, the study of topological band structures and resulting topological phenomena in photonic systems. I will first review basic concepts of topological band structures, and then explain what it means to realize topological band structures in photonic systems. I will particularly emphasize some important differences with respect to solid-state electron systems. I then present some of my own works in topological photonics, such as the synthetic dimensions in photonic systems, which allows one to explore models and phenomena in high dimensions including the four-dimensional quantum Hall effect.

Venue: 1F Meeting Room, AIMR Main Building, Advanced Institute for Materials Research (AIMR), Tohoku University

Event Official Language: English

Workshop

Maskawa Building for Education and Research venue photo

Co-hosted by iTHEMSSUURI-COOL (Kyoto)

iCeMS-iTHEMS Joint Workshop on Interdisciplinary Biology

July 4 (Wed) at 10:00 - 16:30, 2018

This is the first joint workshop between iCeMS (Kyoto Univ.) and iTHEMS (RIKEN). The WS is co-hosted by KUIAS (Kyoto Univ.), iTHEMS (RIKEN) and MACS Program (Kyoto Univ.). By exploring the forefront of experimental and mathematical biology, this workshop aims to stimulate novel research directions in these areas and strengthen the connection between Kyoto Univ. and RIKEN. Those who plan to attend the "get-together", please register before June 22 (Fri.) noon.

Co-hosted by
Kyoto University Institute for Advanced Study (KUIAS), Kyoto Univ.
Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN
MACS Program (MACS), Kyoto Univ.

Venue: #201, Maskawa Building for Education and Research, North Campus, Kyoto University

Event Official Language: English

Seminar

Tomoki Ozawa thumbnail

STAMP Seminar

Introduction to topological band structure

July 6 (Fri) at 10:30 - 17:30, 2018

Tomoki Ozawa (Senior Research Scientist, iTHEMS)

In this seminar, I give an introduction to topological band structures. Topological band structure is the fundamental idea to understand phenomena such as the quantum Hall effect, topological insulators, and topological superconductors. Although originally found in fermionic electron systems, topological band structure is essentially a single-particle property, and thus the same phenomenon can arise also in bosonic systems. In fact, topological band structure does not even need quantum mechanics; topological band structure can arise in classical waves inside a periodic medium, such as electromagnetic waves or classical mechanical waves. In this seminar, I first give a brief introduction to key concepts in topological band structures, such as Berry curvature, Chern number, bulk-edge correspondence, and ten-fold way classification of topological insulators. I then explain how topological band structure can arise in classical systems, giving a brief introduction to the field of topological photonics and topological mechanics.

Venue: Seminar Room #160, 1F Main Research Building, RIKEN

Event Official Language: Japanese

Math Lecture

Introduction to Public-Key Cryptography

Introduction to Public-Key Cryptography (6th)

July 11 (Wed) at 10:30 - 12:00, 2018

Eren Mehmet Kıral (Visiting Researcher, RIKEN Center for Advanced Intelligence Project (AIP))

Venue: Seminar Room #160, 1F Main Research Building, RIKEN

Event Official Language: English

Math Lecture

Yosuke Kubota thumbnail

Theory of Operator Algebras

Theory of Operator Algebras (3rd)

July 12 (Thu) at 15:30 - 17:00, 2018

Yosuke Kubota (Research Scientist, iTHEMS)

Venue: Seminar Room #160, 1F Main Research Building, RIKEN

Event Official Language: English

Workshop

Co-hosted by iTHEMSSUURI-COOL (Kyoto)

The 9th RIKEN-Kyoto University Joint Data Assimilation Workshop

July 17 (Tue) at 13:30 - 17:30, 2018

If you plan to attend the workshop, please register by July 13.

Hosted by Data Assimilation Research Team, RIKEN and Graduate School of Science, Kyoto University
Co-hosted by iTHEMS, RIKEN

Venue: #809 Graduate School of Science Bldg. No 6, Kyoto University

Event Official Language: Japanese

Colloquium

iTHEMS Colloquium

Bell's Theorem, Entanglement, Quantum Teleportation and All That

July 19 (Thu) at 16:00 - 17:30, 2018

Anthony James Leggett (Professor, University of Illinois at Urbana-Champaign, USA)

iTHEMS-CEMS Joint Colloquium.

Professor Leggett is widely recognized as a world leader in the theory of low-temperature physics, and his pioneering work on superfluidity was recognized by the 2003 Nobel Prize in Physics.

Abstract:
One of the most surprising aspects of quantum mechanics is that under certain circumstances it does not allow individual physical systems, even when isolated, to possess properties in their own right. This feature, first clearly appreciated by John Bell in 1964, has over the last half-century been tested experimentally and found (in most people's opinion) to be spectacularly confirmed. More recently it has been realized that it permits various operations which are classically impossible, such as "teleportation" and secure-in-principle cryptography.
This talk is a very basic introduction to the subject, which requires only elementary quantum mechanics.

Venue: Okochi Hall, 1F Laser Science Laboratory, RIKEN

Broadcast: #311, Computational Science Research Building, R-CCS, Kobe Campus, RIKEN / SUURI-COOL (Kyoto), #204-205, 2F Maskawa Building for Education and Research, North Campus, Kyoto University / 2F Seminar Room, AIMR Main Building, Advanced Institute for Materials Research (AIMR), Tohoku University

Event Official Language: English

Seminar

Number Theory Seminar

Number Theory Seminar: 3 Talks

July 24 (Tue) at 10:00 - 12:35, 2018

Masataka Ono (Keio University)
Shingo Sugiyama (Nihon University)
Yoshinosuke Hirakawa (Keio University)

This seminar is aimed at scientists in general, not only to mathematicians.

10:00-10:45
Title: Multiple zeta functions associated with 2-colored rooted trees
Speaker: Dr. Masataka Ono (Keio University)
Abstract: In our recent work, we introduced a combinatorial object and finite sum associated with them which we call finite multiple zeta values associated with 2-colored rooted trees and gave a unified interpretation to some types of finite multiple zeta values. In this talk, we introduce multiple zeta function associated with 2-colored rooted tree and discuss its analytic properties, for example, the possible singularities and functional equations.

10:55-11:40
Title: Modular forms and trace formulas with applications to equidistributions of their Fourier coefficients
Speaker: Dr. Shingo Sugiyama (Nihon University)
Abstract: Modular forms are interesting objects in number theory as they are related to arithmetic problems. Trace formulas of Hecke operators acting on modular forms are very useful tools to study arithmetic invariants: Fourier coefficients, special values of L-functions, Hurwitz class numbers. We will start fundamental notions on modular forms and trace formulas of Hecke operators for non-experts, and introduce our results on a generalization of Serre’s vertical Sato-Tate law. Some results in this talk are based on a joint work with Masao Tsuzuki (Sophia University).

11:50-12:35
Title: On a generalization of Dobinski's formula
Speaker: Yoshinosuke Hirakawa (Keio University)
Abstract: Dobinski's formula is a very classical formula, which expresses the Bell number as an infinite series. Here, the Bell number is the number of partitions of a finite set. Such a "combinatorial-analytic" formula should lead us to more beautiful number theory. In this talk, we introduce a generalization of Dobinski's formula by means of a certain multiple generalization of the exponential function.

Venue: Seminar Room #160, 1F Main Research Building, RIKEN

Event Official Language: English

Conference

Supported by iTHEMS

International Symposium on Quantum Fluids and Solids (QFS)

July 25 (Wed) - 31 (Tue), 2018

The International Symposium on Quantum Fluids and Solids (QFS) will be held at Ito International Research Center (IIRC) on Hongo campus of the University of Tokyo, Japan, from July 25 through 31, 2018. One of the sponsors of this conference is iTHEMS.

The QFS series started forty-three years ago making it one of the oldest series of international conferences in the field of low temperature physics. It has historically been focusing on physics of liquid and solid helium and hydrogen. But in this century its scope is expanding widely from laser cooled cold atoms to topological matters. At QFS2018 in Tokyo, this trend will be continued and with even more interdisciplinary aspects emphasized between the traditional subjects and those in broader physical systems.

Venue: Ito International Research Center (IIRC), Hongo Campus, The University of Tokyo

Event Official Language: English

Person of the Week

Shun Furusawa thumbnail

Self-introduction: Shun Furusawa

2018-06-25

Hello, I am Shun Furusawa, a special postdoctoral researcher of iTHEMS. I received a PhD at Waseda University in September 2013 and then I worked at NAOJ and FIAS as a posdoc. My research area is Nuclear Astrophysics. I am interested in birth, life, and death of various stars and related nuclear physics. At present, I am working on death of massive stars and birth of quark stars. I am looking forward to chatting and discussing with the iTHEMS members.

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