iTHEMS Biology Seminar

We are holding regular seminars and other activities on topics related to biology. Our aim is to lower the boundaries between biology and mathematics/physics, to identify common grounds between biology and mathematics/physics, and to develop ideas for new research topics at the intersection of biology and mathematics or physics.

For further details see iTHEMS Biology Seminar Study Group page.

Seminar

iTHEMS Biology Seminar

Rational design of autonomous, peptide-based ion channels

August 5 at 10:00 - 11:00, 2021

Dr. Ai Niitsu (Postdoctoral Researcher, Theoretical Molecular Science Laboratory, RIKEN)

Designing artificial ion channel proteins has been a major challenge since rational design of membrane proteins is still in its infancy. To address this challenge, we aim to understand the most fundam...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Application of bioenergetics to microbial modeling

July 29 at 10:00 - 11:00, 2021

Prof. Mayumi Seto (Assistant Professor, Department of Chmistry, Biology, and Environmental Science, Faculty of Science, Nara Women's University)

Bioenergetics, the study of thermodynamics as applied to biological systems, aims to understand how energy flows through a living system. Since thermodynamics provides a framework for predicting the p...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

How nucleus size affects chromatin motion? - Experimental measurements and a polymer physics theory

July 1 at 10:00 - 11:00, 2021

Prof. Takahiro Sakaue (Associate Professor, College of Science and Engineering, Department of Physics and Mathematics, Aoyama Gakuin University)

Chromatin moves dynamically inside the cell nucleus, and its motion is often correlated with gene functions such as DNA recombination and transcription. A recent study has shown that during early embr...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Period variability can provide valuable information in oscillatory systems

June 24 at 10:00 - 11:00, 2021

Prof. Fumito Mori (Assistant Professor, Department of Human Science, Faculty of Design, Kyushu University)

Biological clocks generate temporally precise oscillations although they are subjected to various types of noise. In other words, oscillations with only a small variability in the period are observed ...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

The origin and dispersal of buckwheat

June 10 at 10:00 - 11:00, 2021

Dr. Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

Buckwheat, which soba noodles is made from, originated from a wild species that is distributed in southwest China, around Yunnan, Sichuan, and Tibet. We are trying to understand when, where, and how i...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

An overview of genome-wide epistasis and co-selection analysis

June 3 at 10:00 - 11:00, 2021

Dr. Yingying Xu (Special Postdoctoral Researcher, iTHEMS)

This talk is a summary of research that have done by me and my team during 2016~2019. I was a postdoc researcher in Aalto university/Helsinki university in Finland. In the team, a worldwide active col...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

A Mathematical Model for Stem Cell Competition to Maintain a Cell Pool Injured by Radiation Exposure

May 27 at 10:00 - 11:00, 2021

Dr. Kouki Uchinomiya (Central Research Institute of Electric Power Industry)

Cancer risk of low-dose-rate ionizing radiation exposure is one of the most important issues in radiation protection. Tissue stem cells have been considered one of the targets of radiation-induced car...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Organ-to-organ two-way coupling contributes to the stabilization of circadian clock in Arabidopsis.

May 20 at 10:00 - 11:00, 2021

Dr. Kyohei Uemoto (Kyoto University / NARA Institute of Science and Technology)

Circadian clocks increase plant fitness by anticipating periodic environmental changes using unstable temporal information perceived in each tissue/organ. However, little is known about how such local...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Modeling Membrane Morphological Change during Autophagosome Formation

May 14 at 10:00 - 11:00, 2021

Prof. Yuji Sakai (Visiting Scientist (Academia), iTHEMS / Assistant Professor, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo)

Membrane-bound organelles compartmentalize eukaryotic cells and adopt various characteristic shapes such as disk-shaped, tubules, spherical vesicles, and their intermediate structures. Organellar morp...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Kullback-Leibler divergence and stochastic dynamics

May 6 at 10:00 - 11:00, 2021

Dr. Ryosuke Iritani (Research Scientist, iTHEMS)

*Detailed information about the seminar refer to the email.

Event Official Language: English

Seminar

iTHEMS Biology Seminar

The rheotaxis mechanism of swimming ciliates

April 22 at 10:00 - 11:00, 2021

Dr. Yukinori Nishigami (Research Institute for Electronic Science, Hokkaido University)

The swimming unicellular organisms, which live in freshwater, need to resist currents in the environment. Without this ability, their habitat changes with the flow, and they cannot survive in nature f...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Liquid condensates in cell nucleus

April 15 at 10:00 - 11:00, 2021

Dr. Kyosuke Adachi (Special Postdoctoral Researcher, iTHEMS / Special Postdoctoral Researcher, Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research)

I will give a talk in a journal club style. I will introduce recent papers regarding liquid-liquid phase separation in cells. In cell biology, several types of liquid condensates of proteins/RNAs h...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Simple models of cancer growth, MCMC parameter estimation and identifiability

April 8 at 10:00 - 11:00, 2021

Prof. Catherine Beauchemin (Deputy Program Director, iTHEMS / Professor, Department of Physics, Ryerson University, Canada)

I would like to introduce some basic concepts about (very simple) mathematical model of cancer growth, the basic math behind parameter estimation via Markov chain Monte Carlo (MCMC) based on Bayes' th...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Structural reduction of chemical reaction networks based on topology

April 1 at 10:00 - 11:00, 2021

Dr. Yuji Hirono (Assistant Professor, Asia Pacific Center for Theoretical Physics, Republic of Korea)

Chemical reactions form a complex network in living cells and they play vital roles for physiological functions. An amusing question is how the structure of a reaction network is linked to its chemica...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Evolutionary conservativeness and diversification of cycads: Understanding the evolution of living fossils

March 25 at 10:00 - 11:00, 2021

Dr. Jose Said Gutiérrez-Ortega (Assistant Professor, Institute for Excellence in Educational Innovation, Chiba University)

The cycads are a lineage of gymnosperms that represent an example of biological stasis success. Despite their early origin in the seed plant evolution, they survived multiple events of mass extinction...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Microeconomics of metabolism

March 10 at 10:00 - 11:00, 2021

Mr. Jumpei Yamagishi (Kaneko Laboratory, University of Tokyo)

Metabolic behaviors of proliferating cells are often explained as a rational choice to optimize cellular growth rate. In contrast, microeconomics formulates consumption behaviors as optimization probl...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Origin of non-linearity of large deformation on DNA stretched

February 25 at 10:00 - 11:00, 2021

Dr. Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)

Since DNA in a cell is mechanically stretched or rotated by many proteins, the mechanical response of DNA in vitro is expected to be basic point for understanding its behavior. When DNA is stretched b...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

High-throughput laboratory evolution with machine learning reveals constraints for drug resistance evolution

February 18 at 10:00 - 11:00, 2021

Mr. Junichiro Iwasawa (Doctoral course, Department of Physics, Graduate School of Science, The University of Tokyo)

The understanding of evolution is crucial to tackle the problem of antibiotic resistance which is a growing health concern. Although the lack of sufficient data has long hindered the mechanism of evol...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

A machine learning approach for prediction of mitochondrial proteins in non-model organisms

February 12 at 10:00 - 11:00, 2021

Dr. Keitaro Kume (Assistant professor, Faculty of Medicine, University of Tsukuba)

The evolution of the repertoire of proteins localized to organelles is important for understanding the evolutionary process of organelles. However, experimental methods for identifying organelle-local...more

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

System identification of mechano-chemical epithelial sheet dynamics

February 4 at 10:00 - 11:00, 2021

Mr. Yoshifumi Asakura (3rd year doctoral program, Graduate School of BIOSTUDIES, Kyoto University)

Collective migration of epithelial cells is a fundamental process of multi-cellular organisms. Our recent study using live imaging with FRET-based biosensor discovered that cell migration within an ep...more

Venue: via Zoom

Event Official Language: English