iTHEMS Biology Seminar
174 events
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.
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Seminar
Journal Club: Phase separation in a many-component system with random interactions
March 31 (Thu) at 10:00 - 11:00, 2022
Kyosuke Adachi (Special Postdoctoral Researcher, Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research (BDR))
Several kinds of protein condensates have been observed in living cells, and the liquid-liquid phase separation is regarded as a basic mechanism of the condensate formation. However, given that there are thousands of protein species in a cell, it is not clear how the number and the composition of distinct condensates are controlled. One of the physics approaches to this problem is considering a model of many components with random interactions. In this Journal Club, I will introduce a recent paper [1] that applies random-matrix theory to the phase separation dynamics.
Venue: via Zoom
Event Official Language: English
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Seminar
Criticality in stochastic SIR model for infectious diseases based on path-integral approach
March 24 (Thu) at 10:00 - 11:00, 2022
Shigehiro Yasui (Assistant Professor, Center of Medical Information Science, Kochi Medical School)
The susceptible-infected-removed (SIR) model provides us with a basic scheme for the analysis of the epidemic infectious diseases such as the COVID-19. In this presentation, we focus on the stochastic SIR model which describes the stochastic time-evolutions of the population sizes for the susceptible, infected, and removed individuals. We consider the master equation (Kolmogorov forward equation) for the infection transmission and recovery processes (SI->II and I->R), and transform it into the Hamiltonian formalism with the Fock space a la quantum physics. According to the Doi-Peliti prescription, furthermore, we introduce the path-integral formalism similar to the quantum field theory, and perform the perturbative and non-perturbative calculations for the time-evolution of the susceptible, infected, and removed populations. We find that the critical value Rc of the basic reproduction number, which determines the spreading or the convergence of the infectious diseases, can be modified by the stochastic effects in comparison to the Rc in the conventional deterministic SIR model.
Venue: via Zoom
Event Official Language: English
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Seminar
Phylogenomics revealed one of the problems for phylogeny –The monophyly of Archaeplastida including land plant-
March 17 (Thu) at 10:00 - 11:00, 2022
Euki Yazaki (Postdoctoral Researcher, iTHEMS)
There are many problems between large eukaryotic lineages. One of these is the monophyly of Archaeplastida to which land plants and other photosynthetic organisms belong. Although it has been believed that the Archaeplastida are monophyletic because they share common chloroplast structures, several large-scale molecular phylogenetic analyses have failed to reproduce this phylogenetic relationship. In this study, by enhancing the taxon sampling of the data set, the monophyly of Archaeplastida was successfully reconstructed, showing that the taxa critical for the reconstruction are present. Through detailed molecular phylogenetic and statistical analyses, it was estimated that the lack of monophyly ofArchaeplastida is due to the specific evolutionary signals of certain taxa.
Venue: via Zoom
Event Official Language: English
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Seminar
Independent regulation of multiple checkpoints in cell-cycle network system -Biological function originated in the law of localization-
March 10 (Thu) at 10:00 - 11:00, 2022
Atsushi Mochizuki (Professor, Institute for Frontier Life and Medical Sciences, Kyoto University)
In cell cycle, G1-S and G2-M checkpoints are regulated by different protein complexes, Cdc2-Cdc13 and Cdc2-Cig2, respectively. For a normal mitosis, activity of two complexes should rise specifically at different timing. However, the complex formations share common species of proteins and activation reactions conform a complicated network. We study how independent regulation of two checkpoints is realized in the network system by “structural sensitivity analysis”, which was previously established by us. The analyses clarified that activities of two complexes are regulated by disjoint sets of reaction parameters in the system. A series of non-trivial behaviors are generated by “buffering structures with an intersection”, which can generally appear in chemical reaction network including complex formation.
Venue: via Zoom
Event Official Language: English
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Seminar
Stator dynamics of the bacterial flagellar motor
February 24 (Thu) at 17:00 - 18:00, 2022
Ashley Nord (Researcher, Centre de Biologie Structurale, CNRS, France)
Rubén Pérez-Carrasco (Lecturer in Theoretical Systems Biology, Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, UK)The bacterial flagellar motor is the membrane-embedded rotary molecular motor which turns the flagellum that provides thrust to many bacteria for swimming, swarming, and chemotaxis. This large multimeric complex, composed of a few dozen constituent proteins, is a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels which dynamically bind to the cell wall and convert electrochemical energy into torque which is applied to the rotor. The dynamic exchange of stator units is a function of the viscous load on the flagellum, allowing the bacterium to adapt to its local environment, though the molecular mechanisms of this mechanosensitivity remain unknown. Previously, we have shown that stator units behave as a catch bond, a counterintuitive bond which becomes stronger under applied tension. Here, by actively perturbing the steady-state stator stoichiometry of individual motors, we reveal a stoichiometry-dependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of next-neighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models which recapitulate the asymmetry, finding assembly dynamics to be particularly well described by a two-state catch-bond mechanism.
Venue: via Zoom
Event Official Language: English
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Seminar
Hilbert transform and its applications to biology
February 17 (Thu) at 10:00 - 11:00, 2022
Shingo Gibo (Postdoctoral Researcher, iTHEMS)
In chronobiology, the estimation of phase dynamics is important for measuring period and phase shift. However, it is difficult to precisely estimate the phase from time-series data when the frequency and the amplitude are nonstationary. Hilbert transform has been known as a signal processing method for decomposing time-series into the phase and the amplitude dynamics. This method allows us to analyze the phase from nonstationary time-series data. In this talk, I would like to introduce the basic concept of Hilbert transform and a few examples of its applications.
Venue: via Zoom
Event Official Language: English
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Seminar
Stochastic operators: properties and applications
February 10 (Thu) at 10:00 - 11:00, 2022
Gilberto Nakamura (Postdoctoral Researcher, iTHEMS)
Stochastic processes are widely used to model systems in which one or more variables fluctuate randomly. Problems arise when large sets of random variables are allowed to interact with each other, as is often the case with physical and biological systems. Stochastic operators provide a convenient framework for describing the interactions and evolution of the random variables. In this talk, I will discuss techniques and methods typically used in spin systems to deal with stochastic operators and their spectral analysis in the context of random processes. I will briefly review their properties and applications to biological systems. As practical examples, I will present some results of my research in infectious diseases and migration of glioma cells.
Venue: via Zoom
Event Official Language: English
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Seminar
On Flow and Form at Low Reynolds Number
January 27 (Thu) at 10:00 - 11:00, 2022
Kenta Ishimoto (Associate Professor, Research Institute for Mathematical Sciences (RIMS), Kyoto University)
Cell locomotion is mechanically restricted by surrounding viscous fluids. With a focus on swimming cells in a low-Reynolds-number flow, I will give a brief introduction to microbiological fluid dynamics and present a 'hydrodynamic shape' theory at the cellular scale.
Venue: via Zoom
Event Official Language: English
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Seminar
A study of biological systems from topological point of view
January 20 (Thu) at 10:00 - 11:00, 2022
Hiroyasu Miyazaki (Senior Research Scientist, iTHEMS)
A biological body can be regarded as a complicated network of chemical reactions. The chemical reaction network (CRN) is a (hyper)graph-theoretic model of such biological networks. Recently, in the joint work with Yuji Hirono, Takashi Okada and Yoshimasa Hidaka, we applied a topological method to the study of CRNs, and found a suitable way to simplify the networks. Since Professor Hirono has already explained our work in this seminar, I will try to explain it from a slightly different point of view. In the first half of the talk, I will review the entire work. In the second half, I will try to give a rough sketch of the mathematical method we used in the work.
Venue: via Zoom
Event Official Language: English
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Seminar
A comprehensive view of the SARS-CoV-2 infection process
January 13 (Thu) at 10:00 - 11:00, 2022
Wataru Nishima (Scientist, New Mexico Consortium, Mexico)
Nishima et al. recently published a paper about a computational model of SARS-CoV-2 Spike Protein [1]. Although it is still a hypothesis due to the lack of direct experimental evidence, the story comprehensively explains the initial infection process of SARS-CoV-2 consistent with most of the empirical evidence. In the presentation, I would like to explain the overview of the infection process for the non-expert audience and how the hypothesis influences the current COVID-19 situation. If time permits, I would like to briefly explain the current plan of the iTHEMS-NMC COVID project, which is going to be the first case of undergoing an interdisciplinary collaboration framework between Japan and the US.
Venue: via Zoom
Event Official Language: English
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Seminar
Physics of nuclear bodies
January 6 (Thu) at 10:00 - 11:00, 2022
Tetsuya Yamamoto (Specially Appointed Associate Professor, Institute for Chemical Reaction Design and Discovery, Hokkaido University)
Eukaryotic nucleus is not a uniform solution of DNA, but there are a number of nuclear bodies in the interchromatin spaces. There are growing number of experiments that suggest that nuclear bodies are assembled by liquid-liquid phase separation (LLPS). Condensates assembled by LLPS show coarsening or coalescence to decrease the surface energy. However, in some nuclear bodies, such as paraspeckles, nuclear stress bodies, and fibrillar centers in nucleoli, multiple condensates are stably dispersed and are not likely assembled by LLPS. The assembly mechanism of nuclear bodies is relevant to the regulation of the area of condensate surfaces, which are functional in some nuclear bodies, and the mobility of nuclear bodies. Hirose group (Osaka Univ.) has elucidated that nuclear bodies are scaffolded by a class of RNA, called architectural RNA (arcRNA), which forms complexes with RNA binding proteins. This implies that the assembly of nuclear bodies is governed RNA dynamics, such as transcription, degradation, and processing, and the sequence of bases of arcRNA. In the seminar, I will show how the base sequences and the dynamics of RNA are involved in the assembly of paraspeckles and fibrillar centers in nucleoli.
Venue: via Zoom
Event Official Language: English
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Seminar
Hidden Markov Models and their applications
December 23 (Thu) at 10:00 - 11:00, 2021
Takashi Okada (Senior Research Scientist, iTHEMS)
The Hidden Markov models (HMM) have been used in a variety of fields for different purposes. I am going to review statistical inference methods associated with HMM & related biological problems. As an example of their applications, I'll also present my research on the SARS-CoV-2 evolution.
Venue: via Zoom
Event Official Language: English
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Seminar
Revisiting Standard Methods for Phylogenetic Tree Inference
December 16 (Thu) at 10:00 - 11:00, 2021
Motomu Matsui (Research Associate, Graduate School of Science, The University of Tokyo)
Phylogenetic tree inference is the foundation to answer any biological questions, for example, how the living systems were established. However, the existing methods show poor performance to infer the phylogenetic tree when constructing an informative multiple sequence alignment (MSA) is difficult. In this talk, I will first review the current problems in phylogenetics, then introduce the graph splitting (GS), and edge perturbation (EP) method. The GS method rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach; evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees when sequences substantially diverge. The EP method is the bootstrap-like method using pairwise sequence alignment (PSA) instead of MSA, which can provide reliable measurements on the estimated branches. In addition, we can rapidly and reliably reconstruct a phylogenetic tree with problematic MSA switching NJ+EP and GS+EP methods, because the EP method can be applied to the NJ method. These methods not only improve the accuracy of phylogenetic tree inference, but they also could open the door for revisiting phylogenetics.
Venue: via Zoom
Event Official Language: English
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Seminar
Selective inference for testing trees and edges in hierarchical clustering and phylogeny
December 9 (Thu) at 10:00 - 11:00, 2021
Hidetoshi Shimodaira (Professor, Graduate School of Informatics, Kyoto University / Team Leader, Mathematical Statistics Team, RIKEN Center for Advanced Intelligence Project (AIP))
Bootstrap resampling is quite useful for computing “confidence values” or “p-values” of trees and edges. However, they are biased and may lead to false positives (too many wrong discoveries) or false negatives (too few correct discoveries) depending on the “curvature” of the boundary surface of a hypothesis region in the data space. In addition, we face the issue of selection bias because we tend to use the dataset twice for hypothesis selection and its evaluation. I will explain these two types of bias and show methods to adjust the confidence values.
Venue: via Zoom
Event Official Language: English
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Seminar
Spatial structure in ecology: the effects of dispersal network structure on biodiversity pattern and stability in metacommunities
November 18 (Thu) at 10:00 - 11:00, 2021
Yuka Suzuki (Okinawa Institute of Science and Technology Graduate University (OIST))
Ecological dynamics typically take place at a large spatial scale. However, it has been challenging to study them at a scale as large as a country, continent, or ocean. In particular, while there are many studies that consider systems with multiple local patches (known as "metacommunities"), spatial structures assumed in these studies are mostly simple or focused on a particular structure, despite the diverse landscape structures seen in nature. Thus, to understand how spatial structures affect metacommunities in nature, we need to expand our understanding of the role of spatial structure in regulating biodiversity patterns and stability across diverse spatial structures. In my study, I addressed this issue by using computer simulation with theoretical and empirical spatial structures. In this talk, I will show how the use of computational tools and network theoretical concepts aided investigating unexplored aspects of spatial structure and dissecting the complex nature of spatial network structure. Results suggest that how dispersal pathways are distributed in the network space affects total diversity, and the number of patches in a metacommunity is the dominant spatial parameter that regulate stability. Such an improved understanding of the role of spatial structure could contribute to a better conservation planning as well.
Venue: via Zoom
Event Official Language: English
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Seminar
Toward mathematical medicine: development of a new drug and digital medicine for sleep disorders
November 11 (Thu) at 12:30 - 13:30, 2021
Jae Kyoung Kim (Associate Professor, Department of Mathematical Sciences, KAIST, Republic of Korea)
In this talk, I will illustrate collaborative stories between our math group and medical researchers to treat disrupted circadian rhythms and sleep. First, I will illustrate the key molecular mechanism for robust circadian rhythms against spatio-temporal noise, which we identified by analyzing spatio-temporal timeseries data of clock molecules. This explains why Alzheimer's diseases, obesity, and aging cause unstable circadian rhythms and sleep-wake cycle: cytoplasmic traffic jam, which provides a new paradigm to treat sleep disorders. Next, I will talk about our collaboration story with Pfizer Inc: how we used mathematical modeling to help the development of a new drug modulating the circadian phase. Finally, I will introduce our collaboration with Samsung medical center: how we used mathematical modeling to analyze complex sleep patterns of shift workers measured with wearables to find optimal sleep patterns minimizing sleep disorders. This opens the chance for the development of an app providing a personalized sleep schedule for shift workers.
Venue: via Zoom
Event Official Language: English
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Seminar
Protein structure modeling from cryo-electron microscopy data
November 4 (Thu) at 13:30 - 14:30, 2021
Takaharu Mori (Senior research scientist, Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research (CPR))
Recent advances in cryo-electron microscopy (cryo-EM) have enabled us to determine three-dimensional structures of biomolecules at near-atomic resolution. Protein structure modeling from experimental cryo-EM data can be achieved using a molecular dynamics (MD) simulation, called flexible fitting. We have developed MD-based flexible fitting algorithms for efficient and reliable protein structure modeling. In this seminar, I would like to talk about our recent contributions to this field, and propose perspectives towards next-generation structural biology.
Venue: via Zoom
Event Official Language: English
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Seminar
Nonlinear dynamics in frog choruses
October 28 (Thu) at 10:00 - 11:00, 2021
Ikkyu Aihara (Associate Professor, Institute of Systems and Information Engineering, University of Tsukuba)
Male frogs produce sounds to attract conspecific females as well as advertise their own territories to other males. Subsequently male frogs acoustically interact with each other, which induces various types of synchronized behavior. In this seminar, I will introduce the synchronized calling behavior of actual male frogs as well as theoretical studies using a phase oscillator model [1, 2]. Next, I will introduce our recent projects on the identification of the phase oscillator model from empirical data [3] and the extension of the model to a hybrid dynamical system in which male frogs intermittently switch their behavioral mode based on internal condition and also the interaction with other males [4].
Venue: via Zoom
Event Official Language: English
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Seminar
Evaluation of origin of driving force for loop formation in a chromatin fiber
October 21 (Thu) at 10:00 - 11:00, 2021
Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)
During cell division, chromatin fiber is condensed into the rod-like shape which is called chromosome. The rod-like shape of the chromosome is constructed by consecutive chromatin loop structures which are formed by the protein complex named condensin. In this talk, by calculating the driving force for the loop formation, we discuss the mechanism of loop formation which is the one of the controversial issues on chromosome condensation. The driving force is evaluated based on the free energy of the chromatin loop formation by constructing the polymer model. Based on the free energy, the loop growth length in the unit time is also evaluated. These evaluations also lead to the time evolution of the loop length and the mechanism of the loop formation.
Venue: via Zoom
Event Official Language: English
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Seminar
Understanding the effect of defective, interfering influenza virus
October 14 (Thu) at 10:00 - 11:00, 2021
Catherine Beauchemin (Deputy Program Director, iTHEMS)
Defective interfering virus particles (DIPs) are viruses that are defective in a very specific way that allows them to out-compete standard, non-defective virus. It is difficult to count DIPs because they can look too similar to standard virus. So instead, people are counting them based on their effect on suppressing the standard virus population. In this talk, I will explain the basic biology of virus replication, what are DIPs, and how they compete with standard virus. I will present our mathematical model (ordinary differential equation) that describes co-infection competition with DIPs and standard virus. I will use the mathematical model to show how experiments to count DIPs can give incorrect results, and I will propose some solutions.
Venue: via Zoom
Event Official Language: English
174 events