iTHEMS生物学セミナー
174 イベント
生物学に関連する様々なトピックを扱ったセミナーを定期的に開催しています。生物学と数学・物理学との境界を低くし、接点を見つけ出すことで、新しい学際的な研究のアイデアが生まれることを期待しています。
詳細はiTHEMS生物学セミナースタディーグループのページをご覧下さい。
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セミナー
Eco-evolutionary dynamics with novel mutations
2020年9月16日(水) 10:00 - 11:00
Hye Jin Park (Junior Research Group Leader, Statistical physics of ecology and evolution group, Asia Pacific Center for Theoretical Physics, Republic of Korea)
Evolution is driven by individual birth and death that are determined by interactions between individuals. Hence studying interactions is crucial to understand the population evolution. However, traditional approaches dealt with those interaction structures are given while spontaneous random mutations can generate new interactors. We considered “mutant interactors,” which lead to new interactions between the residents and invading mutants that can drive the population away from the previous equilibrium and lead to changes in the population composition. Thus, first, we investigated the changes in the population size induced by mutant interactors[1]. And then, we applied this approach to answer the question about relationships between species[2]: Why is cyclic dominance so rare?
会場: via Zoom
イベント公式言語: 英語
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セミナー
Singular point implies coexistence in adaptive dynamics
2020年9月9日(水) 10:00 - 11:00
立川 正志 (数理創造プログラム 客員研究員 / 京都大学 ウイルス･再⽣医学研究所 ⽣命システム研究部⾨ 准教授)
Adaptive dynamics is a relatively new mathematical framework for studying evolution(~1990s). Under the influence of the mathematical ecology and the game theory, adaptive dynamics considers the effect of resident populations on the fitness landscape. As a result, it explains a possible mechanism of evolutionary branching. In this talk, I introduce adaptive dynamics and Pairwise Invasibility Plot (PIP) analysis, a standard method for understanding the adaptive dynamics. Then, I propose a new approach to analyze the adaptive dynamics which enable us to understand higher dimensional systems than PIP does.
会場: via Zoom
イベント公式言語: 英語
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セミナー
The hitch-hiker’s guide to the concept of adaptive dynamics
2020年9月2日(水) 10:00 - 10:30
入谷 亮介 (数理創造プログラム 研究員)
Adaptation is of multi-causality, composed of mutation and selection processes. I will talk about how we model adaptation on the basis of the adaptive dynamics framework. This is a very quick, conceptual talk, rather than heavily mathematical, to draw attention from more people.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Modeling biological timing
2020年8月26日(水) 10:00 - 11:00
黒澤 元 (数理創造プログラム 専任研究員)
Under stay-at-home situation, some of you may suffer from sleep disorder. Efficacy of a drug often depends on the timing of its prescription. We know this fact about our "timing", but we don't know why. This time, I wish to introduce two big mysteries in regard to biological timing. First is our internal daily clock. In general, biochemical process is believed to accelerate with temperature. In contrast, the period of our daily clock, made up of biochemical reactions is somehow stable to temperature. The prediction from simpler biochemical mathematical model, and its experimental verification will be presented. Second is hibernation. During winter, some birds and mammals decrease drastically their body temperature possibly to decrease their energy expenditure. Many studies about hibernation have been conducted for many years. However, basic mechanisms of hibernation (e.g. how the duration of hibernation is determined?) are largely unknown. Recently, we started to investigate body temperature time-series of hibernating hamsters over 100 days in the collaboration with experimental biologists. Preliminary results will be presented.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Heavy tails in the brain
2020年8月5日(水) 10:00 - 11:00
Lukasz Kusmierz (理化学研究所 脳神経科学研究センター (CBS) 研究員)
In my talk I will discuss the relation between two seemingly unrelated measures in the brain that exhibit heavy tails: neuronal avalanches, i.e. bursts of activity with power-law distributions of sizes and lifetimes, and synaptic weights that are believed to be distributed according to the log-normal distribution. Many current models of neuronal avalanches do not rely on heavy-tailed synaptic weight distributions, suggesting that heavy tails of these two quantities may not be related. However, our recent theoretical considerations indicate that this independence no longer holds if two biologically relevant constraints are introduced, i.e., that neurons (1) receive many incoming connections and (2) do not spike if the membrane potential is below some positive threshold, e.g., in the absence of inputs. Under these assumptions we have shown that heavy tails of synaptic weights are necessary to generate biologically plausible low activity levels and associated neuronal avalanches. Our results suggest that the observed distributions of synaptic weights may play important functional roles in the brain.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Time-dependent bias emerges in population models with broad offspring number distributions
2020年7月29日(水) 10:00 - 11:00
岡田 崇 (数理創造プログラム 上級研究員)
It has been increasingly recognized that natural populations exhibit broad offspring number distributions, either because offspring numbers are strongly variable (e.g. marine organisms) or because range expansion processes generate jackpot events. In this talk, I will review the basic concepts of theoretical population genetics and then discuss how broad offspring number distributions affect the evolutionary dynamics.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Human Time vs. Mouse Time in Embryonic Development
2020年7月17日(金) 16:00 - 17:00
戎家 美紀 (Group Leader, European Molecular Biology Laboratory, Barcelona, Spain)
Different species have different tempos of development: larger animals tend to grow more slowly than smaller animals. My group has been trying to understand the molecular basis of this interspecies difference in developmental time, using the segmentation clock as a model system. The segmentation clock is the oscillatory gene expressions that regulate the timing of body segment formation during early embryogenesis. We have recently succeeded in recapitulating the segmentation clock from both human and mouse pluripotent stem cells, detecting oscillations and traveling waves in vitro. Interestingly, the oscillation period of human segmentation clock was 5-6 hours while that of mouse was 2-3 hours. Taking advantage of our in vitro system and simple mathematical models, we have been comparing the genome sequences and molecular processes of the segmentation clock between human and mouse to explain the interspecies difference in the oscillation period.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Application of geometry to protein structure analysis
2020年7月15日(水) 14:00 - 15:00
根上 春 (東京大学 工学系研究科先端学際工学専攻 博士課程)
Geometry is applied in various fields as a method for revealing the structure of data. In this seminar, I will introduce the topological method, fatgraph model, to classify protein structures. I will also introduce another related geometric model and its application to viral glycoprotein analysis. This method provides an a priori prediction of structural rearrangement of proteins.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Constrained evolution of animal embryogenesis
2020年7月8日(水) 10:00 - 11:00
内田 唯 (理化学研究所 生命機能科学研究センター (BDR) 多階層生命動態研究チーム 基礎科学特別研究員)
Animals have developed a great variety of morphologies during the course of evolution. Despite this, phylogeny-specific features have sometimes been maintained for hundreds of millions of years, suggesting that there are constraints to morphological evolution. In my talk, I will introduce some of general motivations behind the EvoDevo study and talk particularly about the blank space in morphospaces (Each axis of a morphospace corresponds to a variable describing morphological features). It remains to be seen if these blank areas are caused by impossible developmental pathways. However, computer simulations of embryogenesis, which has been proposed in recent years, may provide a clue to a solution. Finally, I’m going to talk about my research plan based on this.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Waveform Analysis of Biological Rhythms
2020年7月1日(水) 10:00 - 11:00
儀保 伸吾 (数理創造プログラム 特別研究員)
Nonlinear oscillatory phenomena often emerge in various systems, for example circadian rhythms in biological systems and acoustic vibrations in engineering. Analysis and control of these oscillatory phenomena are one of the big problems in science and technology. My main research field is biological oscillations, especially circadian clocks. The circadian clocks are based on gene-activity rhythms with approximately 24-hour period, and its temporal waveforms are of various shapes. Recently, we theoretically showed that the period of circadian clocks is proportional to the waveform distortion from sinusoidal waves. Interestingly, we found the waveform is important for periods not only in biological oscillations but also in several other types of nonlinear oscillator models.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Turing Patterns in Biology and Beyond
2020年6月10日(水) 10:00 - 10:45
スクロツキ マーティン (数理創造プログラム 客員研究員 / Fellow, German Academic Scholarship Foundation, Germany)
In his 1952 paper "The chemical basis of morphogenesis", Alan M. Turing presented a model for the formation of skin patterns. While it took several decades, the model has been validated, e.g. in the skin pattern formation of zebrafish. More surprising, seemingly unrelated pattern formations can also be studied via the model, like e.g. the formation of plant patches around termite hills. In 1984, David A. Young proposed a discretization of Turing's model, reducing it to a activator/inhibitor process on a discrete domain. In my talk, I will present both the model of Turing and its discretization. We will then consider a generalization to pattern-formation in three-dimensional space and investigate the related parameter space.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Quantification model of energy of loop structure on biopolymer
2020年6月3日(水) 10:00 - 10:45
横田 宏 (数理創造プログラム 特別研究員)
During cell division, the chromatin fiber condenses into a rod-like shape, which is the so-called chromosome. The chromosome is constructed by consecutive chromatin loop structures whose excluded volume interaction gives chromosome its stiffness. So far, the energy source for the loop growing has remained a controversial issue. In this seminar, we quantify the energy source by calculating the free energy difference before and after a model polymer chain creating a loop structure.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation
2020年5月27日(水) 10:00 - 10:45
加藤 郁佳 (理化学研究所 脳神経科学研究センター (CBS) / 東京大学 博士課程)
Dopamine (DA) has been suggested to have two reward-related roles: (1) representing reward-prediction-error (RPE), and (2) providing motivational drive. Role(1) is based on the physiological results that DA responds to unpredicted but not predicted reward, whereas role(2) is supported by the pharmacological results that blockade of DA signaling causes motivational impairments such as slowdown of self-paced behavior. Whereas synaptic/circuit mechanisms for role(1), i.e., how RPE is calculated in the upstream of DA neurons and how RPE-dependent update of learned-values occurs through DA-dependent synaptic plasticity, have now become clarified, mechanisms for role(2) remain unclear. We modeled self-paced behavior by a series of ‘Go’ or ‘No-Go’ selections in the framework of reinforcement-learning assuming DA's role(1), and demonstrated that incorporation of decay/forgetting of learned-values, which is presumably implemented as decay of synaptic strengths storing learned-values, provides a potential unified mechanistic account for the DA's two roles, together with its various temporal patterns.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Models to describe how virus spreads in vitro
2020年5月13日(水) 10:00 - 10:45
カトゥリン・ボシゥメン (数理創造プログラム 客員主管研究員 / Professor, Department of Physics, Ryerson University, Canada)
This is meant as an introductory talk about my research field, virophysics, in which I apply the rigour and methods of physics to study virology. My focus is primarily in vitro (how virus spreads cell-to-cell in a cell culture) but I occasionally do some in vivo work. Recently, my hobby became tracking COVID-19 spread.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Slip or (k)not: Geometry and mechanical performance of physical knots
2020年5月7日(木) 17:00 - 17:45
佐野 友彦 (PD, École polytechnique fédérale de Lausanne, Switzerland)
Knots can impart unique mechanical function to filamentary structures, with examples ranging across length scales, including DNA, polymer-chains, shoelaces, climbing ropes, tennis racket, and surgical sutures. Even though knot theory has a long history of studies in the realm of mathematics, mechanics-based studies of physical knots are much rarer. The fundamental challenge in the understanding of their mechanics under a wide range of loading conditions stems from the fact that their topology, geometry, elasticity, and friction are all tangled ingredients. In this talk, combining experiments, simulations and theory, we present the recent progress on the predictive framework for the knot performance.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Analyses of large-scale sequence data from “PROTIST” can reveal the eukaryotic phylogeny and evolution
2020年4月30日(木) 10:00 - 10:45
矢﨑 裕規 (数理創造プログラム 特別研究員)
Most of the phylogenetic diversity of eukaryotes is made up of unicellular eukaryotic microorganisms called protists, some of which have not known phylogenetic home (called Orphans). Orphans are likely to hold important keys to the evolution of eukaryotes. In this seminar, I will introduce present case studies that reveal phylogenetic home and organelle evolution of orphan protists through sequence analysis based on large-scale sequence data.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Social evolution in viruses
2020年4月22日(水) 10:00 - 10:45
アッシャー・リークス (数理創造プログラム 国際プログラム・アソシエイト / Ph.D. Student, Department of Zoology, University of Oxford, UK)
Viruses are normally thought of as solitary organisms. However, in reality viruses often interact with one another, and these interactions can have important consequences for how viruses evolve and cause disease. In this talk, I will show how simple models of virus-virus interactions can help us to understand some puzzling aspects of virus biology. At the end, I will also talk about a new modelling project on Covid-19 joint with Ryosuke, which considers how human actions such as social distancing could influence the evolution of virulence.
会場: via Zoom
イベント公式言語: 英語
174 イベント