iTHEMS Biology Seminar
173 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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Singular point implies coexistence in adaptive dynamics
September 9 (Wed) at 10:00 - 11:00, 2020
Masashi Tachikawa (Visiting Scientist, iTHEMS / Associate Professor, Institute for Frontier Life and Medical Sciences, Kyoto University)
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.
Venue: via Zoom
Event Official Language: English
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The hitch-hiker’s guide to the concept of adaptive dynamics
September 2 (Wed) at 10:00 - 10:30, 2020
Ryosuke Iritani (Research Scientist, iTHEMS)
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.
Venue: via Zoom
Event Official Language: English
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Modeling biological timing
August 26 (Wed) at 10:00 - 11:00, 2020
Gen Kurosawa (Senior Research Scientist, iTHEMS)
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.
Venue: via Zoom
Event Official Language: English
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Seminar
Heavy tails in the brain
August 5 (Wed) at 10:00 - 11:00, 2020
Lukasz Kusmierz (research scientist, RIKEN Center for Brain Science (CBS))
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.
Venue: via Zoom
Event Official Language: English
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Time-dependent bias emerges in population models with broad offspring number distributions
July 29 (Wed) at 10:00 - 11:00, 2020
Takashi Okada (Senior Research Scientist, iTHEMS)
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.
Venue: via Zoom
Event Official Language: English
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Seminar
Human Time vs. Mouse Time in Embryonic Development
July 17 (Fri) at 16:00 - 17:00, 2020
Miki Ebisuya (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.
Venue: via Zoom
Event Official Language: English
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Seminar
Application of geometry to protein structure analysis
July 15 (Wed) at 14:00 - 15:00, 2020
Haru Negami-Oono (Ph.D. Student, Institute for Biology and Mathematics of Dynamic Cellular Processes, The University of Tokyo)
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.
Venue: via Zoom
Event Official Language: English
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Seminar
Constrained evolution of animal embryogenesis
July 8 (Wed) at 10:00 - 11:00, 2020
Yui Uchida (Special Postdoctoral Researcher, Laboratory for Multiscale Biosystem Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR))
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.
Venue: via Zoom
Event Official Language: English
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Waveform Analysis of Biological Rhythms
July 1 (Wed) at 10:00 - 11:00, 2020
Shingo Gibo (Postdoctoral Researcher, iTHEMS)
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.
Venue: via Zoom
Event Official Language: English
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Turing Patterns in Biology and Beyond
June 10 (Wed) at 10:00 - 10:45, 2020
Martin Skrodzki (Visiting Scientist, iTHEMS / 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.
Venue: via Zoom
Event Official Language: English
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Quantification model of energy of loop structure on biopolymer
June 3 (Wed) at 10:00 - 10:45, 2020
Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)
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.
Venue: via Zoom
Event Official Language: English
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Seminar
Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation
May 27 (Wed) at 10:00 - 10:45, 2020
Ayaka Kato (RIKEN Center for Brain Science (CBS) / Ph.D. Student, The University of Tokyo)
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.
Venue: via Zoom
Event Official Language: English
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Models to describe how virus spreads in vitro
May 13 (Wed) at 10:00 - 10:45, 2020
Catherine Beauchemin (Senior Visiting Scientist, iTHEMS / 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.
Venue: via Zoom
Event Official Language: English
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Seminar
Slip or (k)not: Geometry and mechanical performance of physical knots
May 7 (Thu) at 17:00 - 17:45, 2020
Tomohiko Sano (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.
Venue: via Zoom
Event Official Language: English
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Analyses of large-scale sequence data from “PROTIST” can reveal the eukaryotic phylogeny and evolution
April 30 (Thu) at 10:00 - 10:45, 2020
Euki Yazaki (Postdoctoral Researcher, iTHEMS)
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.
Venue: via Zoom
Event Official Language: English
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Seminar
Social evolution in viruses
April 22 (Wed) at 10:00 - 10:45, 2020
Asher Leeks (International Program Associate, iTHEMS / 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.
Venue: via Zoom
Event Official Language: English
173 events
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