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

Symmetry and conservation laws in neural networks

November 20 at 10:00 - 11:00, 2020

Dr. Hidenori Tanaka (Group Leader & Senior Scientist, Physics & Informatics Laboratories, NTT Research, Inc., USA / Visiting Scholar, Stanford University, USA)

Symmetry is the central guiding principle in the exploration of the physical world but has been underutilized in understanding and engineering neural networks. We first identify simple yet powerful geometrical properties imposed by symmetry. Then, we apply the theory to answer a series of following important questions: (i) What, if anything, can we quantitatively predict about the complex learning dynamics of real-world deep learning models driven by real-world datasets? (ii) How can we make deep learning models more efficient by removing parameters without disconnecting information flow? (iii) How can we distill experimentally testable neuroscientific hypotheses by reducing the complexity of deep learning models mimicking the brain? Overall, our approach demonstrates how we can harness the principles of symmetry and conservation laws to reduce deep learning models' complexity and make advances in the science and engineering of biological and artificial neural networks.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Evolution of a peak of genetic divergence driven by local adaptation

November 5 at 10:00 - 11:00, 2020

Dr. Takahiro Sakamoto (Postdoctoral Researcher, School of Advanced Sciences, The Graduate University for Advanced Studies (SOKENDAI))

In species that are distributed in various environments, each subpopulation adapts to the local environment. In general, when there is migration between subpopulations, genetic divergence does not proceed because the genomes are exchanged between subpopulations. However, around the loci involved in local adaptation, genetic divergence proceeds. This is because different genotypes are favored between subpopulations, so that the alleles of migrants are purged by natural selection and the exchange of genomes is suppressed. It has not been theoretically known how the degree of genetic differentiation evolves over time, making the interpretation of population genomic data difficult. In this study, we constructed and analyzed a model of population genetics to clarify the dynamics of genetic divergence.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Basics of population genomic data analysis

October 29 at 10:00 - 11:00, 2020

Dr. Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

In recent years, it has become possible to obtain the DNA sequence data of a large number of individuals of the same species. This data set is basically a M (number of samples) x N (number of genomic positions) matrix where each data point is 0 or 1. Using this data set, we try to understand, for example, the relationship between each sample or group of samples, and the population process that has generated the data set. In this talk, I will introduce the basic concepts behind the approaches we use to analyze such data sets.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Bayesian nonparametric estimation of Random Dynamical Systems

October 21 at 14:00 - 15:00, 2020

Dr. Christos Merkatas (Postdoctoral Researcher, Aalto University, Finland)

In this talk, a Bayesian nonparametric framework for the estimation and prediction, from observed time series data, of discretized random dynamical systems is presented [1]. The size of the observed time series can be small and the additive noise may not be Gaussian distributed. We show that as the dynamical noise departs from normality, simple Markov Chain Monte Carlo method (MCMC) models are inefficient. The proposed models assume an unknown error process in the form of a countable mixture of zero mean normals, where a–priori the number of the countable normal components and their variances is unknown. Our method infers the number of unknown components and their variances, i.e., infers the density of the error process directly from the observed data. An extension for the joint estimation and prediction of multiple discrete time random dynamical systems based on multiple time-series observations contaminated by additive dynamical noise is presented [2]. In this case the model assumes an unknown joint error process with a pairwise dependence in the sense that to each pair of unknown dynamical error processes, we assign a– priori an independent Geometric Stick-Breaking process mixture of normals with zero mean. These mixtures a–posteriori will capture common characteristics, if there are any, among the pairs of noise processes. We show numerically that when the unknown error processes share common characteristics, it is possible under suitable prior specification to induce a borrowing of strength relationship among the dynamical error pairs. Then time-series with an inadequate sample size for an independent Bayesian reconstruction can benefit in terms of model estimation accuracy. Finally, possible directions for future research will be discussed.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

A PDE model for the localization and spread of flu in the human respiratory tract

October 14 at 10:00 - 11:00, 2020

Mr. Christian Quirouette (PhD student, Department of Medical Physics, Ryerson University, Canada)

Within the human respiratory tract (HRT), virus diffuses through the periciliary fluid (PCF) bathing the epithelium. But it also undergoes advection: as the mucus layer sitting atop the PCF is pushed along by the ciliated cell's beating cilia, the PCF and its virus contents are also pushed along, upwards towards the nose and mouth. Our PDE model represents the HRT as a one-dimensional track extending from the nose down to the lower HRT, wherein stationary cells interact with virus which moves within (diffusion) and along with (advection) the PCF. In the PDE model, diffusion is negligible in the presence of advection which effectively sweeps away virus, preventing infection from spreading below the depth of deposition. Higher virus production rates (10-fold) are required at higher advection speeds (40 micron/s) to maintain equivalent infection severity and timing. Because virus is entrained upwards, upper parts of the HRT located downstream of the advection flow see more virus than lower parts, and so infection grows, peaks, and resolves later in the lower HRT. Clinically, the infection would appear to progress from the upper towards the lower HRT, as reported in mice. When the PDE model is expanded to include cellular regeneration and an immune response, it reproduces tissue damage levels reported in patients. This new PDE model offers a convenient and unique platform from which to study the localization and spread of respiratory viruses (flu, RSV, COVID-19) within the HRT during an infection.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Phase Transitions in Biological Systems

September 23 at 10:00 - 11:00, 2020

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 (BDR))

Biological systems are built hierarchically by DNA, proteins, cells, tissues, organs, individuals, etc. Recent experiments have clarified the existence of interesting mesoscale phenomena inside cells, where the concept of condensed matter physics such as phase transition can be useful in its understanding. For example, interacting nucleosomes in a chromatin chain can cause the mega-base scale structural change, and sub-micron scale dense droplets of proteins/mRNAs can appear through phase separation. In this talk, I will discuss our recent topics: (i) structural transition of a chromatin with epigenetic marks, (ii) intracellular wetting of phase-separated droplets, and (iii) spontaneous aggregation of self-propelled individuals.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Eco-evolutionary dynamics with novel mutations

September 16 at 10:00 - 11:00, 2020

Dr. 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?

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Singular point implies coexistence in adaptive dynamics

September 9 at 10:00 - 11:00, 2020

Dr. Masashi Tachikawa (Visiting Scientist, iTHEMS / Associate Professor, Kyoto University, Institute for Frontier Life and Medical Sciences)

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

Seminar

iTHEMS Biology Seminar

The hitch-hiker’s guide to 
the concept of 
adaptive dynamics

September 2 at 10:00 - 10:30, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Modeling biological timing

August 26 at 10:00 - 11:00, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Heavy tails in the brain

August 5 at 10:00 - 11:00, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Time-dependent bias emerges in population models with broad offspring number distributions

July 29 at 10:00 - 11:00, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Human Time vs. Mouse Time in Embryonic Development

July 17 at 16:00 - 17:00, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Application of geometry to protein structure analysis

July 15 at 14:00 - 15:00, 2020

Ms. 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

Seminar

iTHEMS Biology Seminar

Constrained evolution of animal embryogenesis

July 8 at 10:00 - 11:00, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Waveform Analysis of Biological Rhythms

July 1 at 10:00 - 11:00, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Turing Patterns in Biology and Beyond

June 10 at 10:00 - 10:45, 2020

Dr. Martin Skrodzki (Visiting Researcher, 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

Seminar

iTHEMS Biology Seminar

Quantification model of energy of loop structure on biopolymer

June 3 at 10:00 - 10:45, 2020

Dr. 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

Seminar

iTHEMS Biology Seminar

Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation

May 27 at 10:00 - 10:45, 2020

Ms. 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

Seminar

iTHEMS Biology Seminar

Models to describe how virus spreads in vitro

May 13 at 10:00 - 10:45, 2020

Prof. 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