Official web site of Takeuchi Lab, Univ. Tokyo

Spontaneous segregation of active matter into dense and sparse domains is ubiquitous. In systems with local interactions, it is usually well described as phase separation, and occurs not only in scalar active matter (``motility-induced phase separation'') but also in vectorial, aligning systems. This is in particular the generic situation for the simple but important case of self-propelled particles locally aligning their velocities against some noise. In such dry aligning active matter, the order-disorder transition is not direct, and the homogeneous orientationally-ordered liquid is generically separated from disorder by a coexistence phase in which dense ordered regions evolve in a remaining vapor.

We show that in collections of aligning circle swimmers with this phase separation scenario is replaced by a condensation phenomenon. The condensates, which take the form of vortices or rotating polar packets, can absorb a finite fraction of the particles in the system, and keep a finite or slowly growing size as their mass increases. Our results are obtained both at particle and continuous levels. We consider both ferromagnetic and nematic alignment, and both identical and disordered chiralities. Condensation implies synchronization, even though our systems are in 2D and bear strictly local interactions. We propose a phenomenological theory based on observed mechanisms that accounts qualitatively for our results.

Comprehending cell death is one of the central topics of biological science. Currently, the criteria for microbial cell death are purely experimental, based on PI staining and regrowth experiments. The debate on how “death” should be defined mathematically, and what mathematical properties the phenomenon of ‘death’ has, is largely untouched. In the present project, we aimed to develop a mathematical framework of cell death based on the controllability of cellular states [1].
We start by defining dead states as cellular states that are not returnable to the predefined "representative living states" regardless of the controllable parameters such as the gene expression level and external culture conditions. The definition requires a method to compute the restricted, global, and nonlinear controllability, for which no general theory exists. We have developed "The Stoichiometric Rays", a simple method to solve the controllability computation for catalytic reaction systems. This allows us to compute how the enzyme concentration should be modulated to control the metabolic state from a given state to a desired state.
Using the stoichiometric rays, we have computed the controllability and hence the dead states of a simple toy model of cellular metabolism as well as a rather realistic in silico metabolic model of E. coli [2]. We have also quantified the boundary that divides the phase space into the live and dead states, called the “Separating Alive and Non-life Zone (SANZ) hypersurface” [3].
In this talk I will present our framework for cell death, including stoichiometric rays. I will also discuss possible connections of the cell death framework to related fields such as dynamical systems, resource theory [4], and viability theory [5].

[1]. Himeoka et al., (2024), arXiv., https://arxiv.org/abs/2403.02169.
[2]. Boecker et al., (2021), Mol. Syst. Biol., 17 (12): e10504.
[3]. The Sanzu hypersurface is derived from a mythical river in the Japanese Buddhist tradition, the Sanzu River that represents the boundary between the world of the living and the afterlife.
[4]. Sagawa, (2022), “Entropy, Divergence, and Majorization in Classical and Quantum Thermodynamics”, Springer
[5]. Aubin et al., (2011), “Viability Theory: New Directions”, Springer

When a single fluid flows through porous media like soils or geological reservoirs, the transport of contaminants, nutrients, microorganisms, and chemicals is relatively well understood. However, when multiple fluids flow together, these transport phenomena have largely not been considered despite their significance in natural systems. Forces between the flowing fluids and the solid boundaries may create large variations in the local flow rates and form time-varying flow pathways, which can in turn accelerate solute spreading. In this study, we employ extensive computer simulations to propose a new theory on solute spread in systems with two fluids flowing through porous media, offering insights that could enhance our understanding and control of transport properties in natural environments.

The concept of odd elasticity is useful in characterizing non-reciprocality in active systems such as micromachines and microswimmers. As an example, we first introduce a model for a thermally driven microswimmer in which three spheres are connected by two springs with odd elasticity. Using Onsager’s variational principle, we derive dynamical equations for a nonequilibrium active system with odd elasticity. We further investigate the emergence of odd elasticity in an elastic microswimmer model using a reinforcement learning method. If time allows, I will discuss a new type of information microswimmer.

Understanding the spatiotemporal development of microbial communities is crucial for biomedical and ecological studies. However, our knowledge of how biological and physical processes shape these structures is limited by the lack of simultaneous gene expression and behavior measurements. In Bacillus subtilis, swarming on soft-agar media forms structured colonies with distinct motility behaviors over time. In this seminar, I will present research that combined spatiotemporal transcriptome data with live-cell microscopic data to map B. subtilis swarm development, revealing subpopulations with unique metabolic states and a cross-feeding mechanism that drives swarm expansion.

Many physical and biological systems are constituted by dense, disordered arrangements of individual units. A broad class of these systems exhibit hyperuniform behavior, whereby density fluctuations are suppressed at large spatial scales.  Here, we find that the arrangement of chromatophores on squid skin behaves in an opposite manner, such that density fluctuations grow with spatial scale, akin to a critical system. We term this behavior `hyperdisordered'. We combine experiments and theory to reveal how this unexpected scaling is due to the interplay between growth and volume exclusion. The ubiquity of these two features implies that the simple mechanism we describe may apply to a broad class of growing systems.

The presence of interfaces makes active matter systems different from their bulk behavior as in other soft matter systems. Also, interfaces act as soft confinement for active particles. Here we study the system of a single light-driven Janus particle confined in a very thin oil droplet at an air-water interface. Activation by a laser leads to the particle's horizontal fast motion of 1mm/s-1cm/s while it rests at the center of the droplet without activation. The particle shows periodic or intermittent motions, which can be related to the three-fluid contact angle. The particle is driven by a local thermal Marangoni flow; however, it always couples with the droplet thickness profile, which results in a time-varying propulsion speed. This might result from complex couplings among heat Marangoni flow, the particle wettability change by heating, hydrodynamic flow, and the capillary force. This new type of coupled dynamics will shed light on the hydrodynamic pressure due to the motion of active particles and provide insight into developing activity-controlled materials.

We will discuss new methods to, in principle, obtain all cumulants of von Neumann entropy over different models of random states. The new methods uncover the structures of cumulants in terms of lower-order joint cumulants involving families of ancillary linear statistics. Importantly, the new methods avoid the tedious tasks of simplifying nested summations that prevent existing methods in the literature to obtain higher-order cumulants. This talk is based on an ongoing joint work with Youyi Huang.

A fingering pattern is observed when a less viscous fluid displaces another less viscous fluid in a small space such as porous media or Hele-Shaw cells. This phenomenon is called Saffman-Taylor instability or viscous fingering(VF). Such study is important for several fields such as energy, biological and environmental fields. The VF studies have been categorized into miscible and immiscible systems. The miscible system has infinite mutual solubility like glycerol and water case, whereas the immiscible system has no mutual solubility like oil and water case. However, the presenter and colleagues have suggested the third category, namely, a partially miscible system, which has finite mutual solubility, and have found that the VF in the partially miscible system shows droplet pattern instead of fingering pattern. This is due to the coupling of hydrodynamic (VF) with chemical thermodynamics (phase separation and Korteweg force). In the lecture, the presenter will show several patterns created in the partially miscible system in experiments, and the numerical simulation.

Bacteria encounter and exert mechanical forces, although this physical dimension has been less studied compared to their eukaryotic cell counterparts. Neisseria meningitidis, or meningococcus, is a bacterial pathogen responsible for human septicaemia and meningitis. Infection caused by this bacterium and its interaction with the human host is largely determined by mechanical forces at several levels. Bacterial adhesion to the endothelium is mediated by a filamentous structure called the type IV pilus, which can generate piconewton traction forces. Bacteria form aggregates inside the vessel lumen that have viscous fluid properties. Once the lumen is filled, the bacteria proliferate in a spatially confined environment. The biological and mechanical processes that occur during these sequential host-pathogen interactions will be described and their implications during the infection process discussed.