東京大学 竹内研究室 公式ウェブページ

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.

We have investigated how one can manipulate the shape of a small cluster of colloids (or nano-particles) using an external field in the presence of thermal fluctuations. This problem can be formulated as a minimization of first passage times in configuration space. We obtain the optimal solution using Dynamic Programming. We then show how the efficiency in Reinforcement-Learning approaches vanish at the nanoscale due to thermal fluctuations.

References:
[1] Reinforcement Learning with thermal fluctuations at the nano-scale. F Boccardo, O Pierre-Louis, arXiv preprint arXiv:2311.17519 2024
[2] Temperature transitions and degeneracy in the control of small clusters with a macroscopic field. F Boccardo, O Pierre-Louis 2022, Journal of Statistical Mechanics: Theory and Experiment (10), 103205 2022
[3] Equilibrium return times of small fluctuating clusters and vacancies. F Boccardo, Y Benamara, O Pierre-Louis,　Physical Review E 106, 024120 2022
[4] Controlling the shape of small clusters with and without macroscopic fields. F Boccardo, O Pierre-Louis, Physical Review Letters 128, 256102 2022

Many synthetic, biological, or bio-inspired fluids show orientational order of the building blocks, and can also be intrinsically active or driven out of equilibrium. Disclination lines are string-like singularities within the orientational field and can show intricate non-equilibrium dynamics. I will present the formalism of describing and modelling disclinations through tensorial order parameter field and the velocity field. I will focus on selected problems, for example, how to determine the stability of a disclination loop with a zero topological charge for different flow profiles, and show the role of disclination dynamics in the context of logic operations, microrobotics, nematic microfluidics, and active nematic fluids.

In an unshaken liquid culture, aerobic bacteria easily evolve to construct cellular mats at the air-liquid interface (ALI), a unique habitat with high oxygen access. Adaptive mutants typically overproduce extracellular matrices to form robust mat structures but grow slower than the ancestor. The genetic basis of mat formation in a model organism, Pseudomonas fluorescens, has been the subject of intensive investigation; however, little is known about the mechanical aspects that affect the emergence and maintenance of slow-growing mat formers. In this work, we revealed the diminished ALI colonization of the adaptive mutants due to the general trade-off between motility and matrix production. The deficiency in colonization and growth was overcome by in-situ mutations and low dispersal from the ALI. These findings proposed a novel evolutionary scenario in which adaptive mutants occupied a spatial niche not by migration but by in-situ mutations, highlighting the importance of pre-colonization by the ancestor and the population size. Given the ubiquity of the trade-off between motility and matrix production across bacteria, the mechanism revealed here is expected to be applicable to numerous environments, such as those affecting the adaptive evolution of crypt-colonizing bacteria in an animal gut.