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In-situ mutations drive adaptive evolution in spatial niches

Speaker: Dr. Yuya Karita (Max Planck Institute for Evolutionary Biology)
Date : Apr. 15 (Mon) 2024, JST 10:30-
Place : Room 512, Faculty of Science Bldg.1; hybrid (register here)

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.

Complex Dynamics in Active Matter Systems, Frustration Effects, Magnus Forces andSynchronization

Speaker: Prof. Charles Reichhardt (Los Alamos National Laboratory)
Date : Apr. 11 (Thu) 2024, JST 10:30-
Place : Room 431, Faculty of Science Bldg.1; hybrid (register here)

Active matter denotes systems with self-propulsion and arises in biological, soft, robotic, and social settings [1]. Here, we outline some of our group's recent efforts in active systems,including active matter interacting with ordered and disordered substrates, where various kinds of active clogging and commensuration effects can occur that have connections with frustrated systems and Mott physics. We also discuss chiral active systems with a Magnus force, where we find edge currents similar to those found for topological systems or charged particles in magnetic fields. In the presence of quenched disorder, the chiral active system also shows side jump effects with an active matter Hall angle. Finally, we discuss coupled active matter swarmulators where, in addition to activity, the particles have an internal degree of freedom that can become synchronized or antisynchronized. This system shows a variety of new kinds of motility-induced phase-separated states, including active matter stripes, frustrated states, gels, cluster fluids, and glassy states.

[1] Active Brownian particles in complex and crowded environments, Clemens Bechinger, Roberto Di Leonardo, Hartmut Lowen, Charles Reichhardt Giorgio Volpe, and Giovanni Volpe, Reviews of Modern Physics 88 045006 (2016).

Collective organization in cyanobacteria

Speaker: Prof. Lucas Goehring (Nottingham Trent Univ.)
Date : Apr. 5 (Fri) 2024, JST 14:00-
Place : Room 512, Faculty of Science Bldg.1; hybrid (register here)

Filamentous cyanobacteria can show fascinating patterns of self-organization, which however are not well-understood from a physical perspective. We investigate the motility and collective organization of colonies of these simple multicellular lifeforms. As their area density increases, linear chains of cells gliding on a substrate show a transition from an isotropic distribution to bundles of filaments arranged in a reticulate pattern. Based on our experimental observations of individual behavior and pairwise interactions, we introduce a model accounting for the filaments' large aspect ratio, fluctuations in curvature, motility, and nematic interactions. This minimal model of active filaments recapitulates the observations, and rationalizes the appearance of a characteristic lengthscale in the system, based on the Peclet number of the cyanobacteria filaments.

Selected Two-Fluid Effects in Soft Condensed Matter

Speaker: Prof. Helmut R. Brand (Univ. Bayreuth)
Date : Apr. 2 (Tue) 2024, JST 10:45-
Place : Room 512, Faculty of Science Bldg.1; hybrid (register here)

Key question addressed in this seminar: importance of two-fluid effects on macroscopic and mesoscopic scales in complex fluids. Topics of central importance are immiscibility and velocity differences. Two-fluid hydrodynamics can be applied to materials with two subsystems, which can move relative to each other. The additional macroscopic variables always include the concentration of one component and the relative velocity. The three specific systems covered here are:
1) Smectic clusters in nematic phases: breakdown of flow alignment and sign change of the anisotropy of electric conductivity [1].
2) Clusters above the glass transition in polymeric and low molecular weight materials [2].
3) Magnetorheological fluids (MRFs): onset of column formation in magnetic fields [3].

[1] H.R. Brand and H. Pleiner, Phys. Rev. E 103, 012705 (2021).
[2] H. Pleiner and H.R. Brand, Rheol. Acta 60, 675 (2021).
[3] H. Pleiner, D. Svensek, T. Potisk, and H.R. Brand, Phys. Rev. E 101, 032601 (2020).

Minimum scaling model and exact exponents for the Nambu-Goldstone modes in the Vicsek Model

Speaker: Prof. Harukuni Ikeda (Gakushuin University)
Date : Mar. 26 (Tue) 2024, JST 10:30-
Place : Room 207, Faculty of Science Bldg. 1

We investigate the scaling behavior of Nambu-Goldstone (NG) modes in the ordered phase of the Vicsek model, introducing a phenomenological equation of motion (EOM) incorporating a previously overlooked non-linear term. This term arises from the interaction between velocity fields and density fluctuations, leading to new scaling behaviors. We derive exact scaling exponents in two dimensions, which reproduce the isotropic scaling behavior reported in a prior numerical simulation.

Individual and collective motion of chiral, regularly organized, and nematic active objects

Speaker: Prof. Andreas Menzel (Univ. Magdeburg)
Date : Mar. 11 (Mon) 2024, JST 11:00-
Place : Room 512, Faculty of Science Bldg.1; hybrid (register here)

Actively propelled objects span a broad variety of actual realizations, from self-propelled bacteria, via vibrated hoppers, to animals and humans. Besides being equipped with a propulsion mechanism, all of these entities share a common feature. There is, ad hoc, no outside mechanism that rigidly dictates their propulsion direction. Instead, they have the freedom to select this direction, even if only through rotational stochastic processes. We here address different scenarios of corresponding systems. First, we address chiral objects that show bent trajectories, move in discrete steps, and tend to head towards a remote target, which leads to pronounced nonlinear dynamics [1]. Next, we consider self-propelling units organized in regular lattice structures, which leads to the onset of collective motion beyond a threshold active drive, while chirality can make collective motion break down [2]. Third, we address nematic actively propelled entities that stochastically reverse their propagation direction, where a formal analogy to a basic quantum mechanical problem is revealed during the analysis of the associated statistics [3]. Overall, we hope to stimulate experimental realizations and investigations of such systems.

[1] A. M. Menzel, Phys. Rev. E 106, 064603 (2022).
[2] Z.-F. Huang, A. M. Menzel, H. Löwen, Phys. Rev. Lett. 125, 218002 (2020).
[3] A. M. Menzel, J. Chem. Phys. 157, 011102 (2022) – Featured Communication.

Dynamic relaxation of active and nonequilibrium materials

Speaker: Prof. Sho Takatori (Univ. California, Santa Barbara)
Date : Feb. 13 (Tue) 2024, JST 11:00-12:30
Place : Room 414, Faculty of Science Bldg.1; hybrid (register here)

Through the magic of ‘active matter,’ which converts chemical energy into mechanical work to drive emergent properties, biology solves a myriad of seemingly impossible physical challenges. I will present my lab's efforts to develop new fluid mechanics models to direct the flow of matter enabled by the use of “active” molecules found within living systems. We design 2D composite materials with tunable inclusions of lipid domains embedded within an active elastic network. These lipid inclusions enable exquisite control over the phase separation and material properties (like failure resistance) of 2D composite materials. If time permits, I will also present our recent work on model predictive control and learning of many-body colloidal interactions driven by active and hydrodynamic forces.

Microswimmers in chiral active fluids: the role of nonreciprocal responses induced by odd viscosity

Speaker: Dr. Yuto Hosaka (Max Planck Institute for Dynamics and Self-Organization)
Date : Jan. 22 (Mon) 2024, JST 10:30-12:00
Place : Room 206, Faculty of Science Bldg.1; hybrid (register here)

Chiral active fluids with broken time-reversal and parity symmetries are prevalent at various scales in nonequilibrium systems, ranging from electron fluids to biological and geophysical flows. In such fluids, a peculiar transport coefficient called odd viscosity arises. This viscosity, which does not contribute to the fluid energy dissipation, leads to novel dynamics, such as nonreciprocal (transverse) transports, free-surface dynamics, or chiral edge currents characterized by topological protection, akin to quantum Hall systems. The lack of time-reversal symmetry leads to an asymmetric response and, thus, to an asymmetric mobility tensor. This suggests that the Lorentz reciprocal theorem, a powerful and versatile principle in low-Reynolds-number fluid dynamics, is violated in chiral active systems.

In this talk, I will present my recent work on the dynamics of microswimmers in chiral active fluids. First, we analyze the behavior of a single linear swimmer in a 2D compressible fluid with odd viscosity [1]. It is found that a microswimmer undergoes circular trajectories whose radius is set by the inverse of the odd viscosity. Moreover, a pair of swimmers exhibits a wealth of two-body dynamics that depends on the initial relative orientation angles as well as on the propulsion mechanism adopted by each swimmer. We then discuss the generalization of the Lorentz reciprocal theorem in fluids with odd viscosity [2]. To demonstrate its applicability, we use the theorem to determine the swimming velocity of two categories of microswimmers in a Stokes flow with odd viscosity. We show that a surface-driven microswimmer, which we call a “twister”, can exhibit vertical dynamics induced by nonreciprocal responses due to the odd viscosity.

[1] Y. Hosaka, R. Golestanian, and A. Daddi-Moussa-Ider, New J. Phys. 25, 083046 (2023).
[2] Y. Hosaka, R. Golestanian, and A. Vilfan, Phys. Rev. Lett. 131, 178303 (2023).

Odd elasticity and Lie brackets: non-reciprocity for modelling and control of microscopic swimmer locomotion

Speaker: Dr. Clément Moreau (RIMS, Kyoto University)
Date : Nov. 8 (Wed) 2023, JST 11:00-
Place : Room 512, Faculty of Science Bldg.1 & Zoom (register here)

The research on swimming micro-organisms and the design of swimming micro-robots is at the crossing between many fields, from theoretical fluid dynamics to biomechanics and medical applications. At the microscopic scale, locomotion through a fluid follows specific laws, due to the predominance of the viscous effects . One of the fundamental principles of locomotion in this regime, famously termed as the scallop theorem, states that non-reciprocal deformation is required to produce a net motion. I would like to elaborate on this simple concept of non-reciprocity and its many forms in microswimming studies, by presenting some of my works on modelling and control of microswimmers.

First, I will talk about our recent research on modelling the internal activity of living matter by non-reciprocal interactions. I will present the framework of ‘odd elasticity’ on which this analysis is based, and how it successfully applies to microscale locomotion, illustrating this on flagellar swimmer models.

Then, I will discuss controllability of microswimming models, which aims at determining whether a given swimmer may or may not reach a given target. To mathematically characterize controllability, one relies on Lie brackets, which are, in this context, a sort of measure of the non-reciprocity of a sequence of moves. Using these, we determined conditions to ensure controllability of magnetically-driven elastic swimmers.

Swimming droplets under confinement

Speaker: Dr. Mathilde Reyssat (ESPCI)
Date : Oct. 4 (Wed) 2023, JST 10:30-
Place : Room 233, Faculty of Science Bldg.1 & Zoom (register here)

Artificial micro-swimmers have recently become a central field of research in soft-matter. A very promising and original type of swimmer developed in our team, consists in pure water droplet swimming in an oil phase containing micelles of surfactant. The droplet’s activity comes from the formation of swollen micelles at its interface which induces Marangoni stresses and then motion of the droplets.

We investigate experimentally the behavior of such self-propelled water-in-oil droplets, confined in capillaries of different square and circular cross-sections. Stretched circular capillaries have been used to explore even stronger confinement. Within the most constricted regions, droplets elongate very strongly. These extremely long droplets reveal unexpected behaviors during their motion, in particular regarding their stability.

We build up on the Bretherthon formalism to rationalize this new kind of self-motion of confined droplets in a tube, not anymore driven by pressure or flow rate but rather by locally-induced interfacial stresses.

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