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Long-range nematic order and anomalous fluctuations in collective motion of swimming filamentous bacteria

Speaker: Dr. Daiki Nishiguchi (The University of Tokyo)
Date : Apr. 28 (Fri) 17:00-18:30
Place : Room 155B, Main Bldg.

Collective motion of self-propelled elements, as seen in bird flocks, fish schools, bacterial swarms, etc., is so ubiquitous that it has driven physicists to search for its possibly universal properties. Evidence for such universality has been provided by many theoretical and numerical studies using simple flocking models such as Vicsek-style models and hydrodynamic theories [1-2]. However, no experiments so far have been fully convincing in demonstrating the existence of this universality.

In this seminar, after introducing standard models of collective motion and giving state-of-the-art interpretations on previous experimental studies, I show our experiments on elongated bacteria swimming in a quasi-two-dimensional fluid layer [3]. Strong confinement and the high aspect ratio of bacteria induce weak nematic alignment upon collision, which gives rise to spontaneous breaking of rotational symmetry and global nematic order at sufficiently high density of bacteria. This homogeneous but fluctuating ordered phase has turned out to exhibit true long-range orientational order, non-trivial giant number fluctuations, and algebraic correlations associated with Nambu-Goldstone modes, which verifies the existence of an active phase predicted to emerge in standard flocking models. Such properties contrast our system with usual bacterial experiments that end up with turbulent states without any global orientational order.

Through our experiments, I will also discuss (i) what might be crucial for the emergence of such universality in reality and (ii) possible discrepancy between our experiments and theoretical predictions with approximations.

[1] F. Ginelli, “The Physics of the Vicsek model”, Eur. Phys. J.: Special Topics, 225, 2099 (2016).
[2] J. Toner, Y. Tu, and S. Ramaswamy. “Hydrodynamics and phases of flocks”, Ann. Phys. (N.Y.), 318, 170 (2005).
[3] D. Nishiguchi, K. H. Nagai, H. Chaté, and M. Sano, “Long-range nematic order and anomalous fluctuations in suspensions of swimming filamentous bacteria”, Phys. Rev. E, 95, 020601(R) (2017).

Reversible-irreversible transitions of particle trajectories in oscillatory sheared systems near the jamming transition

Speaker: Dr. Takeshi Kawasaki (Nagoya University)
Date : Apr. 10 (Mon), 16:30-18:00
Place : Room 155B, Main Bldg.

A reversible-irreversible (RI) transition of particle trajectories was first investigated in a low density periodically driven colloidal system and it was found to be a continuous absorbing state transition [1,2]. It has been also discussed that the transition might belong to the directed percolation universality class [2]. In the higher density systems, on the other hand, a RI transition is observed but the nature of the transition has not been clarified yet.

In this seminar, we present our recent studies on the RI transitions for various densities especially near the jamming transition by using oscillatory sheared molecular dynamics simulations. Here it is revealed that the transition behaviors are dramatically changed at the jamming transition density. In particular, above the transition density, we observe only the discontinuous RI transition and find that it is clearly correlated with the yielding transition [3]. On the other hand, below the jamming transition density, we find that there exist several distinct transitions depending on the density and strain amplitude, i.e., (i) continuous, (ii) reentrant, and (iii) weakly discontinuous RI transitions. We show that these transition behaviors are strongly correlated to the number of the contacts among the particles. This implies that these distinct transitions are explained in the context of the contact percolation and mechanical stability [4].

[1] D. J. Pine, J. P. Gollub, J. F. Brady, and A. M. Leshansky, Nature 438, 997 (2005).
[2] L. Cort?, P. M. Chaikin, J. P. Gollub, and D. J. Pine, Nat Phys 4, 420 (2008).
[3] T. Kawasaki and L. Berthier, Phys. Rev. E 94, 022615 (2016).
[4] K. Nagasawa, K. Miyazaki, and T. Kawasaki (in preparation).

Thermodynamic entropy as a Noether invariant

Speaker: Prof. Shin-ichi Sasa (Kyoto University)
Date : Nov. 24 (Thu), 16:00-17:00
Place : Room W521, West 5 Building

Entropy is a fundamental concept in physics. It appears in thermodynamics, statistical mechanics, information theory, computation theory, and thermodynamics of black holes. Recently, the inter-relations between different types of entropy have been discovered. By synthesizing various aspects of entropy, we thus obtain a deeper understanding of fundamental laws in physics. Now, there is a paper [1], which claims that black hole entropy is obtained as the Noether charge associated with the horizon Killing field. We are then naturally led to ask whether thermodynamic entropy of standard materials is also characterized by a Noether invariant.

In this seminar, we study a classical many-particle system with an external control represented by a time dependent parameter in a Lagrangian. We show that thermodynamic entropy of the system is uniquely characterized as the Noether invariant associated with a symmetry for an infinitesimal non-uniform time translation, where trajectories in the phase space are restricted to those consistent with quasi-static processes in thermodynamics [2]. The most remarkable result of our theory is the emergence of a universal constant of the action dimension, while our theory stands on classical mechanics, classical statistical mechanics, and thermodynamics.

Furthermore, we study a thermally isolated quantum many-body system with an external control represented by a time-dependent parameter. From unitary time evolution of quantum pure states, we derive an effective action for trajectories in a thermodynamic state space. In the action, the entropy appears with its conjugate variable. Especially, for saddle-point trajectories, the conjugate variable provides a time coordinate called thermal time. Then, the symmetry for the uniform translation of the thermal time emerges, which leads to the entropy as a Noether invariant [3].

[1] R. M. Wald, Phys. Rev. D 48 R3427 (1993).
[2] S. Sasa and Y. Yokokura, Phys. Rev. Lett. 116, 140601 (2016).
[3] S. Sasa, S. Sugiura, and Y. Yokokura, in preparation.

Solid-state wetting and dewetting

Speaker: Dr. Olivier Pierre-Louis (ILM, Univ. Lyon 1, CNRS)
Date : Oct. 27 (Thu), 13:30-15:00
Place : Room 155B, Main Bldg.

At the nanoscale, the morphological evolution of solid films and islands under annealing is strongly influenced by wetting properties. Inspired by analogies with recent advances in the wetting behavior of liquids, we explore two situations where solid-state wetting plays a crucial role.

In a first part, we discuss the dewetting dynamics of a thin solid film based on 2D Kinetic Monte Carlo (KMC) simulations and analytical models. We focus on the role of the faceting of the dewetting rim, which changes the asymptotic behavior of the dewetting velocity. In addition, we analyze the instability of the dewetting front, which leads to the formation of fingers. We also discuss the consequences of the wetting potential on the dewetting process and on the triple-line dynamics.

In a second part, we will present some results on the wetting statics and dynamics of islands (or nanoparticles) on surface with topographical structures of large aspect ratio, such as pillars or trenches using 3D KMC simulations including elastic effects.

On the transition to turbulence under the "simplest possible circumstances"

Speaker: Prof. Lennaert van Veen (Univ. Ontario)
Date : Aug. 24 (Wed), 16:00-17:30
Place : Room 155B, Main Bldg.

In his landmark 1883 paper, Osborne Reynolds studied qualitatively different kinds of motion of fluid in a straight pipe. His aim was to demonstrate the transition to “sinuous”, in current terminology turbulent, motion as the flow rate increases. As it turns out, he had picked a set up that is practically simple but mathematically very complicated. The flow state that is void of any turbulence remains asymptotically stable for any experimentally reachable flow rate, and swirling flows occur suddenly and intermittently. Their onset is hysteretic and strongly depends on the way the flow rate is varied. Intrigued by this result, A. N. Kolmogorov introduced a more abstract model of fluid motion, restricting it to two spatial dimensions and discarding material boundaries. However, it soon turned out to be overly restrictive and exclude transitions like the one Reynolds had observed. In this presentation, I will show that extending Kolmogorov’s model to three spatial dimensions places it in the same category as elementary shear flows such as that of fluids in pipes and channels. I will study the hysteretic onset of turbulence and the structure of phase space by numerical bifurcation analysis as well as energy methods. This is joint work with Susumu Goto of Osaka University.

System of interacting grains

Speaker: Dr. François Pétrélis (ENS Paris, CNRS)
Date : June 29 (Wed), 16:30-18:00
Place : Room 155B, Main Bldg.

In most granular media, interactions between grains are dominated by contact events: either dissipative collisions in diluted granular media or friction in denser ones. I consider grains that carry a magnetic dipole and interact through dipole-dipole interactions. I will discuss how these long range interactions modify the behavior of the granular medium. In particular I will present several instabilities such as the formation of peaks at the surface of a dense granular layer or a transition similar to the liquid-gas phase transition.

Active diffusion of chromosomal loci driven by athermal noise

Speaker: Dr. Takahiro Sakaue (Kyushu Univ.)
Date : June 9 (Thu), 10:30-12:00
Place : Room 239, Main Bldg.

Active diffusion, i.e., fluctuating dynamics driven by athermal noise is found in various out-of-equilibrium systems. Here we discuss the nature of the active diffusion of tagged monomers in a flexible polymer. A scaling argument based on the notion of tension propagation clarifies how the polymeric effect is reflected in the anomalous diffusion exponent, which may be of relevance to the dynamics of chromosomal loci in living cells. The idea could be applicable to the behavior of polymers in bacterial suspension as well.

T. Sakaue and T. Saito, Soft Matter, 2016, DOI: 10.1039/C6SM00775A

Roles of cellular phenotypic noise in population growth, acclimation, and evolution

Speaker: Prof. Yuichi Wakamoto (Univ. of Tokyo)
Date : May 27 (Fri), 15:00-16:30
Place : Room 155B, Main Bldg.

Recent advances in single-cell time-lapse microscopy have revealed large phenotypic heterogeneity at the single-cell level in genetically homogeneous cellular populations. It has been often assumed that such phenotypic noise is evolutionary unimportant because phenotypic differences among cells are not encoded on the stable genetic materials, thus non-heritable. However, the evidences are accumulating that many cellular phenotypes have trans-generational "memories", which might drive clonal cellular populations to quickly and efficiently adapt to harsh environments if the heterogeneous phenotypes are correlated with cellular fitness. Using custom microfluidic single-cell measurement devices, we have recently uncovered several biological roles of phenotypic noise at the single-cell level: (1) Heterogeneity in division interval causes clonal proliferation to grow faster than the constituent single cells on average in constant environments, thus a cellular population can grow faster than cells [1]; and (2) noise in the expression level of a survival-correlated gene allows a fraction of cells in the population to survive and persist during antibiotic drug exposures [2]. Also, our ongoing study have revealed that clonal bacterial populations can acclimatize to drug exposures through multi-generational dynamics, which is enabled by some uncharacterized stable intracellular memory not encoded on genome. In this seminar, I will present the overviews of these studies, and discuss the implications of the results for evolution and genetics.

[1] Hashimoto, M. et al. Noise-driven growth rate gain in clonal cellular populations. Proc. Natl. Acad. Sci. 113, 3251–3256 (2016).
[2] Wakamoto, Y. et al. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339, 91–5 (2013).

This seminar will be given in Japanese, but slides are in English.

Nonequilibrium equalities in absolutely irreversible processes and their application to the Gibbs paradox

Speaker: Mr. Yuto Murashita (Univ. of Tokyo)
Date : Mar. 24 (Thu), 10:30-12:00
Place : Room 239, Main Bldg.

Fluctuation theorems have attracted considerable attention in the context of statistical mechanics and information thermodynamics. Although integral fluctuation theorems are valid in rather general nonequilibrium situations, they cannot apply to absolutely irreversible processes, where the forward-path probability vanishes and the entropy production diverges in terms of detailed fluctuation theorems. We identify the mathematical origin of this inapplicability as the singularity of probability measure. As a result, we generalize conventional integral fluctuation theorems to absolutely irreversible processes. The new equalities give a more stringent constraint to the average of the entropy production than the conventional second-law-like inequality does.

As a notable application of the new fluctuation theorems, we discuss the Gibbs paradox in small thermodynamic systems. The Gibbs paradox originated from gas mixing, and has raised fundamental problems in thermodynamics and statistical mechanics. Among them, we here consider the consistency between thermodynamic and statistical-mechanical entropies. In this context, the Gibbs paradox is resolved based on the requirement of extensivity in macroscopic thermodynamic systems. However, this resolution cannot apply to small thermodynamic systems because extensivity breaks down. We offer a resolution applicable to small thermodynamic systems based on our fluctuation theorems.

Hydrodynamic collective effects of active proteins in biological cells

Speaker: Prof. Alexander S. Mikhailov (Fritz Haber Institute of the Max Planck Society)
Date : Nov. 26 (Thu), 16:00-17:30
Place : Room 239, Main Bldg.

Recent in vivo experiments with optical tracking of particles in living biological cells indicate that active forces strongly dominate thermal Brownian forces in the cellular environment, impacting motion of objects from nanometers to microns in scale. As we show [PNAS 112, E3639 (2015)], such non-thermal fluctuating forces can arise from hydrodynamic stirring of the cytoplasm by various protein machines, enzymes and molecular motors that densely populate the cell. Independent of their specific functions, all such macromolecules are repeatedly changing their conformations and act as oscillating stochastic force dipoles. Numerical estimates reveal that hydrodynamic collective effects of active proteins may account for the experimentally observed dramatic diffusion enhancement in the cytoplasm under ATP supply.

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