A03 UCHIDA, Nariya |Proposed Research Projects (2016-2017)

Paper | Original Paper


*Takanobu A. Katoh, Koji Ikegami, *Nariya Uchida, Toshihito Iwase, Daisuke Nakane, Tomoko Masaike, Mitsutoshi Setou, *Takayuki Nishizaka,
Three-dimensional tracking of microbeads attached to the tip of single isolated tracheal cilia beating under external load,
Scientific Reports 8, 15562 (2018).

[Summary] To study the properties of tracheal cilia beating under various conditions, we developed a method to monitor the movement of the ciliary tip. One end of a demembranated cilium was immobilized on the glass surface, while the other end was capped with a polystyrene bead and tracked in three dimensions. The cilium, when activated by ATP, stably repeated asymmetric beating as in vivo. The tip of a cilium in effective and recovery strokes moved in discrete trajectories that differed in height. The trajectory remained asymmetric in highly viscous solutions. Model calculation showed that cilia maintained a constant net flux during one beat cycle irrespective of the medium viscosity. When the bead attached to the end was trapped with optical tweezers, it came to display linear oscillation only in the longitudinal direction. Such a beating-mode transition may be an inherent nature of movement-restricted cilia.

Armando Maestro, Nicolas Bruot, Jurij Kotar, Nariya Uchida, Ramin Golestanian, *Pietro Cicuta,
Control of synchronization in models of hydrodynamically coupled motile cilia,
Communications Physics 1, 28/1-8 (2018).

[Summary] In many organisms, multiple motile cilia coordinate their beating to facilitate swimming or driving of surface flows. Simple models are required to gain a quantitative understanding of how such coordination is achieved; there are two scales of phenomena, within and between cilia, and both host complex non-linear and non-thermal effects. We study here a model that is tractable analytically and can be realized by optical trapping colloidal particles: intra-cilia properties are coarse grained into the parameters chosen to drive particles around closed local orbits. Depending on these effective parameters a variety of phase-locked steady states can be achieved. We derive a theory that includes two mechanisms for synchronization: the flexibility of the motion along the predefined orbit and the modulation of the driving force. We show that modest tuning of the cilia beat properties, as could be achieved biologically, results in dramatic changes in the collective motion arising from hydrodynamic coupling.


Yoshiaki Kinosita, *Nariya Uchida, Daisuke Nakane and *Takayuki Nishizaka,
Direct observation of rotation and steps of the archaellum in the swimming halophilic archaeon Halobacterium salinarum,
Nature Microbiology 1, 16148/1-9 (2016).

[Summary] Motile archaea swim using a rotary filament, the archaellum, a surface appendage that resembles bacterial flagella structurally, but is homologous to bacterial type IV pili. Little is known about the mechanism by which archaella produce motility. To gain insights into this mechanism, we characterized archaellar function in the model organism Halobacterium salinarum. Three-dimensional tracking of quantum dots enabled visualization of the left-handed corkscrewing of archaea in detail. An advanced analysis method combined with total internal reflection fluorescence microscopy, termed cross-kymography, was developed and revealed a right-handed helical structure of archaella with a rotation speed of 23 ± 5 Hz. Using these structural and kinetic parameters, we computationally reproduced the swimming and precession motion with a hydrodynamic model and estimated the archaellar motor torque to be 50 pN nm. Finally, in a tethered-cell assay, we observed intermittent pauses during rotation with ∼36° or 60° intervals, which we speculate may be a unitary step consuming a single adenosine triphosphate molecule, which supplies chemical energy of 80 pN nm when hydrolysed. From an estimate of the energy input as ten or six adenosine triphosphates per revolution, the efficiency of the motor is calculated to be ∼6–10%.

Yi-Teng Hsiao, Kuan-Ting Wu, Nariya Uchida, and *Wei-Yen Woon,
Impurity-tuned non-equilibrium phase transition in a bacterial carpet,
Applied Physics Letters 108, 183701/1-5 (2016).

[Summary] The effects of impurity on the non-equilibrium phase transition in Vibrio alginolyticus bacterialcarpets are investigated through a position-sensitive-diode implemented optical tweezers-microsphere assay. The collective flow increases abruptly as we increase the rotation rate of flagellavia Na þ concentration. The effects of impurities on the transition behavior are examined by mixingcells of a wild type strain (VIO5) with cells of a mutant strain (NMB136) in different swimmingpatterns. For dilute impurities, the transition point is shifted toward higher Na þ concentration.Increasing the impurities’ ratio to over 0.25 leads to a significant drop in the collective force, sug-gesting a partial orientational order with a smaller correlation length.

Paper | Review


*Nariya Uchida, Ramin Golestanian, Rachel R. Bennett,
Synchronization and Collective Dynamics of Flagella and Cilia as Hydrodynamically Coupled Oscillators,
Journal of the Physical Society of Japan 86, 101007/1-8 (2017).

[Summary] Cooperative motion of flagella and cilia faciliates swimming of microorganisms and material transport in the body ofmulticellular organisms. Using minimal models, we address the roles of hydrodynamic interaction in synchronizationand collective dynamics of flagella and cilia. Collective synchronization of bacterial flagella is studied with a model ofbacterial carpets. Cilia and eukaryotic flagella are characterized by periodic modulation of their driving forces, whichproduces various patterns of two-body synchronization and metachronal waves. Long-range nature of the interactionintroduces novel features in the dynamics of these model systems. The flagella of a swimmer synchronize also by aviscous drag force mediated through the swimmer’s body. Recent advance in experimental studies of the collectivedynamics of flagella, cilia and related artificial systems are summarized.

Nariya Uchida,
How Do Nanorobots Swim in Slime?,
JPSJ News and Comments 14, 05 (2017).

[Summary] Yasuda et al. [J. Phys. Soc. Japan 86, 043801 (2017)] identified a new locomotion mode of microswimmers in viscoelastic fluids. They extended the three-sphere model by Najafi and Golestanian to fluids with linear viscoelasticity. By relating the swimming velocity and rheological properties of the fluids, they suggest that microswimmers may serve as a new tool for microrheology. In particular, it is shown that a swimmer with structural asymmetry gains net propulsion velocity even by reciprocal motion, due to the imaginary (elastic) part of the complex viscosity.

International Conferences



*Gilhan Kim, Nariya Uchida,
Lattice-based model of run-and-tumble chemotaxis of bacteria with alignment,
International Symposium on Fluctuation and Structure out of Equilibrium 2017 (Nov. 20-23, 2017), Sendai, Japan.



Nariya Uchida,
Some applications of Smoothed Profile Method for active flow in and out of cells,
International Workshop on Hydrodynamic Flows in/of Cells (Nov. 24-25, 2016), Tokyo, Japan.

Nariya Uchida,
Collective dynamics of flagella, cilia and active filaments near surfaces,
Current and Future Perspectives in Active Matter (Oct. 28-29, 2016), Tokyo, Japan.

Grant-in-Aid for Scientific Research (KAKENHI) on Innovative Areas, MEXT, Japan
Synergy of Fluctuation and Structure : Quest for Universal Laws in Non-Equilibrium Systems