東京大学 竹内研究室 公式ウェブページ

We are active matter. From molecular motors noisily walking in living cells to the mesmerizing swirls in a starling flock, systems driven far from equilibrium by a sustained flux of energy through its constituents routinely exhibit stunning emergent phenomena that pose fundamental challenges to our understanding of the natural world. Much is known about what patterns and dynamics active systems can exhibit, but the inverse problem of controlling active matter is less explored. I will discuss our current work on searching for design principles to control localized excitations, drops etc., in active materials using ideas from control theory, optimal transport and symmetry-based approaches. I will conclude by highlighting future directions for embodying function, programmable response and computation in biological and synthetic active systems.

The rapid and universal emergence of antibiotic resistance in bacterial populations poses a worldwide health care challenge, but also serves as a paradigm of microbial evolution. In many cases the evolution of high levels of resistance requires multiple mutational steps, which can be conceptualized as pathways in the microbial fitness landscape. The talk will use the evolution of a specific antibiotic resistance enzyme to explain the theoretical framework within which this process can be described, and report on recent results on the predictability of pathways that were obtained in a collaborative effort between experiment and theory.

Obligately hydrocarbonoclastic bacteria (OHCB) are cosmopolitan marine bacteria that can survive by consuming hydrocarbons as a sole energy and carbon source. In the ocean, these bacteria are typically found at very low densities but bloom to become the dominant bacteria at the site of oil spills. These organisms have likely evolved to directly utilize the abundant hydrocarbons in the marine environment as part of the cryptic carbon cycle and around natural oil-seeps on the sea floor. They are thought to degrade a significant amount of the worldwide spilled oil, which is why they have been organisms of interest for use as agents of bioremediation.

Alcanivorax borkumensis was the first OHCB sequenced in the mid-2000s. Like most bacteria, it is thought to transition between planktonic and biofilm states. Biofilms are 3D communities of densely packed bacteria encased in a self-secreted matrix of extracellular polymeric substances (EPS) that both protect and help the community remain attached to a surface. However, unlike most environmental bacteria, which typically absorb their carbon (and energy) directly from nutrients in the surrounding water, A. borkumensis biofilms must form on the oil-water interface. Although formation of a biofilm at fluid-fluid interface is not unique and, in some ways, shares some similarity to pellicle formation at the air-liquid interface, the similarities diverge there. Biofilms can generate gradients in the nutrients between the internal and external environments. In the case of an A. borkumensis biofilm surrounding an oil droplet, only the cells at the interface have access to the carbon/energy, while the outward facing cells have access to micronutrients. It is not clear how the obvious nutrient gradients and the fluid interface affects A. borkumensis biofilm formation.

Due to the difficulty in tracking individual droplets over time, biofilm dynamics of this interesting organism have largely been conducted though bulk methods. From an applied ecology perspective, clarifying the microscopic mechanisms of biofilm formation for this and similar OHCB organism may reveal features to be exploited in the management of oil spills in the natural environment. From the active-matter physics perspective, the behavior of self-driven layer at a phase-separated interface of may reveal new physics.

We introduce a microfluidic platform that can trap and store oil microdroplets for weeks. This platform greatly facilitates imaging and analysis of biofilm formation at the oil-water interface. We demonstrate unresolved biofilm dynamics by A. borkumensis, showing its ability to rapidly shred oil drops. We analyze various physical aspects of this organism and correlate them to its ability to align and cooperate at the interface to drive a rapid and large-scale remodeling of the interface. This remodeling appears to be the most egalitarian and efficient distribution of resources.

Wind is a variable energy source whose fluctuations threaten electrical grid stability and complicate dynamical load balancing. The power generated by a wind turbine fluctuates due to the variable wind speed that blows past the turbine. Indeed, the spectrum of wind power fluctuations is widely believed to reflect the Kolmogorov spectrum of atmospheric turbulence; both vary with frequency $f$ as $f^{-5/3}$. This variability decreases when aggregate power fluctuations from geographically distributed wind plants are averaged at the grid via a mechanism known as geographic smoothing. Neither the $f^{-5/3}$ wind power fluctuation spectrum nor the mechanism of geographic smoothing are understood. In this talk, I will chart out the non-equilibrium character of wind power fluctuations, and explain the wind power fluctuation spectrum from the turbine through the grid scales. The $f^{-5/3}$ wind power fluctuation spectrum results from the largest length scales of atmospheric turbulence of order 200 km influencing the small scales where individual turbines operate. This long-range influence correlates outputs from geographically distributed wind plants over a range of frequencies that decreases with increasing inter-farm distance. Consequently, aggregate grid-scale power fluctuations remain correlated, and are smoothed until they reach a limiting $f^{-7/3}$ spectrum, which is confirmed with field data. I will discuss engineering and policy implications of these results and chart out the future directions I intend to pursue in the broad area of energy research.

Microbial attachment to material surfaces is a complex phenomenon involving a complexity of electrostatic, biochemical and physical mechanisms. Despite the major problems associated with medical device-associated infection, infectious disease transmission within healthcare environments, and hospital acquired infections (HAIs), many aspects of microbial surface attachment are not well understood. Rates of HAI remain relatively high, and there is significant concern about the effects of antibiotic resistance, globally. Most approaches to antimicrobial material design still usually just rely on the release of biocidal chemical species (such as Ag ions).
We are interested in how material surface design - factors such as surface chemistry, biochemical functionalization, nano- and microtopography, and wettability – can influence microbial surface attachment and biofilm development. In particular, our work has focussed on strategies to disrupt the early stages of microbial surface attachment in antimicrobial material design, as an alternative to biocidal chemistries. In the context of medical device-associated infections, there is an important advantage to keeping bacteria in a planktonic (swimming) state, as they are much more vulnerable than in a biofilm community.
This talk will summarize several experimental research projects that explore aspects of bacterial cell attachment to material surfaces; (1) The immobilization of glycoside hydrolase enzymes to disrupt pseudomonas aeruginosa biofilms; (2) Nanotopographies in wetting contact (the ‘cicada effect’) ; (3) Nano- and microtopographies in non-wetting (superhydrophobic) contact ; (4) Microbial attraction to topographical surface defects ; and (5) ‘Slippery’ surfaces (SLIPS) in the design of non-specific, non-fouling material. Overall, the application of these various materials chemistry design tools has enabled us to learn something about microbial behaviour, through material surface design.

Microscopic colloids are basic building blocks of soft and biological matter. They also serve as experimental test-beds of Brownian dynamics. By illuminating light-absorbing colloids with a laser beam, one can observe the so-called 'hot-Brownian motion'. This out-of-equilibrium colloidal system can form unconventional assemblies and exhibit evolutionary dynamics that can be tuned by light. In this talk, I will show how structuring optical [1], plasmonic [2] and optothermal forces [3] can influence the translational and rotational dynamics of Brownian colloids. I will further discuss the emergence of unconventional patterns of colloidal assembly that can mimic dynamic networks. I will conclude with a discussion on some challenges and opportunities of studying structured light-biological matter interactions.

[1] Optothermal Evolution of Active Colloidal Matter in a Defocused Laser Trap. ACS Photonics 2022, 9 (10), 3440–3449.

[2] Optothermal Pulling, Trapping, and Assembly of Colloids Using Nanowire Plasmons. Soft Matter 2021, 17 (48), 10903–10909.

[3] Plasmofluidic Single-Molecule Surface-Enhanced Raman Scattering from Dynamic Assembly of Plasmonic Nanoparticles. Nat Commun 2014, 5 (1), 4357.

Active droplets and Janus colloids are popular phoretic swimmers extensively developed to generate emergent collective behaviours reminiscent of biological systems. This development will benefit from a proper understanding of their emergence. Recent modeling has helped us understand how Janus colloids self-organize collectively, whereas it remains largely elusive for active droplets due to the substantially increased difficulty modelling them. Here, we conduct simulations resolving full hydrochemical interactions to examine a model system---a suspension of self-phoretic disks, spanning a parameter space of Péclet number and area fraction. Varying them, the suspension self-organizes into diverse states: triangular lattice crystal, liquid phase, gas-like clusters, and active turbulence. A narrow range of hexatic phase between the liquid and solid phases has been identified, with its emergence well captured by our far-field scaling theory. Our simulations have reproduced a few independently reported experimental observations, including the crossing and reflecting trajectories of two active droplets, and the stationary crystalline structure formed by or turbulent motion of camphor boats (as the macroscopic analogy of active droplets). These findings might illuminate building biomimetic architectures with static patterns, or dynamically adaptive organizations and functionalities.

In recent years, the analysis of diffusion phenomena, including computer viruses and pathogens, has become increasingly important. Among the various diffusion phenomena, one of the most physically exciting and long-studied subjects is the penetration of liquids, which appears, for example, when water is spilled on a towel. Experimental and numerical studies have led to several predictions, such as the existence of specific laws for the fluctuations in the permeation area and the fact that its boundary can be described by a new framework of stochastic partial differential equations called the KPZ equation. Surprisingly, experiments and numerical calculations have confirmed that various diffusion phenomena, such as paper burning and bacterial growth, behave like a solution to the KPZ equation. In (space) dimension one, much work has been concentrated in the past years, and they have succeeded in making sense of the solution to the KPZ equation. Moreover, several works have recently studied the KPZ equation in dimensions two and higher, though many significant problems remain to be solved. In this talk, I will talk about recent work around the KPZ equation for higher dimensions, both from microscopic and macroscopic viewpoints.

Shapes of colloidal particles matter the interparticle interaction at liquid interfaces. In this study, the effect of surface roughness was investigated experimentally and numerically in terms of isotherms and particle configuration changes upon compression. Sufficiently rough particles exhibit an intermediate state between gas-like and solid-like states due to roughness-induced capillary attraction, forming a percolated network. Moreover, the surface roughness decreases the jamming point, attributed to the friction and interlocking due to the particles’ surface asperities. Furthermore, the tangential contact force owing to surface asperities can cause a gradual off-plane collapse of the compressed monolayer. Our study on rough colloids at interfaces will also benefit the development of functional materials. At the end of the talk, I will share possible future directions related to active matter.

In the cell, long DNA molecules carry the genetic information and must be stored yet remain accessible to interact with various biomolecules which control for read out and processing. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein-induced topological domains in DNA, quantitative and time-resolved approaches are required. Here we present a methodology to determine the size and dynamics of topological domains using the analysis of fluctuations: a protein-binding event causes a drop in the variance in the end-end distance of a stretched over-wound DNA molecule. Using a combination of high-speed magnetic tweezers experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We demonstrate how transient (partial) dissociation of DNA bridging proteins results in dynamic sampling of different topological states. Our work highlights how considering DNA extension fluctuations, in addition to the mean extension, provides additional information and enables the investigation of protein-DNA interactions that are otherwise not detectable.

References

1. E. Skoruppa, E. Carlon, "Equilibrium Fluctuations of DNA Plectonemes" Phys. Rev. E 106, 024412 (2022)
https://arxiv.org/pdf/2205.07735.pdf
2. W. Vanderlinden, E. Skoruppa, P. Kolbeck, E. Carlon, J. Lipfert, "DNA fluctuations reveal the size and dynamics of topological domains" biorXiv:2021.12.21.473646
https://www.biorxiv.org/content/10.1101/2021.12.21.473646v1