Extreme Diffusion Measures Statistical Fluctuations of the Environment.

We consider many-particle diffusion in one spatial dimension modeled as "random walks in a random environment." A shared short-range space-time random environment determines the jump distributions that drive the motion of the particles. We determine universal power laws for the environment's contribution to the variance of the extreme first passage time and extreme location.

First-passage time for many-particle diffusion in space-time random environments.

The first-passage time for a single diffusing particle has been studied extensively, but the first-passage time of a system of many diffusing particles, as is often the case in physical systems, has received little attention until recently. We consider two models for many-particle diffusion-one treats each particle as independent simple random walkers while the other treats them as coupled to a common space-time random forcing field that biases particles nearby in space and time in similar ways. The first-passage time of a single diffusing particle under both models shows the same statistics and scaling behavior.

A mucin-regulated adhesin determines the spatial organization and inflammatory character of a bacterial symbiont in the vertebrate gut.

In a healthy gut, microbes are often aggregated with host mucus, yet the molecular basis for this organization and its impact on intestinal health are unclear. Mucus is a viscous physical barrier separating resident microbes from epithelia, but it also provides glycan cues that regulate microbial behaviors. Here, we describe a mucin-sensing pathway in an Aeromonas symbiont of zebrafish, Aer01.

Anomalous fluctuations of extremes in many-particle diffusion.

In many-particle diffusions, particles that move the furthest and fastest can play an outsized role in physical phenomena. A theoretical understanding of the behavior of such extreme particles is nascent. A classical model, in the spirit of Einstein's treatment of single-particle diffusion, has each particle taking independent homogeneous random walks.

Emergence of zero modes in disordered solids under periodic tiling.

In computational models of particle packings with periodic boundary conditions, it is assumed that the packing is attached to exact copies of itself in all possible directions. The periodicity of the boundary then requires that all of the particles' images move together. An infinitely repeated structure, on the other hand, does not necessarily have this constraint.

Predicting Defects in Soft Sphere Packings near Jamming Using the Force Network Ensemble.

Amorphous systems of soft particles above jamming have more contacts than are needed to achieve mechanical equilibrium. The force network of a granular system with a fixed contact network is thus underdetermined and can be characterized as a random instantiation within the space of the force network ensemble. In this Letter, we show that defect contacts that are not necessary for stability of the system can be uniquely identified by examining the boundaries of this space of allowed force networks.

BefA, a microbiota-secreted membrane disrupter, disseminates to the pancreas and increases β cell mass.

Microbiome dysbiosis is a feature of diabetes, but how microbial products influence insulin production is poorly understood. We report the mechanism of BefA, a microbiome-derived protein that increases proliferation of insulin-producing β cells during development in gnotobiotic zebrafish and mice. BefA disseminates systemically by multiple anatomic routes to act directly on pancreatic islets.

Hyperuniform jammed sphere packings have anomalous material properties.

A spatial distribution is hyperuniform if it has local density fluctuations that vanish in the limit of long length scales. Hyperuniformity is a well known property of both crystals and quasicrystals. Of recent interest, however, is disordered hyperuniformity: the presence of hyperuniform scaling without long-range configurational order.

Disaggregation as an interaction mechanism among intestinal bacteria.

The gut microbiome contains hundreds of interacting species that together influence host health and development. The mechanisms by which intestinal microbes can interact, however, remain poorly mapped and are often modeled as spatially unstructured competitions for chemical resources. Recent imaging studies examining the zebrafish gut have shown that patterns of aggregation are central to bacterial population dynamics.

Transient learning degrees of freedom for introducing function in materials.

SignificanceMany protocols used in material design and training have a common theme: they introduce new degrees of freedom, often by relaxing away existing constraints, and then evolve these degrees of freedom based on a rule that leads the material to a desired state at which point these new degrees of freedom are frozen out. By creating a unifying framework for these protocols, we can now understand that some protocols work better than others because the choice of new degrees of freedom matters. For instance, introducing particle sizes as degrees of freedom to the minimization of a jammed particle packing can lead to a highly stable state, whereas particle stiffnesses do not have nearly the same impact.

Dionysian Hard Sphere Packings Are Mechanically Stable at Vanishingly Low Densities.

High strength-to-weight ratio materials can be constructed by either maximizing strength or minimizing weight. Tensegrity structures and aerogels take very different paths to achieving high strength-to-weight ratios but both rely on internal tensile forces. In the absence of tensile forces, removing material eventually destabilizes a structure.

Long-Range Anomalous Decay of the Correlation in Jammed Packings.

We numerically study the structure of the interactions occurring in three-dimensional systems of hard spheres at jamming, focusing on the large-scale behavior. Given the fundamental role in the configuration of jammed packings, we analyze the propagation through the system of the weak forces and of the variation of the coordination number with respect to the isostaticity condition, ΔZ. We show that these correlations can be successfully probed by introducing a correlation function weighted on the density-density fluctuations.

Mean-Field Predictions of Scaling Prefactors Match Low-Dimensional Jammed Packings.

No known analytic framework precisely explains all the phenomena observed in jamming. The replica theory for glasses and jamming is a mean-field theory which attempts to do so by working in the limit of infinite dimensions, such that correlations between neighbors are negligible. As such, results from this mean-field theory are not guaranteed to be observed in finite dimensions.

Direct measurement of force configurational entropy in jamming.

Thermal fluctuations are not large enough to lead to state changes in granular materials. However, in many cases, such materials do achieve reproducible bulk properties, suggesting that they are controlled by an underlying statistical mechanics analogous to thermodynamics. While themodynamic descriptions of granular materials have been explored, they have not yet been concretely connected to their underlying statistical mechanics.

Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation.

Some of the densest microbial ecosystems in nature thrive within the intestines of humans and other animals. To protect mucosal tissues and maintain immune tolerance, animal hosts actively sequester bacteria within the intestinal lumen. In response, numerous bacterial pathogens and pathobionts have evolved strategies to subvert spatial restrictions, thereby undermining immune homeostasis.

Jamming Energy Landscape is Hierarchical and Ultrametric.

The free energy landscape of mean-field marginal glasses is ultrametric. We demonstrate that this feature persists in finite three-dimensional systems that are out of equilibrium by finding sets of minima, which are nearby in configuration space. By calculating the distance between these nearby minima, we produce a small region of the distance metric.

Gardner physics in amorphous solids and beyond.

One of the most remarkable predictions to emerge out of the exact infinite-dimensional solution of the glass problem is the Gardner transition. Although this transition was first theoretically proposed a generation ago for certain mean-field spin glass models, its materials relevance was only realized when a systematic effort to relate glass formation and jamming was undertaken. A number of nontrivial physical signatures associated with the Gardner transition have since been considered in various areas, from models of structural glasses to constraint satisfaction problems.

Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration.

All animals live in intimate association with microorganisms that profoundly influence their health and development, yet the traits that allow microorganisms to establish and maintain host associations are not well understood. To date, most investigations aimed at identifying traits required for host association have focused on intrahost niches. Consequently, little is known about the relative contribution of extrahost factors such as environmental growth and survival and immigration into hosts from the external environment, as promoters of host association.

Bacterial Cohesion Predicts Spatial Distribution in the Larval Zebrafish Intestine.

Are there general biophysical relationships governing the spatial organization of the gut microbiome? Despite growing realization that spatial structure is important for population stability, interbacterial competition, and host functions, it is unclear in any animal gut whether such structure is subject to predictive, unifying rules or if it results from contextual, species-specific behaviors. To explore this, we used light sheet fluorescence microscopy to conduct a high-resolution comparative study of bacterial distribution patterns throughout the entire intestinal volume of live, larval zebrafish. Fluorescently tagged strains of seven bacterial symbionts, representing six different species native to zebrafish, were each separately monoassociated with animals that had been raised initially germ-free.

Modernized Tools for Streamlined Genetic Manipulation and Comparative Study of Wild and Diverse Proteobacterial Lineages.

Correlating the presence of bacteria and the genes they carry with aspects of plant and animal biology is rapidly outpacing the functional characterization of naturally occurring symbioses. A major barrier to mechanistic studies is the lack of tools for the efficient genetic manipulation of wild and diverse bacterial isolates. To address the need for improved molecular tools, we used a collection of proteobacterial isolates native to the zebrafish intestinal microbiota as a testbed to construct a series of modernized vectors that expedite genetic knock-in and knockout procedures across lineages.

Tension Independence of Lipid Diffusion and Membrane Viscosity.

The diffusion of biomolecules at lipid membranes is governed by the viscosity of the underlying two-dimensionally fluid lipid bilayer. For common three-dimensional fluids, viscosity can be modulated by hydrostatic pressure, and pressure-viscosity data have been measured for decades. Remarkably, the two-dimensional analogue of this relationship, the dependence of molecular mobility on tension, has to the best of our knowledge never been measured for lipid bilayers, limiting our understanding of cellular mechanotransduction as well as the fundamental fluid mechanics of membranes.

Echoes of the Glass Transition in Athermal Soft Spheres.

Recent theoretical advances have led to the creation of a unified phase diagram for the thermal glass and athermal jamming transitions. This diagram makes clear that, while related, the mode-coupling-or dynamic-glass transition is distinct from the jamming transition, occurring at a finite temperature and significantly lower density than the jamming transition. Nonetheless, we demonstrate a prejamming transition in athermal frictionless spheres which occurs at the same density as the mode-coupling transition and is marked by percolating clusters of locally rigid particles.

Geometric order parameters derived from the Voronoi tessellation show signatures of the jamming transition.

A jammed packing of frictionless spheres at zero temperature is perfectly specified by the network of contact forces from which mechanical properties can be derived. However, we can alternatively consider a packing as a geometric structure, characterized by a Voronoi tessellation which encodes the local environment around each particle. We find that this local environment characterizes systems both above and below jamming and changes markedly at the transition.

Measuring lipid membrane viscosity using rotational and translational probe diffusion.

The two-dimensional fluidity of lipid bilayers enables the motion of membrane-bound macromolecules and is therefore crucial to biological function. Microrheological methods that measure fluid viscosity via the translational diffusion of tracer particles are challenging to apply and interpret for membranes, due to uncertainty about the local environment of the tracers. Here, we demonstrate a new technique in which determination of both the rotational and translational diffusion coefficients of membrane-linked particles enables quantification of viscosity, measurement of the effective radii of the tracers, and assessment of theoretical models of membrane hydrodynamics.