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Shape-changing objects are prized for applications ranging from acoustics to robotics. We report sub-millimetre bubbles that reversibly and rapidly change not only their shape but also their topological class, from sphere to torus, when subjected to a simple pressure treatment. Stabilized by a solid-like film of nanoscopic protein "particles", the bubbles may persist in toroidal form for several days, most of them with the relative dimensions expected of Clifford tori. The ability to cross topological classes reversibly and quickly is enabled by the expulsion of protein from the strained surfaces in the form of submicron assemblies. Compared to structural modifications of liquid-filled vesicles, for example by slow changes in solution osmolality, the rapid inducement of shape changes in bubbles by application of pressure may hasten experimental investigations of surface mechanics, even as it suggests new routes to lightweight materials with high surface areas.

During the biofilm life cycle, bacteria attach to a surface and then reproduce, forming crowded, growing communities. Many theoretical models of biofilm growth dynamics have been proposed; however, difficulties in accurately measuring biofilm height across relevant time and length scales have prevented testing these models, or their biophysical underpinnings, empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a detailed empirical characterization of vertical growth dynamics. We propose a heuristic model for vertical growth dynamics based on basic biophysical processes inside a biofilm: diffusion and consumption of nutrients and growth and decay of the colony. This model captures the vertical growth dynamics from short to long time scales (10 min to 14 d) of diverse microorganisms, including bacteria and fungi.

Evolutionary arms races are broadly prevalent among organisms including bacteria, which have evolved defensive strategies against various attackers. A common microbial aggression mechanism is the type VI secretion system (T6SS), a contact-dependent bacterial weapon used to deliver toxic effector proteins into adjacent target cells. Sibling cells constitutively express immunity proteins that neutralize effectors. However, less is known about factors that protect non-sibling bacteria from T6SS attacks independently of cognate immunity proteins. In this study, we observe that human Escherichia coli commensal strains sensitive to T6SS attacks from Vibrio cholerae are protected when co-cultured with glucose. We confirm that glucose does not impair V. cholerae T6SS activity. Instead, we find that cells lacking the cAMP receptor protein (CRP), which regulates expression of hundreds of genes in response to glucose, survive significantly better against V. cholerae T6SS attacks even in the absence of glucose. Finally, we show that the glucose-mediated T6SS protection varies with different targets and killers. Our findings highlight the first example of an extracellular small molecule modulating a genetically controlled response for protection against T6SS attacks. This discovery may have major implications for microbial interactions during pathogen-host colonization and survival of bacteria in environmental communities.

Vibrio cholerae is an aquatic Gram-negative bacterium that causes severe diarrheal cholera disease when ingested by humans. To eliminate competitor cells in both the external environment and inside hosts, V. cholerae uses the type VI secretion system (T6SS). The T6SS is a macromolecular contact-dependent weapon employed by many Gram-negative bacteria to deliver cytotoxic proteins into adjacent cells. In addition to canonical T6SS gene clusters encoded by all sequenced V. cholerae isolates, strain BGT49 encodes another locus, which we named auxiliary (Aux) cluster 4. The Aux 4 cluster is located on a mobile genetic element and can be used by killer cells to eliminate both V. cholerae and Escherichia coli cells in a T6SS-dependent manner. A putative toxin encoded in the cluster, which we name TpeV (type VI permeabilizing effector Vibrio), shares no homology to known proteins and does not contain motifs or domains indicative of function. Ectopic expression of TpeV in the periplasm of E. coli permeabilizes cells and disrupts the membrane potential. Using confocal microscopy, we confirm that susceptible target cells become permeabilized when competed with killer cells harboring the Aux 4 cluster. We also determine that tpiV, the gene located immediately downstream of tpeV, encodes an immunity protein that neutralizes the toxicity of TpeV. Finally, we show that TpeV homologs are broadly distributed across important human, animal, and plant pathogens and are localized in proximity to other T6SS genes. Our results suggest that TpeV is a toxin that belongs to a large family of T6SS proteins. IMPORTANCE Bacteria live in polymicrobial communities where competition for resources and space is essential for survival. Proteobacteria use the T6SS to eliminate neighboring cells and cause disease. However, the mechanisms by which many T6SS toxins kill or inhibit susceptible target cells are poorly understood. The sequence of the TpeV toxin that we describe here is unlike any previously described protein. We demonstrate that it has antimicrobial activity by permeabilizing cells, eliminating membrane potentials, and causing severe cytotoxicity. TpeV homologs are found near known T6SS genes in human, animal, and plant bacterial pathogens, indicating that the toxin is a representative member of a broadly distributed protein family. We propose that TpeV-like toxins contribute to the fitness of many bacteria. Finally, since antibiotic resistance is a critical global health threat, the discovery of new antimicrobial mechanisms could lead to the development of new treatments against resistant strains.

The prevalence of multicellular organisms is due in part to their ability to form complex structures. How cells pack in these structures is a fundamental biophysical issue, underlying their functional properties. However, much remains unknown about how cell packing geometries arise, and how they are affected by random noise during growth - especially absent developmental programs. Here, we quantify the statistics of cellular neighborhoods of two different multicellular eukaryotes: lab-evolved “snowflake” yeast and the green alga Volvox carteri. We find that despite large differences in cellular organization, the free space associated with individual cells in both organisms closely fits a modified gamma distribution, consistent with maximum entropy predictions originally developed for granular materials. This ‘entropic’ cellular packing ensures a degree of predictability despite noise, facilitating parent-offspring fidelity even in the absence of developmental regulation. Together with simulations of diverse growth morphologies, these results suggest that gamma-distributed cell neighborhood sizes are a general feature of multicellularity, arising from conserved statistics of cellular packing.

The Major Transitions in evolution include events and processes that result in the emergence of new levels of biological individuality. For collectives to undergo Darwinian evolution, their traits must be heritable, but the emergence of higher-level heritability is poorly understood and has long been considered a stumbling block for nascent evolutionary transitions. A change in the means by which genetic information is utilized and transmitted has been presumed necessary. Using analytical models, synthetic biology, and biologicallyinformed simulations, we explored the emergence of trait heritability during the evolution of multicellularity. Contrary to existing theory, we show that no additional layer of genetic regulation is necessary for traits of nascent multicellular organisms to become heritable; rather, heritability and the capacity to respond to natural selection on multicellular-level traits can arise “for free.” In fact, we find that a key emergent multicellular trait, organism size at reproduction, is usually more heritable than the underlying cell-level trait upon which it is based, given reasonable assumptions.

Background Like many bacteria, Vibrio cholerae deploys a harpoon-like type VI secretion system (T6SS) to compete against other microbes in environmental and host settings. The T6SS punctures adjacent cells and delivers toxic effector proteins that are harmless to bacteria carrying cognate immunity factors. Only four effector/immunity pairs encoded on one large and three auxiliary gene clusters have been characterized from largely clonal, patient-derived strains of V. cholerae. Results We sequence two dozen V. cholerae strain genomes from diverse sources and develop a novel and adaptable bioinformatics tool based on hidden Markov models. We identify two new T6SS auxiliary gene clusters and describe Aux 5 here. Four Aux 5 loci are present in the host strain, each with an atypical effector/immunity gene organization. Structural prediction of the putative effector indicates it is a lipase, which we name TleV1 (type VI lipase effector Vibrio). Ectopic TleV1 expression induces toxicity in Escherichia coli, which is rescued by co-expression of the TliV1a immunity factor. A clinical V. cholerae reference strain expressing the Aux 5 cluster uses TleV1 to lyse its parental strain upon contact via its T6SS but is unable to kill parental cells expressing the TliV1a immunity factor. Conclusion We develop a novel bioinformatics method and identify new T6SS gene clusters in V. cholerae. We also show the TleV1 toxin is delivered in a T6SS manner by V. cholerae and can lyse other bacterial cells. Our web-based tool can be modified to identify additional novel T6SS genomic loci in diverse bacterial species. Electronic supplementary material The online version of this article (10.1186/s13059-019-1765-5) contains supplementary material, which is available to authorized users.

Thousands of black soldier larvae hatch simultaneously from eggs laid within rotting vegetation or animal carcasses. Over the next few weeks, they grow while compressed by both their surroundings and each other. When compressed, these larvae rearrange to reduce the forces upon them. How quickly can larvae rearrange, and what final state do they choose? In this experimental study, we use a universal testing machine to conduct creep tests on larvae, squeezing them to set volume fractions and measuring the time course of their reaction force. Live larvae come to equilibrium at a rate 10 times faster than dead larvae, indicating that their small movements can rearrange them faster than just settling. The relaxation of dead larvae is well described by stretched exponentials, which also characterize hierarchical self-avoiding materials such as polymers or balls of crumpled aluminum foil. The equilibrium pressures of live larvae are comparable to those of dead larvae, suggesting that such pressures are dictated by the physics of their bodies rather than their behavior. Live larvae perform fluctuations to actively maintain this equilibrium pressure. This ability to survive large pressures might have applications in the larvae-rearing industry, where both live and dead larvae are packed in containers for shipping.

Microbes are social organisms, interacting primarily through secreted biomolecules. Many traits have evolved based solely on their effects upon other community members, yet even individually beneficial traits often create social side effects that are mediated by spatial population structure. Predicting the evolution of many microbial traits thus requires a comprehensive understanding of their social consequences. In this review, we examine the critical role of population spatial structure in microbial social evolution. We briefly review key mechanisms structuring microbial communities, focusing primarily on the universal roles of cellular death and reproduction. Finally, we explain how spatial assortment can be efficiently calculated in two-dimensional, surface-attached populations.

Structural hierarchy, in which materials possess distinct features on multiple length scales, is ubiquitous in nature. Diverse biological materials, such as bone, cellulose, and muscle, have as many as 10 hierarchical levels. Structural hierarchy confers many mechanical advantages, including improved toughness and economy of material. However, it also presents a problem: Each hierarchical level adds a new source of assembly errors and substantially increases the information required for proper assembly. This seems to conflict with the prevalence of naturally occurring hierarchical structures, suggesting that a common mechanical source of hierarchical robustness may exist. However, our ability to identify such a unifying phenomenon is limited by the lack of a general mechanical framework for structures exhibiting organization on disparate length scales. Here, we use simulations to substantiate a generalized model for the tensile stiffness of hierarchical filamentous networks with a nested, dilute triangular lattice structure. Following seminal work by Maxwell and others on criteria for stiff frames, we extend the concept of connectivity in network mechanics and find a similar dependence of material stiffness upon each hierarchical level. Using this model, we find that stiffness becomes less sensitive to errors in assembly with additional levels of hierarchy; although surprising, we show that this result is analytically predictable from first principles and thus potentially model independent. More broadly, this work helps account for the success of hierarchical, filamentous materials in biology and materials design and offers a heuristic for ensuring that desired material properties are achieved within the required tolerance.

Vibrio cholerae is an aquatic Gram-negative bacterium that causes severe diarrheal cholera disease when ingested by humans. To eliminate competitor cells in both the external environment and inside hosts, V. cholerae uses the Type VI Secretion System (T6SS). The T6SS is a macromolecular weapon employed by many Gram-negative bacteria to deliver cytotoxic proteins into adjacent cells. In addition to canonical T6SS gene clusters encoded by all sequenced V. cholerae isolates, strain BGT49 encodes an additional locus, which we named auxiliary cluster 4 (Aux 4). The Aux 4 cluster is located on a mobile genetic element and can be used by killer cells to eliminate both V. cholerae and Escherichia coli cells in a T6SS-dependent manner. A putative toxin encoded in the cluster, which we name TpeV (Type VI Permeabilizing Effector Vibrio), shares no homology to known proteins and does not contain motifs or domains indicative of function. Ectopic expression of TpeV in the periplasm of E. coli permeabilizes cells and disrupts the membrane potential. Using confocal microscopy, we confirm that susceptible target cells become permeabilized when competed with killer cells harboring the Aux 4 cluster. We also determine that tpiV, the gene located immediately downstream of tpeV, encodes an immunity protein that neutralizes the toxicity of TpeV. Finally, we show that TpeV homologs are broadly distributed across important animal and plant pathogens and are localized in proximity to other T6SS genes. Our results suggest that TpeV is a toxin that belongs to a large family of T6SS proteins.IMPORTANCEBacteria live in polymicrobial communities where competition for resources and space is essential for survival. Proteobacteria use the T6SS to eliminate neighboring cells and cause disease. However, the mechanisms by which many T6SS toxins kill or inhibit susceptible target cells are poorly understood. The sequence of the TpeV toxin we describe here is unlike any previously described protein. We demonstrate that it has antimicrobial activity by permeabilizing cells, eliminating membrane potentials and causing severe cytotoxicity. TpeV homologs are found near known T6SS genes in human, animal and plant bacterial pathogens, indicating that the toxin is a representative member of a broadly distributed protein family. We propose that TpeV-like toxins contribute to the fitness and pathogenicity of many bacteria. Finally, since antibiotic resistance is a critical global health threat, the discovery of new antimicrobial mechanisms could lead to the development of new treatments against resistant strains.

Reproductive division of labor (e.g., germ-soma specialization) is a hallmark of the evolution of multicellularity, signifying the emergence of a new type of individual and facilitating the evolution of increased organismal complexity. A large body of work from evolutionary biology, economics, and ecology has shown that specialization is beneficial when further division of labor produces an accelerating increase in absolute productivity (i.e., productivity is a convex function of specialization). Here we show that reproductive specialization is qualitatively different from classical models of resource sharing, and can evolve even when the benefits of specialization are saturating (i.e., productivity is a concave function of specialization). Through analytical theory and evolutionary individual based simulations, our work demonstrates that reproductive specialization is strongly favored in sparse networks of cellular interactions, such as trees and filaments, that reflect the morphology of early, simple multicellular organisms, highlighting the importance of restricted social interactions in the evolution of reproductive specialization. More broadly, we find that specialization is strongly favored, despite saturating returns on investment, in a wide range of scenarios in which sharing is asymmetric.

Biofilms are highly structured, densely packed bacterial consortia where many different species can coexist. During biofilm development and growth, the different species often form spatial distribution patterns that govern biofilm composition and function. In some cases, emerging structures have been explained as the result of social interactions between bacteria, e.g. cooperation and competition. Others emphasize the role of local mechanics, where spatial structuring arises from forces exerted between cells or between cells and their environment. Typically, these two lines of argumentation are treated separately. Here, we show that mechanics and social interactions can be strongly interrelated and their combination can crucially impact biofilm formation and dynamics. Using confocal microscopy and bacterial co-culture assays, we examine how bacterial antagonism impacts biofilm mechanics, and vice versa. We study competing Vibrio cholerae strains that kill on contact using the Type 6 secretion system. In case of mutual killers, i.e. two V. cholerae strains that can kill each other on contact, this social interaction leads to the formation of clonal domains of the competing strains (Mc Nally et al., Nat Commun, 2017). Intuitively, an unequal fight may enable a superior killer to invade and quickly eliminate a much weaker competitor. However, we observe that killer cells can coexist with killing-deficient target cells for very long times, and find that this results from the mechanical consequences of the deadly competition. Killing produces dead cells, which accumulates between domains of competing cells and prevents subsequent killing. Counterintuitively, our results suggest that antagonistic interactions stabilize coexistence in diverse communities. The findings demonstrate that the impact of social interactions in bacterial consortia is complex, requiring the understanding of the structural and the statistical-mechanical processes in biofilms.

Evolutionary arms races among organisms are broadly prevalent and bacteria have evolved defensive strategies against various attackers. A common microbial aggression mechanism is the Type VI Secretion System (T6SS), a contact-dependent bacterial weapon used to deliver toxic effector proteins into adjacent target cells. Sibling cells constitutively express immunity proteins that neutralize effectors. However, less is known about mechanisms that allow non-sibling bacteria to respond to external cues and survive T6SS attacks independently of immunity proteins. In this study, we show that resistance to T6SS attacks is promoted by a genetically controlled response to exogenous glucose. We observe that multiple human Escherichia coli commensal strains lacking immunity proteins are sensitive to T6SS attacks from pandemic Vibrio cholerae on nutrient-rich media. By contrast, E. coli cells become resistant to attacks when co-cultured on the same media with glucose. We confirm that glucose does not impair V. cholerae T6SS activity. Instead, we find that cAMP receptor protein (CRP), which alters expression of hundreds of genes in response to glucose, controls resistance to T6SS attacks in E. coli cells. Consistent with the observed resistance on media with glucose, an E. coli crp disruption mutant survives significantly better against V. cholerae T6SS attacks even in the absence of glucose. Finally, we also show that resistance to T6SS attacks depends on the pH of the medium and varies based on the target and killer strains.IMPORTANCEMany Gram-negative bacteria, including important pathogens, encode T6SS genes to deliver toxic effectors and eliminate competitors. Our results uncover a novel defense mechanism against T6SS attacks that is triggered by an external stimulus and mediated by a metabolic response in non-kin target cells. In microbiomes such as those in gastrointestinal tracts where T6SS activity is known to occur, signaling by metabolites like glucose may affect the efficacy of T6SS attacks and alter microbial community composition. Our findings could have vast implications for microbial interactions during pathogen colonization of hosts and survival of bacterial cells in environmental communities. Furthermore, the glucose-mediated resistance observed here might provide a novel example of an evolutionary arms race between killer T6SS cells and target bacteria.

Bacterial communities are governed by a wide variety of social interactions, some of which are antagonistic with potential significance for bacterial warfare. Several antagonistic mechanisms, such as killing via the type VI secretion system (T6SS), require killer cells to directly contact target cells. The T6SS is hypothesized to be a highly potent weapon, capable of facilitating the invasion and defence of bacterial populations. However, we find that the efficacy of contact killing is severely limited by the material consequences of cell death. Through experiments withVibrio choleraestrains that kill via the T6SS, we show that dead cell debris quickly accumulates at the interface that forms between competing strains, preventing physical contact and thus preventing killing. While previous experiments have shown that T6SS killing can reduce a population of target cells by as much as 106-fold, we find that, as a result of the formation of dead cell debris barriers, the impact of contact killing depends sensitively on the initial concentration of killer cells. Killer cells are incapable of invading or eliminating competitors on a community level. Instead, bacterial warfare itself can facilitate coexistence between nominally antagonistic strains. While a variety of defensive strategies against microbial warfare exist, the material consequences of cell death provide target cells with their first line of defence.

Honey bees ( Apis mellifera ) carry pollen back to their hive by mixing it with nectar and forming it into a pellet. The pellet must be firmly attached to their legs during flight, but also easily removable when deposited in the hive. How does the honey bee achieve these contrary aims? In this experimental study, we film honey bees removing pollen pellets and find they peel them off at speeds 2–10 times slower than their typical grooming speeds. Using a self-built pollen scraper, we find that slow removal speeds reduce the force and work required to remove the pellet under shear stress. Creep tests on individual pollen pellets revealed that pollen pellets are viscoelastic materials characterized by a Maxwell model with long relaxation times. The relaxation time enables the pellet to remain a solid during both transport and removal. We hope that this work inspires further research into viscoelastic materials in nature.

Encapsulated microbes have been used for decades to produce commodities ranging from methyl ketone to beer. Encapsulated cells undergo limited replication, which enables them to more efficiently convert substrate to product than planktonic cells and which contributes to their stress resistance. To determine how encapsulated yeast supports long‐term, repeated fed‐batch ethanologenic fermentation, and whether different matrices influence that process, fermentation and indicators of matrix durability and cell viability were monitored in high‐dextrose, fed‐batch culture over 7 weeks. At most timepoints, ethanol yield (g/g) in encapsulated cultures exceeded that in planktonic cultures. And frequently, ethanol yield differed among the four matrices tested: sodium alginate crosslinked with Ca2+ and chitosan, sodium alginate crosslinked with Ca2+, Protanal alginate crosslinked with Ca2+ and chitosan, Protanal alginate crosslinked with Ca2+, with the last of these consistently demonstrating the highest values. Young's modulus and viscosity were higher for matrices crosslinked with chitosan over the first week; thereafter values for both parameters declined and were indistinguishable among treatments. Encapsulated cells exhibited greater heat shock tolerance at 50°C than planktonic cells in either stationary or exponential phase, with similar thermotolerance observed across all four matrix types. Altogether, these data demonstrate the feasibility of re‐using encapsulated yeast to convert dextrose to ethanol over at least 7 weeks.

Summary All multicellular organisms develop through one of two basic routes: they either aggregate from free-living cells, creating potentially chimeric multicellular collectives, or they develop clonally via mother-daughter cellular adhesion. Although evolutionary theory makes clear predictions about trade-offs between these developmental modes, these have never been experimentally tested in otherwise genetically identical organisms. We engineered unicellular baker’s yeast (Saccharomyces cerevisiae) to develop either clonally (“snowflake”; Δace2) or aggregatively (“floc”; GAL1p::FLO1) and examined their fitness in a fluctuating environment characterized by periods of growth and selection for rapid sedimentation. When cultured independently, aggregation was far superior to clonal development, providing a 35% advantage during growth and a 2.5-fold advantage during settling selection. Yet when competed directly, clonally developing snowflake yeast rapidly displaced aggregative floc. This was due to unexpected social exploitation: snowflake yeast, which do not produce adhesive FLO1, nonetheless become incorporated into flocs at a higher frequency than floc cells themselves. Populations of chimeric clusters settle much faster than floc alone, providing snowflake yeast with a fitness advantage during competition. Mathematical modeling suggests that such developmental cheating may be difficult to circumvent; hypothetical “choosy floc” that avoid exploitation by maintaining clonality pay an ecological cost when rare, often leading to their extinction. Our results highlight the conflict at the heart of aggregative development: non-specific cellular binding provides a strong ecological advantage—the ability to quickly form groups—but this very feature leads to its exploitation.

The integration of automotive technology with Internet-connectivity promises to both dramatically improve transportation, while simultaneously introducing the potential for new unknown risks. Internet-connected vehicles are like digital data because they can be targeted for malicious hacking. Unlike digital data, however, Internet-connected vehicles are cyber-physical systems that physically interact with each other and their environment. As such, the extension of cybersecurity concerns into the cyber-physical domain introduces new possibilities for self-organized phenomena in traffic flow. Here, we study a scenario envisioned by cybersecurity experts leading to a large number of Internet-connected vehicles being suddenly and simultaneously disabled. We investigate post-hack traffic using agent-based simulations, and discover the critical relevance of percolation for probabilistically predicting the outcomes on a multi-lane road in the immediate aftermath of a vehicle-targeted cyber attack. We develop an analytic percolation-based model to rapidly assess road conditions given the density of disabled vehicles and apply it to study the street network of Manhattan (NY, USA) revealing the city's vulnerability to this particular cyber-physical attack., 11 pages, 4 figures

BackgroundLike many bacteria, Vibrio cholerae, which causes fatal cholera, deploys a harpoon-like Type VI Secretion System (T6SS) to compete against other microbes in environmental and host settings. The T6SS punctures adjacent cells and delivers toxic effector proteins that are harmless to bacteria carrying cognate immunity factors. Only four effector/immunity pairs encoded on one large and three auxiliary gene clusters have been characterized from largely clonal, patient-derived strains of V. cholerae.ResultsWe sequenced two dozen V. cholerae strain genomes from diverse sources and developed a novel and adaptable bioinformatic tool based on Hidden Markov Models. We identified two new T6SS auxiliary gene clusters; one, Aux 5, is described here. Four Aux 5 loci are present in the host strain, each with an atypical effector/immunity gene organization. Structural prediction of the putative effector indicated it is a lipase, which we name TleV1 (Type VI lipase effector Vibrio, TleV1). Ectopic TleV1 expression induced toxicity in E. coli, which was rescued by co-expression of the TleV1 immunity factor. A clinical V. cholerae reference strain expressing the Aux 5 cluster used TleV1 to lyse its parental strain upon contact via its T6SS but was unable to kill parental cells expressing TleV1’s immunity factor.ConclusionWe developed a novel bioinformatic method and identified new T6SS gene clusters in V. cholerae. We also showed the TleV1 toxin is delivered in a T6SS-manner by V. cholerae and can lyse other bacterial cells. Our web-based tool may be modified to identify additional novel T6SS genomic loci in diverse bacterial species.

Negative frequency-dependent selection (i.e., declining fitness with increased frequency in the population) is thought to be one of the factors that maintains biological diversity. In this paper, we give a concrete mathematical argument supporting this. Our model is as follows: A collection of species derive their fitnesses via a rock-paper-scissors-type game whose precise payoffs are a function of the environment. The new aspect of our model lies in adding a feedback loop: the environment changes according to the relative fitnesses of the species (hence, payoffs change as a function of fitness, which in turn changes as a function of payoffs). The changes in the payoffs are in keeping with the principle of negative frequency-dependent selection, which is widespread in nature. In order to model our game as a continuous time dynamical system, we cast it in the setting of a differential game. We show that for certain parameters, this dynamics cycles, i.e., no species goes extinct and diversity is maintained. We believe that our techniques can be applied to optimization and machine learning to show that first order methods (e.g., gradient descent/ascent) do cycle even in online settings in which the loss function changes with time.

Hypothesis The manipulation of nanosheets on a fluid-fluid interface remains a significant challenge. At this interface, hydrodynamic forces can be used for long-range transport (>1× capillary length) but are difficult to utilize for accurate and repeatable positioning. While capillary multipole interactions have been used for particle trapping, how these interactions manifest on large but thin objects, i.e., nanosheets, remains an open question. Hence, we posit hydrodynamic forces in conjunction with capillary multipole interactions can be used for nanosheet transport and trapping. Experiments We designed and characterized a fluidic device for transporting and trapping nanosheets on the water-air interface. Analytical models were compared against optical measurements of the nanosheet behavior to investigate capillary multipole interactions. Energy-based modeling and dimensional analysis were used to study trapping stability. Findings Hydrodynamic forces and capillary interactions successfully transported and trapped nanosheets at a designated trapping location with a repeatability of 10% of the nanosheet’s length and 12% of its width (length = 1500 µm, width = 1000 µm) and an accuracy of 20% of their length and width. Additionally, this is the first report that surface tension forces acting upon nanoscale-thick objects manifest as capillary quadrupolar interactions and can be used for precision manipulation of nanosheets.

The evolution of multicellularity set the stage for sustained increases in organismal complexity 1–5 . However, a fundamental aspect of this transition remains largely unknown: how do simple clusters of cells evolve increased size when confronted by forces capable of breaking intracellular bonds? Here we show that multicellular snowflake yeast clusters 6–8 fracture due to crowding-induced mechanical stress. Over seven weeks (~291 generations) of daily selection for large size, snowflake clusters evolve to increase their radius 1.7-fold by reducing the accumulation of internal stress. During this period, cells within the clusters evolve to be more elongated, concomitant with a decrease in the cellular volume fraction of the clusters. The associated increase in free space reduces the internal stress caused by cellular growth, thus delaying fracture and increasing cluster size. This work demonstrates how readily natural selection finds simple, physical solutions to spatial constraints that limit the evolution of group size—a fundamental step in the evolution of multicellularity. Understanding how single cells evolved into multicellular organisms requires knowledge of the physical constraints on the evolution of cell clusters. Evidence that an evolution in cell shape delays fracturing offers a route to increased complexity.

The deposition process at the edge of evaporating colloidal drops varies with the shape of suspended particles. Experiments with prolate ellipsoidal particles suggest that the spatiotemporal properties of the deposit depend strongly on particle aspect ratio. As the aspect ratio increases, the particles form less densely-packed deposits and the statistical behavior of the deposit interface crosses over from the Kardar-Parisi-Zhang (KPZ) universality class to another universality class which was suggested to be consistent with the KPZ plus quenched disorder. Here, we numerically study the effect of particle interaction anisotropy on deposit growth. In essence, we model the ellipsoids, at the interface, as disk-like particles with two types of interaction patches that correspond to specific features at the poles and equator of the ellipsoid. The numerical results corroborate experimental observations and further suggest that the deposition transition can stem from interparticle interaction anisotropy. Possible extensions of our model to other systems are also discussed.

All multicellular organisms develop through one of two basic routes: they either aggregate from free-living cells, creating potentially-chimeric multicellular collectives, or they develop clonally via mother-daughter cellular adhesion. While evolutionary theory makes clear predictions about trade-offs between these developmental modes, these have never been experimentally tested in otherwise genetically-identical organisms. We engineered unicellular baker’s yeast (Saccharomyces cerevisiae) to develop either clonally (‘snowflake’, Δace2), or aggregatively (‘floc’,GAL1p::FLO1), and examined their fitness in a fluctuating environment characterized by periods of growth and selection for rapid sedimentation. When cultured independently, aggregation was far superior to clonal development, providing a 35% advantage during growth, and a 2.5-fold advantage during settling selection. Yet when competed directly, clonally-developing snowflake yeast rapidly displaced aggregative floc. This was due to unexpected social exploitation: snowflake yeast, which do not produce adhesive FLO1, nonetheless become incorporated into flocs at a higher frequency than floc cells themselves. Populations of chimeric clusters settle much faster than floc alone, providing snowflake yeast with a fitness advantage during competition. Mathematical modeling suggests that such developmental cheating may be difficult to circumvent; hypothetical ‘choosy floc’ that avoid exploitation by maintaining clonality pay an ecological cost when rare, often leading to their extinction. Our results highlight the conflict at the heart of aggregative development: non-specific cellular binding provides a strong ecological advantage – the ability to quickly form groups – but this very feature leads to its exploitation.

The evolutionary transition to multicellularity transformed life on earth, allowing for the evolution of large, complex organisms. While multicellularity can be strongly advantageous, its earliest stages bring unique physical challenges. Nascent multicellular organisms must contend with a novel constraint: intercellular stresses arising from cell-cell interactions that can limit multicellular size. Among the possible evolutionary routes to overcoming this size limit, two appear obvious: multicellular organisms can increase intercellular bond strength, allowing them to tolerate larger stresses, or, they can slow the rate of stress accumulation by altering their internal structure. Recent experiments demonstrated that multicellular 'snowflake yeast' readily find a solution to this problem via the latter route. By evolving more elongated cells, which decreases cellular packing fraction and thus the rate of internal stress accumulation during growth, snowflake yeast evolve to delay fracture and grow larger. However, it is unclear if snowflake yeast evolved large size along an optimal path, or if the observed path to large size was taken due to proximate biological reasons. Here, we examine the geometric efficiency of both strategies using a minimal model that was previously demonstrated to replicate many experimentally observed structural properties of snowflake yeast. We find that changing geometry is a far more efficient route to large size than evolving increased intercellular adhesion. In fact, increasing cellular aspect ratio is on average ~13 times more effective at increasing the number of cells in a cluster than increasing bond strength. These results suggest that geometrically-imposed physical constraints may have been a key early selective force guiding the emergence of multicellular complexity.

We demonstrate real-time quantitative phase imaging as a new optical approach for measuring the evaporation dynamics of sessile microdroplets. Quantitative phase images of various droplets were captured during evaporation. The images enabled us to generate time-resolved three-dimensional topographic profiles of droplet shape with nanometer accuracy and, without any assumptions about droplet geometry, to directly measure important physical parameters that characterize surface wetting processes. Specifically, the time-dependent variation of the droplet height, volume, contact radius, contact angle distribution along the droplet's perimeter, and mass flux density for two different surface preparations are reported. The studies clearly demonstrate three phases of evaporation reported previously: pinned, depinned, and drying modes; the studies also reveal instances of partial pinning. Finally, the apparatus is employed to investigate the cooperative evaporation of the sprayed droplets. We observe and explain the neighbor-induced reduction in evaporation rate, that is, as compared to predictions for isolated droplets. In the future, the new experimental methods should stimulate the exploration of colloidal particle dynamics on the gas-liquid-solid interface.

Liquid crystals can organize dispersed particles into useful and exotic structures. In the case of lyotropic cholesteric polypeptide liquid crystals, polypeptide-coated particles are appealing because the surface chemistry matches that of the polymeric mesogen, which permits a tighter focus on factors such as extended particle shape. The colloidal particles developed here consist of a magnetic and fluorescent cylindrically symmetric silica core with one rounded, almost hemispherical end. Functionalized with helical poly(γ-stearyl-l-glutamate) (PSLG), the particles were dispersed at different concentrations in cholesteric liquid crystals (ChLC) of the same polymer in tetrahydrofuran (THF). Defects introduced by the particles to the director field of the bulk PSLG/THF host led to a variety of phases. In fresh mixtures, the cholesteric mesophase of the PSLG matrix was distorted, as reflected in the absence of the characteristic fingerprint pattern. Over time, the fingerprint pattern returned, more quickly when the concentration of the PSLG-coated particles was low. At low particle concentration the particles were "guided" by the PSLG liquid crystal to organize into patterns similar to that of the re-formed bulk chiral nematic phase. When their concentration increased, the well-dispersed PSLG-coated particles seemed to map onto the distortions in the bulk host's local director field. The particles located near the glass vial-ChLC interfaces were stacked lengthwise into architectures with apparent two-dimensional hexagonal symmetry. The size of these "crystalline" structures increased with particle concentration. They displayed remarkable stability toward an external magnetic field; hydrophobic interactions between the PSLG polymers in the shell and those in the bulk LC matrix may be responsible. The results show that bio-inspired LCs can assemble suitable colloidal particles into soft crystalline structures.

In a broad class of complex materials a quench leads to a multi-scaled relaxation process known as aging. To explain its commonality and the astounding insensitivity to most microscopic details, record dynamics (RD) posits that a small set of increasingly rare and irreversible events, so called quakes, controls the dynamics. While key predictions of RD are known to concur with a number of experimental and simulational results, its basic assumption on the nature of quake statistics has proven extremely difficult to verify experimentally. The careful distinction of rare ("record") cage-breaking events from in-cage rattle accomplished in previous experiments on jammed colloids, enables us to extract the first direct experimental evidence for the fundamental hypothesis of RD that the rate of quakes decelerates with the inverse of the system age. The resulting description shows the predicted growth of the particle mean square displacement and of a mesoscopic lengthscale with the logarithm of time., 6 pages, RevTex, changed title, many updates and corrections; for related information, see http://www.physics.emory.edu/faculty/boettcher/

SummaryBy nature of their small size, dense growth and frequent need for extracellular metabolism, microbes face persistent public goods dilemmas1–5. Spatial assortment can act as a general solution to social conflict by allowing extracellular goods to be utilized preferentially by productive genotypes1,6,7. Established mechanisms that generate microbial assortment depend on the availability of free space8–14; however, microbes often live in densely-packed environments, wherein these mechanisms are ineffective. Here, we describe a novel class of self-organized pattern formation that facilitates the development of spatial structure within densely-packed bacterial colonies. Contact-mediated killing through the Type VI secretion system (T6SS) drives high levels of assortment by precipitating phase separation, even in initially well-mixed populations that do not necessarily exhibit net growth. We examine these dynamics using three different classes of mathematical models and experiments with mutually antagonistic strains of Vibrio cholerae growing on solid media, and find that all appear to de-mix via the same ‘Model A’ universality class of order-disorder transition. We mathematically demonstrate that contact killing should favour the evolution of public goods cooperation, and empirically examine the relationship between T6SSs and potential cooperation through phylogenetic analysis. Across 26 genera of Proteobacteria and Bacteroidetes, the proportion of a strain’s genome that codes for potentially-exploitable secreted proteins increases significantly with boththe number of Type 6 secretion systems and the number of T6SS effectors that it possesses. This work demonstrates how antagonistic traits—likely evolved for the purpose of killing competitors—can indirectlylead to the evolution of cooperation by driving genetic phase separation.

Single-span membrane proteins (ssMPs) represent approximately one-half of all membrane proteins and play important roles in cellular communications. However, like all membrane proteins, ssMPs are prone to misfolding and aggregation because of the hydrophobicity of transmembrane helices, making them difficult to study using common aqueous solution-based approaches. Detergents and membrane mimetics can solubilize membrane proteins but do not always result in proper folding and functionality. Here, we use cell-free protein synthesis in the presence of oil drops to create a one-pot system for the synthesis, assembly, and display of functional ssMPs. Our studies suggest that oil drops prevent aggregation of some in vitro-synthesized ssMPs by allowing these ssMPs to localize on oil surfaces. We speculate that oil drops may provide a hydrophobic interior for cotranslational insertion of the transmembrane helices and a fluidic surface for proper assembly and display of the ectodomains. These functionalized oil drop surfaces could mimic cell surfaces and allow ssMPs to interact with cell surface receptors under an environment closest to cell-cell communication. Using this approach, we showed that apoptosis-inducing human transmembrane proteins, FasL and TRAIL, synthesized and displayed on oil drops induce apoptosis of cultured tumor cells. In addition, we take advantage of hydrophobic interactions of transmembrane helices to manipulate the assembly of ssMPs and create artificial clusters on oil drop surfaces. Thus, by coupling protein synthesis with self-assembly at the water-oil interface, we create a platform that can use recombinant ssMPs to communicate with cells.

The influence of the small ionic surfactant sodium dodecyl sulfate (SDS) on the evaporation of drying colloidal droplets is quantitatively investigated. The addition of SDS leads to a significantly more uniform deposition of colloidal particles after evaporation (i.e., the so-called "coffee-ring effect" is dramatically altered). We understand this phenomenon in the context of circulating radial Marangoni flows induced by the variation of SDS concentration along the air-water interface. Video microscopy permits the direct visualization of the colloidal particles involved in these flows, revealing a surprisingly stable "Marangoni eddy" that prevents particle deposition at the drop perimeter.

When a drop of liquid dries on a solid surface, its suspended particulate matter is deposited in ring-like fashion. This phenomenon, known as the coffee-ring effect, is familiar to anyone who has observed a drop of coffee dry. During the drying process, drop edges become pinned to the substrate, and capillary flow outward from the centre of the drop brings suspended particles to the edge as evaporation proceeds. After evaporation, suspended particles are left highly concentrated along the original drop edge. The coffee-ring effect is manifested in systems with diverse constituents, ranging from large colloids to nanoparticles and individual molecules. In fact--despite the many practical applications for uniform coatings in printing, biology and complex assembly-the ubiquitous nature of the effect has made it difficult to avoid. Here we show experimentally that the shape of the suspended particles is important and can be used to eliminate the coffee-ring effect: ellipsoidal particles are deposited uniformly during evaporation. The anisotropic shape of the particles significantly deforms interfaces, producing strong interparticle capillary interactions. Thus, after the ellipsoids are carried to the air-water interface by the same outward flow that causes the coffee-ring effect for spheres, strong long-ranged interparticle attractions between ellipsoids lead to the formation of loosely packed or arrested structures on the air-water interface. These structures prevent the suspended particles from reaching the drop edge and ensure uniform deposition. Interestingly, under appropriate conditions, suspensions of spheres mixed with a small number of ellipsoids also produce uniform deposition. Thus, particle shape provides a convenient parameter to control the deposition of particles, without modification of particle or solvent chemistry.

When the packing fraction is increased sufficiently, loose particulates jam to form a rigid solid in which the constituents are no longer free to move. In typical granular materials and foams, the thermal energy is too small to produce structural rearrangements. However, because thermal motion becomes relevant when the particles are small enough, it is imperative to understand the behaviour as the temperature is increased. Zhang et al. use both colloidal experiments and computer simulations to investigate the overlap distance between neighbouring particles beyond the zero-temperature limit. They find that this quantity evolves in an unusual manner, retaining a vestige of its zero-temperature behaviour. When the packing fraction is increased sufficiently, loose particulates jam together to form a rigid solid in which the constituents are no longer free to move. Although in typical granular materials and foams the thermal energy is too small to produce structural rearrangements, thermal motion becomes relevant when the particles are small enough. Here, colloidal experiments and computer simulations are used to investigate the overlap distance between neighbouring particles beyond the zero-temperature limit, revealing some surprising behaviour. When the packing fraction is increased sufficiently, loose particulates jam to form a rigid solid in which the constituents are no longer free to move. In typical granular materials and foams, the thermal energy is too small to produce structural rearrangements. In this zero-temperature (T = 0) limit, multiple diverging1,2,3,4,5,6,7,8 and vanishing2,9,10 length scales characterize the approach to a sharp jamming transition. However, because thermal motion becomes relevant when the particles are small enough, it is imperative to understand how these length scales evolve as the temperature is increased. Here we used both colloidal experiments and computer simulations to progress beyond the zero-temperature limit to track one of the key parameters—the overlap distance between neighbouring particles—which vanishes at the T = 0 jamming transition. We find that this structural feature retains a vestige of its T = 0 behaviour and evolves in an unusual manner, which has masked its appearance until now. It is evident as a function of packing fraction at fixed temperature, but not as a function of temperature at fixed packing fraction or pressure. Our results conclusively demonstrate that length scales associated with the T = 0 jamming transition persist in thermal systems, not only in simulations but also in laboratory experiments.

Geometric frustration arises when lattice structure prevents simultaneous minimization of local interactions. It leads to highly degenerate ground states and, subsequently, complex phases of matter such as water ice, spin ice and frustrated magnetic materials. Here we report a simple geometrically frustrated system composed of closely packed colloidal spheres confined between parallel walls. Diameter-tunable microgel spheres are self-assembled into a buckled triangular lattice with either up or down displacements analogous to an antiferromagnetic Ising model on a triangular lattice. Experiment and theory reveal single-particle dynamics governed by in-plane lattice distortions that partially relieve frustration and produce ground-states with zigzagging stripes and subextensive entropy, rather than the more random configurations and extensive entropy of the antiferromagnetic Ising model. This tunable soft matter system provides an uncharted arena in which the dynamics of frustration, thermal excitations and defects can be directly visualized., (*) These authors contributed equally to this work. Main Text: 6 pages, 5 figures. Supplementary Information and Online Movies available at http://www.physics.upenn.edu/~yair/frustration.html

This review collects and describes experiments that employ colloidal suspensions to probe physics in ordered and disordered solids and related complex fluids. The unifying feature of this body of work is its clever usage of poly(N-isopropylacrylamide) (PNIPAM) microgel particles. These temperature-sensitive colloidal particles provide experimenters with a 'knob' for in situ control of particle size, particle interaction and particle packing fraction that, in turn, influence the structural and dynamical behavior of the complex fluids and solids. A brief summary of PNIPAM particle synthesis and properties is given, followed by a synopsis of current activity in the field. The latter discussion describes a variety of soft matter investigations including those that explore formation and melting of crystals and clusters, and those that probe structure, rearrangement and rheology of disordered (jammed/glassy) and partially ordered matter. The review, therefore, provides a snapshot of a broad range of physics phenomenology which benefits from the unique properties of responsive microgel particles.

We study phonon modes in two-dimensional colloidal crystals composed of soft microgel particles with hard polystyrene particle dopants distributed randomly on the triangular lattice. This experimental approach produces close-packed lattices of spheres with random bond strength disorder, i.e., the effective springs coupling nearest neighbors are very stiff, very soft, or of intermediate stiffness. Particle tracking video microscopy and covariance matrix techniques are then employed to derive the phonon modes of the corresponding "shadow" crystals with bond strength disorder as a function of increasing dopant concentration. At low frequencies, hard and soft particles participate equally in the phonon modes, and the samples exhibit Debye-like density of states behavior characteristic of crystals. For mid- and high-frequency phonons, the relative participation of hard versus soft particles in each mode is found to vary systematically with dopant concentration. Additionally, a few localized modes, primarily associated with hard particle motions, are found at the highest frequencies.

Particle tracking and displacement covariance matrix techniques are employed to investigate the phonon dispersion relations of two-dimensional colloidal glasses composed of soft, thermoresponsive microgel particles whose temperature-sensitive size permits \textit{in situ} variation of particle packing fraction. Bulk, $B$, and shear, $G$, moduli of the colloidal glasses are extracted from the dispersion relations as a function of packing fraction, and variation of the ratio $G/B$ with packing fraction is found to agree quantitatively with predictions for jammed packings of frictional soft particles. In addition, $G$ and $B$ individually agree with numerical predictions for frictional particles. This remarkable level of agreement enabled us to extract an energy scale for the inter-particle interaction from the individual elastic constants and to derive an approximate estimate for the inter-particle friction coefficient.

We study the influence of particle shape on growth processes at the edges of evaporating drops. Aqueous suspensions of colloidal particles evaporate on glass slides, and convective flows during evaporation carry particles from drop center to drop edge, where they accumulate. The resulting particle deposits grow inhomogeneously from the edge in two dimensions, and the deposition front, or growth line, varies spatiotemporally. Measurements of the fluctuations of the deposition front during evaporation enable us to identify distinct growth processes that depend strongly on particle shape. Sphere deposition exhibits a classic Poisson-like growth process; deposition of slightly anisotropic particles, however, belongs to the Kardar-Parisi-Zhang universality class, and deposition of highly anisotropic ellipsoids appears to belong to a third universality class, characterized by Kardar-Parisi-Zhang fluctuations in the presence of quenched disorder.

Water-lutidine mixtures permit the interparticle potentials of colloidal particles suspended therein to be tuned, in situ, from repulsive to attractive. We employ these systems to directly elucidate the effects of interparticle potential on glass dynamics in experimental samples composed of the same particles at the same packing fractions. Cooperative rearrangement regions (CRRs) and heterogeneous dynamics are observed in both types of glasses. Compared to repulsive glasses, the attractive glass dynamics are found to be heterogeneous over a wider range of time and length scales, and its CRRs involve more particles. Additionally, the CRRs are observed to be stringlike structures in repulsive glasses and compact structures in attractive glasses. Thus, the experiments demonstrate explicitly that glassy dynamics can depend on the sign of the interparticle interaction.

We investigate the influence of morphology and size on the vibrational properties of disordered clusters of colloidal particles with attractive interactions. From measurements of displacement correlations between particles in each cluster, we extract vibrational properties of the corresponding "shadow" glassy cluster, with the same geometric configuration and interactions as the "source" cluster but without damping. Spectral features of the vibrational modes are found to depend strongly on the average number of nearest neighbors, $\bar{NN}$, but only weakly on the number of particles in each glassy cluster. In particular, the median phonon frequency, $��_{med}$, is essentially constant for $\bar{NN}$ $2$. This behavior parallels concurrent observations about local isostatic structures, which are absent in clusters with $\bar{NN}$ $2$. Thus, cluster vibrational properties appear to be strongly connected to cluster mechanical stability (i.e., fraction of locally isostatic regions), and the scaling of $��_{med}$ with $\bar{NN}$ is reminiscent of the behavior of packings of spheres with repulsive interactions at the jamming transition. Simulations of random networks of springs corroborate observations and suggest that connections between phonon spectra and nearest neighbor number are generic to disordered networks., 5 pages, 3 figures

We investigate correlations between low-frequency vibrational modes and rearrangements in two-dimensional colloidal glasses composed of thermosensitive microgel particles, which readily permit variation of the sample packing fraction. At each packing fraction, the particle displacement covariance matrix is measured and used to extract the vibrational spectrum of the "shadow" colloidal glass (i.e., the particle network with the same geometry and interactions as the sample colloid but absent damping). Rearrangements are induced by successive, small reductions in the packing fraction. The experimental results suggest that low-frequency quasilocalized phonon modes in colloidal glasses, i.e., modes that present low energy barriers for system rearrangements, are spatially correlated with rearrangements in this thermal system.