Spatial Self-organization Research Articles

Optical pattern formation of laser fields in the Rydberg atomic gases

We study the phenomena of long-wave and short-wave modulation instabilities (LMI and SMI) in Rydberg atomic gases within the framework of the nonlocal nonlinear Schrödinger equations in the local and nonlocal regions (characterized by the ratio of beam radius to radius of Rydberg blockade sphere), respectively. We further reveal the rich soliton dynamics arising from interactions of nonlinear waves triggered by LMI. We also show the variety of spatial self-organization pattern formations and their active manipulation due to SMI. Through a synthesis of theoretical analysis and numerical simulations, the self-organized optical structures reported here provide a way for realizing what we believe to be novel optical patterns and solitons based on Rydberg atomic gases.

Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth

Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance.

Experimental simulation evaluation and control measures of paving segregation for the stone matrix asphalt mixtures

The aggregate segregation for asphalt mixtures, characterized by non-uniform particle distribution, significantly undermines the quality and performance of pavements. This investigation aims to explore and reveal the mechanisms underlying segregation, including raw material properties and construction procedures. Novel evaluation methods, predictive metrics, and control measures were introduced using the developed apparatus. The results indicate that physical properties, particle morphology, and gradation are fundamental factors driving segregation. Spatial hindrance, interfacial friction, collision, and self-organization collectively coordinate particle spatial migration and distribution. Excessive coarse particles induce interstitial displacement, while that of fine particles trigger third-body lubrication. The lubricating-bonding factor η was proposed to characterize asphalt regulation. Segregation prediction based on composite angularity facilitates informed raw material selection. In addition, measures to improve paving quality and efficiency during loading, unloading, and auger mixing were proposed. This research contributes to the understanding of segregation mechanisms, enabling early prevention and effective management strategies.

Carbonate mounds formed by mud volcanism at the Cretaceous-Paleogene boundary, Saudi Arabia

More than 1000 mound structures have been mapped in shallow marine sediments at the Cretaceous-Paleogene boundary in the Rub’ Al-Khali of Saudi Arabia. Mapping used 3D reflection seismic data in a 37,000 km2 study area. No wells penetrate the mounds themselves. The mounds are at a present-day subsurface depth of approximately 1 km, and they are convex-up with diameters of 200–400 m and elevation of 10–15 m. The mounds display spatial self-organization with a mean separation of approximately 3.75 km. Comparison with mound populations in other study areas with known spatial distribution statistics and modes of origin indicates that the mound population in this study has the characteristics of fluid escape structures, and they are interpreted here as mud volcanoes. The observation that the mounds occur at the Cretaceous-Paleogene boundary demands a singular trigger at that moment in time. We develop a model of seismic energy-related mud volcanism mechanism including the Chicxulub asteroid impact as the energy source that accounts for the timing of the mound structures and a drainage cell model based on producing water wells that provides a mechanism for spatial self-organization into a regular pattern.

Robust spatial self-organization in crowds of asynchronous pedestrians.

Human crowds display various self-organized collective behaviours, such as the spontaneous formation of unidirectional lanes in bidirectional pedestrian flows. In addition, parts of pedestrians' footsteps are known to be spontaneously synchronized in one-dimensional, single-file crowds. However, footstep synchronization in crowds with more freedom of movement remains unclear. We conducted experiments on bidirectional pedestrian flows (24 pedestrians in each group) and examined the relationship between collective footsteps and self-organized lane formation. Unlike in previous studies, pedestrians did not spontaneously synchronize their footsteps unless following external auditory cues. Moreover, footstep synchronization generated by external cues disturbed the flexibility of pedestrians' lateral movements and increased the structural instability of spatial organization. These results imply that, without external cues, pedestrians marching out of step with each other can efficiently self-organize into robust structures. Understanding how asynchronous individuals contribute to ordered collective behaviour might bring innovative perspectives to research fields concerned with self-organizing systems.

Experimental study on control of transverse jet mixing by arrayed plasma energy deposition

The efficient and prompt mixing of fuel is crucial in the operation of scramjet engines. This paper presents the findings from wind tunnel experiments that examined the influence of plasma energy deposition on transverse jets at a Mach number of 6.13. The study took into account various inlet flow total pressures and momentum flux ratios between the jet and the main flow. Utilizing a database containing time-resolved intensities from instantaneous schlieren images, we perform turbulence analysis employing various techniques such as the root mean square, fast Fourier transform, proper orthogonal decomposition, and the two-point correlation method. Specifically, we aim to compare and analyze the pulsation characteristics and spatial self-organization of the jet flow field, both with and without energy deposition control. The findings reveal that intermittent “hot bubbles” created by plasma energy deposition interact with the bow shock induced by the jet, resulting in the formation of an array of large-scale vortices. These vortices emerge as the dominant structures within the jet, effectively amplifying its pulsations. At low inlet flow pressures, energy deposition primarily disrupts the jet, causing large-scale vortices to propagate primarily within the jet plume region. However, at high inlet flow pressures, the impact of energy deposition extends to both the jet and the turbulent boundary layer, encompassing their respective disturbance ranges. Increasing the inlet flow pressure constraints the evolution of large-scale vortices, thus limiting the efficacy of energy deposition in governing the mixing process.

Spatial organization of a soil cyanobacterium and its cyanosphere through GABA/Glu signaling to optimize mutualistic nitrogen fixation.

Soil biocrusts are characterized by the spatial self-organization of resident microbial populations at small scales. The cyanobacterium Microcoleus vaginatus, a prominent primary producer and pioneer biocrust former, relies on a mutualistic carbon (C) for nitrogen (N) exchange with its heterotrophic cyanosphere microbiome, a mutualism that may be optimized through the ability of the cyanobacterium to aggregate into bundles of trichomes. Testing both environmental populations and representative isolates, we show that the proximity of mutualistic diazotroph populations results in M. vaginatus bundle formation orchestrated through chemophobic and chemokinetic responses to gamma-aminobutyric acid (GABA) /glutamate (Glu) signals. The signaling system is characterized by: a high GABA sensitivity (nM range) and low Glu sensitivity (μM to mM), the fact that GABA and Glu are produced by the cyanobacterium as an autoinduction response to N deficiency, and by the presence of interspecific signaling by heterotrophs in response to C limitation. Further, it crucially switches from a positive to a negative feedback loop with increasing GABA concentration, thus setting maximal bundle sizes. The unprecedented use of GABA/Glu as an intra- and interspecific signal in the spatial organization of microbiomes highlights the pair as truly universal infochemicals.

Microplastic leachates inhibit small-scale self-organization in mussel beds

Self-organized spatial patterns are increasingly recognized for their contribution to ecosystem functioning. They can improve the ecosystem's ability to respond to perturbation and thus increase its resilience to environmental stress. Plastic pollution has now emerged as major threat to aquatic and terrestrial biota. Under laboratory conditions, we tested whether plastic leachates from pellets collected in the intertidal can impair small-scale, spatial self-organization and byssal threads production of intertidal mussels and whether the effect varied depending on where the pellets come from. Specifically, leachates originating from plastic pellets collected from relatively pristine and polluted areas respectively impaired and inhibited the ability of mussels to self-organize at small-scale and to produce byssal threads compared to control conditions (i.e., seawater without leaching solution). Limitations to natural self-organizing processes and threads formation may translate to a declined capacity of natural ecosystems to avoid tipping points and to a reduced restoration success of disturbed ecosystems.

The primacy of temporal dynamics in driving spatial self-organization of soil iron redox patterns.

This study investigates mechanisms that generate regularly spaced iron-rich bands in upland soils. These striking features appear in soils worldwide, but beyond a generalized association with changing redox, their genesis is yet to be explained. Upland soils exhibit significant redox fluctuations driven by rainfall, groundwater changes, or irrigation. Pattern formation in such systems provides an opportunity to investigate the temporal aspects of spatial self-organization, which have been heretofore understudied. By comparing multiple alternative mechanisms, we found that regular iron banding in upland soils is explained by coupling two sets of scale-dependent feedbacks, the general principle of Turing morphogenesis. First, clay dispersion and coagulation in iron redox fluctuations amplify soil Fe(III) aggregation and crystal growth to a level that negatively affects root growth. Second, the activation of this negative root response to highly crystalline Fe(III) leads to the formation of rhythmic iron bands. In forming iron bands, environmental variability plays a critical role. It creates alternating anoxic and oxic conditions for required pattern-forming processes to occur in distinctly separated times and determines durations of anoxic and oxic episodes, thereby controlling relative rates of processes accompanying oxidation and reduction reactions. As Turing morphogenesis requires ratios of certain process rates to be within a specific range, environmental variability thus modifies the likelihood that pattern formation will occur. Projected changes of climatic regime could significantly alter many spatially self-organized systems, as well as the ecological functioning associated with the striking patterns they present. This temporal dimension of pattern formation merits close attention in the future.

Modelling how negative plant–soil feedbacks across life stages affect the spatial patterning of trees

In this work, we theoretically explore how litter decomposition processes and soil-borne pathogens contribute to negative plant–soil feedbacks, in particular in transient and stable spatial organisation of tropical forest trees and seedlings known as Janzen-Connell distributions. By considering soil-borne pathogens and autotoxicity both separately and in combination in a phenomenological model, we can study how both factors may affect transient dynamics and emerging Janzen–Connell distributions. We also identify parameter regimes associated with different long-term behaviours. Moreover, we compare how the strength of negative plant–soil feedbacks was mediated by tree germination and growth strategies, using a combination of analytical approaches and numerical simulations. Our interdisciplinary investigation, motivated by an ecological question, allows us to construct important links between local feedbacks, spatial self-organisation, and community assembly. Our model analyses contribute to understanding the drivers of biodiversity in tropical ecosystems, by disentangling the abilities of two potential mechanisms to generate Janzen-Connell distributions. Furthermore, our theoretical results may help guiding future field data analyses by identifying spatial signatures in adult tree and seedling distribution data that may reflect the presence of particular plant–soil feedback mechanisms.

Self-organization in mobile populations promotes the evolution of altruistic punishment

Altruistic punishment has been shown to sustain cooperation in social dilemmas. However, the influence of individual migration has often been overlooked in previous studies investigating the emergence of altruistic punishment. In this study, we address this gap by exploring the evolution of altruistic punishment in a mobile population. To capture the complexities of individual migration decisions, we propose a weighted migration model that incorporates individuals’ assessments of potential gains and losses. Our findings reveal that migration prioritizing potential benefits contributes to population clustering, and such spatial self-organization patterns play a vital role in promoting the flourishing of altruistic punishment. Conversely, when individuals are more inclined to avoid losses, it intensifies the dissolution of cooperative clusters and inhibits the evolution of cooperation. Moreover, our results suggest that pro-social punishment can still be maintained during the migration process, even in scenarios with low punishment efficiency, as long as individuals are capable of imposing sufficiently large amounts of punishments. This study provides valuable insights into the emergence and maintenance of altruistic punishment.

Interaction-motif-based classification of self-organizing metabolic cycles

Particles that are catalytically-active and chemotactic can interact through the concentration fields upon which they act, which in turn may lead to wide-scale spatial self-organization. When these active particles interact through several fields, these interactions gain an additional structure, which can result in new forms of collective behavior. Here, we study a mixture of active species which catalyze the conversion of a substrate chemical into a product chemical, and chemotax in concentration gradients of both substrate and product. Such species develop non-reciprocal, specific interactions that we coarse-grain into attractive and repulsive, which can lead to a potentially complex interaction network. We consider the particular case of a metabolic cycle of three species, each of which interacts with itself and both other species in the cycle. We find that the stability of a cycle of species that only chemotax in gradients of their substrate is piloted by a set of two parameter-free conditions, which we use to classify the low number of corresponding interaction networks. In the more general case of substrate- and product-chemotactic species, we can derive a set of two high-dimensional stability conditions, which can be used to classify the stability of all the possible interaction networks based on the self- and pair-interaction motifs they contain. The classification scheme that we introduce can help guide future studies on the dynamics of complex interaction networks and explorations of the corresponding large parameter spaces in such metabolically active complex systems.

SOCIO-CULTURAL APPROACHES AND PRACTICES OF PARTICIPATION IN PROJECTS OF IMPROVEMENT OF YARD TERRITORIES

The practices of forming sustainable local communities by the methods of socio-cultural design of common areas differ depending on the level of spatial self-organization of the community: urban level (urban spaces); district level (neighborhood, group of quarters); the level of the secondary common area (yard spaces). Sociocultural approaches to the formation of local communities in the improvement of courtyard areas are based on the practice of participation and include: reliance on grassroots urban initiatives, assistance in resolving territorial conflicts, artistic practices.

Micropatterning of Quantum Dots for Biofunctionalization and Nanoimaging

Micron-scale patterning of colloidal quantum dots (QDs) is extremely important for the fabrication of high-performance Quantum dot Light-Emitting Diode (QLED) displays, biosensing, and super-resolution imaging. Thus, several nondestructive methods have been recently proposed, such as spatial self-organization. However, none of them can be useful for biofunctionalization or nanoimaging. To address this limitation, we propose a method to create micropatterns of QDs of any shape and size. UV photolithography assisted by a digital micromirror device (DMD) and silanization allow creating an adhesive layer, on which QDs micropatterns can be assembled with a 2 μm resolution. The patterns are composed of a monolayer of CdSe/CdS/CdZnS/ZnS core/multishell QDs (7 ± 1 nm in diameter, emitting at 590 nm) with a high surface density (typically 4000 QDs/μm2). We also demonstrate that it is possible to reversibly bind any kind of His-Tagged proteins on the QDs surface. This is highlighted by measuring FRET (Förster Resonance Energy Transfer) with a dedicated polymer exhibiting on one end Alexa Fluor 647 (AF647) and on the other end eight imidazole cycles, allowing chelation on the quantum dots’ surface. Therefore, this patterning protocol provides a path to combine nanoimaging with cell patterning through a relevant biofunctionalization.

An in vitro culture platform for studying the effect of collective cell migration on spatial self-organization within induced pluripotent stem cell colonies

BackgroundHuman induced pluripotent stem cells (hiPSCs) provide an in vitro system to identify the impact of cell behavior on the earliest stages of cell fate specification during human development. Here, we developed an hiPSC-based model to study the effect of collective cell migration in meso–endodermal lineage segregation and cell fate decisions through the control of space confinement using a detachable ring culture system.ResultsThe actomyosin organization of cells at the edge of undifferentiated colonies formed in a ring barrier differed from that of the cells in the center of the colony. In addition, even in the absence of exogenous supplements, ectoderm, mesoderm, endoderm, and extraembryonic cells differentiated following the induction of collective cell migration at the colony edge by removing the ring-barrier. However, when collective cell migration was inhibited by blocking E-cadherin function, this fate decision within an hiPSC colony was altered to an ectodermal fate. Furthermore, the induction of collective cell migration at the colony edge using an endodermal induction media enhanced endodermal differentiation efficiency in association with cadherin switching, which is involved in the epithelial-mesenchymal transition.ConclusionsOur findings suggest that collective cell migration can be an effective way to drive the segregation of mesoderm and endoderm lineages, and cell fate decisions of hiPSCs.

A unifying method-based classification of robot swarm spatial self-organisation behaviours

Self-organisation in robot swarms can produce collective behaviours, particularly through spatial self-organisation. For example, it can be used to ensure that the robots in a swarm move collectively. However, from a designer’s point of view, understanding precisely what happens in a swarm that allows these behaviours to emerge at the macroscopic level remains a difficult task. The same behaviour can come from multiple different controllers (ie the control algorithm of a robot) and a single controller can give rise to multiple different behaviours, sometimes caused by slight changes in self-organisation. To grasp the causes of these differences, it is necessary to investigate the relationships between the many methods of self-organisation that exist and the various behaviours that can be obtained. The work presented here addresses self-organisation in robot swarms by focusing on the main behaviours that lead to spatial self-organisation of the robots. First, we propose a unified definition of the different behaviours and present an original classification system highlighting ten self-organisation methods that each allow one or more behaviours to be performed. An analysis, based on this classification system, links the identified mechanisms with behaviours that could be considered as obtainable or not. Finally, we discuss some perspectives on this work, notably from the point of view of an operator or designer.

Landscapes of Biochemical Warfare: Spatial Self-Organization Woven from Allelopathic Interactions.

Evidence shows that diversity and spatial distributions of biological communities are largely driven by the race of living organisms in their adaptation to chemicals synthesized by their neighbors. In this report, the emergence of mathematical models on pure spatial self-organization induced by biochemical suppression (allelopathy) and competition between species were investigated through numerical analysis. For both random and patched initial spatial distributions of species, we demonstrate that warfare survivors are self-organized on the landscape in Turing-like patterns driven by diffusive instabilities of allelochemicals. These patterns are simple; either all species coexist at low diffusion rates or are massively extinct, except for a few at high diffusivities, but they are complex and biodiversity-sustained at intermediate diffusion rates. "Defensive alliances" and ecotones seem to be basic mechanisms that sustain great biodiversity in our hybrid cellular automata model. Moreover, species coexistence and extinction exhibit multi-stationarity.

Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals.

Most bacteria live in dense, spatially structured communities such as biofilms. The high density allows cells to alter the local microenvironment, whereas the limited mobility can cause species to become spatially organized. Together, these factors can spatially organize metabolic processes within microbial communities so that cells in different locations perform different metabolic reactions. The overall metabolic activity of a community depends both on how metabolic reactions are arranged in space and on how they are coupled, i.e., how cells in different regions exchange metabolites. Here, we review mechanisms that lead to the spatial organization of metabolic processes in microbial systems. We discuss factors that determine the length scales over which metabolic activities are arranged in space and highlight how the spatial organization of metabolic processes affects the ecology and evolution of microbial communities. Finally, we define key open questions that we believe should be the main focus of future research.

Extracellular Matrix Rigidities Regulate the Tricarboxylic Acid Cycle and Antibiotic Resistance of Three-Dimensionally Confined Bacterial Microcolonies.

As a major cause of clinical chronic infection, microbial biofilms/microcolonies in host tissues essentially live in 3D-constrained microenvironments, which potentially modulate their spatial self-organization and morphodynamics. However, it still remains unclear whether and how mechanical cues of 3D confined microenvironments, for example, extracellular matrix (ECM) stiffness, exert an impact on antibiotic resistance of bacterial biofilms/microcolonies. With a high-throughput antibiotic sensitivity testing (AST) platform, it is revealed that 3D ECM rigidities greatly modulate their resistance to diverse antibiotics. The microcolonies in 3D ECM with human tissue-specific rigidities varying from 0.5 to 20kPa show a ≈2-10 000-fold increase in minimum inhibitory concentration, depending on the types of antibiotics. The authors subsequently identified that the increase in 3D ECM rigidities leads to the downregulation of the tricarboxylic acid (TCA) cycle, which is responsible for enhanced antibiotic resistance. Further, it is shown that fumarate, as a potentiator of TCA cycle activity, can alleviate the elevated antibiotic resistance and thus remarkably improve the efficacy of antibiotics against bacterial microcolonies in 3D confined ECM, as confirmed in the chronic infection mice model. These findings suggest fumarate can be employed as an antibiotic adjuvant to effectively treat infections induced by bacterial biofilms/microcolonies in a 3D-confined environment.

Self-organized sulfide-driven traveling pulses shape seagrass meadows

Seagrasses provide multiple ecosystem services and act as intense carbon sinks in coastal regions around the globe but are threatened by multiple anthropogenic pressures, leading to enhanced seagrass mortality that reflects in the spatial self-organization of the meadows. Spontaneous spatial vegetation patterns appear in such different ecosystems as drylands, peatlands, salt marshes, or seagrass meadows, and the mechanisms behind this phenomenon are still an open question in many cases. Here, we report on the formation of vegetation traveling pulses creating complex spatiotemporal patterns and rings in Mediterranean seagrass meadows. We show that these structures emerge due to an excitable behavior resulting from the coupled dynamics of vegetation and porewater hydrogen sulfide, toxic to seagrass, in the sediment. The resulting spatiotemporal patterns resemble those formed in other physical, chemical, and biological excitable media, but on a much larger scale. Based on theory, we derive a model that reproduces the observed seascapes and predicts the annihilation of these circular structures as they collide, a distinctive feature of excitable pulses. We show also that the patterns in field images and the empirically resolved radial profiles of vegetation density and sediment sulfide concentration across the structures are consistent with predictions from the theoretical model, which shows these structures to have diagnostic value, acting as a harbinger of the terminal state of the seagrass meadows prior to their collapse.