Pattern transitions in spatial epidemics: Mechanisms and emergent properties

Superatoms are nanometer-sized molecules or particles that can form ordered lattices, mimicking their atomic counterparts. Hierarchical assembly of superatoms gives rise to emergent properties in superlattices of quantum-dots, p-block clusters, and fullerenes. Here, we introduce a family of uranium-oxysulfate cluster anions whose hierarchical assembly in water is controlled by two parameters; acidity and the countercation. In acid, larger LnIII (Ln=La-Ho) link hexamer (U6) oxoclusters into body-centered cubic frameworks, while smaller LnIII (Ln=Er-Lu &Y) promote linking of fourteen U6-clusters into hollow superclusters (U84 superatoms). U84 assembles into superlattices including cubic-closest packed, body-centered cubic, and interpenetrating networks, bridged by interstitial countercations, and U6-clusters. Divalent transition metals (TM=MnII and ZnII), with no added acid, charge-balance and promote the fusion of 10 U6 and 10 U-monomers into a wheel–shaped cluster (U70). Dissolution of U70 in organic media reveals (by small-angle Xray scattering) that differing supramolecular assemblies are accessed, controlled by TM-linking of U70-clusters.

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Substrate use prioritization by a coculture of five species of gut bacteria fed mixtures of arabinoxylan, xyloglucan, β-glucan, and pectin

10.26686/wgtn.12585620.v1 ◽

2020 ◽

Author(s):

Y Liu ◽

AL Heath ◽

B Galland ◽

N Rehrer ◽

L Drummond ◽

...

Keyword(s):

Gut Microbiota ◽

Dietary Fiber ◽

Plant Cell Wall ◽

Bacterial Species ◽

Short Chain ◽

Emergent Properties ◽

Human Gut ◽

Fermentation Products ◽

Plant Polysaccharides ◽

Human Gut Microbiota

© 2020 American Society for Microbiology. Dietary fiber provides growth substrates for bacterial species that belong to the colonic microbiota of humans. The microbiota degrades and ferments substrates, producing characteristic short-chain fatty acid profiles. Dietary fiber contains plant cell wall-associated polysaccharides (hemicelluloses and pectins) that are chemically diverse in composition and structure. Thus, depending on plant sources, dietary fiber daily presents the microbiota with mixtures of plant polysaccharides of various types and complexity. We studied the extent and preferential order in which mixtures of plant polysaccharides (arabinoxylan, xyloglucan, β-glucan, and pectin) were utilized by a coculture of five bacterial species (Bacteroides ovatus, Bifidobacterium longum subspecies longum, Megasphaera elsdenii, Ruminococcus gnavus, and Veillonella parvula). These species are members of the human gut microbiota and have the biochemical capacity, collectively, to degrade and ferment the polysaccharides and produce short-chain fatty acids (SCFAs). B. ovatus utilized glycans in the order β-glucan, pectin, xyloglucan, and arabinoxylan, whereas B. longum subsp. longum utilization was in the order arabinoxylan, arabinan, pectin, and β-glucan. Propionate, as a proportion of total SCFAs, was augmented when polysaccharide mixtures contained galactan, resulting in greater succinate production by B. ovatus and conversion of succinate to propionate by V. parvula. Overall, we derived a synthetic ecological community that carries out SCFA production by the common pathways used by bacterial species for this purpose. Systems like this might be used to predict changes to the emergent properties of the gut ecosystem when diet is altered, with the aim of beneficially affecting human physiology. This study addresses the question as to how bacterial species, characteristic of the human gut microbiota, collectively utilize mixtures of plant polysaccharides such as are found in dietary fiber. Five bacterial species with the capacity to degrade polymers and/or produce acidic fermentation products detectable in human feces were used in the experiments. The bacteria showed preferential use of certain polysaccharides over others for growth, and this influenced their fermentation output qualitatively. These kinds of studies are essential in developing concepts of how the gut microbial community shares habitat resources, directly and indirectly, when presented with mixtures of polysaccharides that are found in human diets. The concepts are required in planning dietary interventions that might correct imbalances in the functioning of the human microbiota so as to support measures to reduce metabolic conditions such as obesity.

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Models of decision support in socio-cyber-physical systems

Information and Control Systems ◽

10.31799/1684-8853-2019-3-55-70 ◽

2019 ◽

pp. 55-70 ◽

Cited By ~ 1

Author(s):

A. V. Smirnov ◽

T. V. Levashova

Keyword(s):

Decision Making ◽

Decision Support ◽

Situation Awareness ◽

Cyber Physical Systems ◽

Emergent Behavior ◽

Emergent Properties ◽

Decision Making Process ◽

Physical Systems ◽

Decision Support Models ◽

Common Goals

Introduction: Socio-cyber-physical systems are complex non-linear systems. Such systems display emergent properties. Involvement of humans, as a part of these systems, in the decision-making process contributes to overcoming the consequences of the emergent system behavior, since people can use their experience and intuition, not just the programmed rules and procedures.Purpose: Development of models for decision support in socio-cyber-physical systems.Results: A scheme of decision making in socio-cyber-physical systems, a conceptual framework of decision support in these systems, and stepwise decision support models have been developed. The decision-making scheme is that cybernetic components make their decisions first, and if they cannot do this, they ask humans for help. The stepwise models support the decisions made by components of socio-cyber-physical systems at the conventional stages of the decision-making process: situation awareness, problem identification, development of alternatives, choice of a preferred alternative, and decision implementation. The application of the developed models is illustrated through a scenario for planning the execution of a common task for robots.Practical relevance: The developed models enable you to design plans on solving tasks common for system components or on achievement of common goals, and to implement these plans. The models contribute to overcoming the consequences of the emergent behavior of socio-cyber-physical systems, and to the research on machine learning and mobile robot control.

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Imaging the formation and surface phase separation of the CE phase

npj Quantum Materials ◽

10.1038/s41535-021-00353-2 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Haibiao Zhou ◽

Qiyuan Feng ◽

Yubin Hou ◽

Masao Nakamura ◽

Yoshinori Tokura ◽

...

Keyword(s):

Magnetic Field ◽

Phase Transitions ◽

Charge Ordering ◽

Zero Magnetic Field ◽

Ferromagnetic Phase ◽

Emergent Properties ◽

Orbital Ordering ◽

Strong Electron ◽

Antiferromagnetic Correlation ◽

Ordering Transitions

AbstractThe CE phase is an extraordinary phase exhibiting the simultaneous spin, charge, and orbital ordering due to strong electron correlation. It is an ideal platform to investigate the role of the multiple orderings in the phase transitions and discover emergent properties. Here, we use a cryogenic high-field magnetic force microscope to image the phase transitions and properties of the CE phase in a Pr0.5Ca0.5MnO3 thin film. In a high magnetic field, we observed a clear suppression of magnetic susceptibility at the charge-ordering insulator transition temperature (TCOI), whereas, at the Néel temperature (TN), no significant change is observed. This observation favors the scenario of strong antiferromagnetic correlation developed below TCOI but raises questions about the Zener polaron paramagnetic phase picture. Besides, we discoverd a phase-separated surface state in the CE phase regime. Ferromagnetic phase domains residing at the surface already exist in zero magnetic field and show ultra-high magnetic anisotropy. Our results provide microscopic insights into the unconventional spin- and charge-ordering transitions and revealed essential attributes of the CE phase, highlighting unusual behaviors when multiple electronic orderings are involved.

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Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture

mSphere ◽

10.1128/msphere.00285-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 4

Author(s):

Emily G. Sweeney ◽

Andrew Nishida ◽

Alexandra Weston ◽

Maria S. Bañuelos ◽

Kristin Potter ◽

...

Keyword(s):

Helicobacter Pylori ◽

Three Dimensional ◽

Structural Features ◽

Agent Based Modeling ◽

Emergent Properties ◽

Cellular Interactions ◽

Biofilm Growth ◽

Content Type ◽

Agent Based ◽

H Pylori

ABSTRACTBacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms ofHelicobacter pylori, a common bacterial resident of human stomachs. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterizedH. pyloristrains with various AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis-defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger-scale emergent properties of biofilms.IMPORTANCEMost bacteria exist in aggregated, three-dimensional structures called biofilms. Although biofilms play important ecological roles in natural and engineered settings, they can also pose societal problems, for example, when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown thatHelicobacter pyloribacteria are repulsed by high concentrations of a self-produced molecule, AI-2, and thatH. pylorimutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here, we used computer simulations of biofilm formation to show that localH. pyloribehavior of repulsion from high AI-2 could explain the overall architecture ofH. pyloribiofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.

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Stochastic models support rapid peopling of Late Pleistocene Sahul

Nature Communications ◽

10.1038/s41467-021-21551-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Corey J. A. Bradshaw ◽

Kasih Norman ◽

Sean Ulm ◽

Alan N. Williams ◽

Chris Clarkson ◽

...

Keyword(s):

Stochastic Models ◽

Ecological Model ◽

New Guinea ◽

Emergent Properties ◽

Modern Humans ◽

Global Migration ◽

Early Settlement ◽

Anatomically Modern Humans ◽

Settlement Event ◽

Initial Entry

AbstractThe peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model supports a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers. The model’s emergent properties predict that peopling of the entire continent occurred rapidly across all ecological environments within 156–208 human generations (4368–5599 years) and at a plausible rate of 0.71–0.92 km year−1. More broadly, our methods and approaches can readily inform other global migration debates, with results supporting an exit of anatomically modern humans from Africa 63,000–90,000 years ago, and the peopling of Eurasia in as little as 12,000–15,000 years via inland routes.

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Collision avoidance during group evasive manoeuvres: a comparison of real versus simulated swarms with manipulated vision and surface wave detectors

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.0812 ◽

2014 ◽

Vol 281 (1788) ◽

pp. 20140812 ◽

Cited By ~ 6

Author(s):

William L. Romey ◽

Magenta M. Miller ◽

Jose M. Vidal

Keyword(s):

Surface Wave ◽

Sensory Modality ◽

Simulation Models ◽

Emergent Properties ◽

Control Groups ◽

Group Attraction ◽

Group Motion ◽

Coordinate Group ◽

Group Movements ◽

Simulation Systems

Coordinated group motion has been studied extensively both in real systems (flocks, swarms and schools) and in simulations (self-propelled particle (SPP) models using attraction and repulsion rules). Rarely are attraction and repulsion rules manipulated, and the resulting emergent behaviours of real and simulation systems are compared. We compare swarms of sensory-deprived whirligig beetles with matching simulation models. Whirligigs live at the water's surface and coordinate their grouping using their eyes and antennae. We filmed groups of beetles in which antennae or eyes had been unilaterally obstructed and measured individual and group behaviours. We then developed and compared eight SPP simulation models. Eye-less beetles formed larger diameter resting groups than antenna-less or control groups. Antenna-less groups collided more often with each other during evasive group movements than did eye-less or control groups. Simulations of antenna-less individuals produced no difference from a control (or a slight decrease) in group diameter. Simulations of eye-less individuals produced an increase in group diameter. Our study is important in (i) differentiating between group attraction and repulsion rules, (ii) directly comparing emergent properties of real and simulated groups, and (iii) exploring a new sensory modality (surface wave detection) to coordinate group movement.

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