Example Of Self-organization Research Articles

The Min-protein oscillations in Escherichia coli: an example of self-organized cellular protein waves.

In the rod-shaped bacterium Escherichia coli, selection of the cell centre as the division site involves pole-to-pole oscillations of the proteins MinC, MinD and MinE. This spatio-temporal pattern emerges from interactions among the Min proteins and with the cytoplasmic membrane. Combining experimental studies in vivo and in vitro together with theoretical analysis has led to a fairly good understanding of Min-protein self-organization. In different geometries, the system can, in addition to standing waves, also produce travelling planar and spiral waves as well as coexisting stable stationary distributions. Today it stands as one of the best-studied examples of cellular self-organization of proteins.This article is part of the theme issue 'Self-organization in cell biology'.

Lipid self-assembly and lectin-induced reorganization of the plasma membrane.

The plasma membrane represents an outstanding example of self-organization in biology. It plays a vital role in protecting the integrity of the cell interior and regulates meticulously the import and export of diverse substances. Its major building blocks are proteins and lipids, which self-assemble to a fluid lipid bilayer driven mainly by hydrophobic forces. Even if the plasma membrane appears-globally speaking-homogeneous at physiological temperatures, the existence of specialized nano- to micrometre-sized domains of raft-type character within cellular and synthetic membrane systems has been reported. It is hypothesized that these domains are the origin of a plethora of cellular processes, such as signalling or vesicular trafficking. This review intends to highlight the driving forces of lipid self-assembly into a bilayer membrane and the formation of small, transient domains within the plasma membrane. The mechanisms of self-assembly depend on several factors, such as the lipid composition of the membrane and the geometry of lipids. Moreover, the dynamics and organization of glycosphingolipids into nanometre-sized clusters will be discussed, also in the context of multivalent lectins, which cluster several glycosphingolipid receptor molecules and thus create an asymmetric stress between the two membrane leaflets, leading to tubular plasma membrane invaginations.This article is part of the theme issue 'Self-organization in cell biology'.

Challenges and solutions for studying collective animal behaviour in the wild.

Mobile animal groups provide some of the most compelling examples of self-organization in the natural world. While field observations of songbird flocks wheeling in the sky or anchovy schools fleeing from predators have inspired considerable interest in the mechanics of collective motion, the challenge of simultaneously monitoring multiple animals in the field has historically limited our capacity to study collective behaviour of wild animal groups with precision. However, recent technological advancements now present exciting opportunities to overcome many of these limitations. Here we review existing methods used to collect data on the movements and interactions of multiple animals in a natural setting. We then survey emerging technologies that are poised to revolutionize the study of collective animal behaviour by extending the spatial and temporal scales of inquiry, increasing data volume and quality, and expediting the post-processing of raw data.This article is part of the theme issue 'Collective movement ecology'.

Some Aspects of Nonlinearity and Self-Organization In Biosystems on Examples of Localized Excitations in the DNA Molecule and Generalized Fisher–KPP Model

This review deals with ideas and approaches to nonlinear phenomena, based on different branches of physics and related to biological systems, that focus on how small impacts can significantly change the state of the system at large spatial scales. This problem is very extensive, and it cannot be fully resolved in this paper. Instead, some selected physical effects are briefly reviewed. We consider sine-Gordon solitons and nonlinear Schrodinger solitons in some models of DNA as examples of self-organization at the molecular level, as well as examine features of their formation and dynamics under the influence of external influences. In addition, the formation of patterns in the generalized Fisher–KPP model is viewed as a simple example of self-organization in a system with nonlocal interaction at the cellular level. Symmetries of model equations are employed to analyze the considered nonlinear phenomena. In this context the possible relations between phenomena considered and released activity effect, which is assessed differently in the literature, are discussed.

A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells.

The capacity of pluripotent embryonic stem cells to differentiate into any cell type in the body makes them invaluable in the field of regenerative medicine. However, because of the complexity of both the core pluripotency network and the process of cell fate computation it is not yet possible to control the fate of stem cells. We present a theoretical model of stem cell fate computation that is based on Halley and Winkler’s Branching Process Theory (BPT) and on Greaves et al.’s agent-based computer simulation derived from that theoretical model. BPT abstracts the complex production and action of a Transcription Factor (TF) into a single critical branching process that may dissipate, maintain, or become supercritical. Here we take the single TF model and extend it to multiple interacting TFs, and build an agent-based simulation of multiple TFs to investigate the dynamics of such coupled systems. We have developed the simulation and the theoretical model together, in an iterative manner, with the aim of obtaining a deeper understanding of stem cell fate computation, in order to influence experimental efforts, which may in turn influence the outcome of cellular differentiation. The model used is an example of self-organization and could be more widely applicable to the modelling of other complex systems. The simulation based on this model, though currently limited in scope in terms of the biology it represents, supports the utility of the Halley and Winkler branching process model in describing the behaviour of stem cell gene regulatory networks. Our simulation demonstrates three key features: (i) the existence of a critical value of the branching process parameter, dependent on the details of the cistrome in question; (ii) the ability of an active cistrome to “ignite” an otherwise fully dissipated cistrome, and drive it to criticality; (iii) how coupling cistromes together can reduce their critical branching parameter values needed to drive them to criticality.

Crowd of individuals walking in opposite directions. A toy model to study the segregation of the group into lanes of individuals moving in the same direction

Consider a corridor, street or bridge crowded with pedestrians walking in both directions. The individuals do not walk in a completely straight line. They adjust their path to avoid colliding with incoming pedestrians. As a result of these adjustments, the whole group sometimes end up split into lanes of individuals moving in the same direction. While this formation of lanes facilitates the flow and benefits the whole group, it is believed that results from the actions of the individuals acting only on their behalf, without considering others. This phenomenon is an example of self-organization.We analyze a simple model. We assume that individuals move around a two-lane circular track. All of them at the same speed. Half of them in one direction and the rest in the opposite direction. Each time two individuals collide, one of them moves to the other lane. The individual changing lanes is selected randomly. The system self-organizes. Eventually each lane is occupied with individuals moving in only one direction. We show that the time required for the system to self-organize is bounded by a linear function on the number of individuals. This toy model provides an example where global self-organization occurs even though each member of the group acts without considering the rest.

Self-Organization and the Bypass: Re-Imagining Institutions for More Sustainable Development in Agriculture and Food

In exploring the social dynamics of agrofood movements in Ecuador as examples of self-organization (i.e., locally distributed and resolved development), this article departs from a preoccupation with innovation by means of design and the use of scaling as a metaphor for describing research contributions in agriculture and food. The case material highlights that much development is contingent, unpredictable, and unmanageable as well as unbound to fixed spaces or places. In their study of people’s daily practice, the authors do not find clear boundaries between dichotomies of internal–external, lay–expert, traditional–modern, or local–global organization, but heterogeneous blends of each. For the purposes of sustainable development, this highlights the need for attention to be paid to relationships (social, material, and biological), adaptation (the capacity to innovate), and responsibility (adherence to norms of sustainability). Far from romanticizing self-organization, the authors acknowledge that people and their institutions share varying degrees of complicity for the goods as well as the bads of their economic activity, such as mass soil degradation, agrobiodiversity loss, and poisoning by pesticides. Nevertheless, even under highly difficult conditions, certain actors effectively bypass the limitations of formal institutions in forging a socio-technical course of action (i.e., policy) for relatively healthy living and being. As such, the authors have come to appreciate self-organization as a neglected, if paradoxical, resource for policy transition towards more sustainable agriculture and food.

Socio-Ecological Adaptation of Agricultural Heritage Systems in Modern China: Three Cases in Qingtian County, Zhejiang Province

This paper, on rural restructuring in China, focuses on the ability of agricultural heritage systems to adapt to modernizing conditions in the rural economy. Since 2002, when FAO initiated the protection of Globally Important Agricultural Heritage Systems (GIAHS), the value of agricultural heritage has been widely acknowledged, as has the importance and urgency to protect the systems in which they are embedded. However, such complex systems have not been fully assessed for their contribution to food security, ecosystem services and cultural preservation, as well as their ability to adapt to the demands of modernization. In fact, they have not been effectively evaluated as whole systems, largely because we have not yet devised satisfactory ways of studying complex systems, nor have we been able to assess them fully for their multi-faceted contributions to sustainability. This paper accepts the premise that such systems are sustainable in that they have survived as agro-ecosystems for many hundreds of years, having endured the predations of droughts, famines, plagues, floods and wars. This ability to sustain a rich diversity of biological and human systems is considered, in the theory of Complex Adaptive Systems (CAS), to be a form of resilience, meaning that these systems have either formed a new normal or returned to the old normal after a period of environmental or social stress. In effect, ancient agricultural heritage systems can be seen to represent what has been traditional and normal in China, but which today are faced with the overwhelming forces of modernization. Taking three examples from Qingtian County in Southern China, where physical and political conditions are consistent, the paper shows how similar rice-fish systems adapt differently and sustain themselves in the face of modernization, and particularly to the loss of youth and labor to urbanisation. One system self-adjusts by using remittances from abroad to sustain the system: an example of self-organization. In another township, the pursuit of tourism is the main form of adaptation to large losses of working population and marginal incomes. To maintain the landscape as a key attraction for tourists, this community has re-assembled abandoned rice terraces and is farming them as a collective enterprise under the auspices of a co-operative: an example of land and labor restructuring that has become common as the dominant form of agrarian change in China. In a third example, the local rice-fish system is being strengthened by modern farming technology and scientific techniques: an example of technological adaptation. The discussion explores the three responses as evidence of sustainable practice involving local restructuring, continued ingenuity, and the creative support of local governments in the face of the homogenizing demands of modernization.

Fluid-flow-templated self-assembly of calcium carbonate tubes in the laboratory and in biomineralization: The tubules of the watering-pot shells, Clavagelloidea

We show with laboratory experiments that self-assembled mineral tube formation involving precipitation around a templating jet of fluid — a mechanism well-known in the physical sciences from the tubular growth of so-called chemical gardens — functions with carbonates, and we analyse the microstructures and compositions of the precipitates. We propose that there should exist biological examples of fluid-flow-templated tubes formed from carbonates. We present observational and theoretical modelling evidence that the complex structure of biomineral calcium carbonate tubules that forms the ‘rose’ of the watering-pot shells, Clavagelloidea, may be an instance of this mechanism in biomineralization. We suggest that this is an example of self-organization and self-assembly processes in biomineralization, and that such a mechanism is of interest for the production of tubes as a synthetic biomaterial. Statement of SignificanceThe work discussed in the manuscript concerns the self-assembly of calcium carbonate micro-tubes and nano-tubes under conditions of fluid flow together with chemical reaction. We present the results of laboratory experiments on tube self-assembly together with theoretical calculations. We show how nature may already be making use of this process in molluscan biomineralization of the so-called watering-pot shells, and we propose that we may be able to take advantage of the formation mechanism to produce synthetic biocompatible micro- and nano-tubes.

Taming Self-Organization Dynamics to Dramatically Control Porous Architectures.

We demonstrate templating of functional materials with unexpected and intricate micro- and nanostructures by controlling the condensation, packing, and evaporation of water droplets on a polymer solution. Spontaneous evaporation of a polymer solution induces cooling of the liquid surface and water microdroplet condensation from the ambient vapor. These droplets pack together and act as a template to imprint an entangled polymer film. This breath figure (BF) phenomenon is an example of self-organization that involves the long-range ordering of droplets. Equilibrium-based analysis provides many insights into contact angles and drop stability of individual drops, but the BF phenomenon remains poorly understood thus far, preventing translation to real applications. Here we investigate the dynamics of this phenomenon to separate out the competing influences and then introduce a modulation scheme to ultimately manipulate the water vapor-liquid equilibrium independently from the solvent evaporation. This approach to BF control provides insights into the mechanism, a rationale for microstructure design, and evidence for the benefits of dynamical control of self-organization systems. We finally present dramatically different porous architectures from this approach reminiscent of microscale Petri dishes, conical flasks, and test tubes.

Self-Organization of Spatial Patterning in Human Embryonic Stem Cells.

The developing embryo is a remarkable example of self-organization, where functional units are created in a complex spatiotemporal choreography. Recently, human embryonic stem cells (ESCs) have been used to recapitulate in vitro the self-organization programs that are executed in the embryo in vivo. This represents an unique opportunity to address self-organization in humans that is otherwise not addressable with current technologies. In this chapter, we review the recent literature on self-organization of human ESCs, with a particular focus on two examples: formation of embryonic germ layers and neural rosettes. Intriguingly, both activation and elimination of TGFβ signaling can initiate self-organization, albeit with different molecular underpinnings. We discuss the mechanisms underlying the formation of these structures in vitro and explore future challenges in the field.

Entropy Evolution and Uncertainty Estimation with Dynamical Systems

This paper presents a comprehensive introduction and systematic derivation of the evolutionary equations for absolute entropy H and relative entropy D, some of which exist sporadically in the literature in different forms under different subjects, within the framework of dynamical systems. In general, both H and D are dissipated, and the dissipation bears a form reminiscent of the Fisher information; in the absence of stochasticity, dH/dt is connected to the rate of phase space expansion, and D stays invariant, i.e., the separation of two probability density functions is always conserved. These formulas are validated with linear systems, and put to application with the Lorenz system and a large-dimensional stochastic quasi-geostrophic flow problem. In the Lorenz case, H falls at a constant rate with time, implying that H will eventually become negative, a situation beyond the capability of the commonly used computational technique like coarse-graining and bin counting. For the stochastic flow problem, it is first reduced to a computationally tractable low-dimensional system, using a reduced model approach, and then handled through ensemble prediction. Both the Lorenz system and the stochastic flow system are examples of self-organization in the light of uncertainty reduction. The latter particularly shows that, sometimes stochasticity may actually enhance the self-organization process.

Self-organized enhancement of conductivity in biological ion channels

We discuss an example of self-organization in a biological system. It arises from long-range ion–ion interactions, and it leads us to propose a new kind of enhanced conduction in ion channels. The underlying mechanism involves charge fluctuations near the channel mouth, amplified by the mismatch between the relative permittivities of water and the protein of the channel walls. We use Brownian dynamics simulations to show that, as in conventional ‘knock on’ permeation, these interactions can strongly enhance the channel current; but unlike the conventional mechanism, the enhancement occurs without the instigating bath ion entering the channel. The transition between these two mechanisms is clearly demonstrated, emphasizing their distinction. A simple model accurately reproduces the observed phenomena. We point out that electrolyte plus protein of low relative permittivity are universal in living systems, so that long-range ion–ion correlations of the kind considered must be common.

Growing Self-Organizing Mini-Guts from a Single Intestinal Stem Cell: Mechanism and Applications

Recent examples have highlighted how stem cells have the capability to initiate morphogenesis in vitro; that is, to generate complex structures in culture that closely parallel their in vivo counterparts. Lgr5, the receptor for the Wnt-agonistic R-spondins, marks stem cells in multiple adult organs of mice and humans. In R-spondin-based three-dimensional cultures, these Lgr5 stem cells can grow into ever-expanding epithelial organoids that retain their original organ identity. Single Lgr5 stem cells derived from the intestine can be cultured to build epithelial structures that retain hallmarks of the in vivo epithelium. Here, we review the mechanisms that support this notable example of self-organization and discuss applications of this technology for stem cell research, disease modeling (e.g., for colorectal cancer and cystic fibrosis), and regenerative medicine.

Self-organization in urban development: towards a new perspective on spatial planning

To date, participatory spatial planning has produced disappointing results. We argue that one reason is that time and again participatory planning proposals remain controlled by public government, and that public government seems not to be very adaptive to initiatives that emerge from the dynamics of civil society itself. To find out why and how citizens could and would be motivated to contribute out of their own motivation to urban development, we propose turning the focus outside-in, instead of inside-out. In this article, we therefore introduce the notion of self-organization, referring to initiatives that originate in civil society itself, via autonomous community-based networks of citizens outside government control which participate in developing the ‘urban fabric’ too. We discuss some examples of self-organization and draw preliminary conclusions of the concept's usefulness for the theory and practice of spatial planning.

Self-Organization and Self-Governance

The intuitive difference between a system that choreographs the motion of its parts in the service of goals of its own formulation and a system composed of a collection of parts doing their own thing without coordination has been shaken by now familiar examples of self-organization. There is a broad and growing presumption in parts of philosophy and across the sciences that the appearance of centralized information-processing and control in the service of system-wide goals is mere appearance, i.e., an explanatory heuristic we have evolved to predict behavior, but one that will eventually get swept away in the advancing tide of self-organization. I argue that there is a distinction of central importance here, and that no adequate science of complex systems can dispense with it.

Observation of a Helical Self-Organized State in a Compact Toroidal Plasma

A nonaxisymmetric stable magnetohydrodynamic (MHD) equilibrium within a prolate cylindrical conducting boundary has been produced experimentally. It has m=1 azimuthal symmetry, helical distortion, and flat lambda profile, all in agreement with the computed magnetically relaxed minimum magnetic energy Taylor state. Despite varied initial conditions determined by two helicity injectors on the device, this same equilibrium consistently emerges as the final state. These results therefore describe a new example of self-organization in an MHD plasma.

Migrating Brain Cells Stick Together

Migrating Brain Cells Stick Together

Noise improves collective decision-making by ants in dynamic environments

Recruitment via pheromone trails by ants is arguably one of the best-studied examples of self-organization in animal societies. Yet it is still unclear if and how trail recruitment allows a colony to adapt to changes in its foraging environment. We study foraging decisions by colonies of the ant Pheidole megacephala under dynamic conditions. Our experiments show that P. megacephala, unlike many other mass recruiting species, can make a collective decision for the better of two food sources even when the environment changes dynamically. We developed a stochastic differential equation model that explains our data qualitatively and quantitatively. Analysing this model reveals that both deterministic and stochastic effects (noise) work together to allow colonies to efficiently track changes in the environment. Our study thus suggests that a certain level of noise is not a disturbance in self-organized decision-making but rather serves an important functional role.

Formation of evenly spaced ridges and valleys

Seen from above, it's clear that in many hilly landscapes the ridges and valleys appear uniformly spaced. Current physically based models of landscape evolution produce realistic looking topography, but cannot predict the 'wavelength' typical of evenly spaced ridges and valleys in natural landscapes. Taylor Perron and colleagues use equations of mass conservation and sediment transport to derive a characteristic length scale that is directly proportional to the ridge–valley wavelength in models of landform evolution and at five field study sites across the United States, including Nappa Valley in California and Point of the Mountain in Utah. The findings provide a quantitative explanation for one of the most widely observed characteristics of landscapes and suggest that valley spacing records the effects of material properties and climate on erosional processes. Ridges and valleys in many landscapes are uniformly spaced, but no theory has predicted this fundamental topographic wavelength. A characteristic length scale is now derived from equations of mass conservation and sediment transport; it is found to be directly proportional to the valley spacing in models of landform evolution, and to the measured valley spacing at five study sites in the USA. One of the most striking examples of self-organization in landscapes is the emergence of evenly spaced ridges and valleys1,2,3,4,5,6. Despite the prevalence of uniform valley spacing, no theory has been shown to predict this fundamental topographic wavelength. Models of long-term landscape evolution can produce landforms that look realistic7,8,9, but few metrics exist to assess the similarity between models and natural landscapes. Here we show that the ridge–valley wavelength can be predicted from erosional mechanics. From equations of mass conservation and sediment transport, we derive a characteristic length scale at which the timescales for erosion by diffusive soil creep and advective stream incision are equal. This length scale is directly proportional to the valley spacing that emerges in a numerical model of landform evolution, and to the measured valley spacing at five field sites. Our results provide a quantitative explanation for one of the most widely observed characteristics of landscapes. The findings also imply that valley spacing is a fundamental topographic signature that records how material properties and climate regulate erosional processes.