Ecology of the digital world of Wikipedia.

Wikipedia, a paradigmatic example of online knowledge space is organized in a collaborative, bottom-up way with voluntary contributions, yet it maintains a level of reliability comparable to that of traditional encyclopedias. The lack of selected professional writers and editors makes the judgement about quality and trustworthiness of the articles a real challenge. Here we show that a self-consistent metrics for the network defined by the edit records captures well the character of editors' activity and the articles' level of complexity. Using our metrics, one can better identify the human-labeled high-quality articles, e.g., "featured" ones, and differentiate them from the popular and controversial articles. Furthermore, the dynamics of the editor-article system is also well captured by the metrics, revealing the evolutionary pathways of articles and diverse roles of editors. We demonstrate that the collective effort of the editors indeed drives to the direction of article improvement.

Correction: Transition rates for slip-avalanches in soft athermal disks under quasi-static simple shear deformations.

Correction for 'Transition rates for slip-avalanches in soft athermal disks under quasi-static simple shear deformations' by Kuniyasu Saitoh et al., Soft Matter, 2019, DOI: 10.1039/c8sm01966e.

Temporal inactivation enhances robustness in an evolving system.

We study the robustness of an evolving system that is driven by successive inclusions of new elements or constituents with m random interactions to older ones. Each constitutive element in the model stays either active or is temporarily inactivated depending upon the influence of the other active elements. If the time spent by an element in the inactivated state reaches T W , it gets extinct. The phase diagram of this dynamic model as a function of m and T W is investigated by numerical and analytical methods and as a result both growing (robust) as well as non-growing (volatile) phases are identified. It is also found that larger time limit T W enhances the system's robustness against the inclusion of new elements, mainly due to the system's increased ability to reject 'falling-together' type attacks. Our results suggest that the ability of an element to survive in an unfavourable situation for a while, either as a minority or in a dormant state, could improve the robustness of the entire system.

Transition rates for slip-avalanches in soft athermal disks under quasi-static simple shear deformations.

We study slip-avalanches in two-dimensional soft athermal disks by quasi-static simulations of simple shear deformations. Sharp drops in shear stress, or slip-avalanches, are observed intermittently during steady state. Such stress drops are caused by restructuring of the contact networks, accompanied by drastic changes of the interaction forces, Δf. The changes of the forces happen heterogeneously in space, indicating that collective non-affine motions of the disks are most pronounced when slip-avalanches occur. We analyze and predict the statistics for the force changes, Δf, by transition rates of the contact forces and angles, where slip-avalanches are characterized by wide power-law tails. We find that the transition rates are described by a q-Gaussian distribution regardless of the area fraction of the disks. Because the transition rates quantify structural changes of the force-chains, our findings are an important step towards linking macroscopic observations to a microscopic theory of slip-avalanches in the experimentally accessible quasi-static regime.

Enhanced robustness of evolving open systems by the bidirectionality of interactions between elements.

Living organisms, ecosystems, and social systems are examples of complex systems in which robustness against inclusion of new elements is an essential feature. A recently proposed simple model has revealed a general mechanism by which such systems can become robust against inclusion of elements with totally random interactions when the elements have a moderate number of links. The interaction is, however, in many systems often intrinsically bidirectional like for mutual symbiosis and competition in ecology. This study reports the strong reinforcement effect of the bidirectionality of the interactions on the robustness of evolving systems. We show that the system with purely bidirectional interactions can grow with twofold average degree, in comparison with the purely unidirectional system. This drastic shift of the transition point comes from the reinforcement of each node, not from a change in structure of the emergent system. For systems with partially bidirectional interactions we find that the regime of the growing phase gets expanded. In the dense interaction regime, there exists an optimum proportion of bidirectional interactions for the growth rate at around 1/3. In the sparsely connected systems, small but finite fraction of bidirectional links can change the system's behaviour from non-growing to growing.

Optogenetic perturbation and bioluminescence imaging to analyze cell-to-cell transfer of oscillatory information.

Cells communicate with each other to coordinate their gene activities at the population level through signaling pathways. It has been shown that many gene activities are oscillatory and that the frequency and phase of oscillatory gene expression encode various types of information. However, whether or how such oscillatory information is transmitted from cell to cell remains unknown. Here, we developed an integrated approach that combines optogenetic perturbations and single-cell bioluminescence imaging to visualize and reconstitute synchronized oscillatory gene expression in signal-sending and signal-receiving processes. We found that intracellular and intercellular periodic inputs of Notch signaling entrain intrinsic oscillations by frequency tuning and phase shifting at the single-cell level. In this way, the oscillation dynamics are transmitted through Notch signaling, thereby synchronizing the population of oscillators. Thus, this approach enabled us to control and monitor dynamic cell-to-cell transfer of oscillatory information to coordinate gene expression patterns at the population level.

Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods.

All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca(2+)-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.