This paper is placed at the intersection-point between the study of theoretical computational models aimed at capturing the essence of genetic regulatory networks and the field of Artificial Embryology (or Computational Development). A model is proposed, with the objective of providing an effective way to generate arbitrary forms by using evolutionary-developmental techniques. Preliminary experiments have been performed.
We propose a dynamical model in which a network structure evolves in a self-organized critical (SOC) manner and explain a possible origin of the emergence of fractal and small-world networks. Our model combines a network growth and its decay by failures of nodes. The decay mechanism reflects the instability of large functional networks against cascading overload failures. It is demonstrated that the dynamical system surely exhibits SOC characteristics, such as power-law forms of the avalanche size distribution, the cluster size distribution, and the distribution of the time interval between intermittent avalanches. During the network evolution, fractal networks are spontaneously generated when networks experience critical cascades of failures that lead to a percolation transition. In contrast, networks far from criticality have small-world structures. We also observe the crossover behavior from fractal to small-world structure in the network evolution.
We show that accounting for internal character among interacting, heterogeneous entities generates rich phase transition behavior between isolation and cohesive dynamical grouping. Our analytical and numerical calculations reveal different critical points arising for different character-dependent grouping mechanisms. These critical points move in opposite directions as the populations diversity decreases. Our analytical theory helps explain why a particular class of universality is so common in the real world, despite fundamental differences in the underlying entities. Furthermore, it correctly predicts the non-monotonic temporal variation in connectivity observed recently in one such system.
The abundance of a species population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a well-defined double-exponential (Laplace) distribution. This striking regularity allows us to devise a stochastic model despite seemingly irregular variations in population abundances. The model identifies the effect of reduced growth at low population density as a key factor missed in current approaches of population variability analysis and without which extinction risks are severely underestimated. The model also allows us to separate the effect of demographic stochasticity and show that single-species growth rates are dominantly determined by stochasticity common to all species. This dominance---and the implications it has for interspecies correlations, including co-extinctions---emphasizes the need of ecosystem-level management approaches to reduce the extinction risk of the individual species themselves.
We have carried out car-following experiments with a 25-car-platoon on an open road section to study the relation between a cars speed and its spacing under various traffic conditions, in the hope to resolve a controversy surrounding this fundamental relation of vehicular traffic. In this paper we extend our previous analysis of these experiments, and report new experimental findings. In particular, we reveal that the platoon length (hence the average spacing within a platoon) might be significantly different even if the average velocity of the platoon is essentially the same. The findings further demonstrate that the traffic states span a 2D region in the speed-spacing (or density) plane. The common practice of using a single speed-spacing curve to model vehicular traffic ignores the variability and imprecision of human driving and is therefore inadequate. We have proposed a car-following model based on a mechanism that in certain ranges of speed and spacing, drivers are insensitive to the changes in spacing when the velocity differences between cars are small. It was shown that the model can reproduce the experimental results well.
The power from wind and solar exhibits a nonlinear flickering variability, which typically occurs at time scales of a few seconds. We show that high-frequency monitoring of such renewable powers enables us to detect a transition, controlled by the field size, where the output power qualitatively changes its behaviour from a flickering type to a diffusive stochastic behaviour. We find that the intermittency and strong non-Gaussian behavior in cumulative power of the total field, even for a country-wide installation still survives for both renewable sources. To overcome the short time intermittency, we introduce a time-delayed feedback method for power output of wind farm and solar field that can change further the underlying stochastic process and suppress their strong non- gaussian fluctuations.
Introduced by the late Per Bak and his colleagues, self-organized criticality (SOC) has been one of the most stimulating concepts to come out of statistical mechanics and condensed matter theory in the last few decades, and has played a significant role in the development of complexity science. SOC, and more generally fractals and power laws, have attacted much comment, ranging from the very positive to the polemical. The other papers in this special issue (Aschwanden et al, 2014; McAteer et al, 2014; Sharma et al, 2015) showcase the considerable body of observations in solar, magnetospheric and fusion plasma inspired by the SOC idea, and expose the fertile role the new paradigm has played in approaches to modeling and understanding multiscale plasma instabilities. This very broad impact, and the necessary process of adapting a scientific hypothesis to the conditions of a given physical system, has meant that SOC as studied in these fields has sometimes differed significantly from the definition originally given by its creators. In Baks own field of theoretical physics there are significant observational and theoretical open questions, even 25 years on (Pruessner, 2012). One aim of the present review is to address the dichotomy between the great reception SOC has received in some areas, and its shortcomings, as they became manifest in the controversies it triggered. Our article tries to clear up what we think are misunderstandings of SOC in fields more remote from its origins in statistical mechanics, condensed matter and dynamical systems by revisiting Bak, Tang and Wiesenfelds original papers.
The physics of activated escape of objects out of a metastable state plays a key role in diverse scientific areas involving chemical kinetics, diffusion and dislocation motion in solids, nucleation, electrical transport, motion of flux lines superconductors, charge density waves, and transport processes of macromolecules, to name but a few. The underlying activated processes present the multidimensional extension of the Kramers problem of a single Brownian particle. In comparison to the latter case, however, the dynamics ensuing from the interactions of many coupled units can lead to intriguing novel phenomena that are not present when only a single degree of freedom is involved. In this review we report on a variety of such phenomena that are exhibited by systems consisting of chains of interacting units in the presence of potential barriers. In the first part we consider recent developments in the case of a deterministic dynamics driving cooperative escape processes of coupled nonlinear units out of metastable states. The ability of chains of coupled units to undergo spontaneous conformational transitions can lead to a self-organised escape. The mechanism at work is that the energies of the units become re-arranged, while keeping the total energy conserved, in forming localised energy modes that in turn trigger the cooperative escape. We present scenarios of significantly enhanced noise-free escape rates if compared to the noise-assisted case. The second part deals with the collective directed transport of systems of interacting particles overcoming energetic barriers in periodic potential landscapes. Escape processes in both time-homogeneous and time-dependent driven systems are considered for the emergence of directed motion. It is shown that ballistic channels immersed in the associated high-dimensional phase space are the source for the directed long-range transport.
We find chimera states with respect to amplitude dynamics in a network of Stuart-Landau oscillators. These partially coherent and partially incoherent spatio-temporal patterns appear due to the interplay of nonlocal network topology and symmetry-breaking coupling. As the coupling range is increased, the oscillations are quenched, amplitude chimeras disappear and the network enters a symmetry-breaking stationary state. This particular regime is a novel pattern which we call chimera death. It is characterized by the coexistence of spatially coherent and incoherent inhomogeneous steady states and therefore combines the features of chimera state and oscillation death. Additionally, we show two different transition scenarios from amplitude chimera to chimera death. Moreover, for amplitude chimeras we uncover the mechanism of transition towards in-phase synchronized regime and discuss the role of initial conditions.
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from non-life to life, where the life phase is distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that lifes propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from non-life to life. We discuss the implications of these results for understanding lifes emergence and evolutionary transitions more broadly.
