Measurement in biological systems from the self-organisation point of view

Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological systems as dynamical systems far from not only their chemical equilibrium, but, in most cases, also of their Lyapunov stable states. Thus, in biological experiments, we do not observe states, but distinct trajectories followed by the examined organism. If one of the possible sequences is selected, a minute sub-section of the whole problem is obtained, sometimes in a seemingly highly reproducible manner. But the state of the organism is known only if a complete set of possible trajectories is known. And this is often practically impossible. Therefore, we propose a different framework for reporting and analysis of biological experiments, respecting the view of non-linear mathematics. This view should be used to avoid overoptimistic results, which have to be consequently retracted or largely complemented. An increase of specification of experimental procedures is the way for better understanding of the scope of paths, which the biological system may be evolving. And it is hidden in the evolution of experimental protocols.Comment: 13 pages, 5 figure

Statistics of extinction and survival in Lotka-Volterra systems

We analyze purely competitive many-species Lotka-Volterra systems with random interaction matrices, focusing the attention on statistical properties of their asymptotic states. Generic features of the evolution are outlined from a semiquantitative analysis of the phase-space structure, and extensive numerical simulations are performed to study the statistics of the extinctions. We find that the number of surviving species depends strongly on the statistical properties of the interaction matrix, and that the probability of survival is weakly correlated to specific initial conditions.Comment: Previous version had error in authors. 11 pages, including 5 figure

Resonant nucleation of spatio-temporal order via parametric modal amplification

We investigate, analytically and numerically, the emergence of spatio-temporal order in nonequilibrium scalar field theories. The onset of order is triggered by destabilizing interactions (DIs), which instantaneously change the interacting potential from a single to a double-well, tunable to be either degenerate (SDW) or nondegenerate (ADW). For the SDW case, we observe the emergence of spatio-temporal coherent structures known as oscillons. We show that this emergence is initially synchronized, the result of parametric amplification of the relevant oscillon modes. We also discuss how these ordered structures act as bottlenecks for equipartition. For ADW potentials, we show how the same parametric amplification mechanism may trigger the rapid decay of a metastable state. For a range of temperatures, the decay rates associated with this resonant nucleation can be orders of magnitude larger than those computed by homogeneous nucleation, with time-scales given by a simple power law, $\tau_{\rm RN}\sim[E_b/k_BT]^B$, where $B$ depends weakly on the temperature and $E_b/k_BT$ is the free-energy barrier of a critical fluctuation.Comment: 38 pages, 20 figures now included within the tex

Does the Red Queen reign in the kingdom of digital organisms?

In competition experiments between two RNA viruses of equal or almost equal fitness, often both strains gain in fitness before one eventually excludes the other. This observation has been linked to the Red Queen effect, which describes a situation in which organisms have to constantly adapt just to keep their status quo. I carried out experiments with digital organisms (self-replicating computer programs) in order to clarify how the competing strains' location in fitness space influences the Red-Queen effect. I found that gains in fitness during competition were prevalent for organisms that were taken from the base of a fitness peak, but absent or rare for organisms that were taken from the top of a peak or from a considerable distance away from the nearest peak. In the latter two cases, either neutral drift and loss of the fittest mutants or the waiting time to the first beneficial mutation were more important factors. Moreover, I found that the Red-Queen dynamic in general led to faster exclusion than the other two mechanisms.Comment: 10 pages, 5 eps figure

Square to stripe transition and superlattice patterns in vertically oscillated granular layers

We investigated the physical mechanism for the pattern transition from square lattice to stripes, which appears in vertically oscillating granular layers. We present a continuum model to show that the transition depends on the competition between inertial force and local saturation of transport. By introducing multiple free-flight times, this model further enables us to analyze the formation of superlattices as well as hexagonal lattice

Dynamic Separation of Chaotic Signals in the Presence of Noise

The problem of separation of an observed sum of chaotic signals into the individual components in the presence of noise on the path to the observer is considered. A noise threshold is found above which high-quality separation is impossible. Below the threshold, each signal is recovered with any prescribed accuracy. This effect is shown to be associated with the information content of the chaotic signals and a theoretical estimate is given for the threshold.Comment: PDF, 12 pages, 6 figures, submitted to Phys. Rev.

Mean flow and spiral defect chaos in Rayleigh-Benard convection

We describe a numerical procedure to construct a modified velocity field that does not have any mean flow. Using this procedure, we present two results. Firstly, we show that, in the absence of mean flow, spiral defect chaos collapses to a stationary pattern comprising textures of stripes with angular bends. The quenched patterns are characterized by mean wavenumbers that approach those uniquely selected by focus-type singularities, which, in the absence of mean flow, lie at the zig-zag instability boundary. The quenched patterns also have larger correlation lengths and are comprised of rolls with less curvature. Secondly, we describe how mean flow can contribute to the commonly observed phenomenon of rolls terminating perpendicularly into lateral walls. We show that, in the absence of mean flow, rolls begin to terminate into lateral walls at an oblique angle. This obliqueness increases with Rayleigh number.Comment: 14 pages, 19 figure

Multistable Pulse-like Solutions in a Parametrically Driven Ginzburg-Landau Equation

It is well known that pulse-like solutions of the cubic complex Ginzburg-Landau equation are unstable but can be stabilised by the addition of quintic terms. In this paper we explore an alternative mechanism where the role of the stabilising agent is played by the parametric driver. Our analysis is based on the numerical continuation of solutions in one of the parameters of the Ginzburg-Landau equation (the diffusion coefficient $c$), starting from the nonlinear Schr\"odinger limit (for which $c=0$). The continuation generates, recursively, a sequence of coexisting stable solutions with increasing number of humps. The sequence "converges" to a long pulse which can be interpreted as a bound state of two fronts with opposite polarities.Comment: 13 pages, 6 figures; to appear in PR