Marco Thiel

Cross recurrence plot based synchronization of time series

The method of recurrence plots is extended to the cross recurrence plots (CRP) which, among others, enables the study of synchronization or time differences in two time series. This is emphasized in a distorted main diagonal in the cross recurrence plot, the line of synchronization (LOS). A non-parametrical fit of this LOS can be used to rescale the time axis of the two data series (whereby one of them is compressed or stretched) so that they are synchronized. An application of this method to geophysical sediment core data illustrates its suitability for real data. The rock magnetic data of two different sediment cores from the Makarov Basin can be adjusted to each other by using this method, so that they are comparable.

Influence of observational noise on the recurrence quantification analysis

In this paper, we estimate the errors due to observational noise on the recurrence quantification analysis (RQA). Based on this estimation, we present ways to minimize these errors. We give a criterion to choose the threshold e needed for the optimal computation of the recurrence plot (RP). One important point is to show the limits of interpretability of the results of the RQA if it is applied to measured time series. We show that even though the RQA is very susceptible to observational noise, it can yield reliable results for an optimal choice of e if the noise level is not too high. We apply the results to typical models, such as white noise, the logistic map and the Lorenz system, and to experimental laser data.

Estimation of dynamical invariants without embedding by recurrence plots.

In this paper we show that two dynamical invariants, the second order Renyi entropy and the correlation dimension, can be estimated from recurrence plots (RPs) with arbitrary embedding dimension and delay. This fact is interesting as these quantities are even invariant if no embedding is used. This is an important advantage of RPs compared to other techniques of nonlinear data analysis. These estimates for the correlation dimension and entropy are robust and, moreover, can be obtained at a low numerical cost. We exemplify our results for the Rossler system, the funnel attractor and the Mackey-Glass system. In the last part of the paper we estimate dynamical invariants for data from some fluid dynamical experiments and confirm previous evidence for low dimensional chaos in this experimental system.

Combinatorial stresses kill pathogenic Candida species

Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to the characterization of the adaptive responses to each of these stresses. In the wild, cells are frequently exposed simultaneously to combinations of these stresses and yet the effects of such combinatorial stresses have not been explored. We have developed a common experimental platform to facilitate the comparison of combinatorial stress responses in C. glabrata and C. albicans. This platform is based on the growth of cells in buffered rich medium at 30°C, and was used to define relatively low, medium and high doses of osmotic (NaCl), oxidative (H 2O2) and nitrosative stresses (e.g., dipropylenetriamine (DPTA)-NONOate). The effects of combinatorial stresses were compared with the corresponding individual stresses under these growth conditions. We show for the first time that certain combinations of combinatorial stress are especially potent in terms of their ability to kill C. albicans and C. glabrata and/or inhibit their growth. This was the case for combinations of osmotic plus oxidative stress and for oxidative plus nitrosative stress. We predict that combinatorial stresses may be highly signif cant in host defences against these pathogenic yeasts.

Inference of Granger causal time-dependent influences in noisy multivariate time series.

Inferring Granger-causal interactions between processes promises deeper insights into mechanisms underlying network phenomena, e.g. in the neurosciences where the level of connectivity in neural networks is of particular interest. Renormalized partial directed coherence has been introduced as a means to investigate Granger causality in such multivariate systems. A major challenge in estimating respective coherences is a reliable parameter estimation of vector autoregressive processes. We discuss two shortcomings typical in relevant applications, i.e. non-stationarity of the processes generating the time series and contamination with observational noise. To overcome both, we present a new approach by combining renormalized partial directed coherence with state space modeling. A numerical efficient way to perform both the estimation as well as the statistical inference will be presented.

A max-plus model of ribosome dynamics during mRNA translation.

We examine the dynamics of the translation stage of cellular protein production, in which ribosomes move uni-directionally along an mRNA strand, building amino acid chains as they go. We describe the system using a timed event graph-a class of Petri net useful for studying discrete events, which have to satisfy constraints. We use max-plus algebra to describe a deterministic version of the model, where the constraints represent steric effects which prevent more than one ribosome reading a given codon at a given time and delays associated with the availability of the different tRNAs. We calculate the protein production rate and density of ribosomes on the mRNA and find exact agreement between these analytical results and numerical simulations of the deterministic model, even in the case of heterogeneous mRNAs.

The dynamics of supply and demand in mRNA translation.

We study the elongation stage of mRNA translation in eukaryotes and find that, in contrast to the assumptions of previous models, both the supply and the demand for tRNA resources are important for determining elongation rates. We find that increasing the initiation rate of translation can lead to the depletion of some species of aa-tRNA, which in turn can lead to slow codons and queueing. Particularly striking “competition” effects are observed in simulations of multiple species of mRNA which are reliant on the same pool of tRNA resources. These simulations are based on a recent model of elongation which we use to study the translation of mRNA sequences from the Saccharomyces cerevisiae genome. This model includes the dynamics of the use and recharging of amino acid tRNA complexes, and we show via Monte Carlo simulation that this has a dramatic effect on the protein production behaviour of the system.

Recurrences determine the dynamics.

We show that under suitable assumptions, Poincare recurrences of a dynamical system determine its topology in phase space. Therefore, dynamical systems with the same recurrences are dynamically equivalent. This conclusion can be drawn from a theorem proved in this paper which states that the recurrence matrix determines the topology of closed sets. The theorem states that if a set of points M is mapped onto another set N, such that two points in N are closer than some prescribed fixed distance if and only if the corresponding points in M are closer than some, in general different, prescribed fixed distance, then both sets are homeomorphic, i.e., identical up to a continuous change in the coordinate system. The theorem justifies a range of methods in nonlinear dynamics which are based on recurrence properties.

INFERRING INDIRECT COUPLING BY MEANS OF RECURRENCES

The identification of the coupling direction from measured time series taking place in a group of interacting components is an important challenge for many experimental studies. We propose here a method to uncover the coupling configuration using recurrence properties. The approach hinges on a generalization of conditional probability of recurrence, which was originally introduced to detect and quantify even weak coupling directions between two interacting systems, to the case of multivariate time series where indirect interactions might be present. We test our method by an example of three coupled Lorenz systems. Our results confirm that the proposed method has much potential to identify indirect coupling, which is very relevant for experimental time series analysis.

Generating surrogates from recurrences

In this paper, we present an approach to recover the dynamics from recurrences of a system and then generate (multivariate) twin surrogate (TS) trajectories. In contrast to other approaches, such as the linear-like surrogates, this technique produces surrogates which correspond to an independent copy of the underlying system, i.e. they induce a trajectory of the underlying system visiting the attractor in a different way. We show that these surrogates are well suited to test for complex synchronization, which makes it possible to systematically assess the reliability of synchronization analyses. We then apply the TS to study binocular fixational movements and find strong indications that the fixational movements of the left and right eye are phase synchronized. This result indicates that there might be only one centre in the brain that produces the fixational movements in both eyes or a close link between the two centres.