Improved linear response for stochastically driven systems

The recently developed short-time linear response algorithm, which predicts the average response of a nonlinear chaotic system with forcing and dissipation to small external perturbation, generally yields high precision of the response prediction, although suffers from numerical instability for long response times due to positive Lyapunov exponents. However, in the case of stochastically driven dynamics, one typically resorts to the classical fluctuation-dissipation formula, which has the drawback of explicitly requiring the probability density of the statistical state together with its derivative for computation, which might not be available with sufficient precision in the case of complex dynamics (usually a Gaussian approximation is used). Here we adapt the short-time linear response formula for stochastically driven dynamics, and observe that, for short and moderate response times before numerical instability develops, it is generally superior to the classical formula with Gaussian approximation for both the additive and multiplicative stochastic forcing. Additionally, a suitable blending with classical formula for longer response times eliminates numerical instability and provides an improved response prediction even for long response times

Experimental analysis and computational modeling of interburst intervals in spontaneous activity of cortical neuronal culture

Rhythmic bursting is the most striking behavior of cultured cortical networks and may start in the second week after plating. In this study, we focus on the intervals between spontaneously occurring bursts, and compare experimentally recorded values with model simulations. In the models, we use standard neurons and synapses, with physiologically plausible parameters taken from literature. All networks had a random recurrent architecture with sparsely connected neurons. The number of neurons varied between 500 and 5,000. We find that network models with homogeneous synaptic strengths produce asynchronous spiking or stable regular bursts. The latter, however, are in a range not seen in recordings. By increasing the synaptic strength in a (randomly chosen) subset of neurons, our simulations show interburst intervals (IBIs) that agree better with in vitro experiments. In this regime, called weakly synchronized, the models produce irregular network bursts, which are initiated by neurons with relatively stronger synapses. In some noise-driven networks, a subthreshold, deterministic, input is applied to neurons with strong synapses, to mimic pacemaker network drive. We show that models with such “intrinsically active neurons” (pacemaker-driven models) tend to generate IBIs that are determined by the frequency of the fastest pacemaker and do not resemble experimental data. Alternatively, noise-driven models yield realistic IBIs. Generally, we found that large-scale noise-driven neuronal network models required synaptic strengths with a bimodal distribution to reproduce the experimentally observed IBI range. Our results imply that the results obtained from small network models cannot simply be extrapolated to models of more realistic size. Synaptic strengths in large-scale neuronal network simulations need readjustment to a bimodal distribution, whereas small networks do not require such change

Fluctuations, response, and resonances in a simple atmospheric model

We study the response of a simple quasi-geostrophic barotropic model of the atmosphere to various classes of perturbations affecting its forcing and its dissipation using the formalism of the Ruelle response theory. We investigate the geometry of such perturbations by constructing the covariant Lyapunov vectors of the unperturbed system and discover in one specific case–orographic forcing–a substantial projection of the forcing onto the stable directions of the flow. This results into a resonant response shaped as a Rossby-like wave that has no resemblance to the unforced variability in the same range of spatial and temporal scales. Such a climatic surprise corresponds to a violation of the fluctuation–dissipation theorem, in agreement with the basic tenets of nonequilibrium statistical mechanics. The resonance can be attributed to a specific group of rarely visited unstable periodic orbits of the unperturbed system. Our results reinforce the idea of using basic methods of nonequilibrium statistical mechanics and high-dimensional chaotic dynamical systems to approach the problem of understanding climate dynamics

A new mathematical framework for atmospheric blocking events

We use a simple yet Earth-like hemispheric atmospheric model to propose a new framework for the mathematical properties of blocking events. Using finite-time Lyapunov exponents, we show that the occurrence of blockings is associated with conditions featuring anomalously high instability. Longer-lived blockings are very rare and have typically higher instability. In the case of Atlantic blockings, predictability is especially reduced at the onset and decay of the blocking event, while a relative increase of predictability is found in the mature phase. The opposite holds for Pacific blockings, for which predictability is lowest in the mature phase. Blockings are realised when the trajectory of the system is in the neighbourhood of a specific class of unstable periodic orbits (UPOs), natural modes of variability that cover the attractor the system. UPOs corresponding to blockings have, indeed, a higher degree of instability compared to UPOs associated with zonal flow. Our results provide a rigorous justification for the classical Markov chains-based analysis of transitions between weather regimes. The analysis of UPOs elucidates that the model features a very severe violation of hyperbolicity, due to the presence of a substantial variability in the number of unstable dimensions, which explains why atmospheric states can differ a lot in term of their predictability. The resulting lack of robustness might be a fundamental cause contributing to the difficulty in representing blockings in numerical models and in predicting how their statistics will change as a result of climate change. This corresponds to fundamental issues limiting our ability to construct very accurate numerical models of the atmosphere, in term of predictability of the both the first and of the second kind in the sense of Lorenz

Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem–loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents

SPIKE - Clustering in Neuronal Cultures: Simulations vs. Experimental Data

Computational models of cultured cortical networks require either synaptic noise or pacemaker neurons to trigger activity. We aimed to investigate the behavior of noise-driven neuronal networks (NN). We show that NN with synaptic differentiation reproduces experimental activity better than network with uniformly distributed synaptic weights

Heterogeneity of the Attractor of the Lorenz '96 Model: Lyapunov Analysis, Unstable Periodic Orbits, and Shadowing Properties

The predictability of weather and climate is strongly state-dependent: special and extremely relevant atmospheric states like blockings are associated with anomalous instability. Indeed, typically, the instability of a chaotic dynamical system can vary considerably across its attractor. Such an attractor is in general densely populated by unstable periodic orbits that can be used to approximate any forward trajectory through the so-called shadowing. Dynamical heterogeneity can lead to the presence of unstable periodic orbits with different number of unstable dimensions. This phenomenon - unstable dimensions variability - implies a serious breakdown of hyperbolicity and has considerable implications in terms of the structural stability of the system and of the possibility to describe accurately its behaviour through numerical models. As a step in the direction of better understanding the properties of high-dimensional chaotic systems, we provide here an extensive numerical study of the dynamical heterogeneity of the Lorenz '96 model in a parametric configuration leading to chaotic dynamics. We show that the detected variability in the number of unstable dimensions is associated with the presence of many finite-time Lyapunov exponents that fluctuate about zero also when very long averaging times are considered. The transition between regions of the attractor with different degrees of instability comes with a significant drop of the quality of the shadowing. By performing a coarse graining based on the shadowing unstable periodic orbits, we can characterize the slow fluctuations of the system between regions featuring, on the average, anomalously high and anomalously low instability. In turn, such regions are associated, respectively, with states of anomalously high and low energy, thus providing a clear link between the microscopic and thermodynamical properties of the system.Comment: 28 pages, 11 figures, final accepted versio

On spurious detection of linear response and misuse of the fluctuation–dissipation theorem in finite time series

Using a sensitive statistical test we determine whether or not one can detect the breakdown of linear response given observations of deterministic dynamical systems. A goodness-of-fit statistics is developed for a linear statistical model of the observations, based on results for central limit theorems for deterministic dynamical systems, and used to detect linear response breakdown. We apply the method to discrete maps which do not obey linear response and show that the successful detection of breakdown depends on the length of the time series, the magnitude of the perturbation and on the choice of the observable. We find that in order to reliably reject the assumption of linear response for typical observables sufficiently large data sets are needed. Even for simple systems such as the logistic map, one needs of the order of observations to reliably detect the breakdown with a confidence level of ; if less observations are available one may be falsely led to conclude that linear response theory is valid. The amount of data required is larger the smaller the applied perturbation. For judiciously chosen observables the necessary amount of data can be drastically reduced, but requires detailed a priori knowledge about the invariant measure which is typically not available for complex dynamical systems. Furthermore we explore the use of the fluctuation–dissipation theorem (FDT) in cases with limited data length or coarse-graining of observations. The FDT, if applied naively to a system without linear response, is shown to be very sensitive to the details of the sampling method, resulting in erroneous predictions of the response