Tractable nonlinear memory functions as a tool to capture and explain dynamical behaviours

Mathematical approaches from dynamical systems theory are used in a range of fields. This includes biology where they are used to describe processes such as protein-protein interaction and gene regulatory networks. As such networks increase in size and complexity, detailed dynamical models become cumbersome, making them difficult to explore and decipher. This necessitates the application of simplifying and coarse graining techniques in order to derive explanatory insight. Here we demonstrate that Zwanzig-Mori projection methods can be used to arbitrarily reduce the dimensionality of dynamical networks while retaining their dynamical properties. We show that a systematic expansion around the quasi-steady state approximation allows an explicit solution for memory functions without prior knowledge of the dynamics. The approach not only preserves the same steady states but also replicates the transients of the original system. The method also correctly predicts the dynamics of multistable systems as well as networks producing sustained and damped oscillations. Applying the approach to a gene regulatory network from the vertebrate neural tube, a well characterised developmental transcriptional network, identifies features of the regulatory network responsible dfor its characteristic transient behaviour. Taken together, our analysis shows that this method is broadly applicable to multistable dynamical systems and offers a powerful and efficient approach for understanding their behaviour.Comment: (8 pages, 8 figures

Switchable Genetic Oscillator Operating in Quasi-Stable Mode

Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in transient and stochastic environments such as the cell. We show here that even repressilators possess quasi-stable, travelling-wave periodic solutions that are reachable, long-lived and robust to parameter changes. These solutions underlie the sustained oscillations observed in even rings in the stochastic regime, even if these circuits are expected to behave as switches. The existence of such solutions can also be exploited for control purposes: operation of the system around the quasi-stable orbit allows us to turn on and off the oscillations reliably and on demand. We illustrate these ideas with a simple protocol based on optical interference that can induce oscillations robustly both in the stochastic and deterministic regimes.Comment: 24 pages, 5 main figure

Time Delay and Noise Explaining Cyclical Fluctuations in Prices of Commodities

This paper suggests to model jointly time delay and random effects in economics and finance. It proposes to explain the random and often cyclical fluctuations in commodity prices as a consequence of the interplay between external noise and time delays caused by the time between initiation of production and delivery. The proposed model is formulated as a stochastic delay differential equation. The typical behavior of a commodity price index under this model will be discussed. Methods for parameter estimation and the evaluation of functionals will be proposed.commodity prices; stochastic delay differential equation; cyclical behavior; scenario simulation; parameter estimation; autocorrelation function

Multiscale Computations on Neural Networks: From the Individual Neuron Interactions to the Macroscopic-Level Analysis

We show how the Equation-Free approach for multi-scale computations can be exploited to systematically study the dynamics of neural interactions on a random regular connected graph under a pairwise representation perspective. Using an individual-based microscopic simulator as a black box coarse-grained timestepper and with the aid of simulated annealing we compute the coarse-grained equilibrium bifurcation diagram and analyze the stability of the stationary states sidestepping the necessity of obtaining explicit closures at the macroscopic level. We also exploit the scheme to perform a rare-events analysis by estimating an effective Fokker-Planck describing the evolving probability density function of the corresponding coarse-grained observables

Semiclassical Phase Reduction Theory for Quantum Synchronization

We develop a general theoretical framework of semiclassical phase reduction for analyzing synchronization of quantum limit-cycle oscillators. The dynamics of quantum dissipative systems exhibiting limit-cycle oscillations are reduced to a simple, one-dimensional classical stochastic differential equation approximately describing the phase dynamics of the system under the semiclassical approximation. The density matrix and power spectrum of the original quantum system can be approximately reconstructed from the reduced phase equation. The developed framework enables us to analyze synchronization dynamics of quantum limit-cycle oscillators using the standard methods for classical limit-cycle oscillators in a quantitative way. As an example, we analyze synchronization of a quantum van der Pol oscillator under harmonic driving and squeezing, including the case that the squeezing is strong and the oscillation is asymmetric. The developed framework provides insights into the relation between quantum and classical synchronization and will facilitate systematic analysis and control of quantum nonlinear oscillators.Comment: 20 pages, 5 figure

Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes

Multiple biological processes are driven by oscillatory gene expression at different time scales. Pulsatile dynamics are thought to be widespread, and single-cell live imaging of gene expression has lead to a surge of dynamic, possibly oscillatory, data for different gene networks. However, the regulation of gene expression at the level of an individual cell involves reactions between finite numbers of molecules, and this can result in inherent randomness in expression dynamics, which blurs the boundaries between aperiodic fluctuations and noisy oscillators. Thus, there is an acute need for an objective statistical method for classifying whether an experimentally derived noisy time series is periodic. Here we present a new data analysis method that combines mechanistic stochastic modelling with the powerful methods of non-parametric regression with Gaussian processes. Our method can distinguish oscillatory gene expression from random fluctuations of non-oscillatory expression in single-cell time series, despite peak-to-peak variability in period and amplitude of single-cell oscillations. We show that our method outperforms the Lomb-Scargle periodogram in successfully classifying cells as oscillatory or non-oscillatory in data simulated from a simple genetic oscillator model and in experimental data. Analysis of bioluminescent live cell imaging shows a significantly greater number of oscillatory cells when luciferase is driven by a {\it Hes1} promoter (10/19), which has previously been reported to oscillate, than the constitutive MoMuLV 5' LTR (MMLV) promoter (0/25). The method can be applied to data from any gene network to both quantify the proportion of oscillating cells within a population and to measure the period and quality of oscillations. It is publicly available as a MATLAB package.Comment: 36 pages, 17 figure

On the use of simple dynamical systems for climate predictions: A Bayesian prediction of the next glacial inception

Over the last few decades, climate scientists have devoted much effort to the development of large numerical models of the atmosphere and the ocean. While there is no question that such models provide important and useful information on complicated aspects of atmosphere and ocean dynamics, skillful prediction also requires a phenomenological approach, particularly for very slow processes, such as glacial-interglacial cycles. Phenomenological models are often represented as low-order dynamical systems. These are tractable, and a rich source of insights about climate dynamics, but they also ignore large bodies of information on the climate system, and their parameters are generally not operationally defined. Consequently, if they are to be used to predict actual climate system behaviour, then we must take very careful account of the uncertainty introduced by their limitations. In this paper we consider the problem of the timing of the next glacial inception, about which there is on-going debate. Our model is the three-dimensional stochastic system of Saltzman and Maasch (1991), and our inference takes place within a Bayesian framework that allows both for the limitations of the model as a description of the propagation of the climate state vector, and for parametric uncertainty. Our inference takes the form of a data assimilation with unknown static parameters, which we perform with a variant on a Sequential Monte Carlo technique (`particle filter'). Provisional results indicate peak glacial conditions in 60,000 years.Comment: superseeds the arXiv:0809.0632 (which was published in European Reviews). The Bayesian section has been significantly expanded. The present version has gone scientific peer review and has been published in European Physics Special Topics. (typo in DOI and in Table 1 (psi -> theta) corrected on 25th August 2009

Noninvasive brain stimulation techniques can modulate cognitive processing

Recent methods that allow a noninvasive modulation of brain activity are able to modulate human cognitive behavior. Among these methods are transcranial electric stimulation and transcranial magnetic stimulation that both come in multiple variants. A property of both types of brain stimulation is that they modulate brain activity and in turn modulate cognitive behavior. Here, we describe the methods with their assumed neural mechanisms for readers from the economic and social sciences and little prior knowledge of these techniques. Our emphasis is on available protocols and experimental parameters to choose from when designing a study. We also review a selection of recent studies that have successfully applied them in the respective field. We provide short pointers to limitations that need to be considered and refer to the relevant papers where appropriate

Dissipation in noisy chemical networks: The role of deficiency

We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of complex behavior such as multistability and oscillations, is shown to also characterize the entropic balance. In particular, only when deficiency is zero does the average stochastic dissipation rate equal that of the corresponding deterministic model, where correlations are disregarded. In fact, dissipation can be reduced by the effect of noise, as occurs in a toy model of metabolism that we employ to illustrate our findings. This phenomenon highlights that there is a close interplay between deficiency and the activation of new dissipative pathways at low molecule numbers.Comment: 10 Pages, 6 figure

Frequency Precision of Oscillators Based on High-Q Resonators

We present a method for analyzing the phase noise of oscillators based on feedback driven high quality factor resonators. Our approach is to derive the phase drift of the oscillator by projecting the stochastic oscillator dynamics onto a slow time scale corresponding physically to the long relaxation time of the resonator. We derive general expressions for the phase drift generated by noise sources in the electronic feedback loop of the oscillator. These are mixed with the signal through the nonlinear amplifier, which makes them {cyclostationary}. We also consider noise sources acting directly on the resonator. The expressions allow us to investigate reducing the oscillator phase noise thereby improving the frequency precision using resonator nonlinearity by tuning to special operating points. We illustrate the approach giving explicit results for a phenomenological amplifier model. We also propose a scheme for measuring the slow feedback noise generated by the feedback components in an open-loop driven configuration in experiment or using circuit simulators, which enables the calculation of the closed-loop oscillator phase noise in practical systems