Generalizing the transition from amplitude to oscillation death in coupled oscillators

Peer reviewedPublisher PD

Restoration of rhythmicity in diffusively coupled dynamical networks

We acknowledge financial support from the National Natural Science Foundation of China (No. 11202082, No. 61203235, No. 11371367 and No. 11271290), the Fundamental Research Funds for the Central Universities of China under Grant No. 2014QT005, IRTG1740(DFG-FAPESP), and SERB-DST Fast Track scheme for young scientist under Grant No. ST/FTP/PS-119/2013, NSF CHE-0955555 and Grant No. 229171/2013-3 (CNPq).Peer reviewedPublisher PD

Analysing Dynamical Behavior of Cellular Networks via Stochastic Bifurcations

The dynamical structure of genetic networks determines the occurrence of various biological mechanisms, such as cellular differentiation. However, the question of how cellular diversity evolves in relation to the inherent stochasticity and intercellular communication remains still to be understood. Here, we define a concept of stochastic bifurcations suitable to investigate the dynamical structure of genetic networks, and show that under stochastic influence, the expression of given proteins of interest is defined via the probability distribution of the phase variable, representing one of the genes constituting the system. Moreover, we show that under changing stochastic conditions, the probabilities of expressing certain concentration values are different, leading to different functionality of the cells, and thus to differentiation of the cells in the various types

Timing Cellular Decision Making Under Noise via Cell–Cell Communication

Many cellular processes require decision making mechanisms, which must act reliably even in the unavoidable presence of substantial amounts of noise. However, the multistable genetic switches that underlie most decision-making processes are dominated by fluctuations that can induce random jumps between alternative cellular states. Here we show, via theoretical modeling of a population of noise-driven bistable genetic switches, that reliable timing of decision-making processes can be accomplished for large enough population sizes, as long as cells are globally coupled by chemical means. In the light of these results, we conjecture that cell proliferation, in the presence of cell–cell communication, could provide a mechanism for reliable decision making in the presence of noise, by triggering cellular transitions only when the whole cell population reaches a certain size. In other words, the summation performed by the cell population would average out the noise and reduce its detrimental impact

Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study

Peer reviewedPublisher PD

Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals.

Majority of the theory on cell polarization and the understanding of cellular sensing and responsiveness to localized chemical cues has been based on the idea that non-polarized and polarized cell states can be represented by stable asymptotic switching between them. The existing model classes that describe the dynamics of signaling networks underlying polarization are formulated within the framework of autonomous systems. However these models do not simultaneously capture both, robust maintenance of polarized state longer than the signal duration, and retained responsiveness to signals with complex spatial-temporal distribution. Based on recent experimental evidence for criticality organization of biochemical networks, we challenge the current concepts and demonstrate that non-asymptotic signaling dynamics arising at criticality uniquely ensures optimal responsiveness to changing chemoattractant fields. We provide a framework to characterize non-asymptotic dynamics of system's state trajectories through a non-autonomous treatment of the system, further emphasizing the importance of (long) transient dynamics, as well as the necessity to change the mathematical formalism when describing biological systems that operate in changing environments

Stochastic switching in systems with rare and hidden attractors

Complex biochemical networks are commonly characterised by the coexistence of multiple stable attractors. This endows living systems with plasticity in responses under changing external conditions, thereby enhancing their probability for survival. However, the type of such attractors as well as their positioning can hinder the likelihood to randomly visit these areas in phase space, thereby effectively decreasing the level of multistability in the system. Using a model based on the Hodgkin–Huxley formalism with bistability between a silent state, which is a rare attractor, and oscillatory bursting attractor, we demonstrate that the noise-induced switching between these two stable attractors depends on the structure of the phase space and the disposition of the coexisting attractors to each other

Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study

Background Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices

Characteristics of two coupled oscillators () in the deterministic case () close to the and .

<p>(A) A fragment of the bifurcation diagram. (B) Phase portrait for the multystability region .</p