Related papers: Gene circuit designs for noisy excitable dynamics
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
We report a noise induced delay of bifurcation in a simple pulse-coupled neural circuit. We study the behavior of two neural oscillators, each individually governed by saddle-node dynamics, with reciprocal excitatory synaptic connections.…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…
We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and genes dynamics, with…
The intrinsic stochasticity of gene expression can lead to large variability of protein levels across a population of cells. Variability (or noise) in protein distributions can be modulated by cellular mechanisms of gene regulation; in…
Systems with the coexistence of different stable attractors are widely exploited in systems biology in order to suitably model the differentiating processes arising in living cells. In order to describe genetic regulatory networks several…
A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or…
We employ a typical genetic circuit model to explore how noise can influence the dynamic structure. With the increase of a key interactive parameter, the model will deterministically go through two bifurcations and three dynamic structure…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Local periodic perturbations induce frequency-dependent propagation waves in an excitable spatio-temporally chaotic system. We show how segments of noise-contaminated and chaotic perturbations induce characteristic sequences of excitations…
An electronic circuit device, inspired on the FitzHugh-Nagumo model of neuronal excitability, was constructed and shown to operate with characteristics compatible with those of biological sensory neurons. The nonlinear dynamical model of…
Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein…
Neurons fire irregularly on multiple timescales when stimulated with a periodic pulse train. This raises two questions: Does this irregularity imply significant intrinsic stochasticity? Can existing neuron models be readily extended to…
We study the activation process in large assemblies of type II excitable units whose dynamics is influenced by two independent noise terms. The mean-field approach is applied to explicitly demonstrate that the assembly of excitable units…
We consider the coaction of two distinct noise sources on the activation process of a single and two interacting excitable units, which are mathematically described by the Fitzhugh-Nagumo equations. We determine the most probable activation…
This paper presents an intracellular feedback control strategy, to regulate the gene expression process dynamics. For this purpose, two types of genetic circuits are designed in order to compare concentrations of the input transcription…
The activity generated by an ensemble of neurons is affected by various noise sources. It is a well-recognised challenge to understand the effects of noise on the stability of such networks. We demonstrate that the patterns of activity…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
The structure of a stochastic nonlinear gene regulatory network is uncovered by studying its response to input signal generators. Four applications are studied in detail: a nonlinear connection of two linear systems, the design of a logic…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…