Related papers: Extrinsic noise driven phenotype switching in a se…
Mixed positive and negative feedback loops are often found in biological systems which support oscillations. In this work we consider a prototype of such systems, which has been recently found at the core of many genetic circuits showing…
In this paper we present a framework for investigating coloured noise in reaction-diffusion systems. We start by considering a deterministic reaction-diffusion equation and show how external forcing can cause temporally correlated or…
We formulate a general, high-dimensional kinetic theory describing the internal state (such as gene expression or protein levels) of cells in a stochastically evolving population. The resolution of our kinetic theory also allows one to…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability,…
This paper explores a stochastic Gause predator-prey model with bounded or sub-linear functional response. The model, described by a system of stochastic differential equations, captures the influence of stochastic fluctuations on…
Complex coherent dynamics is present in a wide variety of neural systems. A typical example is the voltage transitions between up and down states observed in cortical areas in the brain. In this work, we study this phenomenon via a…
Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating…
We address the problem of the relative importance of the intrinsic chaos and the external noise in determining the complexity of population dynamics. We use a recently proposed method for studying the complexity of nonlinear random…
Can noise be beneficial to machine-learning prediction of chaotic systems? Utilizing reservoir computers as a paradigm, we find that injecting noise to the training data can induce a stochastic resonance with significant benefits to both…
Some genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the…
A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and…
Gene regulatory circuits show significant stochastic fluctuations in their circuit signals due to the low copy number of transcription factors. When a gene circuit component is connected to an existing circuit, the dynamic properties of the…
Bistable autonomous systems can be found inmany areas of science. When the intrinsic noise intensity is large, these systems exhibits stochastic transitions from onemetastable steady state to another. In electronic bistable memories, these…
Our understanding of cell division control in bacteria still relies largely on interpreting correlations between phenomenological variables, with limited connection to the underlying molecular mechanisms. Here, we analytically solve a…
Living systems implement and execute an extraordinary plethora of computational tasks. The inherent degree of large scale coordination emerges as a global property, from the intricate sea of microscopic interactions. The brain, with its…
Recent theoretical studies have shown that demographic stochasticity can greatly increase the tendency of asexually reproducing phenotypically diverse organisms to spontaneously evolve into localised clusters, suggesting a simple mechanism…
Biological systems are notoriously noisy. Noise, therefore, also plays an important role in many models of neural impulse generation. Noise is not only introduced for more realistic simulations but also to account for cooperative effects…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…