Related papers: Sampling rare switching events in biochemical netw…
We report a detailed study of neuromorphic switching behaviour in inherently complex percolating networks of self-assembled metal nanoparticles. We show that variation of the strength and duration of the electric field applied to this…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
Signal-processing molecules inside cells are often present at low copy number, which necessitates probabilistic models to account for intrinsic noise. Probability distributions have traditionally been found using simulation-based approaches…
We study genetic switches formed from pairs of mutually repressing operons. The switch stability is characterised by a well defined lifetime which grows sub-exponentially with the number of copies of the most-expressed transcription factor,…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
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…
Many cyber-physical systems can naturally be formulated as switched systems with constrained switching. This includes systems where one of the signals in the feedback loop may be lost. Possible sources for losses are shared or unreliable…
Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria,…
Quantum phase transitions encompass a variety of phenomena that occur in quantum systems exhibiting several possible symmetries. Traditionally, these transitions are explored by continuously varying a control parameter that connects two…
External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, fundamentally altering their dynamical function. How might we control and design these transitions in chemical…
We study the problem of coincidence detection in time series data, where we aim to determine whether the appearance of simultaneous or near-simultaneous events in two time series is indicative of some shared underlying signal or…
Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of…
It is well-known that gene activation/deactivation dynamics may be a major source of randomness in genetic networks, also in the case of large concentrations of the transcription factors. In this work, we investigate the effect of realistic…
Mathematical models of stem cell differentiation are commonly based upon the concept of subsequent cell fate decisions, each controlled by a gene regulatory network. These networks exhibit a multistable behavior and cause the system to…
Time is at a premium for recurrent network dynamics, and particularly so when they are stochastic and correlated: the quality of inference from such dynamics fundamentally depends on how fast the neural circuit generates new samples from…
This paper investigates the stability of switched linear systems whose switching signal is modeled as a stochastic process called a regenerative process. We show that the mean stability of such a switched system is characterized by the…
Additive noise is known to produce counter-intuitive behaviors in nonlinear dynamical systems. Previously, it was shown that systems with a deterministic limit cycle can display bistable switching between metastable states in the presence…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
The switch-like character of gene regulation has motivated the use of hybrid, discrete-continuous models of genetic regulatory networks. While powerful techniques for the analysis, verification, and control of hybrid systems have been…