Related papers: Gene circuit designs for noisy excitable dynamics
We disclose the generality of the intrinsic mechanisms underlying multistability in reciprocally inhibitory 3-cell circuits composed of simplified, low-dimensional models of oscillatory neurons, as opposed to those of a detailed Hodgkin-…
Neuronal responses are conspicuously variable. We focus on one particular aspect of that variability: the precision of action potential timing. We show that for common models of noisy spike generation, elementary considerations imply that…
We study the noise characteristics of stochastic oscillations in protein number dynamics of simple genetic oscillatory systems. Using the three-component negative feedback transcription regulatory system called the repressilator as a…
Genes and proteins regulate cellular functions through complex circuits of biochemical reactions. Fluctuations in the components of these regulatory networks result in noise that invariably corrupts the signal, possibly compromising…
It often is emphasized that gene expression is noisy. A seemingly contradictory view is that control mechanisms have been optimized to squeeze as much information as possible out of a limited number of molecules. Here we revisit these…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
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…
Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling.…
Unlike isolated beta-cells, which usually produce continuous spikes or fast and irregular bursts, electrically coupled beta-cells are apt to exhibit robust bursting action potentials. We consider the noise induced by thermal fluctuations as…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…
We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the…
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…
We study by simulation the effect of the diffusive motion of repressor molecules on the noise in mRNA and protein levels in the case of a repressed gene. We find that spatial fluctuations due to diffusion can drastically enhance the noise…
A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…
We characterize the operation of semiconductor microring lasers in an excitable regime. Our experiments reveal a statistical distribution of the characteristics of noise-triggered optical pulses that is not observed in other excitable…
We give a constructive method for realizing an arbitrary directed graph (with no one-cycles) as a heteroclinic or an excitable dynamic network in the phase space of a system of coupled cells of two types. In each case, the system is…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…
A new type of noised-induced phase transitions that should occur in systems of elements with motivated behavior is considered. By way of an example, a simple oscillatory system {x,v} with additive white noise is analyzed numerically. A…