Related papers: Gene circuit designs for noisy excitable dynamics
Tissue dynamics play a crucial role in biological processes ranging from inflammation to morphogenesis. However, these noisy multicellular dynamics are notoriously hard to predict. Here, we introduce a biomimetic machine learning framework…
We explore the dynamics of an integrate-and-fire neuron with an oscillatory stimulus. The frustration due to the competition between the neuron's natural firing period and that of the oscillatory rhythm, leads to a rich structure of…
Stochasticity in gene expression can give rise to fluctuations in protein levels and lead to phenotypic variation across a population of genetically identical cells. Recent experiments indicate that bursting and feedback mechanisms play…
Motivated by a stochastic differential equation describing the dynamics of interfaces, we study the bifurcation behavior of a more general class of such equations. These equations are characterized by a 2-dimensional phase space (describing…
Recent evidence suggests that neural information is encoded in packets and may be flexibly routed from region to region. We have hypothesized that neural circuits are split into sub-circuits where one sub-circuit controls information…
In order to respond to environmental signals, cells often use small molecular circuits to transmit information about their surroundings. Recently, motivated by concrete examples in signaling and gene regulation, a body of work has focused…
Biological systems rely on robust internal information processing: Survival depends on highly reproducible dynamics of regulatory processes. Biological information processing elements, however, are intrinsically noisy (genetic switches,…
Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…
Knowing which mode of combinatorial regulation (typically, AND or OR logic operation) that a gene employs is important for determining its function in regulatory networks. Here, we introduce a dynamic cross-correlation function between the…
We have studied the entropy-driven mechanism leading to stationary patterns formation in stochastic systems with local dynamics and non-Fickian diffusion. We have shown that a multiplicative noise fulfilling a fluctuation-dissipation…
We show that oscillations are excited in a complex system under the influence of the external force, if the parameters of the system experience rapid change due to the changes in its internal structure. This excitation is collision-like and…
Computing circuits composed of noisy logical gates and their ability to represent arbitrary Boolean functions with a given level of error are investigated within a statistical mechanics setting. Bounds on their performance, derived in the…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
In order to describe excitable reaction-diffusion systems, we derive a two-dimensional model with a Hopf and a semilocal saddle-node homoclinic bifurcation. This model gives the theoretical framework for the analysis of the saddle-node…
The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study…
Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as…
A recurrent idea in the study of complex systems is that optimal information processing is to be found near bifurcation points or phase transitions. However, this heuristic hypothesis has few (if any) concrete realizations where a standard…
Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions (called gene expression "noise" or phenotype "fluctuation"). In yeast and Escherichia coli, positive…
In this article, the dynamics and complexity of a noise induced blood flow system have been investigated. Changes in the dynamics have been recognized by measuring the periodicity over significant parameters. Chaotic as well as non-chaotic…