Related papers: Counting statistics for genetic switches based on …
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
We consider stochastic and open quantum systems with a finite number of states, where a stochastic transition between two specific states is monitored by a detector. The long-time counting statistics of the observed realizations of the…
The nonequilibrium stationary state of an exclusive genetic switch is considered. The model comprises two competing species and a single binding site which, when bound to by a protein of one species, causes the other species to be…
We use large deviation methods to calculate rates of noise-induced transitions between states in multistable genetic networks. We analyze a synthetic biochemical circuit, the toggle switch, and compare the results to those obtained from a…
We propose a direct numerical method to calculate the statistics of the number of transitions in stochastic processes, without having to resort to Monte Carlo calculations. The method is based on a generating function method, and arbitrary…
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,…
We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…
There has been an increasing demand for formal methods in the design process of safety-critical synthetic genetic circuits. Probabilistic model checking techniques have demonstrated significant potential in analyzing the intrinsic…
There exists a wide variety of works on the dynamics of large populations ranging from simple heuristic modeling to those based on advanced computer supported methods. Their interconnections, however, remain mostly vague, which…
Since gene regulatory systems contain sometimes only a small number of molecules, these systems are not described well by macroscopic rate equations; a master equation approach is needed for such cases. We develop an approximation scheme…
Stochastic systems feature, in general, both coherent dynamics and incoherent transitions between different states. We propose a method to identify the coherent part in the full counting statistics for the transitions. The proposal is…
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because…
A complete characterization of quantum fluctuations in many-body systems is accessible through the full counting statistics. We present an exact computation of statistical properties of light in a basic model of light-matter interaction: a…
In this study, a two-state Markov switching count-data model is proposed as an alternative to zero-inflated models to account for the preponderance of zeros sometimes observed in transportation count data, such as the number of accidents…
Destructive interference of single-electron tunneling between three quantum dots can trap an electron in a coherent superposition of charge on two of the dots. Coupling to external charges causes decoherence of this superposition, and in…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
The simple genetic algorithm is proposed for the simulation of quantum many body dynamics. It uses the selection of entangled quantum states and has the inbuilt absolute decoherence that comes from the limitation of classical memory. It…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
In this paper we present elementary computations for some Markov modulated counting processes, also called counting processes with regime switching. Regime switching has become an increasingly popular concept in many branches of science. In…
We consider the stochastic gene expression process with inter-state flip-flops. An exact steady-state solution to the master equation is calculated. One of the main goals in this paper is to investigate whether the probability distribution…