相关论文: Phase Reduction of Stochastic Biochemical Oscillat…
We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…
This paper investigates optimal fluctuations for chemical reaction systems with N species, M reactions, and general rate law. In the limit of large volume, large fluctuations for such models occur with overwhelming probability in the…
According to the chemical reaction network theory, the topology of a certain class of chemical reaction networks, regardless of the kinetic details, sets a limit on the dynamical properties that a particular network can potentially admit;…
Chemical reaction networks are widely used to model stochastic dynamics in chemical kinetics, systems biology and epidemiology. Solving the chemical master equation that governs these systems poses a significant challenge due to the large…
The stochastic systems without detailed balance are common in various chemical reaction systems, such as metabolic network systems. In studies of these systems, the concept of potential landscape is useful. However, what are the sufficient…
We address the use of optical parametric oscillator (OPO) to counteract phase-noise in quantum optical communication channels, and demonstrate reduction of phase diffusion for coherent signals travelling through a suitably tuned OPO. In…
In the reaction-diffusion process $A+B \to \varnothing$ on random scale-free (SF) networks with the degree exponent $\gamma$, the particle density decays with time in a power law with an exponent $\alpha$ when initial densities of each…
We propose a new Neural Galerkin Normalizing Flow framework to approximate the transition probability density function of a diffusion process by solving the corresponding Fokker-Planck equation with an atomic initial distribution,…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…
A general phase reduction method for a network of coupled dynamical elements exhibiting collective oscillations, which is applicable to arbitrary networks of heterogeneous dynamical elements, is developed. A set of coupled adjoint equations…
We study a chemotaxis system that includes two competitive prey and one predator species in a two-dimensional domain, where the movement of prey (resp. predators) is driven by chemicals secreted by predators (resp. prey), called mutually…
Oscillatory chemical reactions are functional components in a variety of biological contexts. In chemistry, the construction and identification of even rudimentary oscillators remain elusive and lack a general framework. Using…
Spatially-distributed, nonequilibrium chemical systems described by a Markov chain model are considered. The evolution of such systems arises from a combination of local birth-death reactive events and random walks executed by the particles…
This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…
We propose a method for designing two-dimensional limit-cycle oscillators with prescribed periodic trajectories and phase response properties based on the phase reduction theory, which gives a concise description of weakly-perturbed…
Network interactions between dynamical units are often subject to time delay. We develop a phase reduction method for delay-coupled oscillator networks. The method is based on rewriting the delay-differential equation as an ordinary…
The dynamics of one species chemical kinetics is studied. Chemical reactions are modelled by means of continuous time Markov processes whose probability distribution obeys a suitable master equation. A large deviation theory is formally…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…
Biochemical reactions can happen on different time scales and also the abundance of species in these reactions can be very different from each other. Classical approaches, such as deterministic or stochastic approach, fail to account for or…
We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new resonant reaction…