相关论文: Phase Reduction of Stochastic Biochemical Oscillat…
We perform and extend real-time numerical simulation of a low-dimensional scalar field theory or a quantum mechanical system using stochastic quantization. After a brief review of the quantization method and the complex Langevin dynamics,…
In Bhattacharya et al. (Science Advances, 2020), a set of chemical reactions involved in the dynamics of actin waves in cells was studied. Both at the microscopic level, where the individual chemical reactions are directly modelled using…
The quasi-steady-state approximation (or stochastic averaging principle) is a useful tool in the study of multiscale stochastic systems, giving a practical method by which to reduce the number of degrees of freedom in a model. The method is…
Spontaneous oscillations induced by time delays are observed in many real-world systems. Phase reduction theory for limit-cycle oscillators described by delay-differential equations (DDEs) has been developed to analyze their synchronization…
The phase reduction technique is essential for studying rhythmic phenomena across various scientific fields. It allows the complex dynamics of high-dimensional oscillatory systems to be expressed by a single phase variable. This paper…
We show that solutions of the chemical reaction-diffusion system associated to $A+B\rightleftharpoons C$ in one spatial dimension can be approximated in $L^2$ on any finite time interval by solutions of a space discretized ODE system which…
Algorithmic stability is among the most potent techniques in generalization analysis. However, its derivation usually requires a stepsize $\eta_t = \mathcal{O}(1/t)$ under non-convex training regimes, where $t$ denotes iterations. This…
Oscillators - dynamical systems with stable periodic orbits - arise in many systems of physical, technological, and biological interest. The standard phase reduction, a model reduction technique based on isochrons, can be unsuitable for…
This paper addresses the problem of model reduction for dynamical system models that describe biochemical reaction networks. Inherent in such models are properties such as stability, positivity and network structure. Ideally these…
We introduce a variational method for analyzing limit cycle oscillators in $\mathbb{R}^d$ driven by Gaussian noise. This allows us to derive exact stochastic differential equations (SDEs) for the amplitude and phase of the solution, which…
We study a family of numerical schemes applied to a class of multiscale systems of stochastic differential equations. When the time scale separation parameter vanishes, a well-known homogenization or Wong--Zakai diffusion approximation…
We present an efficient finite difference method for the approximation of second derivatives, with respect to system parameters, of expectations for a class of discrete stochastic chemical reaction networks. The method uses a coupling of…
The phase description is a powerful tool for analyzing noisy limit cycle oscillators. The method, however, has found only limited applications so far, because the present theory is applicable only to the Gaussian noise while noise in the…
A description for regulatory genetic network based on generalized potential energy is constructed. The potential energy is derived from the steady state solution of linearized Fokker-Plank equation, and the result is shown to be equivalent…
We present a simple method for determining the exact noise power spectra in linear chemical reaction networks. We apply the method to networks which are representative of biochemical processes such as gene expression and signal detection.…
In this paper we propose a model-order reduction method for chemical reaction networks governed by general enzyme kinetics, including the mass-action and Michaelis-Menten kinetics. The model-order reduction method is based on the Kron…
The stochastic dynamics of biochemical networks are usually modelled with the chemical master equation (CME). The stationary distributions of CMEs are seldom solvable analytically, and numerical methods typically produce estimates with…
In this paper, we study a numerical approximation for a class of stationary states for reaction-diffusion system with m densities having disjoint support, which are governed by a minimization problem. We use quantitative properties of both…
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement of strand-displacement DNA computing, a large class of…
To identify first-order phase transitions in the dynamical process similar to the relativistic heavy-ion collisions, we investigate the dynamical behaviors of the first-order phase transition criterion in the Fokker-Planck framework. In the…