Related papers: Global Sensitivity Analysis of Biochemical Reactio…
In this paper we study the local instability to the boundary equilibria and the local stability to the positive equilibria for some chemical reaction-diffusion systems. We first analyze a three-species system with boundary equilibria in…
We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…
We consider a reaction-diffusion system which may serve as a model for a ferment catalytic reaction in chemistry. The model consists of a system of reaction diffusion equations with unbounded time dependent coefficients and different…
We present a method for estimating parameters in stochastic models of biochemical reaction networks by fitting steady-state distributions using Wasserstein distances. We simulate a reaction network at different parameter settings and train…
In this paper, the Turing instability in reaction-diffusion models defined on complex networks is studied. Here, we focus on three types of models which generate complex networks, i.e. the Erd\H{o}s-R\'enyi, the Watts-Strogatz, and the…
A reaction network consists of a finite number of species, which interact through predefined reaction channels. Traditionally such networks were modeled deterministically, but it is now well-established that when reactant copy numbers are…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
The ergodicity and the output-controllability of stochastic reaction networks have been shown to be essential properties to fulfill to enable their control using, for instance, antithetic integral control. We propose here to extend those…
The application of the quasi-steady-state approximation to the Michaelis-Menten reaction embedded in large open chemical reaction networks is a popular model reduction technique in deterministic and stochastic simulations of biochemical…
A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…
There is a growing trend in molecular and synthetic biology of using mechanistic (non machine learning) models to design biomolecular networks. Once designed, these networks need to be validated by experimental results to ensure the…
Detailed balance of a chemical reaction network can be defined in several different ways. Here we investigate the relationship among four types of detailed balance conditions: deterministic, stochastic, local, and zero-order local detailed…
Reaction-diffusion models are widely used to study spatially-extended chemical reaction systems. In order to understand how the dynamics of a reaction-diffusion model are affected by changes in its input parameters, efficient methods for…
A fundamental challenge in quantum physics is determining the ground-state properties of many-body systems. Whereas standard approaches, such as variational calculations, consist of writing down a wave function ansatz and minimizing over…
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
We study the set of output stable configurations of chemical reaction deciders (CRDs). It turns out that CRDs with only bimolecular reactions (which are almost equivalent to population protocols) have a special structure that allows for an…
The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in…
We introduce the notion of corresponding a chemical reaction network to a split network translation, and use this novel process to extend the scope of existing network-based theory for characterizing the steady state set of mass-action…
Living systems are maintained out-of-equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…