相关论文: Scaling Methods for Stochastic Chemical Reaction N…
Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the…
Molecular computation based on chemical reaction networks (CRNs) has emerged as a promising paradigm for designing programmable biochemical systems. However, the implementation of complex computations still requires excessively large and…
Chemical systems are interpreted through the species they contain and the reactions they may undergo, i.e., their chemical reaction network (CRN). In spite of their central importance to chemistry, the structure of CRNs continues to be…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection…
We consider Markov logic networks and relational logistic regression as two fundamental representation formalisms in statistical relational artificial intelligence that use weighted formulas in their specification. However, Markov logic…
The dynamics of a chemical reaction network (CRN) is often modelled under the assumption of mass action kinetics by a system of ordinary differential equations (ODEs) with polynomial right-hand sides that describe the time evolution of…
Chemical Reaction Neural Networks (CRNNs) have emerged as an interpretable machine learning framework for discovering reaction kinetics directly from data, while strictly adhering to the Arrhenius and mass action laws. However, standard…
Chemical reaction networks (CRNs) are fundamental computational models used to study the behavior of chemical reactions in well-mixed solutions. They have been used extensively to model a broad range of biological systems, and are primarily…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
Step Chemical Reaction Networks (step CRNs) are an augmentation of the Chemical Reaction Network (CRN) model where additional species may be introduced to the system in a sequence of ``steps.'' We study step CRN systems using a weak subset…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
Well-mixed chemical reaction networks (CRNs) contain many distinct chemical species with copy numbers that fluctuate in correlated ways. While those correlations are typically monitored via Monte Carlo sampling of stochastic trajectories,…
We address a fundamental question: under which conditions do the dynamics and thermodynamics of open chemical reaction networks (CRNs), grounded on the notion of idealized chemostats that exchange selected species, emerge from underlying…
If $(C_n)$ is a Markov chain on a discrete state space ${\mathcal{S}}$, a Markov chain $(C_n,M_n)$ on the product space ${\mathcal{S}}\times{\mathcal{S}}$, the cat and mouse Markov chain, is constructed. The first coordinate of this Markov…
Reaction networks have been widely used as generic models in diverse areas of applied sciences, such as biology, chemistry, ecology, epidemiology, and computer science. A reaction network incorporating noisy effects is modeled as a…
We establish a generalized work theorem for stochastic chemical reaction networks (CRNs). By using a compensated Poisson jump process, we identify a martingale structure in a generalized entropy defined relative to an auxiliary backward…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
We introduce a new model of \emph{step} Chemical Reaction Networks (step CRNs), motivated by the step-wise addition of materials in standard lab procedures. Step CRNs have ordered reactants that transform into products via reaction rules…
A family of results, referred to as inheritance results, tell us which enlargements of a chemical reaction network (CRN) preserve its capacity for nontrivial behaviours such as multistationarity and oscillation. In this paper, the following…