相关论文: Kron-based Model-order Reduction of Open Mass-acti…

In this work, we introduce a flow based machine learning approach, called reaction coordinate (RC) flow, for discovery of low-dimensional kinetic models of molecular systems. The RC flow utilizes a normalizing flow to design the coordinate…

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 show that the Schur-complement reduction of a chemical reaction network (CRN) from Hirono et al. is the categorical complement of the stoichiometric arrow in the arrow category $[\mathbf{A}_2,\mathbf{Vect}]$. This identifies the ambient…

Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…

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…

The asymptotic properties of some Markov processes associated to stochastic chemical reaction networks (CRNs) driven by the kinetics of the law of mass action are analyzed. The scaling regime introduced in the paper assumes that the norm of…

An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…

Predicting stochastic cellular dynamics as emerging from the mechanistic models of molecular interactions is a long-standing challenge in systems biology: low-level chemical reaction network (CRN) models give raise to a highly-dimensional…

Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…

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…

Proposals for molecular communication networks as part of a future internet of bio-nano-things have become more intricate and the question of practical implementation is gaining more importance. One option is to apply detailed chemical…

In this paper we derive a compact mathematical formulation describing the dynamics of chemical reaction networks that are complex-balanced and are governed by mass action kinetics. The formulation is based on the graph of (substrate and…

For fast timescales or long prediction horizons, the AC optimal power flow (OPF) problem becomes a computational challenge for large-scale, realistic AC networks. To overcome this challenge, this paper presents a novel network reduction…

We present an integrated approach for the use of simulated data from full order discretization as well as projection-based Reduced Basis reduced order models for the training of machine learning approaches, in particular Kernel Methods, in…

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…

Inspired by Anderson et al. [J. R. Soc. Interface, 2014] we study the long-term behavior of discrete chemical reaction networks (CRNs). In particular, using techniques from both Petri net theory and CRN theory, we provide a powerful…

Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…

In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both…

This paper presents a novel structure-preserving, Kron-based reduction framework for unbalanced distribution feeders. The method aggregates electrically similar nodes within a mixed-integer optimization (MIP) problem to produce reduced…

Network reduction simplifies complex electrical networks to address computational challenges of large-scale transmission and distribution grids. Traditional network reduction methods are often based on a predefined set of nodes or lines to…