Related papers: Reverse Engineering Chemical Reaction Networks fro…
Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
We introduce inverse transport networks as a learning architecture for inverse rendering problems where, given input image measurements, we seek to infer physical scene parameters such as shape, material, and illumination. During training,…
We explore the perspectives of machine learning techniques in the context of quantum field theories. In particular, we discuss two-dimensional complex scalar field theory at nonzero temperature and chemical potential -- a theory with a…
A major challenge in network science is to determine parameters governing complex network dynamics from experimental observations and theoretical models. In complex chemical reaction networks, for example, such as those describing processes…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…
Causality implies that by measuring an absorption spectrum, the time-dependent linear response function can be retrieved. Recent experiments suggest a link between the shape of spectral lines observed in absorption spectroscopy with the…
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…
Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at…
Exploring large chemical reaction networks with automated exploration approaches and accurate quantum chemical methods can require prohibitively large computational resources. Here, we present an automated exploration approach that focuses…
We consider stochastic reaction networks modeled by continuous-time Markov chains. Such reaction networks often contain many reactions, potentially occurring at different time scales, and have unknown parameters (kinetic rates, total…
To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
Both natural and synthetic chemical systems not only exhibit a range of non-trivial dynamics, but also transition between qualitatively different dynamical behaviours as environmental parameters change. Such transitions are called…
Chemical kinetic mechanisms can be represented by sets of elementary reactions that are easily translated into mathematical terms using physicochemical relationships. The schematic representation of reactions captures the interactions…
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…