Related papers: Identifying Biochemical Reaction Networks From Het…
This work addresses multistationarity of fully open reaction networks equipped with mass action kinetics. We improve upon the existing results relating existence of positive feedback loops in a reaction network and multistationarity; and we…
Databases of gas and surface chemical reactions are a key tool for scientists working in a wide range of physical sciences. In Astrochemistry, databases of chemical reactions are used as inputs to chemical models to determine the abundances…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
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,…
We consider the problem of learning data-driven replicas for stiff systems of ordinary differential equations arising in chemical kinetics that can be evaluated with high computational efficiency. We first focus on training emulators for…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
We consider linear elimination of variables in steady state equations of a chemical reaction network. Particular subsets of variables corresponding to sets of so-called reactant-noninteracting species, are introduced. The steady state…
The detailed balance property is a fundamental property that must be satisfied in all the macroscopic systems with a well defined temperature at each point. On the other hand, many biochemical networks work in non-equilibrium conditions and…
In this paper, we provide a graphic formulation of non-isothermal reaction systems and show that a non-isothermal detailed balanced network system converges (locally) asymptotically to the unique equilibrium within the invariant manifold…
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…
Chemical named entity recognition (NER) models are used in many downstream tasks, from adverse drug reaction identification to pharmacoepidemiology. However, it is unknown whether these models work the same for everyone. Performance…
In many biological processes heterogeneity within cell populations is an important issue. In this work we consider populations where the behavior of every single cell can be described by a system of ordinary differential equations.…
Reaction virtual screening and discovery are fundamental challenges in chemistry and materials science, where traditional graph neural networks (GNNs) struggle to model multi-reactant interactions. In this work, we propose ChemHGNN, a…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
A central challenge in materials science is characterizing chemical processes that are elusive to direct measurement, particularly in functional materials operating under realistic conditions. Here, we demonstrate that mechanical strain…
Biochemical networks play a crucial role in biological systems, implementing a broad range of vital functions. They normally operate at low copy numbers and in spatial settings, but this is often ignored and well-stirred conditions are…
Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…