Related papers: Decomposition of Complex Reaction Networks into Re…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…
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 further clarify the relation between detailed-balanced and complex-balanced equilibria of reversible chemical reaction networks. Our results hold for arbitrary kinetics and also for boundary equilibria. Detailed balance, complex balance,…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
Over the last two decades, network science has greatly advanced our understanding of how the collective behaviors of a complex system emerge from the interactions among its basic units. Multiplex networks, i.e. networks with many layers,…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
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…
Reaction prediction, a critical task in synthetic chemistry, is to predict the outcome of a reaction based on given reactants. Generative models like Transformer have typically been employed to predict the reaction product. However, these…
Complex networks have been shown to be robust against random structural perturbations, but vulnerable against targeted attacks. Robustness analysis usually simulates the removal of individual or sets of nodes, followed by the assessment of…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
Spectral decomposition has been rarely used to investigate complex networks. In this work we apply this concept in order to define two types of link-directed attacks while quantifying their respective effects on the topology. Several other…
We establish a new relationship between monotonicity and contractivity and use this connection to describe a new general class of weakly contractive reaction networks. The new class is characterized by the stoichiometry matrix of the…
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and…
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…
Retrosynthesis is the process of recursively decomposing target molecules into available building blocks. It plays an important role in solving problems in organic synthesis planning. To automate or assist in the retrosynthesis analysis,…
The study of the dynamics of chemical reactions, and in particular phenomena such as oscillating reactions, has led to the recognition that many dynamical properties of a chemical reaction can be predicted from graph theoretical properties…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…