Related papers: Minimal autocatalytic networks
Chemical Reaction Networks (CRNs) are a well-established model of distributed computing characterized by quantities of molecular species that can transform or change through applications of reactions. A fundamental problem in CRNs is the…
For the networks that are linear conjugate to complex balanced systems, the delayed version may include two classes of networks: one class is still linear conjugate to the delayed complex balanced network, the other is not. In this paper,…
Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtolitres. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of…
Emerging reconfigurable optical communication technologies allow to enhance datacenter topologies with demand-aware links optimized towards traffic patterns. This paper studies the algorithmic problem of jointly optimizing topology and…
Heteroclinic cycles and networks are structures in dynamical systems composed of invariant sets and connecting heteroclinic orbits, and can be robust in systems with invariant subspaces. The usual method for analysing the stability of…
Cross-reactions and other systematic issues generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key…
Many decision-making algorithms draw inspiration from the inner workings of individual biological systems. However, it remains unclear whether collective behavior among biological species can also lead to solutions for computational tasks.…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Autocatalytic reaction fronts between two reacting species in the absence of fluid flow, propagate as solitary waves. The coupling between autocatalytic reaction front and forced hydrodynamic flow may lead to stationary front whose velocity…
Reaction networks (RNs) comprise a set $X$ of species and a set $\mathscr{R}$ of reactions $Y\to Y'$, each converting a multiset of educts $Y\subseteq X$ into a multiset $Y'\subseteq X$ of products. RNs are equivalent to directed…
Discrete chemical reaction networks formalize the interactions of molecular species in a well-mixed solution as stochastic events. Given their basic mathematical and physical role, the computational power of chemical reaction networks has…
Oscillatory chemical reactions are functional components in a variety of biological contexts. In chemistry, the construction and identification of even rudimentary oscillators remain elusive and lack a general framework. Using…
Under mass-action kinetics, biochemical reaction networks give rise to polynomial autonomous dynamical systems whose parameters are often difficult to estimate. We deal in this paper with the problem of identifying the kinetic parameters of…
In most natural sciences there is currently the insight that it is necessary to bridge gaps between different processes which can be observed on different scales. This is especially true in the field of chemical reactions where the…
In small systems, quantitative discrepancies between stochastic and deterministic descriptions of chemical kinetics can be significant, with their magnitude depending on the specific reaction network. Here, we study the Finke-Watzky…
Natural systems are modeled by networks with nodes and links. Often the nodes are segregated into communities with different connectivity patterns. Node heterogeneity such as political affiliation in social networks or biological function…
We study self-organization in a minimally nonlinear model of large random ecosystems. Populations evolve over time according to a piecewise linear system of ordinary differential equations subject to a non-negativity constraint resulting in…
Chemical reaction networks (CRNs) model the behavior of molecules in a well-mixed system. The emerging field of molecular programming uses CRNs not only as a descriptive tool, but as a programming language for chemical computation.…
This paper considers the problem of inferring an unknown network of dynamical systems driven by unknown, intrinsic, noise inputs. Equivalently we seek to identify direct causal dependencies among manifest variables only from observations of…
We develop a model-independent reduction method of chemical reaction systems based on the stoichiometry, which determines their network topology. A subnetwork can be eliminated systematically to give a reduced system with fewer degrees of…