Related papers: Timing in chemical reaction networks
The Turing completeness of continuous Chemical Reaction Networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…
Molecular communication is set to play an important role in the design of complex biological and chemical systems. An important class of molecular communication systems is based on the timing channel, where information is encoded in the…
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…
The model of chemical reaction networks is among the oldest and most widely studied and used in natural science. The model describes reactions among abstract chemical species, for instance $A + B \to C$, which indicates that if a molecule…
Our paper reviews some key concepts in chemical reaction network theory and mathematical epidemiology, and examines their intersection, with three goals. The first is to make the case that mathematical epidemiology (ME), and also related…
The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable…
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…
We investigate a class of stochastic chemical reaction networks with $n{\ge}1$ chemical species $S_1$, \ldots, $S_n$, and whose complexes are only of the form $k_iS_i$, $i{=}1$,\ldots, $n$, where $(k_i)$ are integers. The time evolution of…
In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical algorithms must be designed…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
In this contribution, we establish a model for multichannel cognitive radio networks (CRNs) using the theory of priority queues. This model enables us to conduct a performance analysis in the most general form by the derivation of the…
In this essay, we investigate some relations between Chemical Reaction Networks (CRN) and Mathematical Epidemiology (ME) and report on several pleasant surprises which we had simply by putting these two topics together. Firstly, we propose…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Counterexample generation is an indispensable part of model checking process. In stochastic model checking, counterexample generation is a challenging problem as it is not enough to find a single trace that violates the given property.…
We classify the functions $f:\mathbb{N}^2 \rightarrow \mathbb{N}$ which are stably computable by output-oblivious Stochastic Chemical Reaction Networks (CRNs), i.e., systems of reactions in which output species are never reactants. While it…
A chemical reaction mechanism (CRM) is a sequence of molecular-level events involving bond-breaking/forming processes, generating transient intermediates along the reaction pathway as reactants transform into products. Understanding such…
The thermodynamic and dynamical conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics were presented in Srinivas et al. (2023): Unimolecular CRNs can only…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
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…
Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on…