Related papers: Disconnection Rules are Complete for Chemical Reac…
We present a metagrammatical formalism, {\em generic rules}, to give a default interpretation to grammar rules. Our formalism introduces a process of {\em dynamic binding} interfacing the level of pure grammatical knowledge representation…
Regulation of multiple reaction modules is quite common in molecular computation and deep learning networks construction through chemical reactions, as is always a headache for that sequential execution of modules goes against the…
Existential rules are an expressive knowledge representation language mainly developed to query data. In the literature, they are often supposed to be in some normal form that simplifies technical developments. For instance, a common…
We introduce a new motif for constructing robust digital logic circuits using input/output chemical reaction networks. These chemical circuits robustly handle perturbations in input signals, initial concentrations, rate constants, and…
We present an account of the current status of the theoretical treatment of inclusive $(d,p)$ reactions in the breakup-fusion formalism, pointing to some applications and making the connection with current experimental capabilities. Three…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
The task of constructing compositional semantics for network-style diagrammatic languages, such as electrical circuits or chemical reaction networks, has been dubbed the black boxing problem, as it gives semantics that describes the…
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…
Physical kinetic roughening processes are well known to exhibit universal scaling of observables that fluctuate in space and time. Are there analogous dynamic scaling laws that are unique to the chemical reaction mechanisms available…
We introduce in this article a random model of reactivity in which a primitive rule, if accepted, generates an infinite number of rules by context derivation. The model may be thought of as a toy model of chemical reactivity, where…
Chemical reactions involving diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced" (DI). Virtually all biochemical processes in living media can be counted among them, together with those…
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 offer a new formalism for global explanations of pairwise feature dependencies and interactions in supervised models. Building upon SHAP values and SHAP interaction values, our approach decomposes feature contributions into synergistic,…
This paired article aims to develop an automated and programmable biochemical fully connected neural network (BFCNN) with solid theoretical support. In Part I, a concrete design for BFCNN is presented, along with the validation of the…
Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…
The principle of detailed balance states that in equilibrium each elementary process is equilibrated by its reverse process. For many real physico-chemical complex systems (e.g. homogeneous combustion, heterogeneous catalytic oxidation,…
We study the model of continuous chemical reaction networks (CRNs), consisting of reactions such as $A+B \to C+D$ that can transform some continuous, nonnegative real-valued quantity (called a *concentration*) of chemical species $A$ and…
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…
A crucial question is how objective and classical behavior arises from a fundamental physical theory. Here we provide a natural definition of a decoherence process valid in all causal theories, and show how its behavior can be extremely…
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…