相关论文: Hypergraphic Oriented Matroid Relational Dependenc…
Rapid discovery of new reactions and molecules in recent years has been facilitated by the advancements in high throughput screening, accessibility to a much more complex chemical design space, and the development of accurate molecular…
We study families of chemical reaction networks whose positive steady states are toric, and therefore can be parameterized by monomials. Families are constructed algorithmically from a core network; we show that if a family member is…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
This paper proposes an optimization-based framework for the analysis of multiperiod directed multihypergraphs aimed at identifying self-amplifying structures that sustain endogenous growth in complex systems. The approach captures the…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and…
Parsing chemical reaction diagrams from scientific literature is challenging due to heterogeneous layouts, intertwined visual elements, and the difficulty of integrating recognition and reasoning. Existing vision-language models advance…
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…
An oriented hypergraph is an oriented incidence structure that extends the concepts of signed graphs, balanced hypergraphs, and balanced matrices. We introduce hypergraphic structures and techniques that generalize the circuit…
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…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular…
We derive the nonequilibrium conductance matrix for open stationary Chemical Reaction Networks (CRNs) described by a deterministic mass action kinetic equation. As an illustration, we determine the nonequilibrium conductance matrix of a CRN…
A binary frame template is a device for creating binary matroids from graphic or cographic matroids. Such matroids are said to conform or coconform to the template. We introduce a preorder on these templates and determine the nontrivial…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
High-order structures have been recognised as suitable models for systems going beyond the binary relationships for which graph models are appropriate. Despite their importance and surge in research on these structures, their random cases…
The conventional definition of hypergraph has two major issues: (1) there is not a standard definition of directed hypergraph and (2) there is not a formal definition of nested hypergraph. To resolve these issues, we propose a new…
Coarse-grained modeling in molecular simulations serves not only to extend accessible time and length scales beyond atomistic limits, but also to reduce high-dimensional chemical data to low-dimensional representations that expose the…