Related papers: Disconnection Rules are Complete for Chemical Reac…
We consider global dynamics of reaction systems as introduced by Ehrenfeucht and Rozenberg. The dynamics is represented by a directed graph, the so-called transition graph, and two reaction systems are considered equivalent if their…
We consider the chemical reaction networks and study currents in these systems. Reviewing recent decomposition of rate functionals from large deviation theory for Markov processes, we adapt these results for reaction networks. In…
Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from…
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…
We propose a technique to detect and generate patterns in a network of locally interacting dynamical systems. Central to our approach is a novel spatial superposition logic, whose semantics is defined over the quad-tree of a partitioned…
The rules of d-separation provide a framework for deriving conditional independence facts from model structure. However, this theory only applies to simple directed graphical models. We introduce relational d-separation, a theory for…
A decomposition of a chemical reaction network (CRN) is produced by partitioning its set of reactions. The partition induces networks, called subnetworks, that are "smaller" than the given CRN which, at this point, can be called parent…
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…
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…
This note shows how classical tools from linear control theory can be leveraged to provide a global analysis of nonlinear reaction-diffusion models. The approach is differential in nature. It proceeds from classical tools of contraction…
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…
Inspired by decomposition problems in rule-based formalisms in Computational Systems Biology and recent work on compositionality in graph transformation, this paper proposes to use arbitrary colimits to "deconstruct" models of reactions in…
Graph neural networks are widely used to learn global representations of graphs, which are then used for regression or classification tasks. Typically, the graphs in such data sets are connected, i.e. each training sample consists of a…
Reversible logic synthesis is a crucial component in quantum electronic design automation. While rule-based methodologies have gained prominence in reversible circuit optimization, the completeness of the transformation rule systems is a…
Reaction networks have become a major modelling framework in the biological sciences from epidemiology and population biology to genetics and cellular biology. In recent years, much progress has been made on stochastic reaction networks…
In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
We consider general multi-species models of reaction diffusion processes and obtain a set of constraints on the rates which give rise to closed systems of equations for correlation functions. Our results are valid in any dimension and on…
Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…