Related papers: Computing all possible graph structures describing…
In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
Estimating causal interactions in complex dynamical systems is an important problem encountered in many fields of current science. While a theoretical solution for detecting the causal interactions has been previously formulated in the…
Determining whether two graphs are structurally identical is a fundamental problem with applications spanning mathematics, computer science, chemistry, and network science. Despite decades of study, graph isomorphism remains a challenging…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…
In the recent years, several polynomial algorithms of a dynamical nature have been proposed to address the graph isomorphism problem. In this paper we propose a generalization of an approach exposed in cond-mat/0209112 and find that this…
As a partial answer to a question of Rao, a deterministic and customizable efficient algorithm is presented to test whether an arbitrary graphical degree sequence has a bipartite realization. The algorithm can be configured to run in…
We study a graph partitioning problem motivated by the simulation of the physical movement of multi-body systems on an atomistic level, where the forces are calculated from a quantum mechanical description of the electrons. Several advanced…
In the recent research of data mining, frequent structures in a sequence of graphs have been studied intensively, and one of the main concern is changing structures along a sequence of graphs that can capture dynamic properties of data. On…
The paper considers scheduling on parallel machines under the constraint that some pairs of jobs cannot be processed concurrently. Each job has an associated weight, and all jobs have the same deadline. The objective is to maximise the…
Polynomial systems occur in many areas of science and engineering. Unlike general nonlinear systems, the algebraic structure enables to compute all solutions of a polynomial system. We describe our massive parallel predictor-corrector…
In this paper we discuss the question of how to decide when a general chemical reaction system is incapable of admitting multiple equilibria, regardless of parameter values such as reaction rate constants, and regardless of the type of…
We show that the number of $k$-matching in a given undirected graph $G$ is equal to the number of perfect matching of the corresponding graph $G_k$ on an even number of vertices divided by a suitable factor. If $G$ is bipartite then one can…
The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several…
We develop a new characterization of potential maximal cliques of a triconnected planar graph and, using this characterization, give a polynomial delay algorithm generating all potential maximal cliques of a given triconnected planar graph.…
Finding diverse solutions in combinatorial problems recently has received considerable attention (Baste et al. 2020; Fomin et al. 2020; Hanaka et al. 2021). In this paper we study the following type of problems: given an integer $k$, the…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
In this paper, a polynomial time algorithm for finding the set of all cyclic subsets in a graph is presented. The concept of cyclic subsets has already been introduced in an earlier paper. The algorithm finds cyclic subsets in a graph G by…
A polynomial time algorithm which detects all paths and cycles of all lengths in form of vertex pairs (start, finish).