Related papers: Reconstructing biochemical cluster networks
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…
Introducing an active space approximation is inevitable for the quantum computations of chemical systems. However, this approximation ignores the electron correlations related to non-active orbitals. Here, we propose a computational method…
We study transient sequential dynamics of evolving dynamical networks, i.e., those having active nodes and links and activity-dependent topology. We show that such networks can generate sequences of metastable cluster states where each…
This paper addresses the following verification task: Given a graph transformation system and a class of initial graphs, can we guarantee (non-)reachability of a given other class of graphs that characterizes bad or erroneous states? Both…
The present paper is concerned with the concept of the one-way quantum computer, beyond binary-systems, and its relation to the concept of stabilizer quantum codes. This relation is exploited to analyze a particular class of quantum…
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…
This work studies how a suitably-designed classical system generates with a quantum-like (QL) state space mediated by a graph. The graph plays a special dual role by directing the topology of the classical network and defining a state space…
In this work we present a coupled-cluster theory for the propagation of multireference electronic systems initiating at general quantum mechanical states. Our formalism is based on the infinitesimal analysis of modified cluster operators,…
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…
Large datasets with interactions between objects are common to numerous scientific fields (i.e. social science, internet, biology...). The interactions naturally define a graph and a common way to explore or summarize such dataset is graph…
Apart from the role the clustering coefficient plays in the definition of the small-world phenomena, it also has great relevance for practical problems involving networked dynamical systems. To study the impact of the clustering coefficient…
We show that a special type of entangled states, cluster states, can be created with Heisenberg interactions and local rotations in 2d steps where d is the dimension of the lattice. We find that, by tuning the coupling strengths,…
The connection between certain entangled states and graphs has been heavily studied in the context of measurement-based quantum computation as a tool for understanding entanglement. Here we show that this correspondence can be harnessed in…
Local graph clustering is an important algorithmic technique for analysing massive graphs, and has been widely applied in many research fields of data science. While the objective of most (local) graph clustering algorithms is to find a…
Graph-based analyses have gained a lot of relevance in the past years due to their high potential in describing complex systems by detailing the actors involved, their relations and their behaviours. Nevertheless, in scenarios where these…
Clustering is often a challenging problem because of the inherent ambiguity in what the "correct" clustering should be. Even when the number of clusters $K$ is known, this ambiguity often still exists, particularly when there is variation…
We have generalised the concept of graph states to what we have called mixed graph states, which we define in terms of mixed graphs, that is graphs with both directed and undirected edges, as the density matrix stabilized by the associated…
Symmetries in a network connectivity regulate how the graph's functioning organizes into clustered states. Classical methods for tracing the symmetry group of a network require very high computational costs, and therefore they are of hard,…
We study the graph coloring problem over random graphs of finite average connectivity $c$. Given a number $q$ of available colors, we find that graphs with low connectivity admit almost always a proper coloring whereas graphs with high…
As a model problem for clustering, we consider the densest k-disjoint-clique problem of partitioning a weighted complete graph into k disjoint subgraphs such that the sum of the densities of these subgraphs is maximized. We establish that…