Related papers: Verifying Chemical Reaction Network Implementation…
Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
We propose the chemlambda artificial chemistry, whose behavior strongly suggests that real molecules which embed Interaction Nets patterns and real chemical reactions which resemble Interaction Nets graph rewrites could be a realistic path…
The trend to equilibrium for reaction-diffusion systems modelling chemical reaction networks is investigated, in the case when reaction processes happen on subsets of the domain. We prove the convergence to equilibrium by directly showing…
The existing literature on stochastic simulation of chemical reaction networks has a tendency to move as quickly as possible to the abstract formulation of the stochastic dynamics in terms of probabilities based on the concept of the…
Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require…
The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However,…
Mixed-paradigm process models integrate strengths of procedural and declarative representations like Petri nets and Declare. They are specifically interesting for process mining because they allow capturing complex behaviour in a compact…
Recent advances in digital microfluidic (DMF) technologies offer a promising platform for a wide variety of biochemical applications, such as DNA analysis, automated drug discovery, and toxicity monitoring. For on-chip implementation of…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
Approximate solutions of the chemical master equation and the chemical Fokker-Planck equation are an important tool in the analysis of biomolecular reaction networks. Previous studies have highlighted a number of problems with the…
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…
A numerically effective procedure for determining weakly reversible chemical reaction networks that are linearly conjugate to a known reaction network is proposed in this paper. The method is based on translating the structural and…
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…
Link prediction methods use patterns in known network data to infer which connections may be missing. Previous work has shown that continuous-time quantum walks can be used to represent path-based link prediction, which we further study…
Autocatalytic chemical reaction networks can collectively replicate or maintain their constituents despite degradation reactions only above a certain threshold, which we refer to as the decay threshold. When the chemical network has a…
Methods for reconstructing the topology of complex networks from time-resolved observations of node dynamics are gaining relevance across scientific disciplines. Of biggest practical interest are methods that make no assumptions about…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
Understanding the evolution of electrified solid-liquid interfaces during electrochemical reactions is crucial. However, capturing the dynamic behavior of the interfaces with high temporal resolution and accuracy over long timescales…