236,420 research outputs found
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
Modeling molecules as undirected graphs and chemical reactions as graph
rewriting operations is a natural and convenient approach tom odeling
chemistry. Graph grammar rules are most naturally employed to model elementary
reactions like merging, splitting, and isomerisation of molecules. It is often
convenient, in particular in the analysis of larger systems, to summarize
several subsequent reactions into a single composite chemical reaction. We use
a generic approach for composing graph grammar rules to define a chemically
useful rule compositions. We iteratively apply these rule compositions to
elementary transformations in order to automatically infer complex
transformation patterns. This is useful for instance to understand the net
effect of complex catalytic cycles such as the Formose reaction. The
automatically inferred graph grammar rule is a generic representative that also
covers the overall reaction pattern of the Formose cycle, namely two carbonyl
groups that can react with a bound glycolaldehyde to a second glycolaldehyde.
Rule composition also can be used to study polymerization reactions as well as
more complicated iterative reaction schemes. Terpenes and the polyketides, for
instance, form two naturally occurring classes of compounds of utmost
pharmaceutical interest that can be understood as "generalized polymers"
consisting of five-carbon (isoprene) and two-carbon units, respectively
Model validation of simple-graph representations of metabolism
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 simplest type of graph representation, this reduction
can be done in several ways. We investigate different simple network
representations by testing how well they encode information about one
biologically important network structure -- network modularity (the propensity
for edges to be cluster into dense groups that are sparsely connected between
each other). To reach this goal, we design a model of reaction-systems where
network modularity can be controlled and measure how well the reduction to
simple graphs capture the modular structure of the model reaction system. We
find that the network types that best capture the modular structure of the
reaction system are substrate-product networks (where substrates are linked to
products of a reaction) and substance networks (with edges between all
substances participating in a reaction). Furthermore, we argue that the
proposed model for reaction systems with tunable clustering is a general
framework for studies of how reaction-systems are affected by modularity. To
this end, we investigate statistical properties of the model and find, among
other things, that it recreate correlations between degree and mass of the
molecules.Comment: to appear in J. Roy. Soc. Intefac
Bulvallene Reaction Graph
The Monster Graph describing a rapidly reversible degenerate Cope rearrangement of bullvalene molecule is considered. Some global properties of this 1209600-vertex reaction graph, such as shell counts, properties of geodesics connection enantiomers etc., are discussed
Reaction Spreading on Graphs
We study reaction-diffusion processes on graphs through an extension of the
standard reaction-diffusion equation starting from first principles. We focus
on reaction spreading, i.e. on the time evolution of the reaction product,
M(t). At variance with pure diffusive processes, characterized by the spectral
dimension, d_s, for reaction spreading the important quantity is found to be
the connectivity dimension, d_l. Numerical data, in agreement with analytical
estimates based on the features of n independent random walkers on the graph,
show that M(t) ~ t^{d_l}. In the case of Erdos-Renyi random graphs, the
reaction-product is characterized by an exponential growth M(t) ~ e^{a t} with
a proportional to ln, where is the average degree of the graph.Comment: 4 pages, 3 figure
On the Complexity of Reconstructing Chemical Reaction Networks
The analysis of the structure of chemical reaction networks is crucial for a
better understanding of chemical processes. Such networks are well described as
hypergraphs. However, due to the available methods, analyses regarding network
properties are typically made on standard graphs derived from the full
hypergraph description, e.g.\ on the so-called species and reaction graphs.
However, a reconstruction of the underlying hypergraph from these graphs is not
necessarily unique. In this paper, we address the problem of reconstructing a
hypergraph from its species and reaction graph and show NP-completeness of the
problem in its Boolean formulation. Furthermore we study the problem
empirically on random and real world instances in order to investigate its
computational limits in practice
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