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

Generic Strategies for Chemical Space Exploration

Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial explosion. It quickly becomes impossible to test, for all pairs of compounds in a rapidly growing network, whether they can react with each other. More sophisticated and efficient strategies are therefore required to construct very large chemical reaction networks. Undirected labeled graphs and graph rewriting are natural models of chemical compounds and chemical reactions. Borrowing the idea of partial evaluation from functional programming, we introduce partial applications of rewrite rules. Binding substrate to rules increases the number of rules but drastically prunes the substrate sets to which it might match, resulting in dramatically reduced resource requirements. At the same time, exploration strategies can be guided, e.g. based on restrictions on the product molecules to avoid the explicit enumeration of very unlikely compounds. To this end we introduce here a generic framework for the specification of exploration strategies in graph-rewriting systems. Using key examples of complex chemical networks from sugar chemistry and the realm of metabolic networks we demonstrate the feasibility of a high-level strategy framework. The ideas presented here can not only be used for a strategy-based chemical space exploration that has close correspondence of experimental results, but are much more general. In particular, the framework can be used to emulate higher-level transformation models such as illustrated in a small puzzle game

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

Real-time determination of laser beam quality by modal decomposition

We present a real-time method to determine the beam propagation ratio M2 of laser beams. The all-optical measurement of modal amplitudes yields M2 parameters conform to the ISO standard method. The experimental technique is simple and fast, which allows to investigate laser beams under conditions inaccessible to other methods.Comment: 8 pages, 4 figures, published in Optics Expres