Reconstructing biochemical cluster networks

DOI10.1007/S10910-011-9892-6MaRDI QIDQ656982zbMATHOpenAlexFDO

Authors Utz-Uwe Haus, Raymond Hemmecke, Sebastian Pokutta

Publication date 13 January 2012

Published in Journal of Mathematical Chemistry (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0906.1342

zbMATH Keywords

computer algebrabinomial idealscomputational chemistryreaction networkschemical engineeringelementary reactionsreaction mechanismsreactive intermediatesGröbner bases

Mathematics Subject Classification ID

Applications of graph theory (05C90) Biochemistry, molecular biology (92C40) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Classical flows, reactions, etc. in chemistry (92E20)

Abstract: Motivated by fundamental problems in chemistry and biology we study cluster graphs arising from a set of initial states $$ and a set of transitions/reactions $$. The clusters are formed out of states that can be mutually transformed into each other by a sequence of reversible transitions. We provide a solution method from computational commutative algebra that allows for deciding whether two given states belong to the same cluster as well as for the reconstruction of the full cluster graph. Using the cluster graph approach we provide solutions to two fundamental questions: 1) Deciding whether two states are connected, e.g., if the initial state can be turned into the final state by a sequence of transition and 2) listing concisely all reactions processes that can accomplish that. As a computational example, we apply the framework to the permanganate/oxalic acid reaction.

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• On the complexity of reconstructing chemical reaction networks
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Cites work

• scientific article; zbMATH DE number 1515218 (Why is no real title available?)
• A mathematical approach to solve the network reconstruction problem
• A new general algorithmic method in reaction syntheses using linear algebra
• Computing generating sets of lattice ideals and Markov bases of lattices
• Converting bases with the Gröbner walk
• Decomposition of reaction networks: the initial phase of the permanganate/oxalic acid reaction
• Ideals, varieties, and algorithms. An introduction to computational algebraic geometry and commutative algebra
• Siphons in chemical reaction networks
• The complexity of the word problems for commutative semigroups and polynomial ideals

Cited in

(3)

• Cluster compartmentalization may provide resistance to parasites for catalytic networks
• Relevance of dynamic clustering to biological networks
• Parameter reconstruction for biochemical networks using interval analysis

Describes a project that uses

Uses Software

• CoCoA
• GRIN

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