Reconstructing biochemical cluster networks

DOI10.1007/S10910-011-9892-6zbMATH Open1274.92054arXiv0906.1342OpenAlexW3106537555MaRDI QIDQ656982FDOQ656982

Authors: Utz-Uwe Haus, Raymond Hemmecke, Sebastian Pokutta 

Publication date: 13 January 2012

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

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.

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

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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)

Cites Work

• Ideals, varieties, and algorithms. An introduction to computational algebraic geometry and commutative algebra
• Title not available (Why is that?)
• Siphons in chemical reaction networks
• Computing generating sets of lattice ideals and Markov bases of lattices
• The complexity of the word problems for commutative semigroups and polynomial ideals
• Converting bases with the Gröbner walk
• A mathematical approach to solve the network reconstruction problem
• Decomposition of reaction networks: the initial phase of the permanganate/oxalic acid reaction
• A new general algorithmic method in reaction syntheses using linear algebra

Cited In (3)

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

Uses Software

• CoCoA
• GRIN

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