dorsal/arxiv
View SchemaDirectionality is an inherent property of biochemical networks
| Authors | Feng Yang, Feng Qi, Daniel A. Beard |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0701004 |
| URL | https://arxiv.org/abs/q-bio/0701004 |
Abstract
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well established. This work introduces a systematic approach to compute reaction directions, which are constrained by mass balance and thermodynamics, for genome-scale networks. In addition, it is shown that the nonconvex solution space constrained by physicochemical constraints can be approximated by a set of linearized subspaces in which mass and thermodynamic balance are guaranteed. The developed methodology can be used to {\it ab initio} predict reaction directions of genome-scale networks based solely on the network stoichoimetry.
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"abstract": "Thermodynamic constraints on reactions directions are inherent in the\nstructure of a given biochemical network. However, concrete procedures for\ndetermining feasible reaction directions for large-scale metabolic networks are\nnot well established. This work introduces a systematic approach to compute\nreaction directions, which are constrained by mass balance and thermodynamics,\nfor genome-scale networks. In addition, it is shown that the nonconvex solution\nspace constrained by physicochemical constraints can be approximated by a set\nof linearized subspaces in which mass and thermodynamic balance are guaranteed.\nThe developed methodology can be used to {\\it ab initio} predict reaction\ndirections of genome-scale networks based solely on the network stoichoimetry.",
"arxiv_id": "q-bio/0701004",
"authors": [
"Feng Yang",
"Feng Qi",
"Daniel A. Beard"
],
"categories": [
"q-bio.MN"
],
"title": "Directionality is an inherent property of biochemical networks",
"url": "https://arxiv.org/abs/q-bio/0701004"
},
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"variant": "snapshot-2026-03-01",
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