dorsal/arxiv
View SchemaMetabolic Network Modelling: Including Stochastic Effects
| Authors | P. Ao |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0504003 |
| URL | https://arxiv.org/abs/q-bio/0504003 |
Abstract
We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are balanced to determine the network dynamics, which gives arise to a special stochastic differential equation supplemented by a relationship between the stochastic force and the degradation matrix. Important network behaviors can be obtained from the potential function without explicitly solving for the time-dependent solution. The existence of such a potential function suggests a global optimization principle, and the existence stochastic force corresponds natural to the hierarchical structure in metabolic networks. We provide theoretical evidences to justify our proposal by discussing its connections to others large-scale biochemical systems approaches, such as the network thermodynamics theory, biochemical systems theory, metabolic control analysis, and flux balance analysis. Experimental data displaying stochasticity are also pointed out.
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"abstract": "We propose to model the dynamics of metabolic networks from a systems biology\npoint of view by four dynamical structure elements: potential function,\ntransverse matrix, degradation matrix, and stochastic force. These four\nelements are balanced to determine the network dynamics, which gives arise to a\nspecial stochastic differential equation supplemented by a relationship between\nthe stochastic force and the degradation matrix. Important network behaviors\ncan be obtained from the potential function without explicitly solving for the\ntime-dependent solution. The existence of such a potential function suggests a\nglobal optimization principle, and the existence stochastic force corresponds\nnatural to the hierarchical structure in metabolic networks. We provide\ntheoretical evidences to justify our proposal by discussing its connections to\nothers large-scale biochemical systems approaches, such as the network\nthermodynamics theory, biochemical systems theory, metabolic control analysis,\nand flux balance analysis. Experimental data displaying stochasticity are also\npointed out.",
"arxiv_id": "q-bio/0504003",
"authors": [
"P. Ao"
],
"categories": [
"q-bio.MN",
"q-bio.SC"
],
"title": "Metabolic Network Modelling: Including Stochastic Effects",
"url": "https://arxiv.org/abs/q-bio/0504003"
},
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"type": "Model",
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