摘要翻译:
在这项工作中,我们提出了一种新的算法策略,允许有效地表征与代谢约束相容的一整套稳定通量。该算法基于著名的Bethe近似,可以在多项式时间内计算高维非全维凸多面体的体积。该算法的计算结果与基于蒙特卡罗的红细胞代谢网络流量分布的预测结果非常吻合,但所用的时间却非常短。我们还分析了大肠杆菌代谢网络中反应的平均通量的统计性质,最后测试了基因敲除对大肠杆菌中心代谢解空间大小的影响。
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英文标题:
《Estimating the size of the solution space of metabolic networks》
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作者:
Alfredo Braunstein, Roberto Mulet, Andrea Pagnani
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最新提交年份:
2007
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分类信息:
一级分类:Physics 物理学
二级分类:Disordered Systems and Neural Networks 无序系统与神经网络
分类描述:Glasses and spin glasses; properties of random, aperiodic and quasiperiodic systems; transport in disordered media; localization; phenomena mediated by defects and disorder; neural networks
眼镜和旋转眼镜;随机、非周期和准周期系统的性质;无序介质中的传输;本地化;由缺陷和无序介导的现象;神经网络
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一级分类:Physics 物理学
二级分类:Statistical Mechanics 统计力学
分类描述:Phase transitions, thermodynamics, field theory, non-equilibrium phenomena, renormalization group and scaling, integrable models, turbulence
相变,热力学,场论,非平衡现象,重整化群和标度,可积模型,湍流
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一级分类:Quantitative Biology 数量生物学
二级分类:Molecular Networks 分子网络
分类描述:Gene regulation, signal transduction, proteomics, metabolomics, gene and enzymatic networks
基因调控、信号转导、蛋白质组学、代谢组学、基因和酶网络
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一级分类:Quantitative Biology 数量生物学
二级分类:Quantitative Methods 定量方法
分类描述:All experimental, numerical, statistical and mathematical contributions of value to biology
对生物学价值的所有实验、数值、统计和数学贡献
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英文摘要:
In this work we propose a novel algorithmic strategy that allows for an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. The algorithm, based on the well-known Bethe approximation, allows the computation in polynomial time of the volume of a non full-dimensional convex polytope in high dimensions. The result of our algorithm match closely the prediction of Monte Carlo based estimations of the flux distributions of the Red Blood Cell metabolic network but in incomparably shorter time. We also analyze the statistical properties of the average fluxes of the reactions in the E-Coli metabolic network and finally to test the effect of gene knock-outs on the size of the solution space of the E-Coli central metabolism.
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PDF链接:
https://arxiv.org/pdf/709.0922