Renormalization group approach to power-law modeling of complex metabolic networks

Hernández‐Bermejo, Benito

doi:10.1016/j.jtbi.2010.04.024

Cited by 2 publications

(1 citation statement)

References 33 publications

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“…In this format, any power-law term that appears in any equation is included in every equation, if necessary with a multiplier of 0 [142][143][144][145][146][147][148]. As a result, all equations formally contain a sum of the same terms.…”

Section: Other Canonical Modelsmentioning

confidence: 99%

Biochemical Systems Theory: A Review

Voit

2013

ISRN Biomathematics

149

154

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Biochemical systems theory (BST) is the foundation for a set of analytical andmodeling tools that facilitate the analysis of dynamic biological systems. is paper depicts major developments in BST up to the current state of the art in 2012. It discusses its rationale, describes the typical strategies and methods of designing, diagnosing, analyzing, and utilizing BST models, and reviews areas of application. e paper is intended as a guide for investigators entering the fascinating �eld of biological systems analysis and as a resource for practitioners and experts. PreambleBiochemical systems theory (BST) is a mathematical and computational framework for analyzing and simulating systems. It was originally developed for biochemical pathways but by now has become much more widely applied to systems throughout biology and beyond. BST is called "canonical, " which means that model construction, diagnosis, and analysis follow stringent rules, which will be discussed throughout this paper. e key ingredient of BST is the power-law representation of all processes in a system.BST has been the focus of a number of books [1-6], including some in Chinese and Japanese [7][8][9]. e most detailed modern text dedicated speci�cally to BST is [3]. Moreover, since its inception, numerous reviews have portrayed the evolving state of the art in BST. Most of these reviews summarized methodological advances for the analysis of biochemical pathway systems . Others compared BST models with alternative modeling frameworks [32,[51][52][53][54][55][56][57][58][59][60][61][62][63]; some of these comparisons will be discussed later. Yet other reviews focused on specialty areas, such as customized methods for optimizing BST models (e.g., [64][65][66][67]) or estimating their parameters (e.g., [68][69][70][71][72]), strategies for discovering design and operating principles in natural system (e.g., [73][74][75][76][77][78]), and even the use of BST models in statistics [79][80][81]. A historical account of the �rst twenty years of BST was presented in [82].Supporting the methodological developments in the �eld, several soware packages were developed for different aspects of BST analysis. e earliest was ESSYNS [83][84][85], which supported all standard steady-state analyses and also contained a numerical solver that, at the time, was many times faster than any off-the-shelf soware [86,87]; see also [88]. Utilizing advances in computing and an extension of the solver from ESSYNS, Ferreira created the very user-friendly package PLAS, which is openly available and still very widely used [89] (see also [3]). Yamada and colleagues developed soware to translate E-cell models into BST models in PLAS format [90]. Okamoto's group created the soware BestKit, which permits the graphical design and translation of models, along with their analysis [91][92][93]. Vera and colleagues developed the soware tool PLMaddon for analyzing BST models within SBML [94]; see also [95]. It expands the Matlab SBToolbox with speci�c functionalities for power-law repr...

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Section: Other Canonical Modelsmentioning

confidence: 99%

Biochemical Systems Theory: A Review

Voit

2013

ISRN Biomathematics

149

154

View full text Add to dashboard Cite

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RenoRmalization Group and Fractional Calculus Methods in a Complex World: A Review

Li-hong

Chen

Shi

et al. 2021

Fract Calc Appl Anal

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The concept of the renormalization group (RG) emerged from the renormalization of quantum field variables, which is typically used to deal with the issue of divergences to infinity in quantum field theory. Meanwhile, in the study of phase transitions and critical phenomena, it was found that the self–similarity of systems near critical points can be described using RG methods. Furthermore, since self–similarity is often a defining feature of a complex system, the RG method is also devoted to characterizing complexity. In addition, the RG approach has also proven to be a useful tool to analyze the asymptotic behavior of solutions in the singular perturbation theory. In this review paper, we discuss the origin, development, and application of the RG method in a variety of fields from the physical, social and life sciences, in singular perturbation theory, and reveal the need to connect the RG and the fractional calculus (FC). The FC is another basic mathematical approach for describing complexity. RG and FC entail a potentially new world view, which we present as a way of thinking that differs from the classical Newtonian view. In this new framework, we discuss the essential properties of complex systems from different points of view, as well as, presenting recommendations for future research based on this new way of thinking.

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Renormalization group approach to power-law modeling of complex metabolic networks

Cited by 2 publications

References 33 publications

Biochemical Systems Theory: A Review

Biochemical Systems Theory: A Review

RenoRmalization Group and Fractional Calculus Methods in a Complex World: A Review

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