Biochemical systems analysis

SAVAGEAU, M.A., Biochemical Systems Analysis, Addison-Wesley, Reading, MA. 1976, 379 p. 

VOIT, E.O., RADIVOYEVITHC, T., Biochemical systems analysis of genomewide expression data, Bioinformatics, 2000,16, 1023-1037. 

M. A. Savageau, Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J. Theor. Biol. 25, 365 369 (1969). 

Biochemical systems -analysis using Raman spectroscopy [SPECTROSCOPY, OPTICAL] (Vol 22)... 

Many methods have been developed for model analysis for instance, bifurcation and stability analysis [88, 89], parameter sensitivity analysis [90], metabolic control analysis [16, 17, 91] and biochemical systems analysis [18]. One highly important method for model analysis and especially for large models, such as many silicon cell models, is model reduction. Model reduction has a long history in the analysis of biochemical reaction networks and in the analysis of nonlinear dynamics (slow and fast manifolds) [92-104]. In all cases, the aim of model reduction is to derive a simplified model from a larger ancestral model that satisfies a number of criteria. In the following sections we describe a relatively new form of model reduction for biochemical reaction networks, such as metabolic, signaling, or genetic networks. 

Kacser, H. Bums, J. A. The control of flux. Symp Soc Exp Biol 1973, 27 65-104. Savageau, M. A. Biochemical systems analysis a study of function and design in molecular biology. Addison-Wesley, New York, 1976. 

Simulation and analysis of biochemical systems is at the heart of computational and systems biology. This textbook covers mathematical and computational approaches to biochemical systems based on rigorous physical principles. Written with an interdisciplinary audience in mind, this book shows the natural connection between established disciplines of chemistry and physics and the emerging field of systems biology, enabling the reader to take an informed approach to quantitative biochemical systems analysis. 

Savageau, M. A. (1969b). Biochemical systems analysis II. The steady state solutions for an n-pool system using a power-law approximation. J. Theoret. Biol. 25, 370-379. 

Savageau MA (1999) Biochemical system analysis a study of function and design in molecular biology. Addison-Wesley, Reading... 

Savageau, M. A. (1999). Biochemical System Analysis A Study of Function and Design in Molecular Biology, Addison-Wesley, Reading. 

Chemical appHcations of Mn ssbauer spectroscopy are broad (291—293) determination of electron configurations and assignment of oxidation states in stmctural chemistry polymer properties studies of surface chemistry, corrosion, and catalysis and metal-atom bonding in biochemical systems. There are also important appHcations to materials science and metallurgy (294,295) (see Surface and interface analysis). 

Besides the two most well-known cases, the local bifurcations of the saddle-node and Hopf type, biochemical systems may show a variety of transitions between qualitatively different dynamic behavior [13, 17, 293, 294, 297 301]. Transitions between different regimes, induced by variation of kinetic parameters, are usually depicted in a bifurcation diagram. Within the chemical literature, a substantial number of articles seek to identify the possible bifurcation of a chemical system. Two prominent frameworks are Chemical Reaction Network Theory (CRNT), developed mainly by M. Feinberg [79, 80], and Stoichiometric Network Analysis (SNA), developed by B. L. Clarke [81 83]. An analysis of the (local) bifurcations of metabolic networks, as determinants of the dynamic behavior of metabolic states, constitutes the main topic of Section VIII. In addition to the scenarios discussed above, more complicated quasiperiodic or chaotic dynamics is sometimes reported for models of metabolic pathways [302 304]. However, apart from few special cases, the possible relevance of such complicated dynamics is, at best, unclear. Quite on the contrary, at least for central metabolism, we observe a striking absence of complicated dynamic phenomena. To what extent this might be an inherent feature of (bio)chemical systems, or brought about by evolutionary adaption, will be briefly discussed in Section IX. 

Note that MCA is not a tool for dynamic modeling of biochemical systems. Rather, MCA is essentially a generic sensitivity analysis, predominantly... 

Although the importance of a systemic perspective on metabolism has only recently attained widespread attention, a formal frameworks for systemic analysis has already been developed since the late 1960s. Biochemical Systems Theory (BST), put forward by Savageau and others [142, 144 147], seeks to provide a unified framework for the analysis of cellular reaction networks. Predating Metabolic Control Analysis, BST emphasizes three main aspects in the analysis of metabolism [319] (i) the importance of the interconnections, rather than the components, for cellular function (ii) the nonlinearity of biochemical rate equations (iii) the need for a unified mathematical treatment. Similar to MCA, the achievements associated with BST would warrant a more elaborate treatment, here we will focus on BST solely as a tool for the approximation and numerical simulation of complex biochemical reaction networks. 

E. O. Voit, Computational Analysis of Biochemical Systems. A Practical Guide for Biochemists and Molecular Biologists, Cambridge University Press, Cambridge, United Kingdom (2000). 

P. M. DiGrazia, J. W. Blackburn, P. R. Bienkowski, B. Hilton, G. D. Reed, J. M. H. King, and G. S. Sayler. 1989. Development of a systems analysis approach for resolving the structure of biodegrading soil systems. Appl. Biochem. and Biotechnol. In Press. 

I would like to comment on the theoretical analysis of two systems described by Professor Hess, in order to relate the phenomena discussed by Professor Prigogine to the nonequilibrium behavior of biochemical systems. The mechanism of instability in glycolysis is relatively simple, as it involves a limited number of variables. An allosteric model for the phosphofrucktokinase reaction (PFK) has been analyzed, based on the activation of the enzyme by a reaction product. There exists a parameter domain in which the stationary state of the system is unstable in these conditions, sustained oscillations of the limit cycle type arise. Theoretical... 

This review gives a brief summary of the "types of chemically modified electrodes, their fabrication, and some examples of their uses. One especially promising area of application is that of selective chemical analysis. In general, the approach used is to attach to the electrode surface electrochemically reactive molecules which have electrocatalytic activity toward specific substrates or analytes. In addition, the incorporation of biochemical systems should greatly extend the usefulness of these devices for analytical purposes. 

Bottom-up systems biology does not rely that heavily on Omics. It predates top-down systems biology and it developed out of the endeavors associated with the construction of the first mathematical models of metabolism in the 1960s [10, 11], the development of enzyme kinetics [12-15], metabolic control analysis [16, 17], biochemical systems theory [18], nonequilibrium thermodynamics [6, 19, 20], and the pioneering work on emergent aspects of networks by researchers such as Jacob, Monod, and Koshland [21-23]. 

Studd, J. W. Stability analysis of biochemical systems - practical guide. Prog Biophys Mol Biol 1978, 33 99-187. 

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