Open AccessBook
The Regulation of Cellular Systems
TLDR
The basic equations of metabolic control analysis are rewritten in terms of co-response coefficients and internal response coefficients to describe the interaction of optimization methods and the interrelation with evolution.Abstract:
Introduction Fundamentals of biochemical modeling Balance equations Rate laws Generalized mass-action kinetics Various enzyme kinetic rate laws Thermodynamic flow-force relationships Power-law approximation Steady states of biochemical networks General considerations Stable and unstable steady states Multiple steady states Metabolic oscillations Background Mathematical conditions for oscillations Glycolytic oscillations Models of intracellular calcium oscillations A simple three-variable model with only monomolecular and bimolecular reactions Possible physiological significance of oscillations Stoichiometric analysis Conservation relations Linear dependencies between the rows of the stoichiometry matrix Non-negative flux vectors Elementary flux modes Thermodynamic aspects A generalized Wegscheider condition Strictly detailed balanced subnetworks Onsager's reciprocity reactions for coupled enyme reactions Time hierarchy in metabolism Time constants The quasi-steady-state approximation The Rapid equilibrium approximation Modal analysis Metabolic control analysis Basic definitions A systematic approach Theorems of metabolic control analysis Summation theorems Connectivity theorems Calculation of control coefficients using the theorems Geometrical interpretation Control analysis of various systems General remarks Elasticity coefficients for specific rate laws Control coefficients for simple hypothetical pathways Unbranched chains A branched system Control of erythrocyte energy metabolism The reaction system Basic model Interplay of ATP production and ATP consumption Glycolytic energy metabolism and osmotic states A simple model of oxidative phosphorylation A three-step model of serine biosynthesis Time-dependent control coefficients Are control coefficients always parameter independent? Posing the problem A system without conserved moieties A system with a conserved moiety A system including dynamic channeling Normalized versus non-normalized coefficients Analysis in terms of variables other than steady-state concentrations and fluxes General analysis Concentration ratios and free-energy-differences as state variables Entropy production as response variable Control of transient times Control of oscillations A second-order approach A quantitative approach to metabolic regulations Co-response coefficients Fluctuations of internal variables versus parameter perturbations Internal response coefficients Rephrasing the basic equations of metabolic control analysis in terms of co-response coefficients and internal response coefficients Control within and between subsystems Modular approach Overall elasticities Overall control coefficients Flux control insusceptibility Control exerted by elementary steps in enzyme catalysis Control analysis of metabolic channeling Comparison of metabolic control analysis and power-law formalism Computational aspects Application of optimization methods and the interrelation with evolution Optimization of the catalytic properties of single enzymes Basic assumptions Optimal values of elementary rate constants Optimal Michaelis constants Optimization of multienzyme systems Maximization of steady-state flux Influence of osmotic constraints and minimization of intermediate concentrations Minimization of transient times Optimal stoichiometries.read more
Citations
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On Improving Stochastic Simulation for Systems Biology
TL;DR: The screened model of SRI photocycle proposed by Hoff et al.
Posted ContentDOI
Computational modeling of anthocyanin pathway evolution
Lucas C. Wheeler,Stacey D. Smith +1 more
TL;DR: A simple kinetic model of a major plant pigmentation pathway: the anthocyanin pathway is created which provides a theoretical framework that can be used to predict the consequences of new mutations in terms of both pigment phenotypes and pleiotropic effects.
Posted Content
Emergence of multiple time scales in coupled oscillators with plastic frequencies
TL;DR: In this article, a coupled-phase oscillator model where each oscillator has an angular velocity that varies due to the interaction with other oscillators is proposed to deepen the understanding of the relationship between the coexistence and the plasticity of time scales in complex systems.
Book ChapterDOI
Modelling and Simulation of Brain Energy Metabolism: Energy and Parkinson’s Disease
Peter Wellstead,Mathieu Cloutier +1 more
TL;DR: This work begins by describing PD as a multifactorial condition in which energy deficits form a common denominator for known risk factors, followed by a description of a mathematical model of brain energy metabolism, and its structural and dynamic properties.
Dissertation
Efficient Finite-difference Methods for Sensitivity Analysis of Stiff Stochastic Discrete Models of Biochemical Systems
TL;DR: Novel methods for estimating sensitivities of discrete stochastic models of biochemical reaction systems using finite-difference approximations and adaptive tau-leaping strategies are proposed, resulting in significant speed-up in comparison with previously published approaches for a similar accuracy.
References
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Potential, impedance, and rectification in membranes
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Book
Linear Multivariable Control: A Geometric Approach
TL;DR: In this article, the authors present an approach to controlability, feedback assignment, and pole shifting in a single linear functional model, where the observer is assumed to be a dynamic observer.