ArticleBiophysical journal2007
Thermodynamically feasible kinetic models of reaction networks.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed.
- Formalizing the law of diminishing returns in metabolic networks using an electrical analogy.Royal Society open science · 2024Article
- Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors.eLife · 2024Article
- Sensitivity analysis of biochemical systems using bond graphs.Journal of the Royal Society, Interface · 2023Article
- Conditions for the origin of homochirality in primordial catalytic reaction networks.Scientific reports · 2023Article
- Analysis of Hepatic Lipid Metabolism Model: Simulation and Non-Stationary Global Sensitivity Analysis.Nutrients · 2022Article
- Control of cell state transitions.Nature · 2022Article
- Structural Thermokinetic Modelling.Metabolites · 2022Article
- Article
- Analysing and simulating energy-based models in biology using BondGraphTools.The European physical journal. E, Soft matter · 2021Article
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
- Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data.Journal of the Royal Society, Interface · 2021Article
- TopoFilter: a MATLAB package for mechanistic model identification in systems biology.BMC bioinformatics · 2020Article
- Interrogating metabolism as an electron flow system.Current opinion in systems biology · 2019Review
- Necessary and sufficient conditions for protocell growth.Journal of mathematical biology · 2016Article
- Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach.Scientific reports · 2016Article
- Chemical Schemes for Maintaining Different Compositions Across a Semi-permeable Membrane with Application to Proto-cells.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2015Article
- Design Principles as a Guide for Constraint Based and Dynamic Modeling: Towards an Integrative Workflow.Metabolites · 2015Article
- Modeling for (physical) biologists: an introduction to the rule-based approach.Physical biology · 2015Review
- A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions.PLoS computational biology · 2015Article
- A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen.Frontiers in microbiology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The dynamics of biological reaction networks are strongly constrained by thermodynamics. An holistic understanding of their behavior and regulation requires mathematical models that observe these constraints. However, kinetic models may easily violate the constraints imposed by the principle of detailed balance, if no special care is taken. Detailed balance demands that in thermodynamic equilibrium all fluxes vanish. We introduce a thermodynamic-kinetic modeling (TKM) formalism that adapts the concepts of potentials and forces from irreversible thermodynamics to kinetic modeling. In the proposed formalism, the thermokinetic potential of a compound is proportional to its concentration. The proportionality factor is a compound-specific parameter called capacity. The thermokinetic force of a reaction is a function of the potentials. Every reaction has a resistance that is the ratio of thermokinetic force and reaction rate. For mass-action type kinetics, the resistances are constant. Since it relies on the thermodynamic concept of potentials and forces, the TKM formalism structurally observes detailed balance for all values of capacities and resistances. Thus, it provides an easy way to formulate physically feasible, kinetic models of biological reaction networks. The TKM formalism is useful for modeling large biological networks that are subject to many detailed balance relations.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.