A computational approach to the structural analysis of uncertain kinetic systems
From MaRDI portal
Publication:2102477
DOI10.1016/J.CPC.2018.03.002zbMATH Open1498.92346arXiv1704.08633OpenAlexW2611053392WikidataQ130122233 ScholiaQ130122233MaRDI QIDQ2102477FDOQ2102477
Authors: Bernadett Ács, Gergely Szlobodnyik, Gábor Szederkényi 
Publication date: 28 November 2022
Published in: Computer Physics Communications (Search for Journal in Brave)
Abstract: A computation-oriented representation of uncertain kinetic systems is introduced and analysed in this paper. It is assumed that the monomial coefficients of the ODEs belong to a polytopic set, which defines a set of dynamical systems for an uncertain model. An optimization-based computation model is proposed for the structural analysis of uncertain models. It is shown that the so-called dense realization containing the maximum number of reactions (directed edges) is computable in polynomial time, and it forms a super-structure among all the possible reaction graphs corresponding to an uncertain kinetic model, assuming a fixed set of complexes. The set of core reactions present in all reaction graphs of an uncertain model is also studied. Most importantly, an algorithm is proposed to compute all possible reaction graph structures for an uncertain kinetic model.
Full work available at URL: https://arxiv.org/abs/1704.08633
Recommendations
- A new efficient algorithm for determining all structurally different realizations of kinetic systems
- Realization of linearly conjugate and uncertain kinetic systems with time delay
- Computing all possible graph structures describing linearly conjugate realizations of kinetic systems
- Reaction network realizations of rational biochemical systems and their structural properties
- Computing all sparse kinetic structures for a Lorenz system using optimization
Boundary value problems on graphs and networks for ordinary differential equations (34B45) Classical flows, reactions, etc. in chemistry (92E20)
Cites Work
- Linear Matrix Inequalities in System and Control Theory
- On global identifiability for arbitrary model parametrizations
- Identifiable reparametrizations of linear compartment models
- Title not available (Why is that?)
- Nonnegative and compartmental dynamical systems
- Modeling and analysis of mass-action kinetics
- On the identifiability and distinguishability of nonlinear parametric models
- Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction
- Title not available (Why is that?)
- Identification of parametric models from experimental data. Transl. from an upd. French version by the authors, with the help of John Norton
- Computing weakly reversible linearly conjugate chemical reaction networks with minimal defi\-ciency
- Dynamical equivalence and linear conjugacy of chemical reaction networks: new results and methods
- A proof of the global attractor conjecture in the single linkage class case
- A linear programming approach to weak reversibility and linear conjugacy of chemical reaction networks
- Title not available (Why is that?)
- Computing linearly conjugate weakly reversible kinetic structures using optimization and graph theory
- Finding complex balanced and detailed balanced realizations of chemical reaction networks
- Linear conjugacy of chemical reaction networks
- Computing sparse and dense realizations of reaction kinetic systems
- Computing zero deficiency realizations of kinetic systems
- Identifiability of chemical reaction networks
- On the relationship between sloppiness and identifiability
- An algorithm for finding globally identifiable parameter combinations of nonlinear ODE models using Gröbner bases
- Robust Stabilization for Single-Input Polytopic Nonlinear Systems
- A probabilistic algorithm to test local algebraic observability in polynomial time
- Compartmental models with uncertain flow rates
- Computing all possible graph structures describing linearly conjugate realizations of kinetic systems
- An interval approach for dealing with flux distributions and elementary modes activity patterns
- On Stability and Trajectory Boundedness of Lotka–Volterra Systems With Polytopic Uncertainty
- Decision making: uncertainty, imperfection, deliberation and scalability. Extended versions of six selected contributions based on the presentations at the workshop ``Scalable decision making: uncertainty, imperfection, deliberation, Prague, Czech Republic, 2013
- Uncertainty. The soul of modeling, probability and statistics
- A new efficient algorithm for determining all structurally different realizations of kinetic systems
Cited In (7)
- Reachability analysis of low-order discrete state reaction networks obeying conservation laws
- Polynomial time coverability analysis in discrete state chemical reaction network subclasses
- Polynomial time reachability analysis in discrete state chemical reaction networks obeying conservation laws
- Realizations of kinetic differential equations
- Computing all sparse kinetic structures for a Lorenz system using optimization
- Realization of linearly conjugate and uncertain kinetic systems with time delay
- Guaranteed and randomized methods for stability analysis of uncertain metabolic networks
Uses Software
This page was built for publication: A computational approach to the structural analysis of uncertain kinetic systems
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2102477)
