Modeling, simulating, and parameter Fitting of biochemical kinetic experiments
From MaRDI portal
Publication:2805271
DOI10.1137/151004707zbMATH Open1337.92090arXiv1508.05359OpenAlexW2278941722MaRDI QIDQ2805271FDOQ2805271
Publication date: 10 May 2016
Published in: SIAM Review (Search for Journal in Brave)
Abstract: In many chemical and biological applications, systems of differential equations containing unknown parameters are used to explain empirical observations and experimental data. The DEs are typically nonlinear and difficult to analyze, requiring numerical methods to approximate the solutions. Compounding this difficulty are the unknown parameters in the DE system, which must be given specific numerical values in order for simulations to be run. Estrogen receptor protein dimerization is used as an example to demonstrate model construction, reduction, simulation, and parameter estimation. Mathematical, computational, and statistical methods are applied to empirical data to deduce kinetic parameter estimates and guide decisions regarding future experiments and modeling. The process demonstrated serves as a pedagogical example of quantitative methods being used to extract parameter values from biochemical data models.
Full work available at URL: https://arxiv.org/abs/1508.05359
Recommendations
- Parameter estimation for models of chemical reaction networks from experimental data of reaction rates
- Parameter estimates in differential equation models for chemical kinetics
- Parameter estimation of an enzyme kinetic system using computer algebra techniques
- Evaluation of an S-system root-finding method for estimating parameters in a metabolic reaction model
- Parameter estimation and optimum experimental design for differential equation models
optimizationcluster analysissensitivity analysisdifferential equationsconservation lawsparameter fittingmass actiondimerizationchromatographyestrogen receptor protein
Cites Work
- Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
- The MATLAB ODE Suite
- Optimization by Simulated Annealing
- A Simplex Method for Function Minimization
- Title not available (Why is that?)
- Mathematical biology. Vol. 1: An introduction.
- A methodology for performing global uncertainty and sensitivity analysis in systems biology
- Title not available (Why is that?)
- Sensitivity Analysis in Practice
- Efficient algorithms for agglomerative hierarchical clustering methods
- A User’s View of Solving Stiff Ordinary Differential Equations
- Some general implicit processes for the numerical solution of differential equations
- A course in mathematical biology. Quantitative modeling with mathematical and computational methods.
- Minimization by Random Search Techniques
- Multi-Start Methods
- Nelder, Mead, and the other simplex method
- Sensitivity and Robustness in Chemical Reaction Networks
- Title not available (Why is that?)
- A distribution‐matching method for parameter estimation and model selection in computational biology
- Statistics of parameter estimates: a concrete example
Cited In (7)
- Modeling and numerical simulation of biotin carboxylase kinetics: implications for half-sites reactivity
- Time scale simulation of \(\text{V}_{\max}\) of urea cycle enzymes
- Optimality principle and determination of kinetic constants for biochemical reactions
- Parameter estimation of an enzyme kinetic system using computer algebra techniques
- High-throughput screening: establishing mathematical and physical models for bio-target im\-mo\-bilization
- Kinetic model of hybridoma cultures for identification of rate limiting factors and process optimization
- Estimation, model discrimination, and experimental design for implicitly given nonlinear models of enzyme catalyzed chemical reactions
Uses Software
This page was built for publication: Modeling, simulating, and parameter Fitting of biochemical kinetic experiments
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2805271)
