Modeling and simulation of metabolic networks for estimation of biomass accumulation parameters

Download

index.pdf

Date

2009-05-28

Author

Kaplan, U.
TÜRKAY, METİN
Biegler, L.
Karasözen, Bülent

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

195
views

107
downloads

Metabolic networks are defined as the collection of biochemical reactions within a cell that define the functions of that cell. Due to the growing need to understand the functions of biological organisms for industrial and medical purposes, modeling and simulation of metabolic networks has attracted a lot of attention recently. Traditionally, metabolic networks are modeled such as flux-balance analysis that considers the steady state nature of the cell. However, it is important to consider the dynamic behavior of a cell since the environmental conditions change continuously. Sometimes due to the critical changes in the environment some of the reactions exhibit completely different behavior leading to discrete changes in the metabolic network. Therefore, a cell exhibits discrete-continuous behavior in continuous time. Since hybrid systems exhibit the same characteristics modeling a cell as a hybrid system gives an accurate representation. The aim of this paper is to develop a simulation framework to model the evolving structure of the cell metabolism under changes in the environment. The metabolic responses that cell gives, against multiple changes in the environment are not fully understood. Therefore, in this study, a cell is modeled as a hybrid system that is composed of a system of differential and algebraic equations. The changes in the concentration of metabolites in the environment are represented by Ordinary Differential Equations and the intracellular cell metabolism is represented by a set of algebraic equations. TO understand the feedback relationship between intracellular and extracellular changes, the system is solved considering the effects of extracellular stresses on the metabolic responses.

Subject Keywords

Metabolic networks, Hybrid systems, Parameter estimation, Optimization, Dynamic optimization

URI

https://hdl.handle.net/11511/30552

Journal

DISCRETE APPLIED MATHEMATICS

DOI

https://doi.org/10.1016/j.dam.2008.06.048

Collections

Graduate School of Applied Mathematics, Article

Suggestions

OpenMETU
Core

Harnessing DNA intercalation Persil Çetinkol, Özgül (2007-10-01) Numerous small molecules are known to bind to DNA through base pair intercalation. Fluorescent dyes commonly used for nucleic acid staining, such as ethidium, are familiar examples. Biological and physical studies of DNA intercalation have historically been motivated by mutation and drug discovery research. However, this same mode of binding is now being harnessed for the creation of novel molecular assemblies. Recent studies have used DNA scaffolds and intercalators to construct supramolecular assemblies t...
Optimization of internal tagging of inhibitory G-proteins for investigating their interactions with dopamine receptor D2 via fret method Özcan, Gizem; Son, Çağdaş Devrim; Özçubukçu, Salih; Department of Biochemistry (2016) G-Protein Coupled Receptors (GPCRs) constitute a large family of receptors which act by sensing the molecules outside the cell and start a signal transduction inside the cell through interacting with their associated G-proteins. This interaction results in activation or repression of related signaling pathways via associated secondary messengers. Dopamine receptor D2 (D2R) is a member of D2-like Dopamine Receptor group, which also belongs to the GPCR family. It is known that D2R has critical roles in emotio...
Analysis of ligand-receptor cross-linked fragments by mass spectrometry Son, Çağdaş Devrim; Hurst, GB; Naider, F; Becker, JM (Wiley, 2005-03-01) G-protein coupled receptors (GPCRs) are a class of integral membrane receptor proteins that are characterized by a signature seven-transmembrane (7-TM) configuration. The alpha-factor receptor (Ste2p) from Saccharomyces cerevisiae is a GPCR that, upon binding of a peptide ligand, transduces a signal to initiate a cascade of events leading to the mating of haploid yeast cells. This study summarizes the application of affinity purification and of matrix-assisted laser-desorption ionization time-of-flight (MAL...
Bayesian inference for the MAPK/ERK pathway by considering the dependency of the kinetic parameters Purutçuoğlu Gazi, Vilda (Institute of Mathematical Statistics, 2008-01-01) The MAPK/ERK pathway is one of the major signal transduction systems which regulates the cellular growth control of all eukaryotes like the cell proliferation and the apoptosis. Because of its importance in cellular lifecycle, it has been studied intensively, resulting in a number of qualitative descriptions of this regulatory mechanism. In this study we describe the MAPK/ERK pathway as an explicit set of reactions by combining different sources. Our reaction set takes into account the localization and diff...
Visualization of interactions between fluorescently tagged g protein α11, α12/13 subtypes and adenosine 2a, dopamine 2 or homodimer adenosine 2a/2a receptors Kostromin, İrmak Begüm; Son, Çağdaş Devrim; Department of Biology (2018) G-Protein-coupled receptors (GPCRs) belong to one of the largest family of cell surface receptors, which transmit extracellular signals to intracellular responses by interacting with G- proteins. The G proteins are known as molecular switches that regulates different pathways via control of secondary messengers and signaling proteins. Adenosine 2A (A2A) and Dopamine 2 (D2) receptors belong to G-Protein-coupled receptors (GPCRs) family and are located mostly in striatopallidal γ-aminobutyric acid (GABA) cont...

Citation Formats

U. Kaplan, M. TÜRKAY, L. Biegler, and B. Karasözen, “Modeling and simulation of metabolic networks for estimation of biomass accumulation parameters,” DISCRETE APPLIED MATHEMATICS, pp. 2483–2493, 2009, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/30552.