Stochastic simulations of biological networks under impulses

Download

index.pdf

Date

2016

Author

Yazıcı, Müge

Metadata

Show full item record

Item Usage Stats

143
views

48
downloads

The impulses are one of the sources of fluctuations which lead to the sharp changes in the biochemical systems such as the changes in epidemic and population models. In this study, as the novelty, we implement these effects in exact stochastic simulation algorithms, namely, the Gillespie method and the first reaction method, by changing the chemical master equations (CME) with impulses. Hereby in the extension of these approaches with impulses, we consider different scenarios such as the sudden decrease of the number of molecules. Finally, we evaluate each of these alternatives under small and realistically large biochemical systems.

Subject Keywords

Biometry., Algorithms., Biomathematics., Stochastic processes

URI

http://etd.lib.metu.edu.tr/upload/12619937/index.pdf
https://hdl.handle.net/11511/25614

Collections

Graduate School of Natural and Applied Sciences, Thesis

Suggestions

OpenMETU
Core

Application of stochastic simulations of biological networks under different impulsive scenarios Purutçuoğlu Gazi, Vilda (null; 2016-06-01) The impulses are one of the sources of fluctuations which lead to the sharp changes in the biochemical systems such as the changes in epidemic and population models. These effects have been comprehensively studied under deterministic models, whereas, have not been analyzed in stochastic models. Hereby, in this study, we implement these effects in two exact stochastic simulation algorithms, namely, the direct method and the first reaction method under different dimensional systems and impulses scenarios. In ...
Optimal control of stochastic hybrid system with jumps: A numerical approximation Temoçin, Büşra Zeynep; Weber, Gerhard Wilhelm (2014-03-15) The generalized class of stochastic hybrid systems consists of models with regime changes including the occurrence of impulsive behavior. In this paper, the stochastic hybrid processes with jumps are approximated by locally consistent Markov decision processes that preserve local mean and covariance. We further apply a randomized switching policy for approximating the dynamics on the switching boundaries. To investigate the validity of the approximation, we study a stochastic optimal control problem. On the...
Stochastic models in preventive maintenance policies Gölbaşı, Onur; Demirel, Nuray (2014-07-19) In recent decades, philosophy behind maintenance has varied consistently due to the changes in complexity of designs, advances in automation and mechanization, adaptation to the fast growing market demand, commercial computation in the sectors, and environmental issues. In mid-forties, simplicity of designs, limited maintenance opportunities, and immaturity of trade culture made enough to perform only fix it when it broke approach, i.e. corrective maintenance, after failures. Last quarter of the 21th centur...
Functional Impulses in Exact Stochastic Simulation Altıntan, Derya; Purutçuoğlu Gazi, Vilda; Uğur, Ömür (2015-08-20) Jumps which are observed in many population models give rise to fluctuations in the dynamics of systems. Deterministic model which is based on the Impulsive Differential Equations (IDEs) considers these jumps as impulses and defines the dynamics of the system between successive jump times with the Ordinary Differential Equations (ODEs). From our previous studies, we have proposed a model which is the complement of IDEs in the sense that both studies consider the jumps as impulses. The main difference betwee...
Stochastic simulation of large biochemical systems by approximate Gillespie algorithm Purutçuoğlu Gazi, Vilda (IEEE; 2010-06-01) In recent years the fast innovations for the development of new methods and algorithms in system biology enable the biologists to analyze and interpret the complex biochemical structures. One of the speedy development has been seen in mathematical methods for generating these complex systems on the computer. These techniques help the researcher to ask biologically interesting questions and test their expectations before starting their biological experiments. There are a number of methods which can approxima...

Citation Formats

M. Yazıcı, “Stochastic simulations of biological networks under impulses,” M.S. - Master of Science, Middle East Technical University, 2016.