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Phase computations and phase models for discrete molecular oscillators.
1Department of Electrical and Electronics Engineering, College of Engineering, Koç University Rumeli Feneri Yolu 34450 Sariyer Istanbul, Turkey. osuvak@ku.edu.tr.
EURASIP Journal on Bioinformatics & Systems Biology
|June 13, 2012
Summary
We developed new methods to compute the phase of discrete biochemical oscillators, which are essential for cellular functions like circadian clocks. These techniques help analyze the impact of noise on molecular oscillator behavior.
Area of Science:
- Systems Biology
- Biophysics
- Computational Biology
Background:
- Biochemical oscillators are fundamental to cellular processes, including circadian rhythms.
- Oscillator dynamics are best understood using phase, rigorously defined by isochrons.
- Existing phase computation methods for continuous oscillators are noise-robust.
Purpose of the Study:
- Extend isochron-based phase computation to discrete molecular oscillators.
- Develop techniques for calculating instantaneous phase in stochastic simulations.
- Assess the accuracy and feasibility of these novel phase computation methods.
Main Methods:
- Utilized continuous-state approximations of discrete biochemical oscillators.
- Applied isochron theory to define phase for molecular systems.
- Developed phase computation techniques for stochastic simulation algorithm (SSA) sample paths.
Main Results:
- Successfully extended phase computation to discrete molecular oscillators.
- Validated proposed methods on sample paths of known biological oscillators.
- Derived measures to assess the feasibility and accuracy of the phase computation techniques.
Conclusions:
- Proposed phase computation methods can characterize noise impact in molecular oscillators.
- Isochron-based phase computation is applicable to discrete oscillators of any dimension.
- Future work requires a phase model theory for comprehensive analysis of phase noise phenomena.
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