%0 Journal Article
%T Phase computations and phase models for discrete molecular oscillators
%A Onder Suvak
%A Alper Demir
%J EURASIP Journal on Bioinformatics and Systems Biology
%D 2012
%I BioMed Central
%R 10.1186/1687-4153-2012-6
%X In this article, we extend the applicability of these phase computation methods to biochemical oscillators as discrete molecular systems, upon the information obtained from a continuous-state approximation of such oscillators. In particular, we describe techniques for computing the instantaneous phase of discrete, molecular oscillators for stochastic simulation algorithm generated sample paths. We comment on the accuracies and derive certain measures for assessing the feasibilities of the proposed phase computation methods. Phase computation experiments on the sample paths of well-known biological oscillators validate our analyses.The impact of noise that arises from the discrete and random nature of the mechanisms that make up molecular oscillators can be characterized based on the phase computation techniques proposed in this article. The concept of isochrons is the natural choice upon which the phase notion of oscillators can be founded. The isochron-theoretic phase computation methods that we propose can be applied to discrete molecular oscillators of any dimension, provided that the oscillatory behavior observed in discrete-state does not vanish in a continuous-state approximation. Analysis of the full versatility of phase noise phenomena in molecular oscillators will be possible if a proper phase model theory is developed, without resorting to such approximations.Oscillatory behavior is encountered in many types of systems including electronic, optical, mechanical, biological, chemical, financial, social and climatological systems. Carefully designed oscillators are intentionally introduced into many engineered systems to provide essential functionality for system operation. In electronic systems, oscillators are used to generate clock signals that are needed in the synchronization of operations in digital circuits and sampled-data systems. The periodic signal generated by an electronic oscillator or monochromatic light from a laser is used as a carrier and fo
%K discrete molecular oscillators
%K oscillator phase
%K noise
%K phase noise
%K numerical methods
%K Monte Carlo methods
%K Stochastic Simulation Algorithm (SSA)
%K isochrons
%K phase equations
%K phase computation schemes
%K phase models
%U http://bsb.eurasipjournals.com/content/2012/1/6