Efficient Multiscale Simulations of Circadian Rhythms Using Automated Phase Macomodelling Techniques

Shatam Agarwal 1, Jaijeet Roychowdhury 2

1 Indian Institute of Technology, Kanpur; 2 University of Minnesota, Twin Cities
Email: shatam@iitk.ac.in; jr@umn.edu


Pac Symp Biocomput. 2008;:402-413.


Abstract

Circadian rhythm mechanisms involve multi-scale interactions between endogenous DNA-transcription oscillators. We present the application of efficient, numerically wellconditioned algorithms for abstracting (potentially large) systems of differential equation models of circadian oscillators into compact, accurate phase-only macromodels. We apply and validate our auto-extracted phase macromodelling technique on mammalian and Drosophila circadian systems, obtaining speedups of 9 − 13× over conventional timecourse simulation, with insignificant loss of accuracy, for single oscillators being synchronized by day/night light variations. Further, we apply the macromodels to simulate a system of 400 coupled circadian oscillators, achieving speedups of 240× and accurately reproducing synchronization and locking phenomena amongst the oscillators. We also present the use of parameterized phase macromodels for these circadian systems, and elucidate insights into circadian timing effects directly provided by our auto-extracted macromodels.


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