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Modelling the Biological Clock

Modelling the Biological Clock. By Jos Rohling 17 November 2004. Outline. Research Goals Biological Clock First Model: Coupled Oscillators. Research Goals. Creating a (Computer) Model for the Neuronal Activity in the Supra Chiasmatic Nuclei (SCN) Model for a Single Neuron

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Modelling the Biological Clock

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  1. Modelling the Biological Clock By Jos Rohling 17 November 2004

  2. Outline • Research Goals • Biological Clock • First Model: Coupled Oscillators Modelling the Biological Clock

  3. Research Goals • Creating a (Computer) Model for the Neuronal Activity in the Supra Chiasmatic Nuclei (SCN) • Model for a Single Neuron • Model for Network Connections between Neurons Modelling the Biological Clock

  4. In this research existing and well-known methods from computational science are used to define and implement a simulation model for a real part of the brain Computer Science Biology Bio Informatics • Biological mechanisms are used as ideas to define and implement new computational theories.For example: neural networks, DNA computing, P-systems Computer Science Biology Modelling the Biological Clock

  5. The Biological Clock Modelling the Biological Clock

  6. Day and Night Animals Modelling the Biological Clock

  7. Activity Rhythm Modelling the Biological Clock

  8. 24 Hour Rhythms • Activity of brain areas • Hormone levels (Cortisol) • Cognitive functions • Performances, reaction-times • Heartbeat, blood pressure • Sleep needs • Melatonin levels • Temperature • Liver • Sensitivity for medicines (cytostatics) Modelling the Biological Clock

  9. The Suprachiasmatic Nuclei (SCN) Modelling the Biological Clock

  10. The Suprachiasmatic Nuclei (SCN) • Rhythm Generation • Adaptivity • Seasonal Rhythms Modelling the Biological Clock

  11. Electrical Signals Modelling the Biological Clock

  12. Extra-Cellular Recordings Deboer et al., Nat Neurosci. 2003 Oct;6(10):1086-90. Modelling the Biological Clock

  13. Deboer et al., Nat Neurosci. 2003 Oct;6(10):1086-90. Modelling the Biological Clock

  14. Rhythms in Electrical Activity Modelling the Biological Clock

  15. Measurements of Individual Neurons Modelling the Biological Clock

  16. Modelling the Biological Clock

  17. 8 hours light 12 hours light 16 hours light Modelling the Biological Clock

  18. Simulated and Measured Values Modelling the Biological Clock

  19. Results • Individual neurons do not code for day length • Day length coding arises on the neuronal network level Modelling the Biological Clock

  20. Different Organisational Levels function / behavior integrated neuronal network isolated network cell / neuron gene / molecular network Modelling the Biological Clock

  21. Research Goal • Creating a large scale simulation model: • Where one neuron is described at the electrical level • Where a model for the network in which these neurons operate is presented • Where the outcome can account for the behavioural outcomes of the neurophysiological research Modelling the Biological Clock

  22. Research Questions • How to create a biologically feasible model for one neuron? • Examine neurophysiological data of one single neuron • Find patterns in this data that can add to the model • How to find and model the network structure between the neurons? Modelling the Biological Clock

  23. Coupled Oscillators Taken from: • Mirollo, R.E. and Strogatz, S.H., Synchronization of Pulse-Coupled Biological Oscillators, in SIAM Journal on Applied Mathematics, Vol. 50, No. 6, pages 1645-1662; December 1990. • Strogatz, S.H., and Stewart, I., Coupled Oscillators and Biological Synchronization, in Scientific American, Vol. 269, No. 6, pages 102-108; December 1993. Modelling the Biological Clock

  24. Theory of Coupled Oscillators Strogatz and Stewart, Scientific American, December 1993. Modelling the Biological Clock

  25. Coupled Oscillators in Nature Modelling the Biological Clock

  26. Single Oscillator Modelling the Biological Clock

  27. Oscillators Coupled • How is the coupling? • Complete or partial? • Pulse coupling Modelling the Biological Clock

  28. Peskin’s Model (1) Mirollo and Strogatz, SIAM Journal of Applied Mathematics, December 1990; 50(6): 1645-62. Modelling the Biological Clock

  29. Peskin’s Model (2) Modelling the Biological Clock

  30. Peskin’s Conjectures • The system would always eventually become synchronized • It would synchronize even if the oscillators were not identical But Mirollo and Strogatz showed that although synchrony is the simplest state for coupled oscillators, it is not inevitable: • Symmetry Breaking leading to Phase Locking Modelling the Biological Clock

  31. Phase Locking for 2 Coupled Oscillators Modelling the Biological Clock

  32. Phase Locking for 3 Coupled Oscillators Modelling the Biological Clock

  33. Biological Feasibility • Neurons can have different firing-frequencies • Neurons can even change firing-frequency themselves • Are all neurons connected to all other neurons? How is the network topology? Modelling the Biological Clock

  34. Thank you for your attention Questions? Modelling the Biological Clock

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