Lecture

Circadian and Cell Cycle Dynamics: Coupling and Synchronization

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In course

BIO-341: Dynamical systems in biology

Life is non-linear. This course introduces dynamical systems as a technique for modelling simple biological processes. The emphasis is on the qualitative and numerical analysis of non-linear dynamical models. Examples are taken from biology and population ...

Description

This lecture explores the synchronization and coupling of circadian and cell cycles in mammalian cells, focusing on the impact of cell divisions on the circadian period and the absence of gating in 3T3 cells. The instructor discusses the dynamics of two coupled oscillators, the reconstruction of noisy phase dynamics, and the prediction of stable attractors. The lecture also covers the connection between theory and data, including generative models and optimization. Moreover, it delves into the identification of dynamics from data and the influence of cell proliferation on organ-specific time. The presentation concludes by addressing the potential for identifying brain/neuronal states dynamics from data.

Instructors (2)

Felix Naef

Felix Naef studied theoretical physics at the ETHZ and obtained his PhD from the EPFL in 2000. He then received postdoctoral training at the Center for Studies in Physics and Biology at the Rockefeller University (NYC) under the guidance of Prof. Magnasco. His research focuses on the modeling and interpretation of high-throughput functional data and the study of biomolecular oscillators. He joined ISREC as an associate scientist in early 2004 and is currently Associate Professor in the Institute of Bioengineering (IBI).

Julian Charles Shillcock

Julian received his PhD at Simon Fraser University in Canada for work on Monte Carlo simulations of liquid crystal phase transitions and the elastic properties of fluid and polymerized membranes. He was a Group Leader at the Max Planck Institute of Colloids and Interfaces, Germany for five years applying coarse-grained simulation techniques - principally Dissipative Particle Dynamics (DPD) and Brownian Dynamics - to equilibrium and dynamic properties of fluid lipid membranes. A major target of this research was to reveal the molecular rearrangements that occur during vesicle fusion. During this time, he developed a commercially-available, parallel DPD code that is being used by several universities. He was an Associate Professor at MEMPHYS in the Department of Physics and Chemistry, University of Southern Denmark. He has also worked in industry, designing and writing software for communication satellite simulations (British Aerospace, 1986-1990), and fluid simulation software (Accelrys, Inc., 1998-1999). He joined the Blue Brain Project in 2011, and uses mesoscale simulation techniques, together with theoretical analysis and collaborations with experimentalists, to study the dynamics of cellular processes. Current projects include simulating the formation of the post-synaptic density in dendritic spines and developing theoretical models of the supramolecular organisation of synapses. He also teaches Master's and PhD courses in computational cell biology and biophysics. He wrote and maintains an open source dissipative particle dynamics simulation code: https://github.com/Osprey-DPD/osprey-dpd Orcid: orcid.org/0000-0002-7885-735X

Official source

Related concepts (31)

Attractor

In the mathematical field of dynamical systems, an attractor is a set of states toward which a system tends to evolve, for a wide variety of starting conditions of the system. System values that get close enough to the attractor values remain close even if slightly disturbed. In finite-dimensional systems, the evolving variable may be represented algebraically as an n-dimensional vector. The attractor is a region in n-dimensional space.

Circadian rhythm sleep disorder

Circadian rhythm sleep disorders (CRSD), also known as circadian rhythm sleep-wake disorders (CRSWD), are a family of sleep disorders which affect the timing of sleep. CRSDs arise from a persistent pattern of sleep/wake disturbances that can be caused either by dysfunction in one's biological clock system, or by misalignment between one's endogenous oscillator and externally imposed cues. As a result of this mismatch, those affected by circadian rhythm sleep disorders have a tendency to fall asleep at unconventional time points in the day.

Stable manifold

In mathematics, and in particular the study of dynamical systems, the idea of stable and unstable sets or stable and unstable manifolds give a formal mathematical definition to the general notions embodied in the idea of an attractor or repellor. In the case of hyperbolic dynamics, the corresponding notion is that of the hyperbolic set. The gravitational tidal forces acting on the rings of Saturn provide an easy-to-visualize physical example. The tidal forces flatten the ring into the equatorial plane, even as they stretch it out in the radial direction.

Bacterial circadian rhythm

Bacterial circadian rhythms, like other circadian rhythms, are endogenous "biological clocks" that have the following three characteristics: (a) in constant conditions (i.e. constant temperature and either constant light {LL} or constant darkness {DD}) they oscillate with a period that is close to, but not exactly, 24 hours in duration, (b) this "free-running" rhythm is temperature compensated, and (c) the rhythm will entrain to an appropriate environmental cycle. Until the mid-1980s, it was thought that only eukaryotic cells had circadian rhythms.

Circadian clock

A circadian clock, or circadian oscillator, is a biochemical oscillator that cycles with a stable phase and is synchronized with solar time. Such a clock's in vivo period is necessarily almost exactly 24 hours (the earth's current solar day). In most living things, internally synchronized circadian clocks make it possible for the organism to anticipate daily environmental changes corresponding with the day–night cycle and adjust its biology and behavior accordingly.

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