Computational approaches to cellular rhythms

@article{Goldbeter2002ComputationalAT,
  title={Computational approaches to cellular rhythms},
  author={Albert Goldbeter},
  journal={Nature},
  year={2002},
  volume={420},
  pages={238-245}
}
Oscillations arise in genetic and metabolic networks as a result of various modes of cellular regulation. In view of the large number of variables involved and of the complexity of feedback processes that generate oscillations, mathematical models and numerical simulations are needed to fully grasp the molecular mechanisms and functions of biological rhythms. Models are also necessary to comprehend the transition from simple to complex oscillatory behaviour and to delineate the conditions under… 
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References

SHOWING 1-10 OF 109 REFERENCES
A synthetic oscillatory network of transcriptional regulators
TLDR
This work used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli, which periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells.
Robustness of circadian rhythms with respect to molecular noise
TLDR
It is shown that robust circadian oscillations can occur already with a limited number of mRNA and protein molecules, in the range of tens and hundreds, respectively.
Toward a detailed computational model for the mammalian circadian clock
  • J. Leloup, A. Goldbeter
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2003
TLDR
In conditions where the indirect negative autoregulation of Per and Cry expression is inoperative, the model indicates the possibility that sustained oscillations might still arise from the negative autorotation of Bmal1 expression, uncovers the possible existence of multiple sources of oscillatory behavior.
Network dynamics and cell physiology
TLDR
A new breed of theoretical molecular biologists reproduces these networks in computers and in the mathematical language of dynamical systems to understand this dance of complex assemblies of interacting proteins.
Time zones: a comparative genetics of circadian clocks
TLDR
The circadian clock is a widespread cellular mechanism that underlies diverse rhythmic functions in organisms from bacteria and fungi, to plants and animals, and the weight of evidence favours their independent evolutionary origins in different kingdoms.
Oscillatory behavior in enzymatic control processes.
  • B. Goodwin
  • Physics
    Advances in enzyme regulation
  • 1965
Mechanisms of noise-resistance in genetic oscillators
TLDR
It is shown that this type of oscillator is driven mainly by two elements: the concentration of a repressor protein and the dynamics of an activator protein forming an inactive complex with the repressor, which makes it especially resistant to fluctuations.
From simple to complex oscillatory behavior in metabolic and genetic control networks.
TLDR
The case of nonautonomous complex oscillations in a model for circadian oscillations subjected to periodic forcing by a light-dark cycle is considered and it is shown that the occurrence of entrainment versus chaos in these conditions markedly depends on the wave form of periodic forcing.
From Clocks to Chaos: The Rhythms of Life
  • Medicine
  • 1988
TLDR
One of the most interesting features of the book is that it makes a start at explaining "dynamical diseases" that are not the result of infection by pathogens but that stem from abnormalities in the timing of essential functions.
...
1
2
3
4
5
...