BIOMD0000000323
type: SBMLModel
creator:
  ORG:
    orgname: Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
  n:
    given: Jongmin
    family: Kim
reaction: COPASI6
occurs in: http://identifiers.org/taxonomy/131567
species: 202429
created:
  W3 CDTF: Wed Dec 08 16:54:04 GMT 2010
parameter: COPASI5
species: COPASI2
is described by: http://identifiers.org/pubmed/21283141
time units: 749187
name: Kim2011_Oscillator_SimpleIII
is version of: GO:0010468
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name: Hill inhibition
substance units: 749211
reaction: COPASI9
compartment: 202406
notes: This a model from the article: Synthetic in vitro transcriptional oscillators. Kim J, Winfree E Mol. Syst. Biol. 2011 Feb 1;7:465. 21283141 , Abstract: The construction of synthetic biochemical circuits from simple components illuminates how complex behaviors can arise in chemistry and builds a foundation for future biological technologies. A simplified analog of genetic regulatory networks, in vitro transcriptional circuits, provides a modular platform for the systematic construction of arbitrary circuits and requires only two essential enzymes, bacteriophage T7 RNA polymerase and Escherichia coli ribonuclease H, to produce and degrade RNA signals. In this study, we design and experimentally demonstrate three transcriptional oscillators in vitro. First, a negative feedback oscillator comprising two switches, regulated by excitatory and inhibitory RNA signals, showed up to five complete cycles. To demonstrate modularity and to explore the design space further, a positive-feedback loop was added that modulates and extends the oscillatory regime. Finally, a three-switch ring oscillator was constructed and analyzed. Mathematical modeling guided the design process, identified experimental conditions likely to yield oscillations, and explained the system's robust response to interference by short degradation products. Synthetic transcriptional oscillators could prove valuable for systematic exploration of biochemical circuit design principles and for controlling nanoscale devices and orchestrating processes within artificial cells. Notes: The paper describes 7 models (MODEL1012090000-6) and all these are submitted by the authors. This model (MODEL1012090001) corresponds to the Simple model of the three-switch ring oscillator (Design III). The model reproduces figure 6 (central figures) of the reference publication. The time is rescaled by s=v_d/K_I*t where K_I=0.333 and v_d=1 (for alpha = 1) and v_d=0.5 (for alpha = 0.5). i.e. For alpha = 1, s = 0.003 * t (roughly 10 uni…
units def: 749187
reaction: COPASI11
parameter: COPASI3
length unit: length
parameter: COPASI4
volume units: 749163
reaction: COPASI7
name: Simple inhibition
function def: COPASI12
units def: 749211
modified:
  W3 CDTF: Fri Apr 20 22:58:04 BST 2012
species: 202426
reaction: COPASI8
function def: COPASI13
curated: true
reaction: COPASI10
area units: area
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
is: MODEL1012090001

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