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BIOMD0000000323 - Kim2011_Oscillator_SimpleIII

 

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Reference Publication
Publication ID: 21283141
Kim J, Winfree E.
Synthetic in vitro transcriptional oscillators.
Mol. Syst. Biol. 2011 Feb; 7: 465
Department of Biology, California Institute of Technology, Pasadena, CA 91125, USA.  [more]
Model
Original Model: BIOMD0000000323.xml.origin
Submitter: jongmin kim
Submission ID: MODEL1012090001
Submission Date: 09 Dec 2010 23:04:17 UTC
Last Modification Date: 20 Apr 2012 21:58:04 UTC
Creation Date: 08 Dec 2010 16:54:04 UTC
Encoders:  Vijayalakshmi Chelliah
   Jongmin Kim
set #1
bqbiol:occursIn Taxonomy cellular organisms
set #2
bqbiol:isVersionOf Gene Ontology regulation of gene expression
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 unitless time = 1hr; the time-course should be run for 60 timeunits (6hrs) to get figure 6a). For alpha = 2, s= 0.0015 * t (roughly 5 unitless time = 1hr; the time-course shoue be run for 100 timesunits (20hrs) to get figure 6b).

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use .
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 21283141 Submission Date: 09 Dec 2010 23:04:17 UTC Last Modification Date: 20 Apr 2012 21:58:04 UTC Creation Date: 08 Dec 2010 16:54:04 UTC
Mathematical expressions
Reactions
reaction1 reaction2 reaction3 reaction4
reaction5 reaction6    
Physical entities
Compartments Species
compartment x1 x2 x3
Global parameters
alpha beta n  
Reactions (6)
 
 reaction1 [x1] → [x1] + [x3];  
 
 reaction2 [x2] → [x2] + [x1];  
 
 reaction3 [x3] → [x3] + [x2];  
 
 reaction4 [x1] → ;  
 
 reaction5 [x2] → ;  
 
 reaction6 [x3] → ;  
 
Functions (2)
 
 Hill inhibition lambda(V, Shalve, h, substrate, V/(Shalve^h+substrate^h))
 
 Simple inhibition lambda(x, beta, x/beta/(1+x/beta))
 
 compartment Spatial dimensions: 3.0  Compartment size: 1.0
 
 x1
Compartment: compartment
Initial concentration: 0.0
 
 x2
Compartment: compartment
Initial concentration: 0.0
 
 x3
Compartment: compartment
Initial concentration: 0.33
 
Global Parameters (3)
 
 alpha
Value: 1.0
Constant
 
 beta
Value: 0.3
Constant
 
 n
Value: 5.0
Constant
 
reaction1 (1)
 
 Shalve
Value: 1.0
Constant
 
reaction2 (1)
 
 Shalve
Value: 1.0
Constant
 
reaction3 (1)
 
 Shalve
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000323

Curator's comment: (updated: 29 Mar 2011 18:25:57 BST)

This model (MODEL1012090001) corresponds to the Simple model of the three-switch ring oscillator (Design III) described in the paper. 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 unitless time = 1hr; the time-course should be run for 60 timeunits (6hrs) to get figure 6a). For alpha = 2, s= 0.0015 * t (roughly 5 unitless time = 1hr; the time-course should be run for 100 timesunits (20hrs) to get figure 6b).
The model was integrated and simulated using Copasi v4.6 (Build 32). The curation figures were generated using Gnuplot by obtained the plot data from Copasi.

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