BioModels Database logo

BioModels Database

spacer

BIOMD0000000322 - Kim2011_Oscillator_SimpleI

 

 |   |   |  Send feedback
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: BIOMD0000000322.xml.origin
Submitter: jongmin kim
Submission ID: MODEL1012090000
Submission Date: 09 Dec 2010 23:02:57 UTC
Last Modification Date: 07 Jun 2013 15:14:22 UTC
Creation Date: 08 Dec 2010 15:19:59 UTC
Encoders:  Vijayalakshmi Chelliah
   Jongmin Kim
set #1
bqbiol:isVersionOf Gene Ontology regulation of gene expression
bqbiol:occursIn Taxonomy cellular organisms
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 beha viors 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, bacteri ophage T7 RNA polymerase and Escherichia coli ribonuclease H, to produce and degrade RNA signals. In t his 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 si gnals, showed up to five complete cycles. To demonstrate modularity and to explore the design space fu rther, 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 p rocess, identified experimental conditions likely to yield oscillations, and explained the system's ro bust response to interference by short degradation products. Synthetic transcriptional oscillators cou ld prove valuable for systematic exploration of biochemical circuit design principles and for controll ing nanoscale devices and orchestrating processes within artificial cells.

Note:

The paper describes 7 models (MODEL1012090000-6) and all these are submitted by the authors. This model (MODEL1012090000) corresponds to the Simple model for both mode I and II (Design I and II). The model reproduces timecourse figure plotted in the supplementary material (page 10 of Supplementary material) of the reference publication.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


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 23:02:57 UTC Last Modification Date: 07 Jun 2013 15:14:22 UTC Creation Date: 08 Dec 2010 15:19:59 UTC
Mathematical expressions
Reactions
reaction1 reaction2 reaction3 reaction4
reaction5 reaction6 reaction7 reaction8
reaction9      
Physical entities
Compartments Species
compartment x y u
v    
Global parameters
alpha beta gamma n
m delta    
Reactions (9)
 
 reaction1 [x] → ;  
 
 reaction2 [y] → ;  
 
 reaction3 [u] → ;  
 
 reaction4 [v] → ;  
 
 reaction5 [u] → [u] + [x];  
 
 reaction6 [v] → [v] + [y];  
 
 reaction7 [y] → [y] + [u];  
 
 reaction8 [x] → [x] + [v];  
 
 reaction9 [v] → [v] + [x];  
 
Functions (2)
 
 Hill Cooperativity lambda(substrate, Shalve, V, h, V*substrate^h/(Shalve^h+substrate^h))
 
 Hill inhibition lambda(V, Shalve, h, substrate, V/(Shalve^h+substrate^h))
 
 compartment Spatial dimensions: 3.0  Compartment size: 1.0
 
 x
Compartment: compartment
Initial concentration: 0.1
 
 y
Compartment: compartment
Initial concentration: 0.1
 
 u
Compartment: compartment
Initial concentration: 0.1
 
 v
Compartment: compartment
Initial concentration: 0.1
 
Global Parameters (6)
 
 alpha
Value: 0.57
Constant
 
 beta
Value: 2.5
Constant
 
 gamma
Value: 1.0
Constant
 
 n
Value: 6.5
Constant
 
 m
Value: 6.5
Constant
 
 delta
Value: 1.5
Constant
 
reaction1 (1)
 
 k1
Value: 1.0
Constant
 
reaction2 (1)
 
 k1
Value: 1.0
Constant
 
reaction3 (1)
 
 k1
Value: 1.0
Constant
 
reaction4 (1)
 
 k1
Value: 1.0
Constant
 
reaction7 (2)
 
 V
Value: 1.0
Constant
 
 Shalve
Value: 1.0
Constant
 
reaction8 (2)
 
 Shalve
Value: 1.0
Constant
 
 V
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000322

Curator's comment: (updated: 29 Mar 2011 18:23:29 BST)

This model (MODEL1012090000) corresponds to the Simple model for both mode I and II (Design I and II) described in the paper. The model reproduces timecourse figure plotted in the supplementary material (page 10 of Supplementary material) of the reference publication.
The model was integrated and simulated using Copasi v4.6 (Build 32). Curation figure was generated using Gnuplot by obtaining the plot data from Copasi.

spacer
spacer