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Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle
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10.1063/1.3677190
/content/aip/journal/jcp/136/3/10.1063/1.3677190
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/3/10.1063/1.3677190

Figures

Image of FIG. 1.
FIG. 1.

Bistable switch on which Tyson and Novak's model is based.

Image of FIG. 2.
FIG. 2.

Scales of reactions and populations. Region I contains slow reactions whose reactants have low populations; region II contains slow reactions whose reactants have high populations; region III contains fast reactions whose reactants have low populations; region IV contains fast reactions whose reactants have high populations.

Image of FIG. 3.
FIG. 3.

Profile of reactions in Kar's cell cycle model. Data are collected from a sample SSA run for continuous 200 cell cycles. Four partitioning strategies A, B, C, and D are represented. For each of them, the reactions in the box are for the SSA system, while the ones outside the box are for the ODE system.

Image of FIG. 4.
FIG. 4.

mRNA distributions for the hybrid method and the SSA on Kar et al.'s cell cycle model. Partitioning strategy A is used.

Image of FIG. 5.
FIG. 5.

mRNA distributions for the hybrid method and the SSA on Kar et al.'s cell cycle model. Partitioning strategy B is used.

Image of FIG. 6.
FIG. 6.

Time trajectory of the hybrid model.

Image of FIG. 7.
FIG. 7.

mRNA distributions of the hybrid model with hybrid simulation and Kar's model with full SSA simulation.

Image of FIG. 8.
FIG. 8.

Diagrams for the two test models. The steady-state model does not include reactions in the shaded box, while the oscillation model includes them.

Image of FIG. 9.
FIG. 9.

Distribution of mRNA population for the steady-state model.

Image of FIG. 10.
FIG. 10.

Distribution of p population for the steady-state model.

Image of FIG. 11.
FIG. 11.

Distribution of p2 population for the steady state model.

Image of FIG. 12.
FIG. 12.

Distribution of pTotal population for the steady state model.

Image of FIG. 13.
FIG. 13.

Trajectory of pTotal in the oscillation model.

Image of FIG. 14.
FIG. 14.

Trajectory of mRNA in the oscillation model.

Tables

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Table I.

Statistics for different partitioning strategies of the hybrid method and the full Gillespie SSA on Kar's cell cycle model.

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Table II.

ODE system for the hybrid cell cycle model. 〈X〉 denotes the average number of molecules for species X.

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Table III.

SSA system for the hybrid cell cycle model. 〈X〉 denotes the average number of molecules for species X.

Generic image for table
Table IV.

Parameter values for the hybrid cell cycle model.

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Table V.

Row 1 includes the experimental data from a fission yeast cell sample.11 Row 2 includes the experimental data for daughter cells of the budding yeast.13 Rows 3 and 4 are statistics for the SSA on Kar's model and the hybrid method on the hybrid model, respectively.

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Table VI.

Reactions in the steady-state model.

Generic image for table
Table VII.

Reactions of the oscillation model.

Generic image for table
Table VIII.

Statistics for the period of oscillation for different methods simulating the stochastic oscillation model.

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/content/aip/journal/jcp/136/3/10.1063/1.3677190
2012-01-17
2014-04-21
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/3/10.1063/1.3677190
10.1063/1.3677190
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