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A general moment expansion method for stochastic kinetic models
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10.1063/1.4802475
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Affiliations:
1 Division of Molecular Biosciences, Theoretical Systems Biology Group, Imperial College London, London SW7 2AZ, United Kingdom
a) A. Ale and P. Kirk contributed equally to this work.
b) Authors to whom correspondence should be addressed. Electronic addresses: a.ale@imperial.ac.uk and m.stumpf@imperial.ac.uk
J. Chem. Phys. 138, 174101 (2013)
/content/aip/journal/jcp/138/17/10.1063/1.4802475
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## Figures

FIG. 1.

Study of dimerization system, initial values = [301, 0], parameters = [1.66 × 10, 0.2]. (a) Single SSA realisation. (b) Average of 100 000 SSA simulations. (c) and (d) Histogram of SSA runs (grey bars) and probability density of normal distribution (blue line) calculated from mean and variance of SSA runs corresponding to points c and d in (b). (e) Mean for both variables, calculated using SSA, the moment approximation using 1 moment (deterministic) and two central moments (2m). (f) Variance of calculated using SSA, two central moments (2m), three central moments with Gaussian closure (3m), and four central moments (4m). (g) Third central moment calculated using SSA and moment approximation method, fourth central moment calculated using SSA, and moment approximation method.

FIG. 2.

Study of Michaelis-Menten kinetics, with parameters , and initial conditions, (0) = 301, (0) = 0, and (0) = 120. (a) Single SSA realisation. Trajectories calculated using (b) moment approximation including only the mean (deterministic). (c) and (d) Variance of S and covariance between S and P calculated using SSA and approximation using 2 moments. (e) Skewness of S calculated using SSA and approximation with 3 moments. (f) Kurtosis calculated using SSA and approximation up to 4 and 6 moments.

FIG. 3.

Study of p53 model, parameter set = [90, 0.002, 1.7, 1.1, 0.93, 0.96, 0.01]. (a) Single SSA realisation. (b) Average of 100 000 SSA simulations. Trajectories calculated using (c) moment approximation including only the mean (deterministic), (d) linear noise approximation, (e) mean and the variance, (f) up to three central moments, (g) five central moments, and (h) six central moments. (i) and (j) Cumulative difference between mean trajectory calculated with SSA and trajectories calculated using (i) 2 moments and (j) 6 moments.

FIG. 4.

Analysis of distribution for p53 model. (a) Variance calculated based on SSA runs. (b) Variance calculated with SSA, LNA, and moment approximation method. (c) Skewness calculated based on SSA runs (blue line) and skewness for normal distribution (cyan dashed line). (d) and (f) Histograms calculated based on SSA for points d, e, and f in Figure , and probability density function of normal distribution calculated using mean and variance based on SSA (cyan line).

FIG. 5.

Contour plots for the p53 system of the distance between SSA trajectories and trajectories calculated with the moment expansion method. (a) and (b) Contour for varying and , calculated using expansion up to 2 and 6 moments, respectively. (c) and (d) Contour for varying and , calculated using expansion up to 2 and 6 moments, respectively. Red dots indicate parameter values used for SSA simulations.

FIG. 6.

Assessing the sensitivity to parameter of the dimerisation system of Sec. . Initial conditions and parameters are the same as previously, except that we additionally consider a perturbed value of = 1.1 × 1.66 × 10. (a) Average of 100 000 SSA simulations for the original and perturbed values. (b) As (a), except the mean is estimated using the proposed moment expansion approximation with 6 moments. (c) The sensitivity coefficients ∂μ(, [ , ])/∂ and ∂μ(, [ , ])/∂ (where μ and μ represent the means of and , respectively) estimated from the SSA and 6m output via finite different approximations. (d), (e), and (f) As (a), (b), and (c), but for the second central moment. (g), (h), and (i) As (a), (b), and (c), but for the third central moment.

FIG. 7.

Study of the deviation from the mean ( − μ). (a) Deterministic mean and single SSA trajectory for dimerisation system. (b) Deterministic mean and 9 points taken from different SSA trajectories for dimerisation system. (c) Deterministic mean and single SSA trajectory for p53 system. (d) Deterministic mean and 9 points taken from different SSA trajectories for p53 system.

## Tables

Table I.

Error between mean, second, and third central moment calculated with SSA and approximation methods for the dimerization system.

Table II.

Number of potentially nonzero central moment terms to include in moment approximation for different numbers of variables (columns) and number of central moments (rows).

/content/aip/journal/jcp/138/17/10.1063/1.4802475
2013-05-01
2014-04-16

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