stochastic monte carlo (mc) simulation  (MathWorks Inc)

Journal: bioRxiv

Article Title: Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation

doi: 10.1101/2025.02.13.638117

Figure Lengend Snippet: (A) Pulsing (blue) and constant (orange) 0A~P signal used as input to the biofilm matrix production stochastic model. Pulsing signal corresponds to the signal for growth rate equal to 0.4 h −1 predicted by the phosphorelay network model. The constant 0A~P signal corresponds to the mean of the pulsing signal. (B) Stochastic simulations starting from biofilm matrix inactive state for both constant and pulsing 0A~P signal. Matrix production is considered inactive if the number of TapA molecules < 200 (dashed line). (C) Stochastic simulations starting from matrix active state for both constant and pulsing 0A~P signal. Matrix production is considered active if the number of TapA molecules ≥ 200 (dashed line). (D) Fraction of active cells as a function of time for constant (dark orange) and pulsing 0A~P signal (dark blue) estimated from fitting and to the stochastic simulation data of ‘ Initially OFF cells ’ (light blue) and ‘ Initially ON’ (light orange) cells, respectively. All fits have R 2 >= 0.77 and MSE < 0.005. A total of 2000 simulations were performed. (inset) Estimated values of the biofilm activation rate ( k ON ) and of the matrix deactivation rate assuming pulsing and constant 0A~P input .

Article Snippet: The stochastic model was implemented in MATLAB R2023b, and the stochastic simulations ( ) were done using the SimBiology tool of MATLAB R2023b.

Techniques: Activation Assay

Journal: bioRxiv

Article Title: Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation

doi: 10.1101/2025.02.13.638117

Figure Lengend Snippet: Histogram of TapA molecules obtained from 3000 stochastic simulations (blue bars). Simulation time was set to 50 h. Solid lines represent Gaussian fits derived from a Gaussian Mixture Model with 2 components fitted to the data. The value of 200 molecules was set to be the threshold to distinguish between a biofilm matrix production active and inactive.

Article Snippet: The stochastic model was implemented in MATLAB R2023b, and the stochastic simulations ( ) were done using the SimBiology tool of MATLAB R2023b.

Techniques: Derivative Assay

Journal: bioRxiv

Article Title: Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation

doi: 10.1101/2025.02.13.638117

Figure Lengend Snippet:

Article Snippet: The stochastic model was implemented in MATLAB R2023b, and the stochastic simulations ( ) were done using the SimBiology tool of MATLAB R2023b.

Techniques: