MathWorks Simulations

Using the previously derived expressions from our ODEs, we use the Mathworks Simulink package to derive solutions to our system and model our system for a range of parameters. We simulated our equations for cI Protein, sgRNA and anti-CRISPR, shown in Figure 1.

ODE Solution

Solving:

\begin{eqnarray} \frac{x_2}{dt} = \alpha - \gamma x_2 \\ \frac{x_2}{dt} + \gamma x_2 = \alpha \end{eqnarray}

Integrating Factor:

\begin{eqnarray} e^{\int \gamma dt} = e^{\gamma t} \end{eqnarray}

Multiplying both sides by our integrating factor:

\begin{eqnarray} (\frac{x_2}{dt} + \gamma x_2)e^{\gamma t} = \alpha e^{\gamma t}\\ \int (\frac{x_2}{dt} + \gamma x_2)e^{\gamma t} = \int \alpha e^{\gamma t} \\ x_2 = \frac{\alpha}{\gamma} + ce^{-\gamma t} \end{eqnarray}

R plots

Visit our GitHub repositoryfor our code.

R Analysis

Analyzed in R for this model, and got the following values with adjusted R-squared and p-value:

Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 2.87199 0.21773 13.19 1.47e-15 *** c(time, time, time) 0.15267 0.01142 13.37 9.74e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 0.2935 on 37 degrees of freedom Multiple R-squared: 0.8285, Adjusted R-squared: 0.8238 F-statistic: 178.7 on 1 and 37 DF, p-value: 9.741e-16

Intercept represents the equilibrium value of LacILov, our intercept:

\begin{eqnarray} 2.879199 \pm (0.21773)(2.026) \\ 2.879199 \pm 0.44112098 \end{eqnarray}