## 3 Results and Discussion
### Stochastic Simulation and Knockout Based Analysis
\begin{table}
\begin{tabular}{l|l|l|l|l|l} \hline \hline
**Transition** & \begin{tabular}{l} **Kinetic** \\ **Parameter** \\ \end{tabular} & \begin{tabular}{l} **Rate** \\ **Function** \\ \end{tabular} & **Transition** & \
\begin{tabular}{l} **Kinetic** \\ **Parameter** \\ \end{tabular} &
\begin{tabular}{l} **Rate** \\ **Function** \\ \end{tabular} \\ \hline \(t_{35}\) & 0.025 & \(MA\)(0.025) & \(t_{96}\) & 0.05 & \(MA\)(0.05) \\ \hline \(t_{36}\) & 1.0 & \(MA\)(1.0) & \(t_{97}\) & 0.05 & \(MA\)(0.05) \\ \hline \(t_{37}\) & 0.1 & \(MA\)(0.1) & \(t_{98}\) & 0.1 & \(MA\)(0.1) \\ \hline \(t_{38}\) & 1.0 & \(MA\)(1.0) & \(t_{99}\) & 1.0 & \(MA\)(1.0) \\ \hline \(t_{39}\) & 1.0 & \(MA\)(1.0) & \(t_{100}\) & 1.0 & \(MA\)(1.0) \\ \hline \(t_{40}\) & 0.1 & \(MA\)(0.1) & \(t_{101}\) & 0.05 & \(MA\)(0.05) \\ \hline \(t_{41}\) & 0.1 & \(MA\)(0.1) & \(t_{102}\) & 0.1 & \(MA\)(0.1) \\ \hline \(t_{42}\) & 0.1 & \(MA\)(0.1) & \(t_{103}\) & 0.05 & \(MA\)(0.05) \\ \hline \(t_{43}\) & 0.1 & \(MA\)(0.1) & \(t_{104}\) & 0.1 & \(MA\)(0.1) \\ \hline \(t_{44}\) & 0.1 & \(MA\)(0.1) & \(t_{105}\) & 0.05 & \(MA\)(0.05) \\ \hline \(t_{45}\) & 1.0 & \(MA\)(1.0) & \(t_{106}\) & 0.1 & \(MA\)(0.1) \\ \hline \(t_{46}\) & 0.1 & \(MA\)(0.1) & \(t_{107}\) & 0.025 & \(MA\)(0.025) \\ \hline \(t_{47}\) & 0.05 & \(MA\)(0.05) & \(t_{108}\) & 0.0125 & \(MA\)(0.0125) \\ \hline \(t_{48}\) & 0.1 & \(MA\)(0.1) & \(t_{109}\) & 0.05 & \(MA\)(0.05) \\ \hline \(t_{49}\) & 1.0 & \(MA\)(1.0) & \(t_{110}\) & 0.1 & \(MA\)(0.1) \\ \hline \(t_{50}\) & 0.1 & \(MA\)(0.1) & \(t_{111}\) & 0.002 & \(MA\)(0.002) \\ \hline \(t_{51}\) & 0.025 & \(MA\)(0.025) & \(t_{112}\) & 0.0125 & \(MA\)(0.0125) \\ \hline \(t_{52}\) & 1.0 & \(MA\)(1.0) & \(t_{113}\) & 0.025 & \(MA\)(0.025) \\ \hline \(t_{53}\) & 0.1 & \(MA\)(0.1) & \(t_{114}\) & 0.025 & \(MA\)(0.025) \\ \hline \(t_{54}\) & 0.1 & \(MA\)(0.1) & \(t_{115}\) & 0.1 & \(MA\)(0.1) \\ \hline \(t_{55}\) & 0.0125 & \(MA\)(0.0125) & \(t_{116}\) & 0.025 & \(MA\)(0.025) \\ \hline \(t_{56}\) & 1.0 & \(MA\)(1.0) & \(t_{117}\) & 0.1 & \(MA\)(0.1) \\ \hline \(t_{57}\) & 0.1 & \(MA\)(0.1) & \(t_{118}\) & 0.05 & \(MA\)(0.05) \\ \hline \(t_{58}\) & 1.0 & \(MA\)(1.0) & \(t_{119}\) & 0.025 & \(MA\)(0.025) \\ \hline \(t_{59}\) & 0.05 & \(MA\)(0.05) & \(t_{120}\) & 0.0125 & \(MA\)(0.0125) \\ \hline \(t_{60}\) & 0.1 & \(MA\)(0.1) & \(t_{121}\) & 0.0125 & \(MA\)(0.0125) \\ \hline \hline \end{tabular}
\end{table} 
Table 3: _Cont._Finally, we also looked at the place \(p_{56}\) (HDL-3 cholesterol CE in the blood), which represents a molecule that is significantly and inversely associated with arterial stiffness [64]. The findings are depicted in Figure 7B, and it is evident that the HDL-related mechanisms remained unaltered. Figure 5: The outcomes of the in silico knockout analysis performed under Scenario 1, for place \(p_{49}\) (squalene). (**A**) The model has been simulated without anything knocked out. (**B**) The effect of excluding the following transitions: \(t_{39}\), \(t_{46}\), and \(t_{4}\) (Scenario 1A). (**C**) The effect of excluding the following transitions: \(t_{39}\), \(t_{46}\), and \(t_{17}\) (Scenario 1B). (**D**) The effect of excluding the following transitions: \(t_{34}\), \(t_{45}\), and \(t_{62}\) (Scenario 1C). Figure 6: The outcomes of the in silico knockout analysis performed under Scenario 1, for place \(p_{87}\) (foamy cells). (**A**) The model has been simulated without anything knocked out. (**B**) The effect of excluding the following transitions: \(t_{39}\), \(t_{46}\), and \(t_{4}\) (Scenario 1A). (**C**) The effect of excluding the following transitions: \(t_{39}\), \(t_{46}\), \(t_{4}\), and \(t_{117}\) (Scenario 1B). (**D**) The effect of excluding the following transitions: \(t_{34}\), \(t_{45}\), and \(t_{62}\) (Scenario 1C). **Scenario 1B**. _Inhibition of oxidative stress together with HMG-CoA reductase activity._  
Understanding the pathophysiology of atherosclerosis can give rise to new strategies dedicated to preventing and treating patients with this common disease.