## 3 Results and Discussion
### Scandario 3. Modulating reverse cholesterol transport  
In this simulation experiment, we decided to examine the role of ATP-binding cassette protein A1 (ABCA1) in the development of atherosclerosis. ABCA1 plays a crucial role in maintaining cholesterol homeostasis and facilitating reverse cholesterol transport. It helps to prevent the buildup of excess cholesterol within cells and is critical for the formation of nascent HDL particles by mediating cholesterol efflux to the lipid-poor apolipoprotein AI (apoA-I) [22; 72]. Figure 8: The outcomes of the in silico knockout analysis performed under Scenario 2, for place \(p_{87}\) (foamy cells). (**A**) The model has been simulated without anything knocked out. (**B**) The effect of excluding the following transition: \(t_{110}\). (**C**) The effect of excluding the following transitions: \(t_{110}\), and \(t_{117}\). Figure 10: The outcomes of the in silico knockout analysis performed under Scenario 2, for place \(p_{49}\) (squalene). (**A**) The model has been simulated without anything knocked out. (**B**) The effect of excluding the following transition: \(t_{110}\). (**C**) The effect of excluding the following transitions: \(t_{110}\), and \(t_{117}\). Figure 9: The outcomes of the in silico knockout analysis performed under Scenario 2, for place \(p_{53}\) (HDL-3 cholesterol CE in blood). (**A**) The model has been simulated without anything knocked out. (**B**) The effect of excluding the following transition: \(t_{110}\). (**C**) The effect of excluding the following transitions: \(t_{110}\) and \(t_{117}\). Moreover, it was demonstrated that mutations in the ABCA1 gene result in the autosomal recessive genetic disorder Tangier disease, which is characterized by significantly reduced levels of HDL in the blood and an elevated risk for atherosclerosis [73]. Evidence also shows that overexpression of ABCA1 can increase HDL-C and protect against atherosclerosis [22; 74]. Thus, the boosted activity of ABCA1 can possibly remove the excess cholesterol accumulated in the peripheral cells and reduce the cholesterol burden. To confirm this and observe the effect of the reverse cholesterol transport stimulation, we assigned the value 0.1 to the kinetic constant of the transition \(t_{93}\) (ABCA1 synthesis). We decided to monitor the following locations: \(p_{87}\) (foamy cells), \(p_{49}\) (squalene), and \(p_{56}\) (HDL-3 cholesterol CE in the blood) for the same reasons set out in Scenario 1A above. As depicted in Figure 11C, the level of foamy cells formation is highly attenuated as compared to the results shown in Figure 11A (model without any knockout). Next, to mimic the significant increase (up-regulation) in ABCA1-mediated cholesterol efflux, we assigned the kinetic constant of 1 to the transition \(t_{93}\) (ABCA1 synthesis). The results are presented in Figure 11D, and it is evident that the formation of the foamy cell is inhibited. Thereby, atherosclerosis progression is halted. Therefore, if the reverse cholesterol transport is activated, it may be possible to eliminate excess cholesterol that has accumulated in peripheral cells, thereby preventing the development of atherosclerosis. Finally, we excluded transition \(t_{93}\) (ABCA1 synthesis) from the model to analyze the influence of reverse cholesterol transport restraint on atherosclerosis development and progression. As a result, the level of foamy cells increased significantly (see Figure 11B in comparison to the model without any knockout presented in Figure 11A). In all the above-mentioned simulation experiments, both the HDL-3 level (see Figure 12B-D as compared to the results depicted in Figure 12A) and endogenous cholesterol biosynthesis (see Figure 13B,C as compared to the results depicted in Figure 13A) remained unaffected. Figure 11: The outcomes of the in silico knockout analysis performed under Scenario 3, for place \(p_{87}\) (foamy cells). (**A**) The model has been simulated without anything knocked out. (**B**) The effect of excluding the following transition: \(t_{93}\).