Our model achieves a full-level simulation from micro to application.
At the micro level, it predicts gene expression as well as conducts molecular docking and molecular dynamics simulations, which can guide experiments and provide a better understanding of our system.
At the application level, we simulate the diffusion of Trans-aconitic acid (TAA) and its lethal effects on nematodes to evaluate its actual performance in field environments.
In this section, we constructed a salicylic acid biosensor and lysis model using ordinary differential equations to simulate gene expression. The model helps evaluate whether the expression levels of our shRNA are sufficient to achieve gene silencing and if they can reach a peak before cell lysis occurs.
We predicted the 3D structure of aconitate isomerase(TbrA) in engineered bacteria using AlphaFold 2.0, followed by molecular dynamics simulations.Then we predicted the HrpRS-Phrpl complex structure using AlphaFold , followed by binding free energy calculations. Finally, we applied saturation mutagenesis to enhance NahR protein's affinity for SA.We helped verify the loop building by doing these work.
In this section, we used the 3D convection-diffusion equation to simulate the diffusion of TAA secreted by engineered bacteria in soil. The model provides an estimate of the effective lethal range of TAA against nematodes at steady-state diffusion, leading to the conclusion that seed coating is the most effective method of application.
This module verifies the nematocidal effect of engineered bacteria. First, we used a cellular automaton to model nematode infection and movement in the field. Next, we performed a dose-response analysis of TAA toxicity. Finally, combining these with the TAA diffusion model, we demonstrated that the engineered bacteria effectively protect crops from nematode infestation.