In the NAU-CHINA 2024 project, we conducted our work from two aspects: molecular modeling and mathematical modeling. In molecular modeling, we predicted the tertiary structures of some proteins and docked them, which helped us better understand the structure and characteristics of proteins and explain the rationality of experimental design. In addition, we calculated the solvation free energy of proteins through the method of free energy perturbation, which can reflect the hydrophilicity of proteins and enhance the feasibility of experimental schemes. In mathematical modeling, we first designed an algorithm to simulate the working state of underwater soft robots and counted their damage. We found that even small disturbances would remarkably increase the damage rate of soft robots, which proved that our project is of great significance for damage healing. Then we used mathematical modeling to analyze the hydrogen bond network formed between β-sheets, and then determined the differences in protein stability based on varying translation times using circular mRNA (cmRNA). We found that repeated translation of cmRNA can produce more effective proteins. Then we simulated the variation of L-DOPA concentration during the enzymatic reaction through ordinary differential equations and predicted the optimal reaction time for maximum L-DOPA production, which will provide guidance for the experiment and reduce the experiment cost. Finally, we used mathematical theory to calculate and found that using our designed materials will save costs compared with other materials.
We utilized tools such as SWISS-MODEL and AlphaFold3 to predict the structures of Squid Ring Teeth Protein Tandem Repeat n4 (TRn4), Mussel Foot Protein 5 (Mfp5), and the fusion of TRn4-Mfp5 (fusion protein). We then obtained the docking results of TRn5 and fusion proteins using ClusPro 2.0, ZDOCK, and GRAMM. Subsequently, we referred to descriptions in existing literature of the TRn4 and fusion protein to select reliable docking results. Finally, we applied GROMACS to evaluate the stability of these results. Additionally, we calculated the solvation free energy of the fusion protein using the free energy perturbation method in GROMACS, which effectively characterizes the hydrophilicity of the protein.
We designed a path-finding obstacle avoidance & interference algorithm to simulate the working state of underwater soft robots. We generated a simulation map based on the actual terrain and added some factors to simulate the interference suffered by the underwater robot. Finally, we studied the disturbance impact on the robot by counting damage times. Secondly, we simulated the hydrogen bond network formed by β-sheet through MATLAB, and conducted stability analysis on the hydrogen bond network within proteins with different numbers of repetitions and the hydrogen bond network between protein molecules. We found that the more times cmRNA translates, the more stable proteins can be produced. Then we constructed ordinary differential equations to simulate the concentration changes during the L-DOPA reaction and calculated the yield at different reaction times by Michaelis equation, and obtained the optimal time for the reaction. Finally, we used the renewal reward theorem to obtain the optimal maintenance strategy and minimum cost of the soft robot, thereby quantifying the advantages of our designed materials over ordinary materials.
