Application of Static Virus Spread Algorithm in Base-Balanced DNA Fragment Optimization

DNA has found applications in a diverse array of fields such as computing, medical diagnosis, and circuits. Designing DNA fragments that meet specific requirements is crucial for ensuring the smooth execution of tasks in these domains. However, the conventional approach of combining constraints with evolutionary algorithms often encounters challenges like orthogonality and thermodynamic instability. This poses risks to the control of reaction processes. To tackle these challenges, we have undertaken two tasks in this study: expanding constraint sets and innovating evolutionary algorithms. Firstly, we propose a base balance strategy aimed at enhancing the thermodynamic properties within DNA fragment groups by diversifying neighboring base combinations. The addition of this strategy achieves a minimum variance of 0.03 for the melting temperature while ensuring orthogonality. It represents a significant improvement compared to previous results and reduces the complexity of controlling reactions. Secondly, our static virus spread algorithm optimizes target DNA fragments by base mutations and virus amplification. Simultaneously,it demonstrates good performance across 23 benchmark functions, highlighting its optimization potential. This work is expected to further refine theoretical shortcomings and offer a convenient tool for DNA fragment optimization.