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The rise of pathogenic Escherichia coli (E. coli) in food and water sources poses serious public health risks, highlighting the need for rapid, sensitive detection methods like aptamer-based biosensors. Aptamers are nucleic acids that bind specific targets with high affinity. This study explores their interaction with E. coli proteins, such as Shiga Toxin (Stx), using biophysical simulations including molecular docking and free energy calculations. The methodology identifies key structural features and analyzes binding mechanisms. Overall, this research supports the theoretical foundation for developing advanced biosensors, using in-silico approaches to characterize aptamer-target interactions for future diagnostic applications.