The discovery and subsequent clinical usage of antibiotics was a major breakthrough in 20th-century medicine, drastically improving healthcare standards while increasing the average human life expectancy. The antibiotic era, despite its considerable success, was unfortunately short-lived. Once again, the threat of potential lack of treatments for infectious diseases returns, this time due to the emergence of multidrug-resistant bacteria. Limitations in the number of bacterial targets remain among the main challenges in discovering new antibiotics. In order to overcome this shortage, a promising solution is using antimicrobial peptides (AMPs), a strong naturally occurring alternative. We developed a theoretical framework for the interactions of AMPs and bacteria on both the single-cell and population level, with and without considering the synergistic combination of different types of AMPs. Our methods explain the wide spectrum of efficiencies at which different types of AMPs operate while indicating the equivalent significance of the bacterial cell entrance and inhibition processes. Measures of minimal inhibitory concentration (MIC) as well as our cooperativity parameter in the 2-AMP cases were detailed, offering a physical-chemical description of the mechanisms of cooperativity and the overall bacterial clearance dynamics.