This thesis investigates the growing field of biological nanopores, their applications in molecular sensing and their non-linear ion transport. Biological nanopores, naturally evolved to regulate membrane transport, have been adapted for use in biotechnology, particularly in nanopore sensing. This technology has the potential to become vital in genomics, proteomics, and metabolomics due to its ease of use, cost-efficiency, and high throughput, enabling individual molecular analysis with minimal preparation. Despite significant advances, challenges persist, mainly due to the incomplete understanding of the translocation mechanisms and the complexity of observed current signals. The first chapter explores the labelling of cysteine residues on peptides to detect them in nanopore sensing, revealing that while labelling can act as a steric brake, it also presents challenges in translocation. The study underscores the need for a deeper understanding of the interactions between peptide structure, labelling chemistry, and translocation physics to optimize sensing techniques. The second chapter examines ionic transport through biological nanopores, focusing on how lumen charges affect ion transport, particularly in open-pore rectification and gating. The findings point to voltage-induced conformational changes in the transmembrane region as the origin of gating, with implications for improving nanopore sensors and designing high-gating mutants tailored for specific applications. This thesis contributes to the broader understanding of biological nanopores, offering new perspectives on their function and potential. By integrating insights from peptide translocation and ionic nanopore transport, this work lays part of the groundwork for future innovations in nanopore technology, with broad implications for biomedical diagnostics, environmental sensing, and nanoscale computing. The research emphasizes the importance of mastering the underlying physics of nanopores to fully exploit their capabilities across various domains.