Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations.

ABSTRACT: Understanding the molecular mechanisms of pore formation is crucial for elucidating fundamental biological processes and developing therapeutic strategies, such as the design of drug delivery systems and antimicrobial agents. Although experimental methods can provide valuable information, they often lack the temporal and spatial resolution necessary to fully capture the dynamic stages of pore formation. In this study, we present two novel collective variables (CVs) designed to characterize membrane pore behavior, particularly its energetics, through molecular dynamics (MD) simulations. The first CV─termed Full-Path─effectively tracks both the nucleation and expansion phases of pore formation. The second CV─called Rapid─is tailored to accurately assess pore expansion in the limit of large p

SUBMITTER: Rivel T 

PROVIDER: S-EPMC11776052 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature