We use atomistic and coarse-grain molecular dynamics simulations to study the interactions of surfactant micelles and lipid monolayers and bilayers with polymers and proteins. Specific problems include atomistic molecular dynamics simulations of an anionic sodium dodecyl sulfate (SDS) micelle and a nonionic poly(ethylene oxide) (PEO) polymer in aqueous solution. We show that the polymer resides on the micelle surface and at the hydrocarbon-water interface, leading to a selective reduction in the hydrophobic contribution to the solvent-accessible surface area of the micelle. The association is mainly driven by hydrophobic interactions between the polymer and surfactant tails, and produces the commonly accepted “beaded necklace” structure of the SDS-PEO complex. We also investigate “hydrophobic mismatch” in the length of hydrophobic domains of transmembrane peptides relative to the width of the hydrophobic domain of bilayers using model “KALP” peptides consisting of alanine and leucine lipophilic residues capped at both ends by lysines. We find that the peptide/bilayer system compensates for mismatch through a combination of peptide tilting, local bilayer bending, and lysine side-chain “snorkeling,” in the case that the hydrophobic domain of the peptide is shorter than that of the lipid bilayer. Finally, the conditions under which cationic dendrimers can induce pore formation in bilayers are studied by coarse-grained MD simulations and the results compared favorably with recent experiments.