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In this chapter, we discuss the analysis of membrane remodeling by proteins, pep- tides and nanoparticles using multi-scale computational methods; these include mainly molecular dynamics simulations at atomistic and coarse-grained levels, al- though we will also touch upon continuum mechanics models. The discussions will cover several systems that we have analyzed in recent studies, which include Sar1, the ESCRTIII complex, complexin and peptides from SARS-COVID-2; as comparison, we also briefly discuss the impact of polyelectrolyte coacervates and functionalized nanoparticles on membrane properties, including generation of membrane curvature and potential disruption of liposomes. These examples illustrate different molecular properties and mechanisms that are potentially relevant to membrane remodeling at different length scales. The results highlight both the values and limitations of different computational models for the analysis of membrane remodeling, thus underscoring the importance of integrating different computational approaches to cross-validate the results.