ABSTRACT
This chapter illustrates that by integrating insights from particle-based simulations, continuum modeling can be applied to gain unique mechanistic insights into problems. It stimulates the developments that better integrate particle and continuum levels of description for biomolecular applications. The elastic network models (ENMs) are particle-based coarse-grained (CG) models for biomolecules. The particles in ENM can be regarded as nodes of a continuum mechanics model in a mesh representation. One unique advantage of ENM is that the reference structure, by design, is an energy minimum. The chapter reviews the study of the mechanosensitive channels (MscL) gating transition using a finite element approach, but a simpler model is to treat the protein with an ENM. It explores several different pulling strategies, with an ENM that includes only the MscL protein or the MscL embedded in a lipid bilaye. The chapter mentions that many ENM studies compare computed vibrational properties with x-ray crystallographic data such as the Debye–Waller factors.
