Joshi H, Li CY, Aksimentiev A. All-Atom Molecular Dynamics Simulations of Membrane-Spanning
DNA Origami Nanopores.
Methods Mol Biol 2023;
2639:113-128. [PMID:
37166714 DOI:
10.1007/978-1-0716-3028-0_7]
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Abstract
Building on the recent technological advances, all-atom molecular dynamics (MD) simulations have become an indispensable tool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, and mechanical and electrical properties of DNA origami objects. In this chapter we describe a method to build all-atom model of lipid-spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.
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