All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores

Himanshu Joshi, Chen Yu Li, Aleksei Aksimentiev

Research output: Chapter in Book/Report/Conference proceedingChapter


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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages16
StatePublished - 2023
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • DNA origami nanopores
  • Ionic current
  • Lipid bilayer membrane
  • Molecular dynamics simulation

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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