Modeling Nanopores for Sequencing DNA

Jeffrey R. Comer, David B. Wells, Aleksei Aksimentiev

Research output: Chapter in Book/Report/Conference proceedingChapter


Using nanopores to sequence DNA rapidly and at a low cost has the potential to radically transform the field of genomic research. However, despite all the exciting developments in the field, sequencing DNA using a nanopore has yet to be demonstrated. Among the many problems that hinder development of the nanopore sequencing methods is the inability of current experimental techniques to visualize DNA conformations in a nanopore and directly relate the microscopic state of the system to the measured signal. We have recently shown that such tasks could be accomplished through computation. This chapter provides step-by-step instructions of how to build atomic scale models of biological and solid-state nanopore systems, use the molecular dynamics method to simulate the electric field-driven transport of ions and DNA through the nanopores, and analyze the results of such computational experiments.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages42
StatePublished - 2011

Publication series

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


  • Bionanotechnology
  • Computer simulations
  • Membrane proteins
  • Molecular dynamics
  • Nucleic acids
  • Transmembrane transport

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


Dive into the research topics of 'Modeling Nanopores for Sequencing DNA'. Together they form a unique fingerprint.

Cite this