@inbook {35,
	title = {Modeling nanopores for sequencing DNA},
	booktitle = {DNA Nanotechnology: Methods and Protocols},
	volume = {749},
	year = {2011},
	month = {2011},
	pages = {317-358},
	abstract = {<p>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.</p>
},
	keywords = {Base Sequence, Computer Simulation, DNA, Hemolysin Proteins, Models, Molecular, Molecular Conformation, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Sequence Analysis, DNA},
	issn = {1940-6029},
	doi = {10.1007/978-1-61779-142-0_22},
	author = {Jeffrey Comer and David B Wells and Aleksei Aksimentiev},
	editor = {Giampaolo Zuccheri and Bruno Samori}
}
