@article {29,
	title = {Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics},
	journal = {J Phys Chem C Nanomater Interfaces},
	volume = {116},
	year = {2012},
	month = {2012 Feb 9},
	pages = {3376-3393},
	abstract = {<p>It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.</p>},
	issn = {1932-7447},
	doi = {10.1021/jp210641j},
	author = {Jeffrey Comer and Aleksei Aksimentiev}
}
