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Hugh S. C. Martin, Shantenu Jha and Peter V. Coveney Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force Journal of Computational Chemistry 35

Version of Record online: 9 JAN 2014 | DOI: 10.1002/jcc.23525

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The translocation of nucleotide molecules across nanopores has attracted attention as a next-generation technique for sequencing DNA. Computer simulations can provide atomistic-level insight of important states and processes. Two computational methodologies in a nucleotide–nanopore translocation system are compared using the α-hemolysin nanopore. The first uses constant velocity-steered molecular dynamics with Jarzynski's equality; the second applies an adaptive biasing force, which has not previously been applied to the nucleotide–nanopore system.

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