J. Comer, A. Ho and A. Aksimentiev. Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations. Electrophoresis. (Accepted).
D. Wells, M Belkin, J. Comer and A. Aksimentiev. Assessing graphene nanopores for sequencing DNA. Nano Letters, 12:4117–4123 (2012).
Swati Bhattacharya, Ian M. Derrington, Mikhail Pavlenok, Michael Niederweis, Jens H. Gundlach, and Aleksei Aksimentiev. Molecular dynamics study of MspA arginine-mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence. ACS Nano, 6:6960–6968 (2012).
Winston Timp, Jeffrey Comer and Aleksei Aksimentiev. DNA base-calling from a nanopore using a Viterbi algorithm. Biophysical Journal Letters, 102:L37-L39 (2012).
J. Comer and A Aksimentiev. Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics. Journal of Physical Chemistry C 116:3376–3393 (2012).
S. W. Kowalczyk, D B. Wells, A Aksimentiev, and C. Dekker. Slowing down DNA translocation through a nanopore in lithium chloride. Nano Letters, 12:1038–1044 (2012).
C. Maffeo, B. Luan and A. Aksimentiev. End-to-end attraction of short duplex DNA. Nucleic Acids Research, 40:3812-3821 (2012).
J. Yoo and A Aksimentiev. Improved parameterization of Li+, Na+, K+, and Mg2+ ions for all-atom molecular dynamics simulations of nucleic acid systems. Journal of Physical Chemistry Letters, 3:45–50 (2012).
