Pasi M, Maddocks J, Lavery R. Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics. Nucleic Acids Res. 2015;43:2412-23 pubmed publisher
..We also show that, in some special cases, ion distributions converge very slowly and, on a microsecond timescale, do not reflect the symmetry of the corresponding base sequence. ..
Pasi M, Lavery R. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics. Nucleic Acids Res. 2016;44:5450-6 pubmed publisher
..Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. ..
Etheve L, Martin J, Lavery R. Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors. Nucleic Acids Res. 2016;44:9990-10002 pubmed
Etheve L, Martin J, Lavery R. Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction. Nucleic Acids Res. 2016;44:1440-8 pubmed publisher