@article{c317f0a7814f4005ac8ba85404ab1cc2,
title = "DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size",
abstract = "We present a detailed coarse-grained computer simulation and singlemolecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates the ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions.",
author = "Khara, {Dinesh C.} and Schreck, {John S.} and Tomov, {Toma E.} and Yaron Berger and Ouldridge, {Thomas E.} and Doye, {Jonathan P.K.} and Eyal Nir",
note = "Funding Information: Israel Science Foundation [1857/17 to E.N.]; Engineering and Physical Sciences Research Council [EP/J019445/1 to J.S.S., J.P.K.D.]; Royal Society University Research Fellowship (to T.E.O.). Funding for open access charge: Oxford's RCUK Open Access block grant. Funding Information: Israel Science Foundation [1857/17 to E.N.]; Engineering and Physical Sciences Research Council [EP/J019445/1 to J.S.S., J.P.K.D.]; Royal Society University Research Fellowship (to T.E.O.). Funding for open access charge: Oxford{\textquoteright}s RCUK Open Access block grant. Conflict of interest statement. None declared. Funding Information: We acknowledge the use of the University of Oxford Advanced Research Computing (ARC) facility in carrying out this work (http://dx.doi.org/10.5281/zenodo.22558), and support from the European Union under the FP7 (Integrated Infrastructure Initiative N. 262348 European Soft Matter Infrastructure, ESMI). Publisher Copyright: {\textcopyright} The Author(s) 2017.",
year = "2018",
month = feb,
day = "16",
doi = "10.1093/nar/gkx1282",
language = "English",
volume = "46",
pages = "1553--1561",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "3",
}