The free-energy landscape of a mechanically bistable DNA origami

Autor: Wong, Chak Kui, Doye, Jonathan P. K.

Publikováno v: Appl. Sci. 12, 5875 (2022)

Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit

Externí odkaz: http://arxiv.org/abs/2201.08920

The oxDNA coarse-grained model as a tool to simulate DNA origami

Autor: Doye, Jonathan P. K., Fowler, Hannah, Prešern, Domen, Bohlin, Joakim, Rovigatti, Lorenzo, Romano, Flavio, Šulc, Petr, Wong, Chak Kui, Louis, Ard A., Schreck, John S., Engel, Megan C., Matthies, Michael, Benson, Erik, Poppleton, Erik, Snodin, Benedict E. K.

This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.
Comment: 17 pages, 5 figures

Externí odkaz: http://arxiv.org/abs/2004.05052

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The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.

Autor: Doye JPK; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK. jonathan.doye@chem.ox.ac.uk., Fowler H; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK., Prešern D; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK., Bohlin J; Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK., Rovigatti L; Dipartimento di Fisica, Sapienza Universitá di Roma, Rome, Italy., Romano F; Dipartimento di Fisica, Sapienza Universitá di Roma, Rome, Italy., Šulc P; School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA., Wong CK; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK., Louis AA; Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford, UK., Schreck JS; Computational and Information Systems Laboratory, National Center for Atmospheric Research (NCAR), Boulder, USA., Engel MC; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA., Matthies M; School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA., Benson E; Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK., Poppleton E; School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA., Snodin BEK; Department of Philosophy, Future of Humanity Institute, University of Oxford, Oxford, UK.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2023; Vol. 2639, pp. 93-112.