Computing the elastic mechanical properties of rod-like DNA nanostructures

Autor: Chhabra, Hemani, Mishra, Garima, Cao, Yijing, Prešern, Domen, Skoruppa, Enrico, Tortora, Maxime M. C., Doye, Jonathan P. K.

Publikováno v: J. Chem. Theory Comput. 16, 7748-7763 (2020)

To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and twist persist

Externí odkaz: http://arxiv.org/abs/2006.15029

Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis

Autor: Tortora, Maxime M. C., Mishra, Garima, Presern, Domen, Doye, Jonathan P. K.

Publikováno v: Sci. Adv. 6 (2020) eaaw8331

Lyotropic cholesteric liquid crystal phases are ubiquitously observed in biological and synthetic polymer solutions, characterized by a complex interplay between thermal fluctuations, entropic and enthalpic forces. The elucidation of the link between

Externí odkaz: http://arxiv.org/abs/1811.12331

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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.