The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.
暂无分享,去创建一个
Michael Matthies | Jonathan P. K. Doye | Hannah Fowler | Domen Prevsern | Joakim Bohlin | Lorenzo Rovigatti | Flavio Romano | Petr vSulc | Chak Kui Wong | Ard A. Louis | John S. Schreck | Megan C. Engel | Erik Benson | Erik Poppleton | Benedict E. K. Snodin | J. Doye | A. Louis | Domen Prešern | M. Matthies | P. Šulc | B. Snodin | J. Schreck | F. Romano | M. C. Engel | L. Rovigatti | Erik Benson | Erik Poppleton | Megan C Engel | Joakim Bohlin | Hanna Fowler | Petr vSulc | Domen Prevsern
[1] Shawn M. Douglas,et al. Folding DNA into Twisted and Curved Nanoscale Shapes , 2009, Science.
[2] Flavio Romano,et al. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. , 2015, The Journal of chemical physics.
[3] Tim Liedl,et al. Force-Induced Unravelling of DNA Origami. , 2018, ACS nano.
[4] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[5] Carlos E. Castro,et al. Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. , 2017, ACS nano.
[6] Flavio Romano,et al. A nucleotide-level coarse-grained model of RNA. , 2014, The Journal of chemical physics.
[7] Hendrik Dietz,et al. Molecular engineering of chiral colloidal liquid crystals using DNA origami. , 2017, Nature materials.
[8] Hao Yan,et al. Autonomously designed free-form 2D DNA origami , 2019, Science Advances.
[9] Michael Matthies,et al. Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation , 2020, bioRxiv.
[10] Hendrik Dietz,et al. Magnesium-free self-assembly of multi-layer DNA objects , 2012, Nature Communications.
[11] Tine Curk,et al. Coarse-grained simulation of DNA using LAMMPS , 2018, The European physical journal. E, Soft matter.
[12] Mark Bathe,et al. A primer to scaffolded DNA origami , 2011, Nature Methods.
[13] Jonathan P. K. Doye,et al. Direct Simulation of the Self-Assembly of a Small DNA Origami. , 2016, ACS nano.
[14] W. Chiu,et al. Designer nanoscale DNA assemblies programmed from the top down , 2016, Science.
[15] M. C. Engel,et al. Measuring Internal Forces in Single-Stranded DNA , 2019, DNA Systems Under Internal and External Forcing.
[16] Ivan Viola,et al. Adenita: interactive 3D modelling and visualization of DNA nanostructures , 2020, Nucleic acids research.
[17] Flavio Romano,et al. Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model. , 2017, ACS nano.
[18] Lorenzo Rovigatti,et al. TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami , 2019, J. Comput. Chem..
[19] Flavio Romano,et al. Coarse-grained modelling of the structural properties of DNA origami , 2018, Nucleic acids research.
[20] Jejoong Yoo,et al. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations , 2013, Proceedings of the National Academy of Sciences.
[21] Adam H. Marblestone,et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno , 2009, Nucleic acids research.
[22] J. Doye,et al. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. , 2010, The Journal of chemical physics.
[23] Pekka Orponen,et al. DNA rendering of polyhedral meshes at the nanoscale , 2015, Nature.
[24] Christopher Maffeo,et al. MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems , 2020, Nucleic acids research.
[25] Hao Yan,et al. Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures , 2009, DNA.
[26] Hendrik Dietz,et al. Building machines with DNA molecules , 2019, Nature Reviews Genetics.
[27] Hendrik Dietz,et al. Gigadalton-scale shape-programmable DNA assemblies , 2017, Nature.
[28] H. Dietz,et al. Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components , 2015, Science.
[29] P. Rothemund. Folding DNA to create nanoscale shapes and patterns , 2006, Nature.
[30] Wah Chiu,et al. Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges. , 2019, ACS nano.
[31] Hai-Jun Su,et al. Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis. , 2019, Nanoscale.
[32] T. G. Martin,et al. Cryo-EM structure of a 3D DNA-origami object , 2012, Proceedings of the National Academy of Sciences.
[33] G. Arya,et al. Free energy landscape of salt-actuated reconfigurable DNA nanodevices , 2019, Nucleic acids research.
[34] M. Bathe,et al. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures , 2011, Nucleic acids research.
[35] Hai-Jun Su,et al. Paper Origami-Inspired Design and Actuation of DNA Nanomachines with Complex Motions. , 2018, Small.
[36] I. Z. Reguly,et al. A comparison between parallelization approaches in molecular dynamics simulations on GPUs , 2014, J. Comput. Chem..
[37] John Russo,et al. Reversible gels of patchy particles: role of the valence. , 2009, The Journal of chemical physics.