Advanced search

Filter By:

Journal Check one or more journals to show results from those journals only.

Choose more journals

Article type Check one or more article types to show results from those article types only.
Subject Check one or more subjects to show results from those subjects only.
Date Choose a date option to show results from those dates only.

Custom date range

Clear all filters
Sort by:
Showing 1–11 of 11 results
Advanced filters: Author: Do-Nyun Kim Clear advanced filters

  • AI-based inverse design of DNA origami has been limited by the scarcity of large, standardised datasets. Here, the authors present a diffusion-based design framework trained on simulated equilibrium conformations, highlighting the promise of generative AI models empowered by physical simulation for de novo design of DNA origami.

    • Chien Truong-Quoc
    • Kyounghwa Jeon
    • Do-Nyun Kim
    ResearchOpen Access
    Nature Communications
    P: 1-10

  • DNA may be used to fabricate functional nanostructures with various possible geometries, but first being able to predict these structures is a challenging task. Here, the authors use coarse-grained modelling to predict the shape of artificial DNA nanostructures in solution.

    • Keyao Pan
    • Do-Nyun Kim
    • Mark Bathe
    ResearchOpen Access
    Nature Communications
    Volume: 5, P: 1-7

  • A method is presented to harness the paper-folding mechanism of reconfigurable macroscale systems to create reconfigurable DNA origami structures, in anticipation that it will advance the development of complex molecular systems.

    • Myoungseok Kim
    • Chanseok Lee
    • Do-Nyun Kim
    Research
    Nature
    Volume: 619, P: 78-86

  • Limited datasets hinder the accurate prediction of DNA origami structures. A data-driven and physics-informed approach for model training is presented using a graph neural network to facilitate the rapid virtual prototyping of DNA-based nanostructures.

    • Chien Truong-Quoc
    • Jae Young Lee
    • Do-Nyun Kim
    Research
    Nature Materials
    Volume: 23, P: 984-992

  • Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands is promising for biological and therapeutic applications, but it is elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, the authors present a computational framework for simulating chemo-mechanical change of structured DNA assemblies, using ethidium bromide intercalation as an example.

    • Jae Young Lee
    • Yanggyun Kim
    • Do-Nyun Kim
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-10

  • Controlling the threshold response in synthetic molecular structures is challenging. Here, the authors report on the buckling of ring-shaped DNA origami structures into twisted architectures via mechanical instability, induced by DNA intercalators.

    • Young-Joo Kim
    • Junho Park
    • Do-Nyun Kim
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-8

  • Computational frameworks for structural dynamics are in continuous need of being developed. Here the authors present a a computational framework based on Langevin dynamics to analyze structural dynamics and reconfiguration of DNA assemblies, offering a rational method for designing responsive and reconfigurable DNA machines

    • Jae Young Lee
    • Heeyuen Koh
    • Do-Nyun Kim
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-12

  • The use of staple strands paired with scaffold strands allows the creation of a diverse array of DNA origami nanostructures. Here the authors rationally design a set of staples with variable hinges allowing controllable geometry and flexibility of the final structure.

    • Chanseok Lee
    • Jae Young Lee
    • Do-Nyun Kim
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-8