Multiscale & multiphysics modeling and simulation
Multiscale modeling and simulation is the research field of solving problems which have important nature at multiple scales including DNA and proteins. Multiscale modeling is aimed to the calculation of mechanical properties on one scale using information from different scales and approach such as quantum mechanics, molecular dynamics, coarse-grained models, and continuum mechanics.
* Chanseok Lee, Jae Young Lee, Do-Nyun Kim, "Polymorphic design of DNA origami structures through mechanical control of modular components", Nature Communications (2017).
* Kim, Young-Joo, and Do-Nyun Kim. "Structural Basis for Elastic Mechanical Properties of the DNA Double Helix." PloS One (2016).
* Kim, Young-Joo, and Do-Nyun Kim. "Sensitivity Analysis for the Mechanical Properties of DNA Bundles." Journal of Nanomaterials (2016).
* Keyao Pan, Do-Nyun Kim, Fei Zhang, Matthew R. Adendorff, Hao Yan, Mark Bathe, "Lattice-free prediction of three-dimensional structure of programmed DNA assemblies." Nature Communications (2014).
* Do-Nyun Kim, Fabian Kilchherr, Hendrik Dietz, Mark Bathe, "Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures." Nucleic Acids Research (2011).
* Carlos Ernesto Castro, Fabian Kilchherr, Do-Nyun Kim, Enrique Lin Shiao, Tobias Wauer, Philipp Wortmann, Mark Bathe, Hendrik Dietz, "A primer to scaffolded DNA origami." Nature Methods (2011).