Publication

SNUPI: A computational framework for rapid mechanical analysis of structured DNA assemblies

Jun Hyeong Park, Do-Nyun Kim*, Jae Young Lee*

Submitted

DNA origami directed nanometer-scale integration of colloidal quantum emitters with silicon photonics

Xin Luo, Luigi Ranno, Tara Sverko, Jae Young Lee, Nicholas Sbalbi, Annette Jones, Chi Chen, Moungi G. Bawendi, Juejun Hu, Robert J. Macfarlane*, Mark Bathe*

Submitted

Elasticity of swollen and folded polyacrylamide hydrogel using the MARTINI coarse-grained model

Seunghyok Rho, Heeyuen Koh, Ji Woong Yu, Hye Been Koo, Sebin Kim, Je-Yeon Jung, EunYeong Jung, Chongyong Nam, Jae Young Lee, Kyounghwa Jeon, Jae-Byum Chang*, Do-Nyun Kim*, Won Bo Lee*

ACS Applied Materials & Interfaces (2025) [Link] [PDF]

Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies

Jae Young Lee, Yanggyun Kim, Do-Nyun Kim*

Nature Communications (2024) [Link] [PDF]

DNA hydrogels with programmable condensation, expansion, and degradation for molecular carriers

Kyounghwa Jeon, Chanseok Lee, Jae Young Lee, Do-Nyun Kim*

ACS Applied Materials & Interfaces (2024) [Link] [PDF]

Prediction of DNA origami shape using graph neural network

Chien Truong-Quoc†, Jae Young Lee†, Kyung Soo Kim, Do-Nyun Kim*

Nature Materials (2024) [Link] [PDF]

Controlling chiroptical responses via chemo-mechanical deformation of DNA origami structures

Taehwi Kim, Chanseok Lee, Jae Young Lee, Do-Nyun Kim*

ACS Nano (2024) [Link] [PDF]

A computational model for structural dynamics and reconfiguration of DNA assemblies

Jae Young Lee, Heeyuen Koh, Do-Nyun Kim*

Nature Communications (2023) [Link] [PDF]

Harnessing a paper-folding mechanism for reconfigurable DNA origami

Myoungseok Kim, Chanseok Lee, Kyounghwa Jeon, Jae Young Lee, Young-Joo Kim, Jae Gyung Lee, Hyunsu Kim, Maenghyo Cho, Do-Nyun Kim*

Nature (2023) [Link] [PDF]

Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy

Heng Ni†, Xiao Fan†, Feng Zhou, Galio Guo, Jae Young Lee, Nadrian C. Seeman, Do-Nyun Kim, Nan Yao*, Paul M. Chaikin*, Yimo Han*

iScience (2022) [Link] [PDF]

Formation of non-base-pairing DNA microgels using directed phase transition of amphiphilic monomers

Chanseok Lee†, Sungho Do†, Jae Young Lee, Minju Kim, Sang Moon Kim, Yongdae Shin*, Do-Nyun Kim*

Nucleic Acids Research (2022) [Link] [PDF]

Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint

Jae Gyung Lee, Kyung Soo Kim, Jae Young Lee, Do-Nyun Kim*

ACS Nano (2022) [Link] [PDF]

Characterizing and harnessing the mechanical properties of short single-stranded DNA in structured assemblies

Jae Young Lee†, Myoungseok Kim†, Chanseok Lee, Do-Nyun Kim*

ACS Nano (2021) [Link] [PDF]

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Chanseok Lee†, Young-Joo Kim†, Kyung Soo Kim, Jae Young Lee, Do-Nyun Kim*

Nucleic Acids Research (2021) [Link] [PDF]

Design approaches and computational tools for DNA nanostructures

Heeyuen Koh, Jae Gyung Lee, Jae Young Lee, Ryan Kim, Osamu Tabata, Jin-Woo Kim*, Do-Nyun Kim*

IEEE Open Journal of Nanotechnology (2021) [Link] [PDF]

Programming ultrasensitive threshold response through chemo-mechanical instability

Young-Joo Kim, Junho Park, Jae Young Lee, Do-Nyun Kim*

Nature Communications (2021) [Link] [PDF]

Rapid computational analysis of structured DNA assemblies at near-atomic resolution

Jae Young Lee, Jae Gyung Lee, Giseok Yun, Chanseok Lee, Young-Joo Kim, Kyung Soo Kim, Tae Hwi Kim, Do-Nyun Kim*

ACS Nano (2021) [Link] [PDF]

Tailoring the mechanical stiffness of DNA nanostructures using engineered defects

Chanseok Lee†, Kyung Soo Kim†, Young-Joo Kim, Jae Young Lee, Do-Nyun Kim*

ACS Nano (2019) [Link] [PDF]

Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design

Jae Young Lee, Young-Joo Kim, Chanseok Lee, Jae Gyung Lee, Hiromasa Yagyu, Osamu Tabata, Do-Nyun Kim*

Nucleic Acids Research (2019) [Link] [PDF]

A framework of finite element procedures for the analysis of proteins

Reza Sharifi Sedeh, Giseok Yun, Jae Young Lee, Klaus-Jürgen Bathe, Do-Nyun Kim*

Computers & Structures (2018) [Link] [PDF]

Polymorphic design of DNA origami structures through mechanical control of modular components

Chanseok Lee, Jae Young Lee, Do-Nyun Kim*

Nature Communications (2017) [Link] [PDF]

Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design

Hiromasa Yagyu*, Jae Young Lee, Do-Nyun Kim, Osamu Tabata

Journal of Physical Chemistry B (2017) [Link] [PDF]

Ignition characteristics of laser-ablated aluminum at shock pressures up to 2 GPa

Kyung-Cheol Lee, Tsubasa Taira, Goon Mo Koo, Jae Young Lee, Jack J. Yoh*

Journal of Applied Physics (2014) [Link] [PDF]

_ Lab members, † Contributed equally, * Corresponding author

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