Publications

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† Equal contribution * Corresponding author

41. Jejoong Yoo*, Sangwoo Park, Christopher Maffeo, Taekjip Ha* & Aleksei Aksimentiev*

DNA Sequence and Methylation Prescribe the Inside-Out Conforma- tional Dynamics and Bending Energetics of DNA Minicircles

Nucleic Acids Research, Accepted

40.Sehui Bae, Inrok Oh, Jejoong Yoo & Jun Soo Kim*

Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA

ACS Omega, 6, 18728–18736, 2021

39. Jejoong Yoo*

On the stability of protein–DNA complexes in molecular dynamics simulations using the CUFIX corrections

Journal of the Korean Physical Society, 78:461–466, 2021

38. Hyuk-Joon Lee, Hyeongseop Jeong, Jaekyung Hyun, Bumhan Ryu, Kunwoong Park, Hyun-Ho Lim, Jejoong Yoo & Jae-Sung Woo*

Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel

Science Advances, 6:eaba4996, 2020

37. Jejoong Yoo*, David Winogradoff & Aleksei Aksimentiev*

Molecular Dynamics Simulations of DNA-DNA and DNA-Protein Interactions

Current Opinion in Structural Biology, 64:88–96, 2020

36. Seonju You, Hong-guen Lee, Kimoon Kim & Jejoong Yoo*

Improved Parameterization of Protein–DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA

Journal of Chemical Theory and Computation, 16:4006–4013, 2020

35. Wooseup Hwang, Jejoong Yoo, In-Chul Hwang, Jiyeon Lee, Young Ho Ko, Hyun Woo Kim, Younghoon Kim, Yeonsang Lee, Moon Young Hur, Kyeng Min Park, Jongcheol Seo, Kangkyun Baek & Kimoon Kim

Hierarchical Self-assembly of Polypseudorotaxanes into Artificial Microtubules

Angewandte Chemie International Edition, 59:3460–3464, 2020

34. Younghoon Kim, Jaehyoung Koo, In-Chul Hwang, Rahul Dev Mukhopadhyay, Soonsang Hong, Jejoong Yoo, Ajaz Dar, Ikjin Kim, Dohyun Moon, Tae Joo Shin, Young Ko & Kimoon Kim

Rational Design and Construction of Hierarchical Superstructures Using Shape-persistent Organic Cages: Porphyrin Box-based Metallosupramolecular Assemblies

Journal of the American Chemical Society, 140:14547–14551, 2018

33. Hyunju Kang, Jejoong Yoo, Hong Soo Lee, Byeong-Kwon Sohn, Seung-Won Lee, Wenjie Ma, Jung-Min Kee, Aleksei Aksimentiev* & Hajin Kim*

Sequence-dependent DNA condensation as a driving force of DNA phase separation

Nucleic Acids Research, 46:9401–9413, 2018

32. Alexander Ohmann, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N Baumann, Kerstin Gopfrich, Jejoong Yoo, Ulrich F Keyser* & Aleksei Aksimentiev*

A synthetic enzyme built from DNA flips 10^7 lipids per second in biological membranes

Nature Communications, 9:2426, 2018

31. Jejoong Yoo & Aleksei Aksimentiev

New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

Physical Chemistry Chemical Physics, 20:8432–8449, 2018 (2018 PCCP Hot Articles)

30. Kyeng Min Park, Kangkyun Baek, Young Ho Ko, Annadka Shrinidhi, James Murray, Won Hyuk Jang, Ki Hean Kim, Jun-Seok Lee, Jejoong Yoo, Sungwan Kim & Kimoon Kim

Mono-allyloxylated Cucurbit[7]uril Acts as an Unconventional Amphiphile to Form Light-responsive Vesicles

Angewandte Chemie International Edition, 57:3132–3136, 2018

29. Jejoong Yoo & Aleksei Aksimentiev

Refined Parametrization of Non-bonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations

The Journal of Physical Chemistry Letters, 7:3812–3818, 2016

28. Kerstin Gopfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev & Ulrich F. Keyser

Large-Conductance Transmembrane Porin Made from DNA Origami

ACS Nano, 10:8207–8214, 2016

27. Kerstin Gopfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev & Ulrich F. Keyser

Ion channels made from a single membrane-spanning DNA duplex

Nano Letters, 16:4665–4669, 2016

26. Scott Michael Slone, Chen-Yu Li, Jejoong Yoo & Aleksei Aksimentiev “Molecular mechanics of DNA bricks: In situ structure, mechanical properties and ionic conductivity.” New Journal of Physics, 18:055012, 2016 [Full text]

25. Jejoong Yoo, James Wilson & Aleksei Aksimentiev

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

Biopolymers, 105:752–763, 2016

24. Swati Bhattacharya, Jejoong Yoo& Aleksei Aksimentiev

Water mediates recognition of DNA sequence via ionic current blockade in a biological nanopore.

ACS Nano, 10:4644–4651, 2016

23. Chris Maffeo, Jejoong Yoo & Aleksei Aksimentiev

De novo prediction of DNA origami structures through atomistic molecular dynamics simulation

Nucleic Acids Research, 44:3013–3019, 2016

22. Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev & Taekjip Ha

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

Nature Communications, 7:11045, 2016

21. Thuy Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei Aksimentiev & Taekjip Ha

Effect of cytosine modifications on DNA flexibility and nucleosome mechanical stability

Nature Communications, 7:10813, 2016

20. Jejoong Yoo & Aleksei Aksimentiev

The structure and intermolecular forces of DNA condensates

Nucleic Acids Research, 44:2036–2046, 2016

19. Jejoong Yoo & Aleksei Aksimentiev

Improved parameterization of amine–carboxyate and amine–phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields

Journal of Chemical Theory and Computation, 12:430–443, 2016

18. Jejoong Yoo & Aleksei Aksimentiev

Molecular dynamics of membrane-spanning DNA channels: Conductance mechanism, electro-osmotic transport and mechanical gating

The Journal of Physical Chemistry Letters, 6:4680–4687, 2015

17. Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernandez-Ainsa, Ulrich F. Keyser & Aleksei Aksimentiev

Ionic conductivity, structural deformation and programmable anisotropy of DNA origami in electric field.

ACS Nano, 9:1420–1433, 2015

16. Chris Maffeo, Jejoong Yoo, Jeffrey Comer, David Wells, Binquan Luan & Aleksei Aksimentiev

Close encounters with DNA.

J. Phys.: Condens. Matter, 26:413101, 2014

15. Jejoong Yoo & Aleksei Aksimentiev

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

Proceedings of the National Academy of Sciences, 110:20099–20104, 2013.

14. Jejoong Yoo, Meyer Jackson & Qiang Cui

A comparison of coarse-grained and continuum models for membrane bending in lipid bilayer fusion pores.

Biophysical Journal, 104:841–852, 2013.

13. Jejoong Yoo & Qiang Cui

Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-grained simulation analysis of gramicidin A association.

Biophysical Journal, 104:128–138, 2013. (Cover)

12. Jejoong Yoo & Qiang Cui

Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A.

Biophysical Journal, 104:117–127, 2013.

11. Chris Maffeo, Swati Bhattacharya, Jejoong Yoo, David Wells & Aleksei Aksimentiev

Modeling and simulation of ion channels.

Chemical Reviews, 112:6250–6284, 2012. (Cover)

10. Jejoong Yoo & Aleksei Aksimentiev

Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations.

The Journal of Physical Chemistry B, 43:12946–12954, 2012.

9. Jejoong Yoo & Aleksei Aksimentiev

Improved parametrization of Li+, Na+, K+, and Mg2+ ions for all-atom molecular dynamics simulations of nucleic acid systems.

The Journal of Physical Chemistry Letters, 3:45–50, 2012

8. Jejoong Yoo & Qiang Cui

Chemical versus mechanical perturbations on the protonation state of arginine in complex lipid membranes: insights from microscopic pKa calculations.

Biophysical Journal, 99:1529–1538, 2010.

7. Jejoong Yoo & Qiang Cui

Curvature generation and pressure profile modulation in membrane by lysolipids: Insights from Coarse-Grained Simulations.

Biophysical Journal, 97:2267–76, 2009.

6. Yuye Tang, Xi Chen, Jejoong Yoo, Arun Yethiraj & Qiang Cui

Numerical simulation of nanoindentation and patch clamp experiments on mechanosensitive channels of large conductance in escherichia coli.

Exp. Mech., 49(1): 35–46, 2009.

5. Jejoong Yoo & Qiang Cui

Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations.

Biophysical Journal, 94, L61–L63, 2008.

4. Xi Chen, Qiang Cui, Yuye Tang, Jejoong Yoo & Arun Yethiraj

Gating mechanisms of mechanosensitive channels of large conductance, I: a continuum mechanics-based hierarchical framework.

Biophysical Journal, 95:563–580, 2008. (Cover)

3. Yuye Tang, Jejoong Yoo, Arun Yethiraj, Qiang Cui & Xi Chen

Gating mechanisms of mechanosensitive channels of large conductance, II: systematic study of conformational transitions.

Biophysical Journal, 95:581–596, 2008.

2. Yuye Tang, Jejoong Yoo, Arun Yethiraj, Qiang Cui & Xi Chen

Mechanosensitive channels: insights from continuum-based simulations.

Cell. Biochem. Biophys., 52:1–18, 2008.

1. Yuye Tang, Guoxin Cao, Xi Chen, Jejoong Yoo, Arun Yethiraj & Qiang Cui

A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL.

Biophysical Journal, 91:1248–1263, 2006. (Cover)

Equal contribution

* Corresponding author