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List of works by Jejoong Yoo

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

scientific article published on February 2013

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

scientific article

A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes.

scientific article

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

scientific article

Close encounters with DNA

scientific article

Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations ⬇️

scientific article published on October 19, 2012

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

scientific article published on 28 August 2020

Curvature generation and pressure profile modulation in membrane by lysolipids: insights from coarse-grained simulations

scientific article published on October 2009

DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles

scientific article published on 01 November 2021

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

scientific article published on 14 March 2016

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

scientific article published on 22 March 2016

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

scientific article published on 16 January 2008

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

scientific article published on 24 February 2016

Hierarchical Self-Assembly of Poly-Pseudorotaxanes into Artificial Microtubules

scientific article published on 29 January 2020

Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

scientific article published on 2 December 2015

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

article

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

scientific article published on 4 May 2016

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

scientific article

Ion Channels Made from a Single Membrane-Spanning DNA Duplex

scientific article

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

scientific article

Large-Conductance Transmembrane Porin Made from DNA Origami

scientific article (publication date: 27 September 2016)

Mechanosensitive channels: insights from continuum-based simulations

scientific article published on 12 September 2008

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

scientific article published on 8 January 2013

Modeling and simulation of ion channels

scientific article

Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating

scientific article published on 9 November 2015

Molecular mechanics of DNA bricks:in situstructure, mechanical properties and ionic conductivity

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

scientific article published on 29 January 2018

NUMERICAL SIMULATION OF NANOINDENTATION AND PATCH CLAMP EXPERIMENTS ON MECHANOSENSITIVE CHANNELS OF LARGE CONDUCTANCE IN ESCHERICHIA COLI

scientific article

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

scientific article published on 16 March 2018

Outperforming nature: synthetic enzyme built from DNA flips lipids of biological membranes at record rates

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

article

Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations

scientific article published on 12 September 2016

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

scientific article published on 01 October 2018

The structure and intermolecular forces of DNA condensates

scientific article published on 15 February 2016

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

scientific article published on 8 January 2013

Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore

scientific article published on 7 April 2016

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