Publications — Harold Kim

2024

A new twist on PIFE: photoisomerisation-related fluorescence enhancement

Evelyn Ploetz, Benjamin Ambrose, Anders Barth, Richard Börner, Felix Erichson, Achillefs N Kapanidis, Harold D Kim, Marcia Levitus, Timothy M Lohman, Abhishek Mazumder

Methods and Applications in Fluorescence (2024)

2023

Weak tension accelerates hybridization and dehybridization of short oligonucleotides

Derek J Hart, Jiyoun Jeong, James C Gumbart, Harold D Kim

Nucleic Acids Research (2023)

Toward a 3D physical model of diffusive polymer chains

Andras Karsai, Grace Cassidy, Aradhya Rajanala, Lixinhao Yang, Deniz Kerimoglu, JC Gumbart, Harold Kim, and Dan Goldman

Frontiers in Physics (2023)

2022

Development of a highly sensitive lateral flow strip device for nucleic acid detection using molecular beacons

Youngkwang Moon, Hyeokgyun Moon, Junhyuck Chang, Harold D. Kim, Jung Heon Lee, and Jinkee Lee

Frontiers in Sensors (2022)

Fishing on a budget

Gable Wadsworth and Harold D. Kim

Methods in Molecular Biology (2022)

2021

First passage time study of DNA strand displacement

D.W. Bo Broadwater, Alexander W. Cook, and Harold D. Kim

Biophysical Journal (2021)

Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding

Nicholas M. Gravina, James C. Gumbart, and Harold D. Kim

Journal of Physical Chemistry B (2021)

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Eitan Lerner, Harold D. Kim, Olga Boudker, and others

eLife (2021)

2020

Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP

P. Daniela Garcia, Robert W. Leach, Gable M. Wadsworth, Krishna Choudhary, Hua Li, Sharon Aviran, Harold D. Kim, and Virginia A. Zakian

Nature Communications (2020)

Determinants of cyclization-decyclization kinetics of short DNA with sticky ends

Jiyoun Jeong and Harold D. Kim

Nucleic Acids Research (2020)

2019

Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking

Jiyoun Jeong and Harold D. Kim

Physical Review Letters (2019)

ERASE: A novel surface reconditioning strategy for single-molecule experiments

Bo D.W. Broadwater, Roger B. Altman, Scott C. Blanchard, and Harold D. Kim

Nucleic Acids Research (2019)

2017

mRNA detection in budding yeast with single fluorophores

Gable M. Wadsworth, Rasesh Y. Parikh, John S. Choy, and Harold D. Kim

Nucleic Acids Research (2017)

2016

Transitions of Double-Stranded DNA between the A- and B-Forms

James T. Waters, Xiang-Jun Lu, Rodrigo Galindo-Murillo, James C. Gumbart, Harold D. Kim, Thomas E. Cheatham, and Stephen C. Harvey

Journal of Physical Chemistry B (2016)

Single-molecule fluorescence studies on DNA looping

Jiyoun Jeong, Tung T. Le, and Harold D. Kim

Methods (2016)

DNA Scrunching in the Packaging of Viral Genomes

James T. Waters, Harold D. Kim, James C. Gumbart, Xiang-Jun Lu, and Stephen C. Harvey

Journal of Physical Chemistry B (2016)

Force distribution in a semiflexible loop

James T. Waters and Harold D. Kim

Physical Review E (2016)

The Effect of Basepair Mismatch on DNA Strand Displacement

D. W. Bo Broadwater and Harold D. Kim

Biophysical Journal (2016)

2015

Calculation of a fluctuating entropic force by phase space sampling

James T. Waters and Harold D. Kim

Physical Review E (2015)

Biofilm formation in geometries with different surface curvature and oxygen availability

Ya-Wen Chang, Alexandros A. Fragkopoulos, Samantha M. Marquez, Harold D. Kim, Thomas E. Angelini, and Alberto Fernández-Nieves

New Journal of Physics (2015)