Publications

Intro News People Publications Location

pdf HTMLPloetz, E., Ambrose, B., Barth, A., Börner, R., Erichson, F., Kapanidis, A. N., Kim, H. D., Levitus, M., Lohman, T. M., Mazumder, A., Rueda, D. S., Steffen, F. D., Cordes, T., Magennis, S. W., & Lerner, E. (2023). A new twist on PIFE: Photoisomerisation-related fluorescence enhancement. Methods and Applications in Fluorescence.

pdf HTMLKarsai, A., Cassidy, G. J., Rajanala, A. P., Yang, L., Kerimoglu, D., Gumbart, J. C., Kim, H. D., & Goldman, D. I. (2023). Toward a 3D physical model of diffusive polymer chains. Frontiers in Physics.

pdf HTML Hart, D. J., Jeong, J., Gumbart, J. C., & Kim, H. D. (2023). Weak tension accelerates hybridization and dehybridization of short oligonucleotides. Nucleic Acids Research.

pdf HTML Moon, Y., Moon, H., Chang, J., Kim, H. D., Lee, J. H., & Lee, J. (2022). Development of a highly sensitive lateral flow strip device for nucleic acid detection using molecular beacons. Frontiers in Sensors.

pdf HTML Gravina, N. M., Gumbart, J. C., & Kim, H. D. (2021). Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding. The Journal of Physical Chemistry B.

pdf HTML Broadwater, D. W. B., Cook, A. W., & Kim, H. D. (2021). First passage time study of DNA strand displacement. Biophysical Journal. ("New and Notable")

pdf HTML Lerner, E., et al. (2021). FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. ELife.

pdf HTML Garcia, P. D., et al. (2020). Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nature Communications.

pdf HTML Jeong, J., & Kim, H. D. (2020). Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Research.

pdf HTML Jeong, J., & Kim, H. D. (2019). Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking. Physical Review Letters.

pdf HTML Broadwater, D. W. B., Altman, R. B., Blanchard, S. C., & Kim, H. D. (2019). ERASE: A novel surface reconditioning strategy for single-molecule experiments. Nucleic Acids Research.

pdf HTML Wadsworth, G. M., Parikh, R. Y., Choy, J. S., & Kim, H. D. (2017). mRNA detection in budding yeast with single fluorophores. Nucleic Acids Research.

pdf HTML Waters, J. T., Lu, X.-J., Galindo-Murillo, R., Gumbart, J. C., Kim, H. D., Cheatham, T. E., & Harvey, S. C. (2016). Transitions of Double-Stranded DNA Between the A- and B-Forms. The Journal of Physical Chemistry B.

pdf HTML Waters, J. T., Kim, H. D., Gumbart, J. C., Lu, X.-J., & Harvey, S. C. (2016). DNA Scrunching in the Packaging of Viral Genomes. The Journal of Physical Chemistry B.

pdf HTML Waters, J. T., & Kim, H. D. (2016). Force distribution in a semiflexible loop. Physical Review E.

pdf HTML Jeong, J., Le, T. T., & Kim, H. D. (2016). Single-molecule fluorescence studies on DNA looping. Methods.

pdf HTML Broadwater, D. W. B., & Kim, H. D. (2016). The Effect of Basepair Mismatch on DNA Strand Displacement. Biophysical Journal.

pdf HTML Waters, J. T., & Kim, H. D. (2015). Calculation of a fluctuating entropic force by phase space sampling. Physical Review E.

pdf HTML Chang, Y.-W., Fragkopoulos, A. A., Marquez, S. M., Kim, H. D., Angelini, T. E., & Fernandez-Nieves, A. (2015). Biofilm formation in geometries with different surface curvature and oxygen availability. New Journal of Physics.

pdf HTML Le, T. T., & Kim, H. D. (2014). Probing the elastic limit of DNA bending. Nucleic Acids Research.

pdf HTML Lee, T. J., Parikh, R. Y., Weitz, J. S., & Kim, H. D. (2014). Suppression of Expression Between Adjacent Genes Within Heterologous Modules in Yeast. G3: Genes, Genomes, Genetics.

pdf HTML Le, T. T., & Kim, H. D. (2014). Studying DNA Looping by Single-Molecule FRET. JoVE (Journal of Visualized Experiments).

pdf HTML Waters, J. T., & Kim, H. D. (2013). Equilibrium Statistics of a Surface-Pinned Semiflexible Polymer. Macromolecules.

pdf HTML Parikh, R. Y., & Kim, H. D. (2013). The Effect of an Intervening Promoter Nucleosome on Gene Expression. PLOS ONE.

pdf HTML Le, T. T., & Kim, H. D. (2013). Measuring Shape-Dependent Looping Probability of DNA. Biophysical Journal.


Select publications before Kim lab

Kim, H. D., & O'Shea, E. K. (2008). A Quantitative Model of Transcription Factor-Activated Gene Expression. Nature Structural & Molecular Biology.

Kim, H. D., Puglisi, J. D., & Chu, S. (2007). Fluctuations of Transfer RNAs between Classical and Hybrid States. Biophysical Journal.

Kim, H. D., Nienhaus, G. U., Ha, T., Orr, J. W., Williamson, J. R., & Chu, S. (2002). Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proceedings of the National Academy of Sciences.