Publications
* : correspondence, + : equal contribution
2024
50. Y. Song, J. S. Kim*, "Structure and dynamics of double-stranded DNA rotaxanes",
Nanoscale 16, 4317-4324 (2024) link - Feb 28, 2024
49. G. Kim, J. S. Kim*, "Design of a Brownian Ratchet based on repetitive aggregation and dispersion of stimuli-responsive molecules",
J. Chem. Phys. 160, 064908 (2024) link - Feb 14, 2024
2022
48. I. Oh, J. Song, H. R. Hyun, S. H. Lee, J. S. Kim*, "Brownian ratchet for directional nanoparticle transport by repetitive stretch-relaxation of DNA",
Phys. Rev. E, 106, 054117 (2022) link
47. H. R. Hyun+, J. Han+, J. Lim, Y. J. Park, B. Choi, C. Baik*, J. S. Kim*, "Liquid-like properties of cyclopentadienyl complexes of barium: molecular dynamics simulations of nanoscale droplets",
Phys. Chem. Chem. Phys. 24, 15982-15990 (2022) link
46. M. Kim, C. C. Hong, S. Lee, J. S. Kim*, "Dynamics of a DNA minicircle: poloidal rotation and in-plane circular vibration",
Bull. Kor. Chem. Soc. 43, 523-528 (2022), invited for a special issue of "Advances of Physical Chemistry in Korea" link
45. M. Kim*, J. S. Kim, "A model for cascading failures with the probability of failure described as a logistic function",
Sci. Rep. 12, 989 (2022) link
2021
44. M. Kim, S. Bae, I. Oh, J. Yoo, J. S. Kim*, "Sequence-dependent twist-bend coupling in DNA minicircles",
Nanoscale 13, 20186-20196 (2021) link
43. S. Bae, J. S. Kim*, "Potential of mean force for DNA wrapping around a cationic nanoparticle",
J. Chem. Theory Comput. 17, 7952-7961 (2021) link
42. S. Bae, I. Oh, J. Yoo, J. S. Kim*, "Effect of DNA flexibility on complex formation of a cationic nanoparticle with double-stranded DNA",
ACS Omega 6, 18728-18736 (2021) link
2020
41. H. W. Cho+, H. Kim+, B. J. Sung*, J. S. Kim*, "Tracer diffusion in tightly-meshed homogeneous polymer networks: a Brownian dynamics simulation study",
Polymers 12, 2067 (2020) link
40. K. H. Kil, A. Yethiraj*, J. S. Kim*, "Nematic ordering of hard rods under strong confinement in a dense array of nanoposts",
Phys. Rev. E 101, 032705 (2020) link
2019
39. H. J. Lee, U. J. Yang, K. N. Kim, S. Park, K. H. Kil, J. S. Kim, A. M. Wodtke, W. J. Choi*, M. H. Kim*, J. M. Baik*, "Directional Ostwald ripening for producing aligned arrays of nanowires",
Nano Lett. 19, 4306 (2019) link
38. S. Song, S. J. Park, M. Kim, J. S. Kim, B. J. Sung, S. Lee, J.-H. Kim*, J. Sung*, "Transport dynamics of complex fluids",
Proc. Natl. Acad. Sci. U. S. A. 116, 12733 (2019) link
37. S. Kwon, S. Lee, H. W. Cho, J. Kim, J. S. Kim*, B. J.. Sung*, “The breakdown of the local thermal equilibrium approximation for a polymer chain during packaging”,
J. Chem. Phys. 150, 204901 (2019) link
36. S. Park, J. Song, J. S. Kim*, “In silico construction of a flexibility-based DNA Brownian ratchet for directional nanoparticle delivery”,
Science Advances 5, eaav4943 (2019) links to Article; 한국연구재단; 언론보도
35. M. Kim, E. Kim, S. Lee, J. S. Kim*, S. Lee*, “New method for constant-NPT molecular dynamics”,
J. Phys. Chem. A 123, 1689 (2019) link
34. J. Park, M. Seo, E. Jang, H. Kim, J. S. Kim*, S.-J. Park*, “Vesicle-like assemblies of ligand-stabilized nanoparticles with controllable membrane composition and properties”,
Nanoscale 11, 1837 (2019) link
2018
33. J. S. Kim* , “Macromolecular crowding and nanoscale confinement on the structural regulation of chromatins/DNAs”,
Bull. Chem. Soc. Jpn. 91, 1343 (2018) invited as an Award Account link
32. H. Kim+, Y. Kang+, E. Jang*, J. B. Lee*, C. H. Park, M. S. Park, J. S. Kim* , “Monolayer and bilayer structures of mixtures of ceramide IIIb and c16-alkyl glucosides”,
Bull. Kor. Chem. Soc . 39, 982 (2018) link
31. I. Oh, S. Choi, Y. Jung*, J. S. Kim* , “Entropic effect of macromolecular crowding enhances binding between nucleosome clutches in heterochromatin, but not in euchromatin”,
Scientific Reports 8, 5469 (2018) link
30. S. Park, H. Joo, J. S. Kim* , “Directional rolling of positively charged nanoparticles along a flexibility gradient on long DNA molecules”,
Soft Matter 14, 817 (2018) link
2017
29. C. Yu+, M. A. Shoaib+, N. Iqbal, J. S. Kim*, H.-J. Ha*, E. J. Cho*, "Selective ring-opening of N-alkyl pyrrolidines with chloroformates to 4-chlorobutyl carbamates",
J. Org. Chem. 82, 6615 (2017) link
28. H. Joo, J. S. Kim*, “Confinement-driven organization of a histone-complexed DNA molecule in a dense array of nanoposts”,
Nanoscale 9, 6391 (2017) link
27. T. Chatterjee, G.-b. Roh, M. A. Shoaib, C.-H. Suhl, J. S. Kim*, C.-G. Cho*, E. J. Cho*, “Visible-light-induced synthesis of carbazoles by in situ formation of photosensitizing intermediate”,
Org. Lett. 19, 1906 (2017) link
2016
26. Y. Kang, H. Joo, J. S. Kim*, “Collapse-swelling transitions of a thermoresponsive, single poly(N-isopropylacrylamide) chain in water”,
J. Phys. Chem. B, 120, 13184 (2016) link
25. J. Kim, J. Chae, J. S. Kim, S.-H. Goh, Y. Choi*, “Photosensitizer-conjugated tryptophan-containing peptide ligands as new dual-targeted theranostics for cancers”,
Int. J. Pharm, 513, 584 (2016) link
24. Y. Choi, T. Chatterjee, J. Kim, J. S. Kim, E. J. Cho*, “Synthesis of cyclopenta-fused polycyclic aromatic hydrocarbons utilizing aryl-substituted anilines”,
Org. Biomol. Chem., 14, 6804 (2016) link
23. Y. Choi, C. Yu, J. S. Kim, E. J. Cho*, “Visible-light-induced arylthiofluoroalkylations of unactivated heteroatomatics and alkenes”,
Org. Lett., 18, 3246 (2016) link
22. J. Jung, E. Jang, M. A. Shoaib, K. Jo*, J. S. Kim*, “Droplet formation and growth inside a polymer network: A molecular dynamics simulation study”,
J. Chem. Phys., 144, 134502 (2016) link
2015
21. H. Joo, J. S. Kim* , “Confinement and partitioning of a single polymer chain in a dense array of nanoposts”,
Soft Matter, 11, 8262 (2015) link
20. I. Oh, S. Choi, Y. Jung*, J. S. Kim* , “Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications to the nuclear body formation near chromosomes”,
Soft Matter, 11, 6450 (2015) link
19. J. Jung, J. Lee, J. S. Kim* , “Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dyamics and Brownian dynamics simulations”,
Chem. Phys., 449, 1 (2015) link
2014
18. I. Oh, S. Choi, Y. Jung*, J. S. Kim* , “Unusual size-dependence of effective interactions between collapsed polymers in crowded environments”,
Soft Matter, 10, 9098 (2014) link
17. S. Shin, H.-I. Kang, J. S. Kim* , H. Kang*, “Phase transitions of amorphous solid acetone in confined geometry investigated by reflection absorption infrared spectroscopy”,
J. Phys. Chem. B, 118, 13349 (2014), in a special issue on Physics and Chemistry of Ice link
16. S. Choi+ , E. Jang+ , J. S. Kim* , "In-layer stacking competition during ice growth",
J. Chem. Phys., 140, 014701 (2014) link
15. J. S. Kim* , I. Szleifer, "Nuclear compartmentalization in a crowded nuclear environment: insights from computer simulations",
Int. Rev. Cell Mol. Biol., 307, 73 (2014) link
2013
14. C. Y. Son, J. Kim, J.-H. Kim, J. S. Kim , S. Lee* , "An accurate expression for the rates of diffusion-influenced bimolecular reactions with long-range reactivity",
J. Chem. Phys. , 138 , 164123 (2013) link
2012
13. M. Seo + , E. Jang + , K. Kim, S. Choi, J. S. Kim* , "Understanding anisotropic growth behavior of hexagonal ice on a molecular scale: a molecular dynamics simulation study",
J. Chem. Phys. , 137 , 154503 (2012) link
12 . J. S. Kim , Z. Wu, A. R. Morrow, A. Yethiraj, A. Yethiraj* , "Self-diffusion and viscosity in electrolyte solutions",
J. Phys. Chem. B , 116 , 12007-12013 (2012) link
11. E. J. Cho, J. S. Kim* , "Crowding effects on the formation and maintenance of nuclear bodies: insights from molecular dynamics simulations of simple spherical model particles",
Biophys. J. , 103 , 424-433 (2012) link
10. E. J. Cho, J. S. Kim* , "Crowding-induced phase separation of Lennard-Jones particles: implications to nuclear structures in a biological cell",
J. Phys. Chem. B , 116 , 3874-3879 (2012) link
2011
9. J. S. Kim , V. Backman, I. Szleifer*, Crowding-induced structural alterations of random-loop chromosome model,
Phys. Rev. Lett. , 106 , 168102 (2011) link
8. J. S. Kim , P. Pradhan, V. Backman, I. Szleifer* , Influence of chromosome density variations on the increase in nuclear order strength in carcinogenesis,
Phys. Biol. , 8 , 015004 (2011), in special issue on physical oncology link
7. J. S. Kim , A. Yethiraj* , Crowding effects on protein association: The effect of interactions between crowding agents,
J. Phys. Chem. B , 115 , 347 (2011) link
2009
4. J. S. Kim , S. Damodaran, A. Yethiraj* , Retardation of ice crystallization by short peptides,
J. Phys. Chem. A , 113 , 4403 (2009) link
3. J. S. Kim , A. Yethiraj* , The effect of macromolecular crowding on reaction rates: a computational and theoretical study,
Biophys. J. , 96 , 1333 (2009) link
2008
2. J. S. Kim , A. Yethiraj* , The effect of salt on the melting of ice : a molecular dynamics simulation study,
J. Chem. Phys. , 129 , 124504 (2008) link
1. J. S. Kim, A. Yethiraj* , A diffusive anomaly of water in aqueous sodium chloride solutions at low temperatures,
J. Phys. Chem. B , 112 , 1729 (2008) link