Publications

* : correspondence, + : equal contribution

2021


44. M. Kim, S. Bae, I. Oh, J. Yoo, J. S. Kim*, "Sequence-dependent Twist-bend Coupling in DNA Minicircles",

Nanoscale published online (2021) link


43. S. Bae, J. S. Kim*, "Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle",

J. Chem. Theory Comput. published online (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

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. 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

2010

6. J. S. Kim , I. Szleifer* , Depletion effect on polymers induced by small depleting spheres,

J. Phys. Chem. C , 114 , 20864 (2010) link

5. J. S. Kim , A. Yethiraj* , Crowding effects on association reactions at membranes,

Biophys. J . , 98 , 951 (2010) selected as a Feature Article 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