* : correspondence, + : equal contribution 


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


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 


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 


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 


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



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


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



 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



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



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



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



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 (2012link   


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   



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 (2011link   



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    



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  



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