Stretching biomolecules

RNA & Protein folding

Molecular Motors

Single molecule force spectroscopy

Deciphering the energy landscape of biomolecules

Polymer Physics

Allostery
   
    Publications in reverse chronological order / publications by category

  1. "Ultrasensitivity of water exchange kinetics to the size of metal ion" Y. Lee, D. Thirumalai, C. Hyeon. J. Am. Chem. Soc. (Communication) (2017) 139, 12334-12337. , SI
  2. "Physical insight into the thermodynamic uncertainty relation using Brownian motion in tilted periodic potentials" C. Hyeon, W. Hwang, Phys. Rev. E. (2017) 96, 012156
  3. "Heterogeneity in kinesin function" B. J. N Reddy, S. Tripathy, M. Vershinin, M. Tanenbaum, J. Xu, M. Mattson-Hoss, K. Arabi, D. Chapman, T. Doolin, C. Hyeon, S. P. Gross Traffic (2017) 18, 658-671
  4. "Heterogeneous morphology and dynamics of polyelectrolyte brush condensates in trivalent counterion solution" L. Liu, P. A. Pincus, C. Hyeon, Macromolecules (2017) 50, 1579-1588
  5. "Kinetic Model for the Activation of Mammalian Olfactory Receptor" S. Jang, C. Hyeon, J. Phys. Chem. B (2017) 121, 1304-1311 .
  6. "Quantifying the Heat Dissipation from a Molecular Motor's Transport Properties in Nonequilibrium Steady States" W. Hwang, C. Hyeon J. Phys. Chem. Lett. (2017) vol. 8, 250-256 , SI
  7. "Ripping RNA by Force using Gaussian Network Models" C. Hyeon, D. Thirumalai J. Phys. Chem. B (2017) vol. 121, 3515-3522 .
  8. "Decoding Single Molecule Time Traces with Dynamic Disorder" W. Hwang, I. -B. Lee, S. -C. Hong, C. Hyeon PLoS Comp. Biol. (2016) 12(12), e1005286
  9. "Effects of dimethyl sulfoxide on surface water near phospholipid bilayers" Y. Lee, P. A. Pincus, C. Hyeon Biophys. J. (2016) vol. 111, 2481-2491 (Cover Article)   Featured in Biophysical Society Blog
  10. "How are molecular crowding and the spatial organization of a biopolymer interrelated" C. Jeon, C. Hyeon, Y. Jung, B.-Y. Ha Soft Matter (2016) vol. 12, 9786-9796
  11. "Ultraslow water-mediated transmembrane interactions regulate the activation of A2A adenosine receptor" Y. Lee, S. Kim, S. Choi, C. Hyeon Biophys. J. (2016) vol. 111, 1180-1191 , SI Movie 1 Movie 2 Movie 3 Movie 4
  12. "Directly measuring single-molecule heterogeneity using force spectroscopy" M. Hinczewski, C. Hyeon, D. Thirumalai Proc. Natl. Acad. Sci. USA (2016) vo. 113, E3852-E3861 
  13. "Contact statistics highlight distinct organizing principles of RNA and proteins" L. Liu & C. Hyeon Biophys. J. (2016) vol. 110, 2320-2327  , SI , New and Notable Access the recommendation on
                                    F1000Prime
  14. “Confinement-induced glassy dynamics in a model for chromosome organization” H. Kang, Y.-G. Yoon, D. Thirumalai, C. Hyeon Phys. Rev. Lett. (2015) vol. 115, 198102 SM
  15. "Unexpected swelling of stiff DNA in a polydisperse crowded environment" H. Kang, N. M. Toan, C. Hyeon, D. Thirumalai J. Am. Chem. Soc. (2015) vol. 137, 10970-10978
  16. "Deciphering kinetic information from single molecule FRET data that show slow transitions" S. E. Kim, I. -B. Lee, C. Hyeon, S.-C. Hong J. Phys. Chem. B. (2015) vol. 119, 6974–6978
  17. "Spring-loaded unraveling of a single SNARE complex by NSF in one round of ATP turnover" J.-K. Ryu, D. Min, S.-H. Rah, S. J. Kim, Y. Park, H. Kim, C. Hyeon, H. M. Kim, R. Jahn, T.-Y. Yoon Science (2015) vol. 347, 1485-1489 , SI
  18. "Effects of macromolecular crowding on the collapse of biopolymers" H. Kang, P. A. Pincus, C. Hyeon, D. Thirumalai Phys. Rev. Lett. (2015) vol. 114, 068303  , SI
  19. “Using Simulations and kinetic network models to reveal the dynamics and functions of riboswitches” J.-C. Lin, J. Yoon, C. Hyeon, D. Thirumalai, Methods in Enzymology (2015) 553, 235-258
  20. "Communication over the network of binary switches regulates the activation of A2A adenosine receptor" Y. Lee, S. Choi, C. Hyeon PLoS Comp. Biol. (2015) 11(2): e1004044. , SI , movie M1 .
  21. "Programmed folding of DNA origami structures through single-molecule force control" W. Bae , K. Kim, D. Min, J.-K. Ryu, C. Hyeon, T.-Y. Yoon Nat. Commun (2014) vol. 5, 5654 SI
  22. "Dynamical Transition and Heterogeneous Hydration Dynamics in RNA" J. Yoon, J.-C. Lin, C. Hyeon, D. Thirumalai J. Phys. Chem. B. (2014) vol. 118, 7910-7919
  23. "Destabilization of i-motif by submolar concentrations of a monovalent cation" S. Kim, I.-B. Lee, C. Hyeon, S.-C. Hong J. Phys. Chem. B. (2014) vol. 118, 4753-4760.
  24. "Evidence of disorder in biological molecules from single molecule pulling experiments" C. Hyeon, M. Hinczewski, D. Thirumalai Phys. Rev. Lett. (2014) vol. 112, 138101 SI
  25. "Development and applications of Coarse Grained models for RNA" C. Hyeon, N. A. Denesyuk, D. Thirumalai Israel J. Chem. (2014) vol. 54, 1358-1373
  26. “Sequence-dependent folding landscapes of adenine riboswitch aptamers” J.-C. Lin, C. Hyeon, D. Thirumalai Phys. Chem. Chem. Phys. (2014) vol. 16, 6376
  27. "Mapping the intramolecular signal transduction of G-protein coupled receptors" Y. Lee, S. Choi, & C. Hyeon Proteins: Struct. Func. Bioinfo. (2014) vol. 82, 727-743  SI-I , SI-II
  28. "Generalized Iterative Annealing Model for the action of RNA chaperones" C. Hyeon & D. Thirumalai J. Chem. Phys. (2013) vol. 139, 121924  
  29. "Urea-induced denaturation of preQ1-riboswitch" J. Yoon, D. Thirumalai, C. Hyeon J. Am. Chem. Soc. (2013) vol. 135, 12112-12121 SI Movie 1 , Movie 2 , Movie 3 , Movie 4 , Movie 5 , Movie 5 (detailed) featured in JACS spotlights 
  30. "Real-Time Observation of Multiple Protein-Complex Formation with Single-Molecule FRET " W. Bae, M.-G. Choi, C. Hyeon, Y.-K. Shin, T.-Y. Yoon J. Am. Chem. Soc. (Communication) (2013) vol. 135, 10254-10257 SI
  31. "Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism" D. Min, K. Kim, C. Hyeon, Y. H. Cho, Y.-K. Shin, T.-Y. Yoon Nat. Commun. (2013) vol. 4, 1705 SI
  32. "Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signaling dynamics" H.-W. Lee, T. Kyung, J. Yoo, T. Kim, C. Chung, J.Y. Ryu, H. Lee, K. Park, S. Lee, W.D. Jones, D.-S. Lim, C. Hyeon, W.D. Heo, T.-Y. Yoon Nat. Commun. (2013) vol. 4, 1505 SI
  33. "RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity" J.-C. Lin, C. Hyeon, D. Thirumalai J. Phys. Chem. Lett. (2012) vol. 3, 3616-3625
  34. "The origin of minus-end directionality and mechanochemistry of Ncd motors" B. Jana, C. Hyeon, J. N. Onuchic PLoS Comp. Biol. (2012) 8(11): e1002783   
  35. "Hidden Complexity in the Isomerization Dynamics of Holliday Junctions" C. Hyeon, J. Lee, J. Yoon, S. Hohng, D. Thirumalai Nature Chemistry (2012) vol. 4, 907-914 SI
  36. "Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension" W. K. Kim,  C. Hyeon & W. Sung Proc. Natl. Acad. Sci. USA. (2012) vol. 109, 14410-14415
  37. "Multiple barriers in forced rupture of protein complexes" C. Hyeon & D. Thirumalai J. Chem. Phys. (2012) vol. 137, 055103
  38. "Efficient Functional Delivery of siRNA using Mesoporous Silica Nanoparticles with Ultralarge Pores" H.-K. Na, M.-H. Kim, K. Park, S.-R. Ryoo, K.E. Lee, H. Jeon, R. Ryoo, C. Hyeon, D.-H. Min, Small (2012) vol. 8, 1752-1761 , SI
  39. "Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape" C. Hyeon Bull. Korean Chem. Soc. - K. J. Shin Festshrift (2012) vol. 33, 897-900 http://arxiv.org/abs/1201.2449
  40. "Chain Length Determines the Folding Rates of RNA" C. Hyeon & D. Thirumalai Biophys. J. (2012) vol. 102, L11-L13 .
  41. "A structural perspective on the dynamics of kinesin motors" C. Hyeon & J. N. Onuchic Biophys. J. (2011) vol. 101, 2749 , SI
  42. "Link between Allosteric Signal Transduction and Functional Dynamics in a Multisubunit Enzyme: S-Adenosylhomocysteine Hydrolase" Y. Lee, L.S. Jeong, S. Choi, & C. Hyeon J. Am. Chem. Soc.  (2011) vol. 133, 19807-19815  ,  SI , Movie  .
  43. "Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models" C. Hyeon & D. Thirumalai Nat. Commun. (2011) vol 2, 487
  44. "Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments" G. Morrison, C. Hyeon, M. Hinczewski & D. Thirumalai Phys. Rev. Lett. (2011) vol. 106, 138102
  45. "Theoretical Perspectives on Protein Folding" D. Thirumalai, E. P. O'Brien, G. Morrison & C. Hyeon Annu. Rev. Biophys. (2010) vol. 39, 159-183
  46. "Dynamic Ca2+-Dependent Stimulation of Vesicle Fusion by Membrane-Anchored Synaptotagmin 1" H. -K. Lee, Y. Yang, Z. Su, C. Hyeon, T. -S. Lee, H. -W. Lee, D. -H. Kweon, Y. -K. Shin & T. -Y. Yoon Science (2010) vol. 328, 760-763 , SOM
  47. "Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases" U. D. Priyakumar, C. Hyeon, D. Thirumalai & A. D. MacKerell Jr. J. Am. Chem. Soc. (Communication) (2009) vol.131, 17759-17761 , Supporting Info   featured in C&EN news
  48. "Refolding dynamics of stretched biopolymers upon force-quench" C. Hyeon, G. Morrison, D. L. Pincus, & D. Thirumalai, Proc. Natl. Acad. Sci. USA. (2009) vol. 106, 20288-20293 , Supporting Info
  49. "Metal Ion Dependence of Cooperative Collapse Transitions in RNA" S. Moghaddam, G. Caliskan, S. Chauhan, C. Hyeon, R. M. Briber, D. Thirumalai & S. A. Woodson, J.  Mol. Biol. (2009) vol. 393, 753-764
  50. "Kinesin's Backsteps under Mechanical Load" C. Hyeon, S. Klumpp & J. N. Onuchic, Phys. Chem. Chem. Phys. (2009) vol. 11, 4899-4910
  51. "Ligand-induced global transition in the catalytic domain of protein kinase A" C. Hyeon, P. A. Jennings, J. A. Adams & J. N. Onuchic, Proc. Natl. Acad. Sci. USA. (2009) vol. 106, 3023-3028,  Supporting  info , Movie  .
  52. "Force dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes" C. Hyeon, G. Morrison & D. Thirumalai, Proc. Natl. Acad. Sci. USA. (2008) vol. 105, 9604-9609 ,  Supporting  info.
  53. "Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the stability of RNA hairpins" D. L. Pincus, C. Hyeon & D. Thirumalai, J. Am. Chem. Soc. (2008) vol. 130, 7364-7372 ,  Supporting  info   featured in JACSβ
  54. "Kinetics of loop formation in polymer chains" N. M. Toan, G. Morrison, C. Hyeon & D. Thirumalai, J. Phys. Chem. B (2008) vol. 112, 6094-6106 
  55. "Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins" C. Hyeon & D. Thirumalai, J. Am. Chem. Soc. (Communication) (2008) vol. 130, 1538-1539  Supporting Info. 
  56. "Revealing the bifurcation in the unfolding pathways of GFP using single molecule experiments and simulations" M. Michkler, R. I. Dima, H. Dietz, C. Hyeon, D. Thirumalai & M. Rief Proc. Natl. Acad. Sci. USA. (2007) vol. 104, 20268-20273 
  57. "Mechanical control of the directional stepping dynamics of the kinesin motor" C. Hyeon & J. N. Onuchic, Proc. Natl. Acad. Sci. USA. (2007) vol. 104, 17382-17387 , Supporting Info. 
  58. "Stretching Homopolymers" G. Morrison, C. Hyeon, N. M. Toan, B. -Y. Ha & D. Thirumalai, Macromolecules (2007) vol. 40, 7343-7353 
  59. "Charge density of divalent metal cations determines RNA stability" E. Koculi, C. Hyeon, D. Thirumalai, & S. A. Woodson, J. Am. Chem. Soc. (2007) vol. 129, 2676-2682 
  60. "Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments" C. Hyeon & D. Thirumalai, J. Phys.:Condens. Matter (2007) vol. 19, 113101 
  61. "Internal strain regulates the nucleotide binding site of the kinesin leading head" C. Hyeon & J. N. Onuchic, Proc. Natl. Acad. Sci. USA (2007) vol. 104, 2175-2180 , Supporting Info. , SI Fig.6 , SI Fig.7 , SI Fig.8 , SI Fig.9 
  62. "Mechanical unfolding of RNA: From hairpins to structures with internal multiloops" C. Hyeon & D. Thirumalai, Biophys. J. (2007) vol. 92, 731-743 
  63. "Dynamics of allosteric transitions in GroEL" C. Hyeon, G.H. Lorimer & D. Thirumalai, Proc. Natl. Acad. Sci. USA (2006) vol. 103, 18939-18944 ,      Supporting materials 
  64. "Size, Shape, and flexibility of RNA structures" C. Hyeon, R. I. Dima, & D. Thirumalai, J. Chem. Phys. (2006) vol. 125, 194905 
  65. "Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins" C. Hyeon, R.I. Dima, & D. Thirumalai, Structure (2006) vol. 14, 1633-1645 
  66. "Forced-Unfolding and Force-Quench Refolding of RNA Hairpins" C. Hyeon & D. Thirumalai, Biophys. J. (2006) vol. 90, 3410-3427 
  67. "Kinetics of interior loop formation in semiflexible chains" C. Hyeon & D. Thirumalai, J. Chem. Phys. (2006) vol. 124, 104905 
  68. "Persistence Length Changes Dramatically as RNA Folds" G. Caliskan, C. Hyeon, U. Perez-Salas, B.M. Briber, S.A. Woodson, & D. Thirumalai, Phys. Rev. Lett. (2005) vol. 95, 268303 
  69. "RNA and Protein Folding: Common Themes and Variations" D. Thirumalai & C. Hyeon, Biochemistry (2005) vol. 44, 4957-4970 
  70. "Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures" R.I. Dima, C. Hyeon, and D. Thirumalai, J. Mol. Biol. (2005) vol. 347, 53-69 
  71. "Mechanical unfolding of RNA hairpins" C. Hyeon & D. Thirumalai, Proc. Natl. Acad. Sci. USA (2005) vol. 102, 6789-6794  
  72. "Can energy landscape roughness of proteins and RNA be measured using mechanical unfolding experiments?" C. Hyeon & D. Thirumalai, Proc. Natl. Acad. Sci. USA (2003) vol. 100, 10249-10253 
  73. "One-pot Template Synthesis and Properties of a Molecular Bowl: Dodecaaza Macrotetracycle with mu(3)-Oxo and mu(3)-Hydroxo Tricopper(II) Cores" M. Paik Suh, M.Y. Han, J.H.Lee K.S.Min, & C. Hyeon. J. Am. Chem. Soc. (Communication) (1998) vol. 120, 3819-3820 
  74. "Effects of a quantum-mechanically driven two-state gating mode on the diffusion-influenced bimolecular reactions" Y. Jung, C. Hyeon, S. Shin, & S. Lee, J. Chem. Phys. (1997) vol. 107, 9864  


Book Chapter
  1. "Minimal Models for the Structure and Dynamics of Nucleic Acids" C. Hyeon and D. Thirumalai, Chapter 5 in "Molecular Modeling at the Atomic Scale" edited by Ruhong Zhou (2014) CRC Press.
  2. "Exploring the energy landscape of biopolymers using single-molecule force spectroscopy and molecular simulations" C. Hyeon in Chapter 5 in "Simulations in Nanobiotechnology" edited by K. Eom (2011) Taylor & Francis
  3. "Energy balance and Dynamics of Kinesin Motors" C. Hyeon, & José N. Onuchic in Chapter 1 in "Proteins: Energy, Heat and Signal Flow" edited by D. M. Leitner and J. E. Straub (2009) CRC Press (Part of the book is scanned, available in google book. Follow this web link)
  4. D.L. Pincus, S.S. Cho, C. Hyeon, & D. Thirumalai, "Minimal Models for Protein and RNA: From Folding to Function", Chapter 6 in Progress in Molecular Biology and Translational Science edited by P. Michael Conn (2008) Academic Press, Vol. 84.
  5. "Theory of RNA Folding: From Hairpins to Ribozymes" D. Thirumalai & C. Hyeon, Chapter 2 in Non-Protein Coding RNAs edited by Nils G. Walter, Sarah A. Woodson, and Robert T. Batey (2008) Springer Series in Biophysics, Vol. 13 (Part of the book is scanned in google book. Follow this web link)
  6. "Coarse-Grained Structure-Based Simulations of Proteins and RNA" A. Schug, C. Hyeon, & J. N. Onuchic, Chapter 9 in Coarse-Graining of Condensed Phase and Biomolecular Systems edited by G. A. Voth (2008) CRC Press (Part of the book is scanned in google book. Follow this web link)


Essay

  1. "책장을 정리하며" 고등과학원 20주년 기념 `자연과학자들의 수필집'에 수록 
  2. 생체고분자의 동역학 연구를 통한 생명의 이해 (지식의 지평 2014, 16호 수록)
  3. Phys. Rev. Lett. (2014) 112, 138101 소개 (Physics Plaza, 물리학과 첨단기술, 2014년 7/8월호 48쪽) 
  4. 전산모사를 이용한 생체분자모터 동역학의 이해 (물리학과 첨단기술, May 2011, 27-31)
  5. 열적 요동과 생물물리학 (고등과학원 소식지, "과학의 지평" no.43, 2010)
  6. 생물물리학의 방법론 (한국생물물리학회 Newsletter 제14권 1호 2009.05)


Contact Information : Changbong Hyeon, Professor, School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
+82-2-958-3810 (tel)

© 2010 KIAS Theoretical and Computational Biophysics Group