1. "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
2. "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.
3. "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
4. "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
5. "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
6. "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
7. "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
8. "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
9. "Multiple barriers in forced rupture of protein complexes" C. Hyeon & D. Thirumalai J. Chem. Phys. (2012) vol. 137, 055103
10. "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
11. "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
12. (Book Chapter) "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
13. (Review) "Theoretical Perspectives on Protein Folding" D. Thirumalai, E. P. O'Brien, G. Morrison & C. Hyeon Annu. Rev. Biophys. (2010) vol. 39, 159-183
14. "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
15. "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.
16. "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 
17. (Review) "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 
18. "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 
19. "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 

1. "Communication over the network of binary switches regulates the activation of A_2A adenosine receptor" Y. Lee, S. Choi, C. Hyeon PLoS Comp. Biol. (2015) 11(2): e1004044. , movie M1 .
2. "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
3. "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
4. "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
5. "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  ,  .
6. (Review) "Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models" C. Hyeon & D. Thirumalai Nature Communications (2011) vol 2, 487
7. "A structural perspective on the dynamics of kinesin motors" C. Hyeon & J. N. Onuchic Biophys. J. (2011) vol. 101, 2749 , SI
8. "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
9. "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  .
10. "Kinesin's Backsteps under Mechanical Load" C. Hyeon, S. Klumpp & J. N. Onuchic, Phys. Chem. Chem. Phys. (2009) vol. 11, 4899-4910
11. (Book Chpater) "Energy balance amd 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)
12. (Book Chapter) D.L. Pincus, S.S. Cho, C. Hyeon, & D. Thirumalai, "Minimal Models for Proteins 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.
13. (Book Chapter) "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)
14. "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. 
15. "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 
16. "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 
    

   Polymer Physics

1. "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
2. "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
3. "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 
4. "Stretching Homopolymers" G. Morrison, C. Hyeon, N. M. Toan, B. -Y. Ha & D. Thirumalai, Macromolecules (2007) vol. 40, 7343-7353 
5. "Kinetics of interior loop formation in semiflexible chains" C. Hyeon & D. Thirumalai, J. Chem. Phys. (2006) vol. 124, 104905 

    RNA

1. “Sequence-dependent folding landscapes of adenine riboswitch aptamers” J.-C. Lin, C. Hyeon, D. Thirumalai Phys. Chem. Chem. Phys. (2014) vol. 16, 6376
2. "Development and applications of Coarse Grained models for RNA" C. Hyeon, N. A. Denesyuk, D. Thirumalai Israel J. Chem. (2014) vol. 54, 1358-1373
3. "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
4. “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
5. "Generalized Iterative Annealing Model for the action of RNA chaperones" C. Hyeon & D. Thirumalai J. Chem. Phys. (2013) vol. 139, 121924  
6. "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
   
7. (Perspective) "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
8. "Chain Length Determines the Folding Rates of RNA" C. Hyeon & D. Thirumalai Biophys. J. (2012) vol. 102, L11-L13 .
9. "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
10. "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.
11. "Size, Shape, and flexibility of RNA structures" C. Hyeon, R. I. Dima, & D. Thirumalai, J. Chem. Phys. (2006) vol. 125, 194905 
12. "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 
13. "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. 
14. "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
15. (Book Chapter) "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)
16. "Mechanical unfolding of RNA: From hairpins to structures with internal multiloops" C. Hyeon & D. Thirumalai, Biophys. J. (2007) vol. 92, 731-743 
17. "Forced-Unfolding and Force-Quench Refolding of RNA Hairpins" C. Hyeon & D. Thirumalai, Biophys. J. (2006) vol. 90, 3410-3427 
18. "RNA and Protein Folding: Common Themes and Variations" D. Thirumalai & C. Hyeon, Biochemistry (2005) vol. 44, 4957-4970 
19. "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 
20. "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 
21. "Mechanical unfolding of RNA hairpins" C. Hyeon & D. Thirumalai, Proc. Natl. Acad. Sci. USA (2005) vol. 102, 6789-6794  

    Miscellaneous

1. "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 Nature Communications (2013) vol. 4, 1505 SI
2. "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
3. "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 
4. "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