List of Publications

 

Year 2009

1.        J.-H. Kim, Sangyoub Lee, “A Rigorous Foundation of the Diffusion-influenced Bimolecular Reaction Kinetics ”, J. Chem. Phys. 131, 014503 (2009)

2.        Aeri Kang, J.-H. Kim, Sangyoub Lee, and H. Park, “Diffusion-influenced Reactions Involving a Reactant with Two Active Sites ”, J. Chem. Phys. 130, 094507 (2009)

Before 2009

1.        S. Ko, W. Lee, Sangyoub Lee, and H. Park, “Nanosecond Molecular Dynamics Simulations of Cdc25B and its Complex with a 1,4-Naphthoquinone Inhibitor: Implications for Rational Inhibitor Design”, J. Mol. Graph. Model. 26, 13-19 (2008)

2.        J.-H. Kim, W. Lee, J. Sung, and Sangyoub Lee, “Excluded Volume Effects on the Intrachain Reaction Kinetics”, J. Phys. Chem. B 112, 6250-6258 (2008).

3.        W. Lee, H. Park, and Sangyoub Lee, “Molecular Dynamics Free Energy Simulation Study to Rationalize the Relative Activities of PPARδ Agonists”, Bull. Korean Chem. Soc., 29, 363-371 (2008).

4.        J.-H. Kim and Sangyoub Lee, “Theory of Non-Markovian Rate Processes”, J. Phys. Chem. B 112, 577-584 (2008).

5.        C. Eun, J.-H. Kim, J. Lee, J. H. Bae, Y. R. Lim, Sangyoub Lee, and J. Sung, “Mean First Passage Time for the Contact between the Ends of a Chain Polymer”, J. Phys. Chem. B 111, 10468-10473 (2007).

6.        M. G. Kim, M.-S. Kim, H. Park, Sangyoub Lee, and J. Suh, “Theoretical Analysis and Prediction of Catalysts for Oxidative Decarboxylation of Melanin-Concentrating Hormone”, Bull. Korean Chem. Soc., 28, 1151-1155 (2007).

7.        J.-H. Kim, D. Huh, J. Lee, Sangyoub Lee, J. Sung, K. Seki, and M. Tachiya, “Subdiffusion-Assisted Reaction Kinetics in Disordered Media”, Journal of Physics: Condensed Matter, 19, 065116 (14pp) (2007).

8.        H. Park, J. Lee, and Sangyoub Lee, “Critical Assessment of the Automated AutoDock as a New Docking Tool for Virtual Screening”, PROTEINS: Structure, Function, and Bioinformatics, 65, 549-554 (2006).

9.        J. Uhm, J. Lee, C. Eun, and Sangyoub Lee, “Generalization of Wilemski-Fixman-Weiss decoupling approximation to the case involving multiple sinks of different sizes, shapes, and reactivities”, J. Chem. Phys., 125, 054911 (2006).

10.    J. Uhm, J. Lee, C. Eun, and Sangyoub Lee, “Diffusion-Controlled Reactions Involving a Reactant with Two Reaction Sites: Evaluation of the Utility of Wilemski-Fixman Closure Approximation”, Bull. Korean Chem. Soc., 27, 1181-1185 (2006).

11.    H. Park and Sangyoub Lee, “Role of Solvent Dynamics in Stabilizing the Transition State of RNA Hydrolysis by Hairpin Ribozyme”, Journal of Chemical Theory and Computation, 2, 858-862 (2006).

12.    J. Lee, J. Uhm, W. Lee, Sangyoub Lee, and J. Sung, “Reversible Excited-State Proton Transfer: Effect of the Switching of Interaction Potential by Reaction”, Bull. Korean Chem. Soc., 27, 197-202 (2006).

13.    J. Lee, J. Uhm, W. Lee, Sangyoub Lee, and J. Sung, “Nonequilibrium Distribution Function Theory of Many-Particle Effects in the Reversible Reactions of the Type A+B↔C+B”, Bull. Korean Chem. Soc., 26, 1986-1990 (2005).

14.    D. Huh, J. Lee, and Sangyoub Lee, “Fractional Diffusion Equation Approach to the Anomalous Diffusion on Fractal Lattices”, Bull. Korean Chem. Soc., 26, 1723-1727 (2005).

15.    H. Park, Sangyoub Lee, and J. Suh, “Structural and Dynamical Basis of Broad Substrate Specificity, Catalytic Mechanism, and Inhibition of Cytochrome P450 3A4”, J. Am. Chem. Soc. 127, 13634-13642 (2005).

16.    E.-M. Choi, Y.-H. Yoon, Sangyoub Lee, H. Kang, “Freezing Transition of Interfacial Water at Room Temperature under Electric Fields”, Phys. Rev. Lett., 95, 085701 (2005).

17.    H. Park and Sangyoub Lee, “Free Energy Perturbation Approach to the Critical Assessment of Selective Cyclooxygenase-2 Inhibitors”, J. Computer-Aided Molecular Design  19, 17-31 (2005).

18.    H. Park and Sangyoub Lee, “Prediction of the Mutation-Induced Change in Thermodynamic Stabilities of Membrane Proteins from Free Energy Simulations”, Biophysical Chemistry 114, 191-197 (2005).

19.    P. S. Chae, M.-S. Kim, C.-S. Jeung, S. D. Lee, H. Park, Sangyoub Lee, and J. Suh, “Peptide-Cleaving Catalyst Selective for Peptide Deformylase”, J. Am. Chem. Soc. 127, 2396-2397 (2005).

20.    J.-H. Kim and Sangyoub Lee, “The optimized Rouse–Zimm theory of excluded volume effects on chain dynamics”, J. Chem. Phys., 121, 12640-12649 (2004).

21.    H. Park and Sangyoub Lee, “Homology Modeling, Force Field Design, and Free Energy Simulation Studies to Optimize the Activities of Histone Deacetylase Inhibitors”, J. Computer-Aided Molecular Design  18, 375-388 (2004).

22.    H. Park, M. S. Yeom and Sangyoub Lee, “Loop Flexibility and Solvent Dynamics as Determinants for the Selective Inhibition of Cyclin-Dependent Kinase 4: Comparative Molecular Dynamics Simulation Studies of CDK2 and CDK4”, ChemBioChem 5, 1662-1672 (2004).

23.    J. Lee, S. Yang, J. Kim and Sangyoub Lee, “An efficient molecular dynamics simulation method for calculating the diffusion-influenced reaction rates”, J. Chem. Phys. 120, 7564-7575 (2004).

24.    P. J. Park and Sangyoub Lee, “Diffusion-Controlled Reaction between Polymers and Receptors on Membranes”, J. Korean Phys. Soc. 44, 584-588 (2004).

25.    H. Park and Sangyoub Lee, “Determination of the Active Site Protonation State of b-Secretase from Molecular Dynamics Simulation and Docking Experiment: Implications for Structure-based Inhibitor Design”, J. Am. Chem. Soc. 125, 16416-16422 (2003).

26.    J.-H. Kim and Sangyoub Lee, “Effects of chain-stiffness on the quenching of an excited polymer by small quenchers”, J. Chem. Phys., 119, 11957-11970 (2003).

27.    J. Sung, P. J. Park, J. Lee, W. Lee, J.-H. Kim, and Sangyoub Lee, “Diffusion-influenced kinetics of reactions involving polymers”, Bull. Korean Chem. Soc., 24, 843-852 (2003).

28.    P. J. Park and Sangyoub Lee, “Quenching of an excitation moving on a flexible polymer”, J. Chem. Phys., 118, 1514-1520 (2003).

29.    J. Sung, J. Lee, and Sangyoub Lee, “Theory of intrapolymer excimer-formation kinetics”, J. Chem. Phys., 118, 414-424 (2003).

30.    H. Park, J. Suh, and Sangyoub Lee, “Theoretical evaluation of the electrophilic catalyses in successive enolization and reketonization reactions by Δ5-3-ketosteroid isomerase”, Bull. Korean Chem. Soc., 23, 837-844 (2002).

31.    J. Sung, E. Barkai, R. J. Silbey, and Sangyoub Lee, “Fractional dynamics approach to diffusion-assisted reactions in disordered media” J. Chem. Phys., 116, 2338-2341 (2002).

32.    P. J. Park and Sangyoub Lee, “Diffusion-influenced reversible energy transfer reactions between polymers”, J. Chem. Phys., 115, 9594-9600 (2001).

33.    J. Sung and Sangyoub Lee, “Intrachain fluorescence quenching in a flexible polymer: A theory for frequency-domain fluorometric experiments”, J. Chem. Phys., 115, 9050-9054 (2001).

34.    S. Yang, H. Han, and Sangyoub Lee, “An efficient Brownian dynamics method for evaluating inertial dynamic effects on diffusion-influenced reactions” J. Phys. Chem. B 105, 6017-6024 (2001).

35.    J. Sung, H. Park and Sangyoub Lee, “Green's function approach to nonclassical reaction kinetics in fractal media”, Phys. Rev. Lett., 86, 2463-2466 (2001).

36.    J. Lee, J. Sung and Sangyoub Lee, “Excluded volume effects on the diffusion-influenced reaction: The many-particle kernel approach”, J. Chem. Phys., 113, 8686-8692 (2000).

37.    J.-H. Choi and Sangyoub Lee, “Correlation between the roughness degree of a protein surface and the mobility of solvent molecules on the surface”, J. Chem. Phys., 113, 6325-6329 (2000).

38.    H. Park, J. Suh and Sangyoub Lee, “Ab Initio Studies on the Catalytic Mechanism of Aspartic Proteinases: Nucleophilic versus General Acid/General Base Mechanism”, J. Am. Chem. Soc. 122, 3901-3908 (2000).

39.    J. Sung and Sangyoub Lee, “Relations Among the Modern Theories of Diffusion-Influenced Reactions. II. Reduced Distribution Function Theory versus Modified Integral Encounter Theory”, J. Chem. Phys., 112, 2128-2138 (2000).

40.    J. Sung and Sangyoub Lee, “Relations Among the Modern Theories of Diffusion-Influenced Reactions. I. Reduced Distribution Function Theory versus Memory Function Theory of Yang, Lee, and Shin”, J. Chem. Phys., 111, 10159-10170 (1999).

41.    S. Yang, J. Kim and Sangyoub Lee, “An Efficient Brownian Dynamics Method for Calculating the Time-Dependent Rate Coefficients of Diffusion-Influenced Reactions”, J. Chem. Phys., 111, 10119-10125 (1999).

42.    H. Park, J. Suh and Sangyoub Lee, “Ab Initio Studies of the Intramolecular Amide Hydrolysis in N-Methylmaleamic Acids”, J. Mol. Structure (Theochem), 490, 47-54 (1999).

43.    J. Sung, J. Chi and Sangyoub Lee, “Nonequilibrium Distribution Function Theory of Diffusion-Influenced Reversible Energy-Transfer Reactions”, J. Chem. Phys., 111, 804-815 (1999).

44.    J. Sung and Sangyoub Lee, “Nonequilibrium Distribution Function Formalism for Diffusion-Influenced Bimolecular Reactions: Beyond the Superposition Approximation”, J. Chem. Phys., 111, 796-803 (1999).

45.    H. Park and Sangyoub Lee, “Ab Initio Investigations of the Pyrrole Dimer: A Direct Observation of the p-Facial Hydrogen Bond”, Chem. Phys. Lett. 301, 487-492 (1999).

46.    J. Sung, K. J. Shin and Sangyoub Lee, “Relaxation Kinetics of Diffusion-Influenced Reactions of the Type  Perturbed by Flash Photolysis”, J. Chem. Phys. 109, 9101-9116 (1998).

47.    J.-H. Choi, H. Kim and Sangyoub Lee, “Correlation Dimension as a Measure of Surface Roughness of Globular Protein Molecules”, J. Chem. Phys. 109, 7001-7004 (1998).

48.    E. Lee, C. H. Yoon, T. H. Lee, S. Y. Kim, T. J. Ha, Y.-S. Sung, S.-H. Park, and Sangyoub Lee, “8-Endo Cyclization of (Alkoxycarbonyl)methyl Radicals: Radical Ways for Preparation of Eight-Membered-Ring Lactones”, J. Am. Chem. Soc. 120, 7469-7478 (1998).

49.    H. Park and Sangyoub Lee, “Effect of Multifractalities of Catalyst Surface: A Monte Carlo Study of Catalytic CO Oxidation”, Surf. Sci. 411, 1-9 (1998).

50.    M. Yang, Sangyoub Lee and K. J. Shin, “Kinetic Theory of Bimolecular Reactions in Liquid. III. Reversible Association-Dissociation: ”, J. Chem. Phys. 108, 9069-9085 (1998).

51.    M. Yang, Sangyoub Lee and K. J. Shin, “Kinetic Theory of Bimolecular Reactions in Liquid. II. Reversible Reaction ”, J. Chem. Phys. 108, 8557-8571 (1998).

52.    M. Yang, Sangyoub Lee and K. J. Shin, “Kinetic Theory of Bimolecular Reactions in Liquid. I. Steady-State Fluorescence Quenching Kinetics”, J. Chem. Phys. 108, 117-133 (1998).

53.    Y. Jung, C. Hyeon, S. Shin and Sangyoub Lee, “Effects of a Quantum-Mechanically Driven Two-State Gating Mode on the Diffusion-Influenced Bimolecular Reactions”, J. Chem. Phys. 107, 9864-9877 (1997).

54.    J. Sung, K. J. Shin and Sangyoub Lee, “Many-Particle Effects on the Relaxation Kinetics of Fast Reversible Reactions of the Type ”, J. Chem. Phys. 107, 9418-9436 (1997).

55.    M. Yang, Sangyoub Lee and K. J. Shin, “Power Law Behavior in the Asymptotic Relaxation of Reversible Diffusion-Influenced Reaction  Perturbed by Photolysis”, Phys. Rev. Lett. 79, 3783-3786 (1997).

56.    Y. Jung and Sangyoub Lee, “Excluded Volume Effect on the Diffusion-Influenced Bimolecular Reactions”, J. Phys. Chem. A 101, 5255-5261 (1997).

57.    H. Park, H. Kim and Sangyoub Lee, “Monte Carlo Simulations of Catalytic CO Oxidation on Fractal Surfaces of Dimension between Two and Three”, Surf. Sci., 380, 514-521 (1997).

58.    Sangyoub Lee and J. T. Hynes, “Tunneling Rate Constants for Intramolecular Hydrogen Atom Transfer Reactions in Solution”, J. de Chim. Phys. 93, 1783-1807 (1996).

59.    H. Kim, S. Shin, Sangyoub Lee and K. J. Shin, “Monte Carlo Simulation Study of Recombination Dynamics in Solution”, J. Chem. Phys. 105, 7705-7711 (1996).

60.    J. Kim, Y. Jung, J. Jeon, K. J. Shin and Sangyoub Lee, “Diffusion-Influenced Radical Recombination in the Presence of a Scavenger”, J. Chem. Phys. 104, 5784-5797 (1996).

61.    K. Kwac, S. Shin, Sangyoub Lee and K. J. Shin, “Theoretical Studies of Surface Diffusion: Multidimensional TST and Effect of Surface Vibrations”, Bull. Korean Chem. Soc. 17, 192-198 (1996).

62.    K. Kwac, Sangyoub Lee and K. J. Shin, “Multidimensional Frictional Coupling Effect in the Photoisomerization of trans-Stilbene”, Bull. Korean Chem. Soc. 16, 427-432 (1995).

63.    S. Jang, K. J. Shin and Sangyoub Lee,  "Effects of Excitation Migration and Translational Diffusion in the Luminescence Quenching Dynamics", J. Chem. Phys. 102, 815-827 (1995).

64.    Y. Jung and Sangyoub Lee,  "Equivalence of the Radical Recombination Rate Theories of Waite and Szabo ", Chem. Phys. Lett. 231, 429-438 (1994).

65.    J. Sung, K. J. Shin and Sangyoub Lee,  "Effect of Light Intensity on the Fluorescence Quenching Kinetics Probed by Frequency-Domain Fluorometry", J. Chem. Phys. 101, 7241-7247 (1994).

66.    M. H. Ryu, D. J. Lee, Sangyoub Lee and K. J. Shin, "A Nonlinear Theory for the Oregonator Model with an External Input", Bull. Korean Chem. Soc., 15, 488-496 (1994).

67.    Sangyoub Lee, J.-J. Lee and K. J. Shin, "Theory of Diffusion-Influenced Radical Recombination: Interplay between Geminate and Bulk Recombination", Bull. Korean Chem. Soc., 15, 311-320 (1994).

68.    J. Sung, K. J. Shin and Sangyoub Lee,  "Effects of Static Quenching and Light Pulse Intensity on the Time-Dependent Fluorescence Quenching Kinetics", Chem. Phys. 179, 23-37 (1994).

69.    M. Yang, Sangyoub Lee, S. K. Kim, K. J. Shin, M. H. Ryu, S. H. Lee and D. J. Lee, "A Nonlinear Theory for the Lotka-Volterra Model with an External Input", Bull. Korean Chem. Soc., 13, 560-565 (1992).

70.    J. Sung, K. J. Shin and Sangyoub Lee, "Theory of Diffusion-Influenced Fluorescence Quenching: Effects of Static Quenching On the Stern-Volmer Curve", Chem. Phys., 167, 17-36 (1992).

71.    J. Kim and Sangyoub Lee, "Theory of Diffusion-Influenced Bimolecular Reactions in Solution: Effects of a Stochastic Gating Mode", Bull. Korean Chem. Soc., 13, 398-404 (1992).

72.    M. Yang, Sangyoub Lee, K. J. Shin, K. Y. Choo and D. Lee, "Effects of Light Pulse Intensity and Quencher Concentration on the Time-Dependent Fluorescence Quenching Kinetics", Bull. Korean Chem. Soc., 13, 325-331 (1992).

73.    D. Kim and Sangyoub Lee, "Application of Reaction Path Smoluchowski Equation Formalism to the Photoisomerization of trans-Stilbene", Bull. Korean Chem. Soc., 12, 692-698 (1991).

74.    N. W. Song, K. J. Shin, Sangyoub Lee, K. H. Jung, K. Y. Choo and S. K. Kim, "Infrared Multiphoton Dissociation of CF2HCl: Laser Fluence Dependence and the Effect of Intermolecular Collisions", Bull. Korean Chem. Soc., 12, 652-658 (1991).

75.    M. Yang, Sangyoub Lee, K. J. Shin, K. Y. Choo and D. Lee, "Effects of Light Intensity on the Steady-State Fluorescence Quenching Kinetics", Bull. Korean Chem. Soc., 12, 414-423 (1991).

76.    Sangyoub Lee, M. Yang, K. J. Shin, K. Y. Choo and D. Lee, "Theory of Diffusion-Influenced Fluorescence Quenching: Dependence of the Stern-Volmer Curve on Light Intensity", Chem. Phys., 156, 339-357, (1991).

77.    D. Kim and Sangyoub Lee, "Theory of Multidimensional Barrier Crossing Processes in Highly Viscous Medium: Reaction Path Smoluchowski Equation Approach", Chem. Phys. Lett., 177, 139-145 (1991).

78.    D. Kim and Sangyoub Lee, "A Brownian Dynamics Method for Systems of Nonspherical Brownian Particles", Bull. Korean Chem. Soc., 11, 127-131 (1990).

79.    M. Yang, Sangyoub Lee, Y. S. Kim and K. J. Shin, "Study of Diffusion-Controlled Reactions in Liquids: A Perturbation Series Solution and a Numerical Solution of the Smoluchowski Equation", Bull. Korean Chem. Soc., 10, 529-535 (1989).

80.    D. C. Borgis, Sangyoub Lee and J. T. Hynes, "A Dynamical Theory of Nonadiabatic Proton and Hydrogen Atom Transfer Reaction Rates in Solution", Chem. Phys. Lett., 162, 19-26 (1989).

81.    B. J. Gertner, K. R. Wilson, D. A. Zichi, Sangyoub Lee and J. T. Hynes, "Nonequilibrium Solvation in SN1 and SN2 Reactions in Polar Solvents", Discuss. Faraday Soc., 85, 297-308 (1988).

82.    Sangyoub Lee and J. T. Hynes, "Solution Reaction Path Hamiltonian for Reactions in Polar Solvents. II. Applications", J. Chem. Phys., 88, 6863-6869 (1988).

83.    Sangyoub Lee and J. T. Hynes, "Solution Reaction Path Hamiltonian for Reactions in Polar Solvents. I. Formulation", J. Chem. Phys., 88, 6853-6862 (1988).

84.    Sangyoub Lee and M. Karplus, "Dynamics of Reactions Involving Diffusive Multidimensional Barrier Crossing", J. Phys. Chem., 92, 1075-1086 (1988).

85.    Sangyoub Lee, M. Karplus, D. Bashford and D. Weaver, "Brownian Dynamics Simulation of Protein Folding: A Study of the Diffusion-Collision Model", Biopolymers, 26, 481-506 (1987).

86.    Sangyoub Lee and M. Karplus, "Kinetics of Diffusion-Influenced Bimolecular Reactions in Solution. II. Effects of the Gating Mode and Orientation-Dependent Reactivity", J. Chem. Phys., 86, 1904-1921 (1987).

87.    Sangyoub Lee and M. Karplus, "Kinetics of Diffusion-Influenced Bimolecular Reactions in Solution. I. General Formalism and Relaxation Kinetics of Fast Reversible Reactions", J. Chem. Phys., 86, 1883-1903 (1987); Erratum, ibid., 96, 1663 (1992).

88.    B. J. Gertner, J. P. Bergsma, K. R. Wilson, Sangyoub Lee and J. T. Hynes, "Nonadiabatic Solvation Model for SN2 Reactions in Polar Solvents", J. Chem. Phys., 86, 1377-1386 (1987).

89.    Sangyoub Lee, "Dynamics and Reactions of Macromolecules in Solution", Ph. D. Thesis, Harvard University (1986).

90.    Sangyoub Lee and M. Karplus, "Brownian Dynamics Simulations: Statistical Error of Correlation Functions", J. Chem. Phys., 81, 6106-6118 (1984).

91.    Sangyoub Lee and Y. S. Kim, "N2-N2 Repulsive Interactions Obtained Through a Combining Rule", J. Chem. Phys., 73, 5131-5134 (1980); Erratum, ibid., 74, 4218 (1981).

92.    Sangyoub Lee and Y. S. Kim, "Study of the Ar-N2 Interaction. II. Modification of the Electron Gas Model Potential at Intermediate and Large Distances", J. Chem. Phys., 70, 4856-4863 (1979).

93.    H. Kim and Sangyoub Lee, "A Study of the Cubic Field Splitting Parameter 10Dq by Means of One-Center Expansion of Complex MO", J. Korean Chem. Soc., 22, 67-77 (1978).