Protein Native Fold


About Group
Research Interests
Publications

  Title
Curriculum Vitae
 
  1. "Comparison of Convergence for the Schwinger, Optimized Anomaly-Free and Optimized Minimum-Norm Variational Methods for Potential Scattering", D. Thirumalai and D. G. Truhlar, Chem. Phys. Lett. 70, 330-335 (1980).

2. "Excitation of the Asymmetric Stretch of CO2 by Electron Impact", D. Thirumalai, K. Onda and D. G. Truhlar, J. Phys. B 13, L619-L622 (1980).

3. "Elastic Scattering and Rotational Excitation of a Polyatomic Molecule by Electron Impact: Acetylene", D. Thirumalai, K. Onda and D. G. Truhlar, J. Chem. Phys. 74, 526-534 (1981).

4. "Electron Scattering by CO2: Elastic Scattering, Rotational Excitation and Excitation of the Asymmetric Stretch at 10 eV Impact Energy", D. Thirumalai, K. Onda and D. G. Truhlar, J. Chem. Phys. 4, 6792-6805 (1981).

5. "Improved Calculation of the Cross Section for Excitation of the Asymmetric Stretch of CO2 by Electron Impact", D. Thirumalai and D. G. Truhlar, J. Chem. Phys. 75, 5207-5209 (1981).

6. "Dispersion-Equation Approach to Obtaining Complex Potentials for Electron Scattering", S. M. Valone, D. Thirumalai, D. G. Truhlar, Int. J. Quant. Chem. Symp. 15, 341 (1981).

7. "Full Response Pseudo Channels: A New Method for Converging Coupled-Channel Scattering Calculations: Theory and Examples", D. Thirumalai and D. G. Truhlar, J. Chem. Phys. 76, 385-389 (1982).

8. "Polarization and Absorption Effects in e-He Scattering at 30-400 eV", D. Thirumalai, D. G. Truhlar, M. A. Brandt, R. A. Eades and D. A. Dixon, Phys. Rev. A 25, 2946-2958 (1982).

9. "A Localized Second-Order Optical Potential for Electron Scattering in Terms of Imaginary Frequency Susceptibilities", S. M. Valone, D. G. Truhlar and D. Thirumalai, Phys. Rev. A 25, 3003-3014 (1982).

10. "Application of Variational Matrix Effective Potential Formalism for e-Ne Scattering and Comparisons to Optical Potential Calculations", D. Thirumalai and D. G. Truhlar, Phys. Rev. A 25, 3058-3071 (1982).

11. "Rapid Convergence of V-V Energy Transfer Calculations Using Adiabatic Basis Functions. I. An Accurate Two State Model for Low-Energy Resonant V-V Energy Transfer. II.", D. Thirumalai and D. G. Truhlar, J. Chem. Phys. 76, 5287-5294 (1982).

12. "Energy Dependent Polarization Potential, Dispersion Relation Absorption Potential and Matrix Effective Potential for Electron-Neon Scattering at 10-100 eV", D. Thirumalai and D. G. Truhlar, Phys. Rev. A 26, 793-807 (1982).

13. "Tests of Semiclassical Polarization Approximation foe Electron Scattering by Helium and Neon", D. Thirumalai and D. G. Truhlar, Phys. Rev. A 27, 158-166 (1982).

14. "Electron Scattering by Methane. Elastic Scattering and Rotational Excitation Cross Sections by ab-Initio Potential", N. Abusalbi, R. A. Eades, T. Nam, D. Thirumalai, D. A. Dixon, D. G. Truhlar and M. Dupuis, J. Chem. Phys. 78, 1213-1227 (1983).

15. "Tests of Quasiclassical Trajectory Cross-Correlation Moment Method Against Accurate Quantum Dynamics for V-V Energy Transfer in HF-HF Collisions", D. W. Schwenke, D. Thirumalai, D. G. Truhlar and M. E. Coltrin, J. Chem. Phys. 78, 3078-3083 (1983).

16. "Non-Empirical Model for Imaginary Part of the Optical Potential for Electron Scattering", G. Staszewska, D. W. Schwenke, D. Thirumalai and D. G. Truhlar, J. Phys. B 16, L281-L287 (1983).

17. "On the Calculation of Time Correlation Functions in Quantum Systems: Path Integral Techniques", D. Thirumalai and B. J. Berne, J. Chem. Phys. 79, 5029-5033 (1983).

18. "An Iterative Scheme for the Evaluation of Discretized Path Integrals", D. Thirumalai, E. J. Bruskin and B. J. Berne, J. Chem. Phys. 79, 5063-5069 (1983).

19. "Quasifree Scattering Model for the Imaginary Part of the Optical Potential for Electron Scattering", G. Staszewska, D. W. Schwenke, D. Thirumalai and D. G. Truhlar, Phys. Rev. A 28, 2740-2751 (1983).

20. "Accurate, Smooth, Local, Energy Dependent Optical Potentials for Electron Scattering", D. W. Schwenke, D. Thirumalai and D. G. Truhlar, Phys. Rev. A 28, 3258-3267 (1983).

21. "Rational Fraction Analytic Continuation Method for Complex Resonance Energies in Multidimensional Systems", D. Thirumalai, T. C. Thompson and D. G. Truhlar, J. Chem. Phys. 80, 5864-5865 (1984).

22. "Time Correlation Functions in Quantum Systems", D. Thirumalai and B. J. Berne, J. Chem. Phys. 81, 2512-2513 (1984).

23. "A Path Integral Monte Carlo Study of Liquid Neon and the Quantum Effective Pair Potential", D. Thirumalai, R. W. Hall and B. J. Berne, J. Chem. Phys. 81, 2523-2527 (1984).

24. "Adiabatic and Nonadiabatic Methods for Energies, Lifetimes, and Branching Probabilities of Bimolecular Reactive Collisions", B. C. Garrett, D. W. Schwenke, R. T. Skodje, D. Thirumalai, T. C. Thompson and D. G. Truhlar, A. C. S. Symposia Series 263, 375-400 (1984).

25. "On the Use of Semiclassical Dynamics in Determining Electronic Spectra of Br2 in Ar Matrix", D. Thirumalai, E. J. Bruskin and B. J. Berne, J. Chem. Phys. 83, 230-238 (1985).

26. "Path Integral Methods for Simulating Electronic Spectra", D. Thirumalai and B. J. Berne, Chem. Phys. Lett. 116, 471-473 (1985).

27. "Evaluation of Microcanonical Rate Constants for Bimolecular Reactions by Path Integral< Techniques", D. Thirumalai, B. C. Garrett and B. J. Berne, J. Chem. Phys. 83, 2972-2975 (1985).

28. "Path Integral Monte Carlo Simulations of Electron Localization in Water Clusters", D. Thirumalai, A. Wallqvist and B. J. Berne, J. Stat. Phys. 43, 973-984 (1986).

29. "Effect of Elongational Flow on the Isotropic Nematic Phase Transitions in Rod-like Systems", D. Thirumalai, J. Chem. Phys. 84, 5869-5873 (1986).

30. "Localization of an Electron in Water Clusters", A. Wallqvist, D. Thirumalai and B. J. Berne,< J. Chem. Phys. 85, 1583-1591 (1986).

31. "Structure and Dynamics of Screened Coulomb Colloidal Liquids", R. O. Rosenberg and D. Thirumalai, Phys. Rev. A 33, 4473-4476 (1986) (Rapid Communication).

32. "Lifshitz Tails in a Spatially Correlated Random Potential", D. Thirumalai, J. Phys. C 19, L397-L401 (1986).

33. "On the Simulation of Quantum Systems: Path Integral Methods", B. J. Berne and D. Thirumalai, Ann. Rev. Phys. Chem. 37, 401-424 (1986).

34. "On the Use of Dispersion Relations in Obtaining Local Optical Model Potential for Electron Scattering", D. Thirumalai, G. Staszewska, and D. G. Truhlar, Comm. At. Mol. Phys. 20, 217-243 (1987).

35. "Flow Induced Transitions in Smectic Liquid Crystals", C. A. Condat and D. Thirumalai, J. Chem. Phys. 86, 4548-4554 (1987).

36. "Relaxation of Anisotropic Correlations in (Two Component) Supercooled Liquids", D. Thirumalai and R. D. Mountain, J. Phys. C 20, L399-L405 (1987).

37. "Path Integral Monte Carlo Study of the Hydrated Electron", A. Wallqvist, D. Thirumalai and B. J. Berne, J. Chem. Phys. 86, 6404-6418 (1987).

38. "Dynamics of the Structural Glass Transition and the p-Spin Interaction Spin Glass Model", T. R. Kirkpatrick and D. Thirumalai, Phys. Rev. Lett. 58, 2091-2094 (1987).

39. "Path Integral Monte Carlo Studies of the Behavior of Excess Electrons in Simple Fluids", D. F. Coker, D. Thirumalai and B. J. Berne, J. Chem. Phys. 86, 5689-5702 (1987).

40. "Molecular Dynamics Study of Glassy and Supercooled States of a Binary Mixture of Soft Spheres", R. D. Mountain and D. Thirumalai, Phys. Rev. A 36, 3300-3311 (1987).

41. "Order-Disorder Transition in Colloidal Suspensions", R. O. Rosenberg and D. Thirumalai, Phys. Rev. A 36, 5690-5700 (1987).

42. "p-Spin Interaction Model: Connections with the Structural Glass Problem", T. R. Kirkpatrick and D. Thirumalai, Phys. Rev B 36, 5388-5397 (1987).

43. "A Mean Field Soft Spin Potts Glass Model: Statics and Dynamics", T. R. Kirkpatrick and D. Thirumalai, Phys. Rev. B 37, 5342-5350 (1988).

44. "Isolated Polymer Molecule in a Random Environment", D. Thirumalai, Phys. Rev. A 37, 269-276 (1988).

45. "Freezing of a Colloidal Liquid Subject to Shear Flow", B. Bagchi and D. Thirumalai, Phys. Rev. A 37, 2530-2538 (1988).

46. "Electron Localization by Atomic and Molecular Clusters", in Large Finite Systems, 231-240, eds. J. Jortner and B. Pullman (Reidel Publishing, 1988).

47. "A Comparison Between Dynamical Theories and Metastable States in Regular and Glassy Mean Field Spin Models with Underlying First Order Like Transitions", T. R. Kirkpatrick and D. Thirumalai, Phys. Rev. A 38, 4439-4448 (1988).

48. "Mean Field Potts Glass Model: Initial Condition Effects on Dynamics and Properties of Metastable States", D. Thirumalai and T. R. Kirkpatrick, Phys. Rev. B 38, 4881-4892 (1988).

49. "Random Solutions From a Regular Density Functional Hamiltonian: A Static and Dynamical Theory for the Structural Glass Transition", T. R. Kirkpatrick and D. Thirumalai, J. Phys. A 22, L149-L159 (1989).

50. "Polymer Chains in Porous Media", J. D. Honeycutt, D. Thirumalai and D. K. Klimov, J. Phys. A 22, L169-L175 (1989).

51. "Ergodic Behavior in Supercooled Liquids and in Glasses", D. Thirumalai, R. D. Mountain and T. R. Kirkpatrick, Phys. Rev. A 39, 3563-3574 (1989).

52. "Static Properties of Polymer Chains in Porous Media", J. D. Honeycutt and D. Thirumalai, J. Chem. Phys. 90, 4542-4559 (1989).

53. "Liquid and Crystalline States of Monodisperse Charged Colloidal Particles", D. Thirumalai, J. Phys. Chem. 93. 5637-5644 (1989).

54. "Scaling and Droplet Notions for the Dynamics of Viscous Liquids Near an Ideal Glassy State", T. R. Kirkpatrick, D. Thirumalai and P. G. Wolynes, Phys. Rev. A 40, 1045-1054 (1989).

55. "Liquid, Crystalline and Glassy States of Binary Charged Colloidal Suspensions", R. O. Rosenberg, D. Thirumalai and R. D. Mountain, J. Phys. Condensed Matter 1, 2109-2114 (1989).

56. "Probes of Equipartition in Nonlinear Hamiltonian Systems", D. Thirumalai and R. D. Mountain, J. Stat. Phys. 57, 789-801 (1989). 

57. "Infinite Range Ising Spin Glass in a Transverse Field", D. Thirumalai, Q. Li and T. R. Kirkpatrick, J. Phys. A 22, 3339-3349 (1989).

58. "Measures of Effective Ergodic Convergence in Liquids", R. D. Mountain and D. Thirumalai, J. Phys. Chem. 93, 6975-6979 (1989).

59. "Dynamical Aspects of Anisotropic Correlations in Supercooled Liquids", R. D. Mountain and D. Thirumalai, J. Chem. Phys. 92, 6116-6122 (1990). 

60. "Metastability of the Folded States of Globular Proteins", J. D. Honeycutt and D. Thirumalai,< Proc. Natl. Acad. Sci. 87, 3526-3529 (1990).

61. "Variational Theories for Localized States of an Excess Electron in Fluids", M. R. Shaw and D. Thirumalai, J. Chem. Phys. 93, 3460-3470 (1990).

62. "Ergodic Convergences in Liquids and Glasses", R. D. Mountain and D. Thirumalai, Int. J. Mod. Phys. C 1, 77-89 (1990).

63. "1/p Expansions for p-Spin Interaction Model in a Transverse Field", V. Dobrosavljevic and D. Thirumalai, J. Phys. A 23, L767-L774 (1990).

64. "Ergodic Convergence Properties of Supercooled Liquids and Glasses", D. Thirumalai and R. D. Mountain, Phys. Rev. A 42, 4574-4587 (1990).

65. "Influence of Optimal Cavity Shapes on the Size of Polymer Molecules in Random Media", J. D. Honeycutt and D. Thirumalai, J. Chem. Phys. 93, 6851-6858 (1990).

66. "Drag Reduction in Turbulent Flows by Polymers", J. K. Bhattacharjee and D. Thirumalai, Phys. Rev. Lett. 67, 196-199 (1991).

67. "Ergodic Measures for the Simulation of Dielectric Properties of Water", R. D. Mountain and D. Thirumalai, Comp. Phys. Comm. 62, 352-359 (1991).

68. "Methods for Simulating Time Correlation Functions in Quantum Systems", D. Thirumalai and B. J. Berne, Comp. Phys. Comm. 63, 415-426 (1991).

69. "Free Polymer in a Colloidal Solution", M. R. Shaw and D. Thirumalai, Phys. Rev. A 44, R4797-R4800 (1991).

70. "Topologically Entangled Polymers", D. Thirumalai, Theor. Chem. Acta. 82, 407-417 (1992).

71. "The Nature of Folded States of Globular Proteins", J. D. Honeycutt and D. Thirumalai, Biopolymers 32, 695-709 (1992).

72. "Ergodicity and Activated Dynamics in Supercooled Liquids", R. D. Mountain and D. Thirumalai, Phys. Rev. A 45, R3380-R3383 (1992).

73. "Loss in Ergodicity in Supercooled Liquids", R. D. Mountain and D. Thirumalai, "Slow Dynamics in Condensed Matter", edited by K. Kawazaki, T. Kawakatsu, and M. Tokuyama, AIP Conference Proceedings, 256, 165-172 (1992).

74. "Folding Kinetics of Proteins: A Model Study", Z. Guo, D. Thirumalai and J. D. Honeycutt, J. Chem. Phys. 97, 525-535 (1992).

75. "Conformations of Polyelectrolyte Chain", B.-Y. Ha and D. Thirumalai, Phys. Rev. A 46, R3012-R3015 (1992).

76. "Theoretical Probes of Conformational Fluctuations in Proteins with Applications to S. Peptide and RNase A/3' - UMP Enzyme/Product Complex", J. E. Straub and D. Thirumalai, Proteins: Structure, Function, and Genetics 15, 360-373 (1993).

77. "Kinetics and Thermodynamics of Folding in Model Proteins", C. J. Camacho and D. Thirumalai, Proc. Natl. Acad. Sci. 90, 6369-6372 (1993).

78. "Exploring the Energy Landscape in Proteins", J. E. Straub and D. Thirumalai, Proc. Natl. Acad. Sci. (USA) 90, 809-813 (1993).

79. "Relationship Between the Fluctuation Metric and the Non-ergodicity Parameter: Incoherent Scattering Function", R. D. Mountain and D. Thirumalai, Physica A 192, 543-549 (1993).

80. "Activated Dynamics, Loss of Ergodicity, and Transport in Supercooled Liquids", D. Thirumalai and R. D. Mountain, Phys. Rev. E 47, 479-489 (1993).

81. "Minimum Energy Compact Structures of Random Sequences of Heteropolymers", Phys. Rev. Lett. 71, 2505-2508 (1993).

82. "Dynamics in Rugged Energy Landscapes with Applications to the S-peptide and Ribonuclease A", J. E. Straub, A. B. Rashkin, and D. Thirumalai, J. Am. Chem. Soc. 116, 2049-2063 (1994).

83. "Rotational Relaxation of a Spherocylinder and a Semirigid Molecule in Concentrated Solutions", D. Thirumalai, J. Phys. Chem. 98, 9265-9269 (1994).

84. "Theoretical Perspectives on in vitro and in vivo Protein Folding", D. Thirumalai, in Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, edited by S. Doniach p. 115-134, (Plenum Press, NY, 1994).

85. "Quantitative Measure of Efficiency of Monte Carlo Simulations", R. D. Mountain and D. Thirumalai, Physica A 210, 453-460 (1994).

86. "Theoretical Predictions of Folding Pathways Using the Proximity Rule with Applications to BPTI", C. J. Camacho and D. Thirumalai, Proc. Nat'l. Acad. Sci. 92, 1277 (1995).

87. "Nucleation Mechanism for Protein Folding and Theoretical Predictions for Hydrogen-Exchange Labelling Experiments", D. Thirumalai and Z. Guo, Biopolymers (Research Communications 37, 137-140 (1995)).

88. "Modelling Disulfide Bonds in Globular Proteins: Entropic Barriers and Pathways", C. J. Camacho and D. Thirumalai, Proteins: Structure, Function and Genetics, 22. 28-40 (1995).

89. "Kinetics of Protein Folding: Nucleation Mechanism, Time Scales, and Pathways", Z. Guo and D. Thirumalai, Biopolymers, 36, 83-102 (1995).

90. "Electrostatic Persistence Length of a Polyelectrolyte Chain", B. Ha and D. Thirumalai, Macromolecules 28, 577-581 (1995).

91. "The Cavity Approach to Metastable Glassy States Near Random First Order Phase Transition", T. R. Kirkpatrick and D. Thirumalai, J. Physique I 5, 771-786 (1995).

92. "Are Disordered Spin Models Relevant for the Structural Glass Problem?", T. R. Kirkpatrick and D. Thirumalai, Transp. Theory and Stat. Mech., 24 927-945 (1995).

93. "From Minimal Models to Proteins: Time Scales for Protein Folding Kinetics", D. Thirumalai, J. Physique (Paris), 5, 1457-1467 (1995).

94. "Navigating the Folding Routes", P. G. Wolynes, J. Onuchic, and D. Thirumalai, Science, 267, 1619-1620 (1995).

95. "A Mean Field Model for Semiflexible Chains", B. Y. Ha and D. Thirumalai, J. Chem. Phys., 103, 9408-9412 (1995).

96. "Energy Landscape and Folding Mechanisms in Proteins", Z. Guo and D. Thirumalai, In Protein Folds: a distance based approach edited by H. Bohr and S. Brunak (CRC Press, Boca Raton, FL, 1995) 233-239.

97. "Analytical Theories of Protein Folding", T. Garel, H. Orland, and D. Thirumalai, in New Developments in Theoretical Studies of Protein Folding edited by R. Elber (World Scientific, in press, 1996) pp. 197-268.

98. "Internal Constraints Induce Localization in an Isolated Polymer Molecule", J. D. Bryngelson and D. Thirumalai, Phys. Rev. Lett. 76, 542-545 (1996).

99. "A Criterion That Determines the Foldability of Protein", D. Klimov and D. Thirumalai, Phys. Rev. Lett. 76, 4070-4073 (1996).

100. "Kinetics of Folding of Proteins and RNA", D. Thirumalai and S. A. Woodson, Acc. Chem. Res. 29, 433-439 (1996).

101. "Factors Governing the Foldability of Proteins", D. K. Klimov and D. Thirumalai, Proteins: Structure, Function, and Genetics, 26, 411-441 (1996).

102. "Energy Landscape Perspective of in Vitro and in Vivo Protein Folding", D. Thirumalai, J. de Physique I 6, 51-53 (1996).

103 "Dynamics of Random Hydrophobic-Hydrophilic Copolymers with Implications for Protein Folding", D. Thirumalai, V. Ashwin, and J. K. Bhattacharjee, Phys. Rev. Lett. 77, 5385-5388 (1996).

104. "Kinetics and Thermodynamics of Folding of a de novo Designed four Helix Bundle", Z. Guo and D. Thirumalai, J. Mol. Biol., 263, 323-343 (1996).

105. "Denaturants Can Accelerate Folding in a Class of Globular Proteins", C. J. Camacho and D. Thirumalai, Protein Science, 5, 1826-1832 (1996).

106. "Polymer Induced Drag Reduction in Turbulent Flows", D. Thirumalai and J. K. Bhattacharjee, Phys. Rev. E, 53, 546-551 (1996).

107. "A Criterion that Determines Fast Folding of Proteins: A Model Study", C. J. Camacho and D. Thirumalai, Europhys. Lett., 35, 627-632 (1996).

108. "Chaperonins-Facilitated Protein Folding: Optimization of Rate and Yield by an Iterative Annealing Mechanism", M. J. Todd, G. H. Lorimer, and D. Thirumalai, Proc. Natl. Acad. Sci. (USA), 93, 4030-4075 (1996).

109. "Protein Folding Kinetics: Time Scales, Pathways, and Energy Landscapes in Terms of Sequence-Dependent Properties", T. Veitshans, D. K. Klimov and D. Thirumalai, Folding & Design, 2, 1-22 (1997).

110. "Shapes of Confined Polymer Chains", C. Cordeiro, M. Molisana, and D. Thirumalai, J. Phys. II (France) 7, 433-447 (1997).

111. "Persistence Length of Intrinsically Stiff Polyampholyte Chain", B. Y. Ha and D. Thirumalai, J. Phys. II (France)7, 887-902 (1997).

112. "A Kinetic Model for Chaperonin Assisted Folding of Protein", H. Orland and D. Thirumalai, J. Phys. I (France) 7, 553-560 (1997).

113. "Semiflexible Chains Under Tension", B. Y. Ha and D. Thirumalai, J. Chem. Phys.106, 4243-4247 (1997).

114. "Viscosity Dependence of Folding Rates of Protein", D. K. Klimov and D. Thirumalai, Phys. Rev. Lett., 79, 317-320 (1997).

115. "Kinetic Partitioning Mechanism as a Unifying Theme in the Folding of Biomolecules", D. Thirumalai, D. K. Klimov, and S. A. Woodson, Theoretical Chemistry Accounts, 1, 23-30 (1997).

116. "Folding of RNA Involves Parallel Pathways", J. Pan, D. Thirumalai, and S. A. Woodson, J. Mol. Biol., 273, 7-13 (1997).

117. "Kinetics of Peptide Folding: Computer Simulations of SYPFDU and Peptide Variants in Water", D. Mohanty, R. Elber, D. Thirumalai, D. Beglov, and B. Roux, J. Mol. Biol., 272, 423-442 (1997).

118. "The Nucleation-Collapse Mechanism in Protein Folding: Evidence for the Non-Uniqueness of the Folding Nucleus", Zhuyan Guo and D. Thirumalai, Folding & Design, 2, 277-341 (1997).

119. "Thermodynamic Stability of Folded Proteins Against Mutations", H. J. Bussemaker, D. Thirumalai, and J. K. Bhattacharjee, Phys. Rev. Lett., 79, 3530-3533 (1997).

120. "Hydrophobic Interactions in Aqueous Urea Solutions with Implications for Mechanisms of Protein Denaturation", A. Wallqvist, D. G. Covell, and D. Thirumalai, J. Am. Chem. Soc., 120, 427-428 (1998).

121. "Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins", D. K. Klimov and D. Thirumalai, Folding & Design, 3, 127-139 (1998).

122. "Exploring the Folding Mechanisms in Proteins Using Lattice Models", D. Thirumalai, D. K. Klimov, and M. R. Betancourt in Monte Carlo Approach to Biopolymers and Protein Folding edited by P. Grasssberger, G. J. Barkema and H. Nadler (World Scientific),19-28 (1998).

123. "Hydration for Series of Hydrocarbons", R. D. Mountain and D. Thirumalai, Proc. Natl. Acad. Sci., (USA) 95, 8436-8440 (1998).

124. "Virtual Atom Representation of Hydrogen Bonds in Minimal Off-lattice models of ?-Helices: Effect on Stability, Cooperativity, and Kinetics", D. K. Klimov, M. R. Betancourt, and D. Thirumalai, Folding & Design, 3, 481-496 (1998).

125. "Fishing for Folding Nuclei in Lattice Models and Proteins", D. Thirumalai and D. K. Klimov, Folding & Design, 3, R112-R118 (1998).

126. "Native Secondary Structure Formation in RNA may be Slave to Tertiary Folding", D. Thirumalai, Proc. Natl. Acad. Sci. 95, 11506-11508 (1998).

127. "Statistical Mechanics of Stiff Chains", D. Thirumalai and B.-Y. Ha, in Theoretical and Mathematical Methods in Polymer Research edited by A. Y. Grosberg (Academic Press, New York), 1-35, (1998).

128. "Lattice Models for Proteins Reveal Multiple Folding Nuclei for Nucleation-Collapse< Mechanism", D. K. Klimov and D. Thirumalai, J. Mol. Biol. 282, 471-492 (1998).

129. "Linking Rates of Folding in Lattice Models of Proteins with Underlying Thermodynamic Characteristics", D. K. Klimov and D. Thirumalai, J. Chem. Phys. 109, 4119-4125 (1998).

130. "Exploring the Kinetic Requirements for Enhancement of Protein Folding Rates in the GroEL Cavity", M. R. Betancourt and D. Thirumalai, J. Mol. Biol. 287, 627-644 (1999).

131. "Pair Potentials for Protein Folding: Choice of Reference States and Sensitivity of Predicted Motive States to Variations in the Interaction Schemes", M. R. Betancourt and D. Thirumalai, Protein Science 8, 361-389 (1999).

132. "Fractal Analysis of Protein Potential Energy Landscapes", D. A. Lidar, D. Thirumalai, R. Elber, and R. B. Gerber, Phys. Rev. E 59, 2231-2243 (1999).

133. "Deciphering the Time Scales and Mechanisms of Protein Folding Using Minimal Off-Lattice Models", D. Thirumalai and D. K. Klimov, Curr. Opin. Struct. Biol. 9, 197-207 (1999).

134. "Magnesium-Dependent Folding of Self-Splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics", Proc. Natl. Acad. Sci. 96, 6149-6154 (1999).

135. "Stretching Single Domain Proteins: Phase diagram and kinetics of force-induced unfolding", D.K. Klimov and D. Thirumalai, Proc. Natl. Acad. Sci. 96, 6166-6170 (1999).

136. "Persistence Length of Flexible Polyelectrolyte Chains;", B. Y. Ha and D. Thirumalai, J. Chem. Phys. 110, 7533-7541 (1999).

137. "Time Scales for the Formation of the Most Probable Contacts in Proteins with Applications to Cytochrome C", D. Thirumalai, J. Phys. Chem. B 103, 608-610 (1999).

138. "Stretching DNA: Effect of electrostatic interactions", N. K. Lee and D. Thirumalai, Europhys. J.B. 12, 599-605 (1999).

139. "Emergence of Stable and Fast Folding Protein Structures", D. Thirumalai and D. K. Klimov, in Stochastic Dynamics and Pattern Formation in Biological and Complex Systems edited by S. Kim, K. J. Lu and W. Song, (American Institute of Physics) 95-111 (2000).

140. "Mechanisms and Kinetics of beta-Hairpin Formation", D. K. Klimov and D. Thirumalai, Proc. Natl. Acad. Sci. 97, 2544-2549 (2000)

141. "Native topology determines force-induced unfolding pathways in globular proteins", D. K. Klimov and D. Thirumalai, Proc. Natl. Acad. Sci. 97, 7254-7259 (2000)

142. "Multiple protein folding nuclei and the transition state ensemble in two state proteins", D. K. Klimov and D. Thirumalai, Proteins Struct. Funct. Gen., 43, 465-475 (2001)

143. "Early events in RNA folding", D. Thirumalai, N. Lee, S.A.. Woodson and D.K. Klimov, Ann. Rev. Phys. Chem. 52,751-762 (2001) 
 

144. "Role of Counterion Condensation in Folding of the Tetrahymena Ribozyme II. Counterion-dependence of Folding Kinetics", S.L. Heilman-Miller, J. Pan, D. Thirumalai and S.A. Woodson J. Mol. Biol. 309, 57-68 (2001)

145. "Protein threading using novel inter-residue contact potentials" Straub JE, Buchete NV, Thirumalai D BIOPHYSICAL JOURNAL 80 (1): 2514 Part 2 JAN 2001 .4000 4.6000

146. "Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations" Heilman-Miller SL, Thirumalai D, Woodson SA JOURNAL OF MOLECULAR BIOLOGY 306 (5): 1157-1166 MAR 9 2001


149.
"Dynamics of collapse of flexible polyelectrolytes in poor solvents"  Lee N, Thirumalai D MACROMOLECULES 34 (10): 3446-3457 MAY 8 2001

150.  "Chaperonin-mediated protein folding" Thirumalai D, Lorimer GH ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 30: 245-269 2001

151. "Lattice model studies of force-induced unfolding of proteins"  Klimov DK, Thirumalai D JOURNAL OF PHYSICAL CHEMISTRY B 105 (28): 6648-6654 JUL 19 2001

152. "Bruce Berne Festschrift - Foreword" Pechukas P, Thirumalai D JOURNAL OF PHYSICAL CHEMISTRY B 105 (28): 6453-6454 JUL 19 2001


153. "Kinetic partitioning mechanism in protein folding."  Thirumalai D JOURNAL OF PHYSICAL CHEMISTRY B 106 (3): 599-609 JAN 24 2002

154. "Is there a unique melting temperature for two-state proteins?" Klimov DK, Thirumalai D JOURNAL OF COMPUTATIONAL CHEMISTRY 23 (1): 161-165 JAN 15 2002

155. "Protein sequence design by energy landscaping" Betancourt MR, Thirumalai D JOURNAL OF PHYSICAL CHEMISTRY B 106 (3): 599-609 JAN 24 2002

156. "Folding pathways of RNA by cation binding" Perez-Salas UA, Krueger S, Woodson S, et al. BIOPHYSICAL JOURNAL 82 (1): 644 Part 2 JAN 2002

157. "Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics" Dima RI, Thirumalai D PROTEIN SCIENCE 11 (5): 1036-1049 MAY 2002

158. "Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in S" Klimov DK, Thirumalai D  JOURNAL OF MOLECULAR BIOLOGY 317 (5): 721-737 APR 12 2002

159. "Simulations of beta-hairpin folding confined to spherical pores using distributed computing" Klimov DK, Newfield D, Thirumalai D PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 99 (12): 8019-8024 JUN 11

160. "Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared t
o E22Q Dutch mutant" Massi F, Klimov D, Thirumalai D, et al. PROTEIN SCIENCE 11 (7): 1639-1647 JUL 2002

161. "Insights into specific problems in protein folding using simple concepts" Thirumalai D, Klimov DK, Dima RI DVANCES IN CHEMICAL PHYSICS 120: 35-76 2002

162. "Dependence of folding rates on protein length" Li MS, Klimov DK, Thirumalai D JOURNAL OF PHYSICAL CHEMISTRY B 106 (33): 8302-8305 AUG 22 2002

163. "Exploring the propensities of helices in PrPc to form beta sheet using NMR structures and sequence alignments" Dima RI, Thirumalai D BIOPHYSICAL JOURNAL 83 (3): 1268-1280 SEP 2002

164. "Folding in lattice models with side chains" Li MS, Klimov DK, Thirumalai D COMPUTER PHYSICS COMMUNICATIONS 147 (1-2): 625-628 AUG 1 2002

165. "Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution" Mountain RD, Thirumalai D JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 125 (7): 1950-1957 FEB 19 2003


166. "The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study"  Tobi D, Elber R, Thirumalai D BIOPOLYMERS 68 (3): 359-369 MAR 2003

167. "Dissecting the assembly of A beta(16-22) amyloid peptides into antiparallel beta sheets" Klimov DK, Thirumalai D STRUCTURE 11 (3): 295-307 MAR 2003

168. "Annealing function of GroEL: structural and bioinformatic analysis" Stan G, Thirumalai D, Lorimer GH, et al BIOPHYSICAL CHEMISTRY 100 (1-3): 453-467 Sp. Iss. SI 2003

169. "Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures" Buchete NV, Straub JE, Thirumalai D JOURNAL OF CHEMICAL PHYSICS 118 (16): 7658-7671 APR 22 2003

170. "Emerging ideas on the molecular basis of protein and peptide aggregation" Thirumalai D, Klimov DK, Dima RI CURRENT OPINION IN STRUCTURAL BIOLOGY 13 (2): 146-159 APR 2003

171. "Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?" Hyeon CB, Thirumalai D PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100 (18): 10249-10253 SEP 2 2003

172. "Caging helps proteins fold" Thirumalai D, Klimov DK, Lorimer GH PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100 (20): 11195-11197 SEP 30 2003

173. Ha BY, Thirumalai D
Bending rigidity of stiff polyelectrolyte chains: A single chain and a bundle of multichains
MACROMOLECULES 36 (25): 9658-9666 DEC 16 2003

174. Buchete NV, Straub JE, Thirumalai D
Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases
POLYMER 45 (2): 597-608 JAN 15 2004

175. Li MS, Klimov DK, Thirumalai D
Thermal denaturation and folding rates of single domain proteins: size matters
POLYMER 45 (2): 573-579 JAN 15 2004

176. Perez-Salas UA, Rangan P, Krueger S, et al.
Compaction of a bacterial group I ribozyme coincides with the assembly of core helices
BIOCHEMISTRY 43 (6): 1746-1753 FEB 17 2004

177. Klimov DK, Thirumalai D
Kinetics of the assembly of A beta(16-22) Alzheimer's oligomers: A molecular dynamics study
BIOPHYSICAL JOURNAL 86 (1): 507A-507A Part 2 Suppl. S JAN 2004

178. Buchete NV, Straub JE, Thirumalai D
Orientational potentials extracted from protein structures improve native fold recognition
PROTEIN SCIENCE 13 (4): 862-874 APR 2004

179. Lee NK, Thirumalai D
Pulling-speed-dependent force-extension profiles for semiflexible chains
BIOPHYSICAL JOURNAL 86 (5): 2641-2649 MAY 2004

180. Buchete NV, Straub JE, Thirumalai D
Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis
JOURNAL OF MOLECULAR GRAPHICS & MODELLING 22 (5): 441-450 Sp. Iss. SI MAY 2004

181. Buchete NV, Straub JE, Thirumalai D
Development of novel statistical potentials for protein fold recognition
CURRENT OPINION IN STRUCTURAL BIOLOGY 14 (2): 225-232 APR 2004

182. Mountain RD, Thirumalai D
Importance of excluded volume on the solvation of urea in water
JOURNAL OF PHYSICAL CHEMISTRY B 108 (21): 6826-6831 MAY 27 2004

183. Dima RI, Thirumalai D
Asymmetry in the shapes of folded and denatured states of proteins
JOURNAL OF PHYSICAL CHEMISTRY B 108 (21): 6564-6570 MAY 27 2004

184. Koculi E, Lee NK, Thirumalai D, et al.
Folding of the Tetrahymena ribozyme by polyamines: Importance of counterion valence and size
JOURNAL OF MOLECULAR BIOLOGY 341 (1): 27-36 JUL 30 2004

185. Dima RI, Thirumalai D
Proteins associated with diseases show enhanced sequence correlation between charged residues
BIOINFORMATICS 20 (15): 2345-2354 OCT 12 2004

186. Dokholyan N, Glabe C, Holtzman D, et al.
Live discussion: Protein folding and neurodegeneration: Biophysics to the rescue?
JOURNAL OF ALZHEIMERS DISEASE 6 (1): 99-105 FEB 2004

187. Klimov DK, Straub JE, Thirumalai D
Aqueous urea solution destabilizes A beta(16-22) oligomers
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (41): 14760-14765 OCT 12 2004

188. Dima RI, Thirumalai D
Probing the instabilities in the dynamics of helical fragments from mouse PrPc
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (43): 15335-15340 OCT 26 2004

189. Klimov DK, Thirumalai D
Progressing from folding trajectories to transition state ensemble in proteins
CHEMICAL PHYSICS 307 (2-3): 251-258 DEC 27 2004

190. Mountain RD, Thirumalai D
Alterations in water structure induced by guanidinium and sodium ions
JOURNAL OF PHYSICAL CHEMISTRY B 108 (51): 19711-19716 DEC 23 2004

191. Li MS, Klimov DK, Thirumalai D
Finite size effects on thermal denaturation of globular proteins
PHYSICAL REVIEW LETTERS 93 (26): Art. No. 268107 DEC 31 2004

192. Stan G, Brooks BR, Lorimer GH, et al.
Identifying natural substrates for chaperonins using a sequence-based approach
PROTEIN SCIENCE 14 (1): 193-201 JAN 2005

193. Tarus B, Straub JE, Thirumalai D
Probing the initial stage of aggregation of the A beta(10-35)-protein: Assessing the propensity for peptide dimerization
JOURNAL OF MOLECULAR BIOLOGY 345 (5): 1141-1156 FEB 4 2005

194. Barsegov V, Thirumalai D
Dynamics of unbinding of cell adhesion molecules: Transition from catch to slip bonds
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (6): 1835-1839 FEB 8 2005

195. Dima RI, Hyeon C, Thirumalai D
Extracting stacking interaction parameters for RNA from the data set of native structures 
JOURNAL OF MOLECULAR BIOLOGY 347 (1): 53-69 MAR 18 2005

196. Li MS, Klimov DK, Thirumalai D
Finite size effects on calorimetric cooperativity of two-state proteins 
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 350 (1): 38-44 MAY 1 200

197. Cheung MS, Klimov D, Thirumalai D
Molecular crowding enhances native state stability and refolding rates of globular proteins 
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (13): 4753-4758 MAR 29 2005

198. Thirumalai D, Hyeon C
RNA and protein folding: Common themes and variations 
BIOCHEMISTRY 44 (13): 4957-4970 APR 5 2005

199. Zheng WJ, Brooks BR, Doniach S, et al.
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved 
STRUCTURE 13 (4): 565-577 APR 2005

200. Hyeon C, Thirumalai D
Mechanical unfolding of RNA hairpins 
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (19): 6789-6794 MAY 10 2005


201. Morrison G, Thirumalai D
The shape of a flexible polymer in a cylindrical pore 
JOURNAL OF CHEMICAL PHYSICS 122 (19): Art. No. 194907 MAY 15 2005