Protein Native Fold


About Group
Research Interests
Publications

 

Title
Curriculum Vitae
 
 
  DEVARAJAN THIRUMALAI     

Department of Chemistry and Biochemistry and
Institute for Physical Science and Technology
University of Maryland
College Park, Maryland 20742
(301) 405-4803

FIELD OF SPECIALIZATION -- Theoretical and Computational Chemistry and Biology

EDUCATIONAL BACKGROUND:

1972-1977: M.Sc. (First Class) Received from the Indian Institute of Technology, Kanpur, India (took 50% courses in basic engineering)

Undergraduate Thesis: The E.S.R. Spectra of Some Aromatic Nitro Compounds

1977-1982: Ph.D. Candidate in Physical Chemistry, University of Minnesota
Research Advisor: Professor Donald G. Truhlar

Graduate Thesis Title: Effective Potential Studies of Electron-Atom and Electron-Molecule Collisions

PROFESSIONAL EXPERIENCE:

1982-1985: Postdoctoral Research Associate, Columbia University, New York
Research Advisor: Professor Bruce J. Berne

1985-1989: Assistant Professor, University of Maryland

1989-1993: Associate Professor, University of Maryland

1993- Professor, University of Maryland

1990-present: Guest Worker, National Institute for Standards and Technology, Gaithersburg, MD 20899

July 1995 Visiting Professor, Service de Physique Theorique, Saclay, France

March-June 1996 Visiting Forcheimer Professor, Hebrew University, Jerusalem, Israel

October 1998- Fellow, Institute for Advanced Study, Hebrew University, Jerusalem

January 1999
I certify that this curriculum vitae is corrected and up to date:
Signed/Date

PROFESSIONAL SERVICE:

Editorial Board: Theoretical Chemistry Accounts (1997-present)

Panel Member: NSF Postdoctoral Fellowship in Computations (1997)

Panel Member: NSF Career Awards (1997)

Panel Member: Special Emphasis Panel on Material Theory Programs (1997)

SPECIAL LECTURE SERIES:

A mini course (10 lectures) on "Folding of Biomolecules" in Institute for Theoretical Physics, Santa Barbara, CA, July 1997.

AWARDS:

National Science Talent Research Fellow, India 1972-1977

Camille and Henry Dreyfus Foundation 1985-1987

Distinguished New Faculty Award

Alfred P. Sloan Fellowship 1986-1988

Presidential Young Investigator Award 1987-1992

Outstanding Junior Faculty Award 1989

University of Maryland

Camille and Henry Dreyfus Foundation 1990

Teacher Scholar Award

Maryland Outstanding Young Scientist 1995

Distinguished Faculty Research Fellowship Award 1998

University of Maryland

LIST OF PUBLICATIONS

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 à-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", 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 -Hairpin Formation", D. K. Klimov and D. Thirumalai, Proc. Natl. Acad. Sci. (in press)

INVITED TALKS (Last Five Years) (All talks are 1 hour except when stated otherwise)

1. Department of Physics, University of Pittsburg, May 12, 1994.

2. ACS Meeting, Washington, D.C., "Flow Induced Structure in Polymers", August 22, 1994.

3. Workshop on "Biomolecular Materials", Institute of Theoretical Physics, Santa Barbara, August 26, 1994.

4. National Institutes of Health, Bethesda, MD, November 4, 1994.

5. Symposium on Distance-Based Approach to Protein Structure Determination II (Copenhagen, Denmark) November 11, 1994.

6. Los Alamos National Labs, New Mexico, January 18, 1995.

7. APS Meeting, March, 1995 (invited talk).

8. University of Pennsylvania, Department of Chemistry, March 30, 1995.

9. Department of Physics, University of California at San Diego, Arpil 27, 1995.

10. International Meeting in Disordered Systems and Spin Glasses, Saclay, France, July, 1995.

11. "Physics of Biology: from Molecules to Species", Humlabek, Denmark, August, 1995.

12. Department of Chemistry, Brown University, December, 1995.

13. Physics and Biology: Aspen Winter Meeting, January, 1996.

14. National Institutes of Health, Bethesda, MD, February 2, 1996.

15. Department of Physics, Pennsylvania State University, University Park, PA, February 9, 1996.

16. Department of Physical Chemistry, Hebrew University, Jerusalem, April 15, 1996.

17. Department of Physics, University of California, Santa Barbara, CA, May, 1996.

18. Department of Chemistry, University of California, Los Angeles, CA, May, 1996.

19. Indian Institute of Cultivation Sciences, Calcutta, India, July, 1996.

20. International Center for Theoretical Physics, Trieste, Italy, July, 1996 (1 « hours).

INVITED TALKS (cont'd.)

21. International Center for Theoretical Physics, Trieste, Italy, August 1, 1996 (1 « hours).

22. International Center for Theoretical Physics, Trieste, Italy, August 2, 1996 (1 « hours).

23. American Chemical Society Meeting, Protein Folding, Orlando, FL, May, 1996.

24. Institute for Physical Science and Technology, University of Maryland, College Park, MD, September, 1996.

25. Cornell Theory Center, Cornell University, Ithaca, NY, October, 1996. (45 minutes).

26. Supercomputer Center, University of Minnesota, Minneapolis, MN, December, 1996).

27. Statistical Mechanics Meeting, Rutgers, NJ, December, 1996. (25 minutes).

28. Rockefeller University, Center for Physics nd Biology, New York, May 1997.

29. Conference in Julich, Germany on Monte Carlo Methods in Protein Folding, December 1997.

30. Department of Biochemistry, University of Regansburg, December 1997.

31. Biozentrum, Basel, Switzerland, December 1997.

32. American Physical Society Meeting, March 1998, Los Angeles, (45 min.)

33. CECAM Workshop on Protein Structure and Function, June, 1998, Torino, Italy.

34. Conference on "Computations in Protein Folding", Institute for Advanced Study, Hebrew

University, Jerusalem, October, 1998.

35. Special Lecture on "Protein Folding Kinetics I", Institute for Advanced Study, Hebrew

University, Jerusalem, November, 1998, (90 min.)

36. Special Lecture on "Protein Folding Kinetics II", Institute for Advanced Study, Hebrew

University, Jerusalem, November, 1998, (90 min.)

37. Colloquium Weizmann Institute, Rehovot, Israel, December, 1998.

38. Colloquium Tel Aviv University, Rehovot, Israel, December, 1998.

39. University of Regensburg, Germany, "Regensburger Faltertag" (protein folding meeting) April, 1999.

40. Department of Chemistry, Louisiana State University, April, 1999.

41. Department of Physics, Michigan Technological University, May, 1999.

42. CECAM Meeting on "Phase Space and Energy Landscape in Disordered Systems", Lyon, France, (Plenary Lecture), June, 1999.

43. 4th Claude Itzykan Meeting on "Soft Condensed Matter Physics", Saclay, France, June, 1999.

44. Conference on "Stochastic Dynamics and Pattern Formation in Biological Systems" (Seoul, Korea) July, 1999.

45. Conference on "Complex Material Science", University of California, Santa Barbara, August, 1999.

46. CECAM Workshop "Algorithm for Enhanced Sampling in Simulations of Condensed Matter Systems", Lyon, France, September, 1999. 

47. Protein Folding Symposium in honor of G. Nemethy, Mount Sinai Medical Scool, New York, October, 1999.

48. Biophysics Colloquium, Cornell University, October, 1999.

49. Department of Chemistry, SUNY, Stonybrook, November, 1999.

50. Department of Physics, Johns Hopkins University, November, 1999.

51. Scripps Research Institute, February 4, 2000

52. IBM Research Laboratory, February 16, 2000

53. 41st Quantum Chemistry Sanibel Symposium, March 3, 2000