Refereed Publications:

  1. "Stable calculation of coordinates from distance information" by G.M. Crippen and T.F. Havel, Acta Cryst. A34:282-284 (1978).

  2. "Effects of distance constraints on macromolecular conformation. II. Simulation of experimental results and theoretical predictions" by T.F. Havel, G.M. Crippen and I.D. Kuntz, Biopolymers 18:73-81 (1979).

  3. "A distance geometry study of ring systems: Application to cyclooctane, 18-crown-6, cyclododecane and androstanedione" by P. Weiner, S. Profeta, G. Wipff, T.F. Havel, I.D. Kuntz, R. Langeridge and P. Kolmann, Tetrahedron 39:1113-1121 (1983).

  4. "The theory and practice of distance geometry" by T.F. Havel, I.D. Kuntz and G.M. Crippen, Bull. Math. Biol. 45:665-720 (1983).

  5. "The combinatorial distance geometry approach to the calculation of molecular conformation. I. A new approach to an old problem" by T.F. Havel, I.D. Kuntz and G.M. Crippen, J. Theor. Biol. 104:359-381 (1983).

  6. "The combinatorial distance geometry approach to the calculation of molecular conformation. II. Sample problems and computational statistics" by T.F. Havel, I.D. Kuntz and G.M. Crippen, J. Theor. Biol. 104:383-400 (1983).

  7. "A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of 1H-1H proximities in solution" by T.F. Havel and K. Wüthrich, Bull. Math. Biol. 46:673-698 (1984).

  8. "An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformation in solution" by T.F. Havel and K. Wüthrich, J. Mol. Biol. 182:281-294 (1985).

  9. "Tertiary structure of the proteinase inhibitor IIA from bull seminal plasma" by M.P. Williamson, T.F. Havel and K. Wüthrich, J. Mol. Biol. 182:295-315 (1985).

  10. "Some combinatorial properties of discriminants in metric vector spaces" by A. Dress and T.F. Havel, Adv. Math. 62:285-312 (1986).

  11. "The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization" by M. Billeter, T.F. Havel, K. Wüthrich, J. Comput. Chem. 8:132-141 (1986).

  12. "A new approach to the problem of docking two molecules: The ellipsoid algorithm" by M. Billeter, T.F. Havel, I.D. Kuntz, Biopolymers 26:777-793 (1987).

  13. "Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN" by G. Wagner, W. Braun, T.F. Havel, T. Schaumann, N. Gô; and K. Wüthrich, J. Mol. Biol. 196:611-639 (1987).

  14. "Three-dimensional solution structure of plastocyanin from the green algae Scenedesmus obliquus" by J.M. Moore, D.A. Case, W.J. Chazin, G.P. Gippert, T.F. Havel, R. Powls, and P.E. Wright, Science 240:314-317 (1988).

  15. "Shortest-path problems and molecular conformation" by A. Dress and T.F. Havel, Disc. Appl. Math. 19:129-144 (1988).

  16. "Computational experience with an algorithm for tetrangle inequality bound smoothing" by P.L. Easthope and T.F. Havel, Bull. Math. Biol. 51:173-194 (1988).

  17. "Criteria for the global consistency of two-threshold preference relations in terms of forbidden subconfigurations" by A. Dress and T.F. Havel, Adv. Appl. Math. 10:379-395 (1989).

  18. "The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations" by T.F. Havel, Biopolymers 29:1565-1585 (1990).

  19. "Global energy minimization by rotational energy embedding" by G.M.Crippen and T.F. Havel, J. Chem. Inform. Sci. 30:222-227 (1990).

  20. "A new method for building protein conformations from sequence alignments with homologues of known structure" by T.F. Havel and M.E. Snow, J. Mol. Biol. 217:1-7 (1991).

  21. "Alternating zinc fingers in the human male-associated protein ZFY: 2D-NMR structure of an even finger and implications for "jumping-linker" DNA recognition" by M. Kochoyan, T.F. Havel, D.T. Nguyen, C.E. Dahl, H.T. Keutmann and M.A. Weiss. Biochemistry 30:3371-3386 (1991).

  22. "An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by NMR spectroscopy" by T.F. Havel, Prog. Biophys. molec. Biol. 56:43-78 (1991).

  23. "Some examples of the use of distances as coordinates for Euclidean geometry" by T.F. Havel, J. Symbolic Comput. 11:579-593 (1991).

  24. "Bound smoothing under chirality constraints" by A.W.M. Dress and T.F. Havel, SIAM J. Disc. Math. 4:535-549 (1991).

  25. "Δ-matroids and metroids" by A. Bouchet, A.W.M. Dress and T.F. Havel, Adv. Math. 91:136-142 (1992).

  26. "A high-resolution solution structure of eglin c based on measurements of many NOEs and coupling constants" by S.G. Hyberts, M.S. Goldberg, T.F. Havel and G. Wagner, Protein Sci. 1:736-751 (1992).

  27. "A least-squares approach to the evaluation of protein structures computed from NMR data" by J.-X. Yang and T.F. Havel, J. Biomol. NMR 3:355-360 (1993).

  28. "Predicting the structure of the flavodoxin from E.coli by homology modeling, distance geometry and molecular dynamics" by T.F. Havel, Molec. Simul. 10:175-210 (1993).

  29. "Distance geometry and geometric algebra" by A.W.M. Dress and T.F. Havel, Foundations of Physics 23:1357-1374 (1993).

  30. "Applications of geometric algebra to the theory of molecular conformation. I. The optimum alignment problem" by T.F. Havel and I. Najfeld, TheoChem 308:241-262 (1994).

  31. "Matrix decompositions of two-dimensional nuclear magnetic resonance spectra" by T.F. Havel, I. Najfeld and J.-X. Yang, Proc. Natl. Acad. Sci. USA 91:7962-7966 (1994).

  32. "Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry" by D.P. Yee, H.S. Chan, T.F. Havel and K.A. Dill, J. Mol. Biol. 241:557-573 (1994).

  33. "An evaluation of least-squares fits to COSY spectra as a means of estimating scalar coupling constants. Part I. Simulated test problems" by J.-X. Yang and T.F. Havel, J. Biomol. NMR 4:807-826 (1994).

  34. "An evaluation of least-squares fits to COSY spectra as a means of estimating scalar coupling constants. Part II. Application to polypeptides" by J.-X. Yang, P. Schmieder, A. Krezel, G. Wagner and T.F. Havel, J. Biomol. NMR 4:827-844 (1994).

  35. "Applications of geometric algebra to the theory of molecular conformation. II. The local deformation problem" by T.F. Havel and I. Najfeld, TheoChem 336:175-189 (1995).

  36. "Derivatives of the matrix exponential and their computation" by I. Najfeld and T.F. Havel, Adv. Appl. Math. 16:321-375 (1995).

  37. "A new system of equations, based on geometric algebra, for ring closure in cyclic molecules" by T.F. Havel and I. Najfeld, in Computer Algebra in Science and Engineering (edited by J. Fleischer, J. Grabmeier, W. Hehl & W. Küchlin), pp. 243-259, World Scientific (1995).

  38. "A robust method for estimating cross-relaxation rates from simultaneous fits to build-up and decay curves" by I. Najfeld, K.T. Dayie, T.F Havel and G. Wagner, J. Magn. Reson. 124:372-382 (1997).

  39. "Ensemble quantum computing by NMR spectroscopy" by D.G. Cory, A.F. Fahmy and T.F. Havel, Proc. Natl. Acad. Sci. 94:1634-1639 (1997).

  40. "Embedding with a rigid substructure" by I. Najfeld and T.F. Havel, J. Math. Chem. 21:223-260 (1997).

  41. "Recent advances in molecular distance geometry" by T.F. Havel, S.G. Hyberts and I. Najfeld, in Bioinformatics (eds. R. Hofestädt, T. Lengauer, M. Löffler & D. Schomburg), Lect. Notes in Comput. Sci. 1278:62-71, Springer-Verlag (1997).

  42. "Computational synthetic geometry with Clifford algebra" by T.F. Havel, in Automated Deduction in Geometry (ed. Dongming Wang), Lect. Notes Artif. Intel. 1360:102-114, Springer-Verlag (1997).

  43. "Expressing the operations of quantum computing in multiparticle geometric algebra" by S.S. Somaroo, D.G. Cory and T.F. Havel, Phys. Lett. A 240:1-7 (1998).

  44. "Nuclear magnetic resonance spectroscopy: An experimentally accessible paradigm for quantum computing" by D.G. Cory, M.D. Price and T.F. Havel, Physica D 120:82-101 (1998).

  45. "Experimental quantum error correction" by D.G. Cory, W. Mass, M. Price, E. Knill, R. Laflamme, W.H. Zurek, T.F. Havel and S.S. Somaroo, Phys. Rev. Lett. 81:2152-2155 (1998).

  46. "Quantum simulations on a quantum computer" by S.S. Somaroo, C.-H. Tseng, T.F. Havel, R. Laflamme and D.G. Cory, Phys. Rev. Lett. 82:5381-5384 (1999).

  47. "Construction and implementation of NMR quantum logic gates for two-spin systems" by M.D. Price, S.S. Somaroo, C.-H. Tseng, J.C. Gore, A.F. Fahmy, T.F. Havel and D.G. Cory, J. Magn. Reson. 140:371-378 (1999).

  48. Generalized (controlled)n-NOT quantum logic gates" by M.D. Price, S.S. Somaroo, A.E. Dunlop, T.F. Havel and D.G. Cory, Phys. Rev. A 60:2777-2780 (1999).

  49. "Quantum simulation of a three-body interaction Hamiltonian on an NMR quantum computer" by C.-H. Tseng, S. Somaroo, Y. Sharf, E. Knill, R. Laflamme, T.F. Havel and D.G. Cory, Phys. Rev. A 61:012302 (2000).

  50. "Principles and demonstrations of quantum information processing by NMR spectroscopy" by T.F. Havel, S.S. Somaroo, C.-H. Tseng and D.G. Cory, Springer series on Applicable Algebra in Engineering, Communication and Computing 10:339-374 (2000).

  51. "Geometric algebra methods in quantum information processing by NMR spectroscopy" by T.F. Havel, D.G. Cory, S.S. Somaroo and C.-H. Tseng, in Geometrical Algebras with Applications in Science and Engineering (eds E. Bayro-Corrochanno & G. Sobczyk), Birkhauser (2001).

  52. "A study of quantum error correction by geometric algebra and liquid-state NMR spectroscopy" by T.F. Havel, S.S. Somaroo, Y. Sharf, D.G. Cory, E. Knill, R. Laflamme and W.H. Zurek, Mol. Phys. 98:1347-1363 (2000).

  53. "Quantum simulation with natural decoherence" by C.-H. Tseng, S.S. Somaroo, Y. Sharf, E. Knill, R. Laflamme, T.F. Havel & D.G. Cory, Phys. Rev. A 62:032309 (2000) .

  54. "Quantum codes for controlling coherent evolution" by Y. Sharf, T.F. Havel and D.G. Cory, J. Chem. Phys. 113:10878-10885 (2000).

  55. "NMR based quantum information processing: Achievements and prospects" by D.G. Cory, R. Laflamme, E. Knill, L. Viola, T.F. Havel, N. Boulant, G. Boutis, E. Fortunato, S. Lloyd, R. Martinez, C. Negrevergne, M. Pravia, Y. Sharf, G. Teklemariam, Y.S. Weinstein and W.H. Zurek, Fortschritte der Physik (Progress in Physics) 48:875-907 (2000)

  56. "Spatially encoded pseudo-pure states for NMR quantum information processing" by Y. Sharf, T.F. Havel and D.G. Cory, Phys. Rev. A 62:052314 (2000).

  57. "Hadamard products of product operators and the design of gradient-diffusion experiments for simulating decoherence by NMR spectroscopy" by T.F. Havel, Y. Sharf, L. Viola and D.G. Cory, Phys. Lett. A 280:282-288 (2001).

  58. "An NMR analog of the quantum disentanglement eraser" by G. Teklemariam, E.M. Fortunato, T.F. Havel and D.G. Cory, Phys. Rev. Lett. 86:5845-5849 (2001).

  59. "Entanglement transfer experiment in NMR quantum information processing" by N. Boulant, E.M. Fortunato, M.A. Pravia, G. Teklemariam, D.G. Cory and T.F. Havel, Phys. Rev. A 65:024302 (2002).

  60. "Experimental concatentation of quantum error correction and decoupling" by 58. N. Boulant, M.A. Pravia, E.M. Fortunato, T.F. Havel and D.G. Cory, Quantum Inform. Processing 1:135-144 (2002).

  61. "Quantum erasers and probing classifications of entanglement via nuclear magnetic resonance" by G. Teklemariam, E.M. Fortunato, M.A. Pravia, Y. Sharf, T.F. Havel, D.G. Cory, A. Bhattaharyya and J. Hou, Phys. Rev. A 66:012309 (2002).

  62. "Quantum information processing by nuclear magnetic resonance spectroscopy" by T.F. Havel, D.G. Cory, S. Lloyd, N. Boulant, E.M. Fortunato, M.A. Pravia, G. Teklemariam, Y.S. Weinstein, A. Bhattacharyya and J. Hou, Am. J. Phys. 70:345-362 (2002).

  63. "The real density matrix" by T.F. Havel, Quantum Information Processing 1:511-538 (2002).

  64. "Design of strongly modulating pulses to implement precise effective hamiltonians for quantum information processing" by E.M. Fortunato, M.A. Pravia, N. Boulant, G. Teklemariam, T.F. Havel and D.G. Cory, J. Chem. Phys., 116:7599-7606 (2002).

  65. "Robust procedures for converting among Kraus, Lindblad and matrix representations of quantum dynamical semigroups" by T.F. Havel, J. Math. Phys. 44:534-557 (2003).

  66. "A robust method for estimating the Lindblad operators of a dissipative quantum process from measurements of the density operator at multiple time points" by N. Boulant, T.F. Havel, M.A. Pravia and D.G. Cory, Phys. Rev. A 67:042322 (2003).

  67. "Exploring noiseless subsystems via nuclear magnetic resonance" by E.M. Fortunato, L. Viola, M.A. Pravia, E. Knill, R. Laflamme, T.F. Havel and D.G. Cory, Phys. Rev. A 67:062303 (2003).

  68. "Experimental investigations of decoherence on a quantum information processor" by G. Teklemariam, E.M. Fortunato, M.A. Pravia, T.F. Havel and D.G. Cory, Chaos, Solitons and Fractals 16:457-465 (2003).

  69. "A method for modeling decoherence on a quantum information processor" by G. Teklemariam, E.M. Fortunato, C.C. Lopez, J. Emerson, J.-P. Paz, T.F. Havel and D.G. Cory, Phys. Rev. A 67:062316 (2003).

  70. "Robust control of quantum information" by M.A. Pravia, N. Boulant, J. Emerson, A. Farid, E.M. Fortunato, T.F. Havel, R. Martinez and D.G. Cory, J. Chem. Phys. 119:9993-10001 (2003).

  71. "Experimental simulation of spin squeezing by nuclear magnetic resonance" by Suddhasattwa Sinha, T.F. Havel, J. Emerson, N. Boulant, E.M. Fortunato and D.G. Cory, Quantum Inform. Processing 2:433-448 (2003).

  72. "Incoherent noise in quantum information processing" by N. Boulant, J. Emerson, T.F. Havel, D.G. Cory and S. Furuta, J. Chem. Phys. 121:2955-2961 (2004).

  73. "Geometric algebra and transition-selective implementations of the controlled-NOT gate" by T.F. Havel, S.S. Somaroo, W. Zhang and D.G. Cory, Concepts in Magn. Reson. 23A:49-62 (2004).

  74. "Quantum process tomography of the quantum Fourier transform" by Y.S. Weinstein, T.F. Havel, J. Emerson, N. Boulant, M. Saracenos, S. Lloyd and D.G. Cory, J. Chem. Phys. 121:6117-6133 (2004).

  75. "Selective coherence transfers in homonuclear dipolar coupled spin systems" by Chandrasekhar Ramanathan, Suddhasattwa Sinha, J. Baugh, T.F. Havel, and D.G. Cory, Phys. Rev. A 71:020303(R) (2005).

  76. "Reflection symmetries for multiqubit density operators" by C. Altafini and T.F. Havel, J. Math. Phys. 47:032104 (2006).

  77. "Solid-state NMR three-qubit homonuclear system for quantum-information processing: Control and characterization" by J. Baugh, O. Moussa, C.A. Ryan, R. Laflamme, C. Ramanathan, T.F. Havel and D.G. Cory, Phys. Rev. A 73:022305 (2006).

  78. "Quantum control of nuclear spins" by J.S. Hodges, P. Cappellaro, T.F. Havel and D.G. Cory, Proc. 45th IEEE Conf. Decision & Control, pp. 2488-2494 (2006).

  79. "Principles of control for decoherence-free subsystems" by P. Cappellaro, J.S. Hodges, T.F. Havel and D.G. Cory, J. Chem. Phys. 125:044514 (2006).

  80. "Experimental implementation of a logical Bell state encoding" by J.S. Hodges, P. Cappellaro, T.F. Havel, R. Martinez and D.G. Cory, Phys. Rev. A 75:042320 (2007).

  81. "Subsystem pseudopure states" by P. Cappellaro, J.S. Hodges, T.F. Havel and D.G. Cory, Phys. Rev. A 75:042321 (2007).

  82. "Storing elastic energy in carbon nanotubes" by F. A. Hill, T.F. Havel, A.J. Hart and C. Livermore, Micromech. Microengin. 19:094015-5 (2009).

  83. "Modeling mechanical energy storage in springs based on carbon nanotubes" by F. A. Hill, T.F. Havel and C. Livermore, Nanotechnology 20:255704-12 (2009).