This is as close to an accurate list of my publications as I have. For the most part I do not have them on line so you'll have to go to the journals to find them. The last time I updated this page is at the bottom. Diacritical marks from names are missing (sorry) as are any greeks or symbols. The page is in plain HTML and the translation is less than perfect. The numbering is rough in places as I used to number them by submission; now I use when they are in press.

(1) "Potential Energy Surface for the Collinear Reaction of Ne and HeH+ ," J. Chem. Phys., 69, 2264-2265 (1978); R.L. Matcha, P. Meier, P. Pendergast, and B.M. Pettitt.

(2) "Theoretical Compton Profile Anisotropies in Molecules and Solids III. Re- lation of Parallel and Perpendicular Anisotropies in Alkali-Chloride Molecules," J. Chem. Phys., 69, 3025-3033 (1978); R.L. Matcha, B.M. Pettitt, B.I. Ramirez, and W.R. McIntire.

(3) "Theoretical Compton Profile Anisotropies in Molecules and Solids V. Lithium and Sodium Bromide Diatomics," J. Chem. Phys., 70, 558-564 (1979); R.L. Matcha, B.M. Pettitt, B.I. Ramirez, and W.R. McIntire.

(4) "Theoretical Compton Profile Anisotropies in Molecules and Solids VI. Compton Profile Anisotropies and Chemical Binding," J. Chem. Phys., 70, 3130-3132 (1979); R.L. Matcha and B.M. Pettitt.

(5) "Theoretical Compton Profile Anisotropies in Molecules and Solids IV. Parallel-Per- pendicular Anisotropies in Alkali-Fluoride Molecules," J. Chem. Phys., 71, 991-996 (1979); R.L. Matcha, B.M. Pettitt, B.I. Ramirez and W.R. McIntire.

(6) "Collinear Reaction Surface for He and ArH + ," J. Chem. Phys., 72, 2892-2894 (1980); B.M. Pettitt, K. Jacobson, and R.L. Matcha.

(7) "Theory of the Chemical Bond V. Bond Polarities of the Post-transition Hydrides," J. Chem. Phys., 72, 3944-3946 (1980); R.L. Matcha, S. King, and B.M. Pettitt.

(8) "Theoretical Compton Profile Anisotropies in Molecules and Solids VII. Zero-Point Compton Profile Anisotropies and Bond Polarities in Alkali-Halide Diatomic Molecules," J. Chem. Phys., 72, 4588-4590 (1980); R.L. Matcha and B.M. Pettitt.

(9) "Theoretical Compton Profile Anisotropies in Molecules and Solids VIII. Vibrational, Rotational and Temperature-Dependent Diatomic Alkali-Halide Anisotropies," Int. J. Quant. Chem., S14, 697-706 (1980); B.M. Pettitt, S.R. Gadre, and R.L. Matcha.

(10) "Application of an Extended RISM Equation to Dipolar and Quadrupolar Fluids," J. Chem. Phys., 77, 509-520 (1982); F. Hirata, B.M. Pettitt, and P.J. Rossky.

(11) "Integral Equation Predictions of Liquid State Structure for Water-like Intermolecular Potentials," J. Chem. Phys., 77, 1451-1457 (1982); B.M. Pettitt and P.J. Rossky.

 (12) "The Interionic Potential of Mean Force in a Polar Molecular Solvent from an Extended RISM Equation," J. Chem. Phys., 78, 4133-4144 (1983); F. Hirata, P.J. Rossky, and B.M. Pettitt.

(13) "Contribution of Hydrogen Bonding to the Structure of Liquid Methanol," J. Chem. Phys., 78, 7296-7299 (1983); B.M. Pettitt and P.J. Rossky.

(14) "Theoretical Compton Profile Anisotropies in Molecules and Solids IX. Chem- ical Bonding and 0-90 Anisotropies in the First-row Diatomic Hydrides, AH," J. Chem. Phys., 79, 2913-2917 (1983); B.M. Pettitt, R.L. Matcha, and B.I. Ramirez.

(15) "The Coupling of Long and Short-ranged Correlations in ISM Liquids," Mol. Phys., 50, 1263-1271 (1983); P.J. Rossky, B.M. Pettitt, and G. Stell.

(16) "Entropy of Macromolecules," Proceedings of the Workshop on Dynamics Methods and Protein Structure, UNC Chapel Hill, (1984); M. Karplus, J. Brady, B. Brooks, J. Kushick, B.M. Pettitt.

(17) "The Role of Electrostatics in the Structure, Energy and Dynamics of Biomolecules: A Model Study of N-Methyl Alanyl Acetamide," J. Am. Chem. Soc., 107, 1166-1173 (1985); B.M. Pettitt and M. Karplus.

(18) "Calculation of Temperature Dependent Multimode Raman Spectra from Harmonic Potential Surfaces," J. Chem. Phys., 82, 2918-2926 (1985); R. Friesner, B.M. Pettitt, and J. Jean.

(19) "The Intermolecular Potential of Mean Force Between Polyatomics in a Polar Molecular Solvent," J. Chem. Phys., 83, 781-789 (1985); B.M. Pettitt and M. Karplus.

(20) "The Potential of Mean Force for the Alanine Dipeptide in Water: A Theoretical Approach," Chem. Phys. Lett., 121, 194 (1985); B.M. Pettitt and M. Karplus.

(21) "The Effects of Terminating Long-ranged Forces in Fluids," J. Chem. Phys., 83, 5897- 5908 (1985); C.L. Brooks, B.M. Pettitt, and M. Karplus.

(22) "Alkali-Halides in Water: Ion-Solvent Correlations and Ion-Ion Potentials of Mean Force at Infinite Dilution," J. Chem. Phys., 84, 5836-5844 (1986); B.M. Pettitt and P.J. Rossky.

(23) "Interaction Energies," Topics in Molecular Pharmacology: Molecular Graphics and Drug Design, (A.S.V. Burgen, G.C.K. Roberts and M.S. Tute, eds.), Vol. 3, (Elsevier, London, 1986) pp. 75-114; B.M. Pettitt and M. Karplus.

(24) "An Integral Equation Model for Aqueous Solvation of Polyatomic Solutes," J. Phys. Chem., 90, 6335-6345 (1986); B.M. Pettitt, M. Karplus, and P.J. Rossky.

(25) "New Approaches to Solvent Mediated Interactions," Israel J. Chem., 27, 156-162 (1986); B.M. Pettitt and P.J. Rossky.

(26) "On the Structure of High Density Water at Constant Temperature," J. Phys. Chem., 91, 1541-1545 (1987); B.M. Pettitt and D.F. Calef.

(27) "The Structure of Water Surrounding a Dipeptide: A Theoretical Approach," Chem. Phys. Lett., 136, 383-386(1987); B.M. Pettitt and M. Karplus.

(28) "Two-dimensional Fluids in a Periodic External Potential: Intercalation in Graphite," Chem. Phys. Lett., 137, 72-76 (1987); O.A. Karim and B.M. Pettitt.

(29) "Solvated Chloride Ions at Contact," J. Chem. Phys., 86, 6560-6561 (1987); L.X. Dang and B.M. Pettitt.

 (30) "Simple Intramolecular Model Potentials for Water," J. Phys. Chem., 91, 3349-3354 (1987); L.X. Dang and B.M. Pettitt.

(31) "Chloride Ion Pairs in Water," J. Am. Chem. Soc., 109, 5531-5532 (1987); L.X. Dang and B.M. Pettitt.

(32) "Theoretical Study of the Structure of Shocked Water," Chem. Phys. Lett., 139, 129- 133 (1987); B.M. Pettitt and D.F. Calef.

(33) "Proteins," McGraw-Hill World Book Encyclopedia 1988 Yearbook of Science and Technology, ed. S. Parker, 360-362 (1987); B.M. Pettitt.

(34) "Molecular Dynamics Studies on Antiviral Agents: Thermodynamics of Solvation and Binding," UCLA Symp. Mol. Cell. Biol., 69, 227-233(1987); T.P. Lybrand, W.F. Lau, J.A. McCammon, and B.M. Pettitt.

(35) "Conformations of the Glycine Dipeptide in Water," Biopolymers, 26, 1817- 1831(1987); W.F. Lau and B.M. Pettitt.

(36) "Geometric Considerations in the Calculation of Relative Free Energies of Activation," Chem. Phys. Lett., 141, 83 (1987); J.D. Madura, B.M. Pettitt, and J.A. McCammon.

(37) "Configurational Entropy of Native Proteins," Biophys. J., 52, 1083-1085 (1987); M. Karplus, T. Ichiye, and B.M. Pettitt.

(38) "The Conformational Properties of the Delta Opioid Peptide Bis-D-penicillamine En- kephalin in Aqueous Solutions Determined by NMR and Energy Minimization Calcula- tions," J. Am. Chem. Soc., 110, 3351-3359 (1988); V.J. Hruby, J. Kao, B.M. Pettitt, and M. Karplus.

(39) "Water Under High Pressure," Molecular Phys., 64, 325-336 (1988); J.D. Madura, B.M. Pettitt, and D.F. Calef.

(40) "The Conformational Free Energy of Hydration for the Alanine Dipeptide: Thermody- namic Analysis," J. Phys. Chem., 92, 3994-3997 (1988); B.M. Pettitt and M. Karplus.

(41) "A Theoretical Study of the Inclusion Complexes of beta-Quinol," J. Chem. Phys., 89, 968-974 (1988); L.X. Dang and B.M. Pettitt.

(42) "A Theory of the Interionic Structure of Graphite Intercalation Synthetic Metals: Variations with Respect to Interactions and State," J. Chem. Phys., 89, 1042-1048 (1988); Z.M. Chen, O.A. Karim, and B.M. Pettitt.

(43) "Effects of Truncating Long-range Interactions in Aqueous Ionic Solution Simula- tions," Chem. Phys. Lett., 150 105-108 (1988); J. Madura and B.M. Pettitt.

(44) "Proteins: A theoretical perspective on Structure, Dynamics and Thermodynamics," Adv. Chem. Phys., 71, 1-259 (1988); C.L. Brooks, M. Karplus, and B.M. Pettitt.

(45) "Molecular Dynamics Simulation of Coat Proteins of the Human Rhinovirus," Molec- ular Simulation, 5, 385-398 (1988); W.F. Lau, B.M. Pettitt, and T.P. Lybrand.

(46) "Conformational Constraints in the Design of Receptor Selective Peptides: Conforma- tional Analysis and Molecular Dynamics," Molecular Biology of Brain and Endocrine Peptidergic Systems, ed. M. Chretien and K.W. McKerns (Plenum, New York NY, 1988) pp 13-27; V.J. Hruby, W. Kazmierski, B.M. Pettitt, and F. Al-Obeidi.

(47) "Methods for Calculating Geometries of Transition States in Solution," Chem. Phys. Lett., 129, 185-191 (1989); J.D. Madura, B.M. Pettitt, and J.A. McCammon.

(48) "Conformational-Biological Activity Relationships for Receptor Selective, Conforma- tionally Constrained Opioid Peptides," in Computer-Aided Drug Design , ed. T.J. Perun and C.L. Probst, (Dekker, New York,1989) pp 405-452; V.J. Hruby and B.M. Pettitt.

(49) "Successes, Failures and Curiosities in Free Energy Calculations," in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, ed. W.F. van Gunsteren and P.K. Weiner, (ESCOM, Leiden, 1989) pp 94-100; B.M. Pettitt.

(50) "Design of A New Class of Superpotent Cyclic -Melanotropins Based on Quenched Dynamic Simulations," J. Am. Chem. Soc., 111, 3413-3416 (1989); F.A. Al-Obeidi, M.E. Hadley, B.M. Pettitt, and V.J. Hruby.

(51) "Diatomic Guests in beta-Quinol Clathrates," J. Phys. Chem., 93, 3794-3799 (1989); L.X. Dang and B.M. Pettitt.

(52) "Dynamics of an Oxazole Compound Bound to a Common Cold Virus," J. Am. Chem. Soc., 111, 4111-4113 (1989); W.F. Lau and B.M. Pettitt.

(53) "The Elastic Constants of Nickel: Variations with Respect to Temperature and Pressure," Phys. Rev. B, 39, 12484-12491 (1989); Tahir Cagin and B.M. Pettitt.

(54) "Selective Elimination of Interactions: A method for assessing thermodynamic contri- butions to ligand binding with applications to rhinovirus antivirals," J. Med. Chem., 32, 2542-2547 (1989); W.F. Lau and B.M. Pettitt.

(55) "Flexibility of Tripeptides in Solution: Free Energy Molecular Mechanics," Inter- national Journal of Peptide and Protein Research, 35, 315-327 (1990); G. Rame', W.F. Lau and B.M. Pettitt.

(56) "A Theoretical Study of Like Ion Pairs in Solution," J. Phys. Chem., 94, 4303-4308 (1990); L.X. Dang and B.M. Pettitt.

(57) "Free Energy of Intercalation: The Structure of Graphite Intercalation Compounds," Studies in Physical and Theoretical Chemistry, ed. J.L. Rivail, 71, 103-117 (1990); Z.-M. Chen, O.A. Karim and B.M. Pettitt.

(58) "Diatomic Intercalation in Lamellar Graphite Compounds," Phys. Rev. B, 42, 8173- 8178 (1990); Zhuo-Min Chen and B.M. Pettitt.

(59) "A Study of Model Energetics and Conformational Properties of Polynucleotide Triplexes," Biopolymers, 30, 517-532 (1990); H.W.T. van Vlijmen, G.L. Rame', and B.M. Pettitt.

(60) "Modeling of Solvation Effects in Biopolymer Solutions," in Theoretical Biochemistry and Molecular Biophysics, vol. 2 ,223-229 eds. D.L. Beveridge and R. Lavery, (Adenine Press, New York, 1990); B.M. Pettitt and P.J. Rossky.

(61) "Simulation of the Structure and Dynamics of the Bis-Penicillamine Zwitterion," J. Am. Chem. Soc. , 113, 67-73 (1991); P. Smith, L.X. Dang and B.M. Pettitt.

(62) "Molecular Dynamics with a Variable Number of Molecules," Mol. Phys., 72, 169-175 (1991); T. Cagin and B.M. Pettitt.

(63) "Convergence of the Chemical Potential in Aqueous Solutions," Molecular Simulations, 6, 1-4 (1991); M. Mazor and B.M. Pettitt.

(64) "Grand Molecular Dynamics: A method for open systems," Molecular Simulations, 6, 5-26 (1991); Tahir Cagin and B.M. Pettitt.

 (65) "Time Scales and Fluctuations of Protein Dynamics: Metmyoglobin in Aqueous Solu- tion," in Principles of Molecular Recognition, ed A.D. Buckingham (Chapman Hall, London, 1993) pp 168-193; L. Findsen, S. Subramanian, V. Lounnas, and B.M. Pettitt.

(66) "Aqueous Solvation of N-methyl Acetamide Conformers: Comparison of Simulations and Integral Equation Theories," J. Am. Chem. Soc., 113, 2425-2434 (1991); H.- A. Yu, B.M. Pettitt, and M. Karplus.

(67) "A Method for Modeling Icosahedral Virions: Rotational Symmetry Boundary Conditions," J. Comp. Chem., 12, 627-634, (1991); T. Cagin, M. Holder, and B.M. Pettitt.

(68) "Aspects of the Design of Conformationally Constrained Peptides," Methods in Enzymology, 202, 411-436 (1991); P.E. Smith, F. Al-Obeidi, and B.M. Pettitt.

(69) "Effects of Salt on the Structure and dynamics of the Bis(penicillamine) Enkephalin Zwitterion: A Simulation Study," J. Am. Chem. Soc., 113, 6029-6037 (1991); P.E. Smith and B.M. Pettitt.

(70) "Binding of Triple Helix Forming Oligonucleotides to Sites in Gene Promoters," Biochemistry, 30, 9246-9255 (1991); R.H. Durland, D.J. Kessler, S. Gunnell, M. Duvic, B.M. Pettitt, and M. Hogan.

(71) "Dynamical Search for Bis-Penicillamine Enkephalin Conformations: Quenched Molecular Dynamics," Biophysical J., 60, 1540-1544 (1991); B.M. Pettitt, T. Mat- sunaga, F. Al-Obeidi, C. Gehrig, V.J. Hruby, and M. Karplus

(72) "Peptides in Ionic Solution: A Comparison of Ewald and Switching Function Techniques," J. Chem. Phys., 95, 8430-8441 (1991); P.E. Smith and B.M. Pettitt.

(73) "Dynamic Simulations of Water at Constant Chemical Potential," J. Chem. Phys., 96, 1333-1342 (1992); J. Ji, T. Cagin, and B.M. Pettitt.

(74) "On the Correlations Between Like Ion Pairs in Water," J. Chem. Phys., 96, 4046- 4047 (1992); L.X. Dang, B.M. Pettitt, and P.J. Rossky.

(75) "A Dielectrically Consistent Interaction Site Theory for Solvent-Electrolyte Mixtures," Chem. Phys. Lett. 190, 626-630 (1992); J.S. Perkyns and B.M. Pettitt.

(76) "Hoogsteen vs Reverse Hoogsteen Pairing: DNA Triple Helices," J. Am. Chem. Soc. 114, 4465-4474 (1992); Y.-K. Cheng and B.M. Pettitt.

(77) "Quenched Molecular Dynamics Simulations of Tuftsin and Proposed Cyclic Analogs," J. Med Chem. 35, 2870-2881 (1992); S. O'Connor, P.E. Smith, F. Al-Obeidi, and B.M. Pettitt.

(78) "Forms of Molecular Dynamics," Landolt-Bornstein 00; P.E. Smith and B.M. Pettitt.

(79) " Continuum Model Calculations of Solvation Free Energies: Accurate Evaluation of Electrostatic Contributions", J. Phys. Chem. 96, 6428-6431 (1992); V.Mohan, M.E. Davis, J.A. McCammon, and B.M. Pettitt.

(80) "Comparison of Structural Theories for Graphite Intercalation Compounds," Phys. Rev. B, 46 10476-10478 (1992); Z.M. Chen, B.M. Pettitt, G. Reiter, S.C. Moss, and O.A. Karim.

(81) "A Microscopic View of Protein Solvation," J. Phys. Chem., 96, 7157-7158 (1992); V. Lounnas, B.M. Pettitt, L. Findsen, and S. Subramanian.

 (82) "Amino Acid Side Chain Populations in Aqueous and Saline Solution: Bis- Penicillamine Enkephalin," Biopolymers, 32, 1623-1629 (1992); P.E. Smith and B.M. Pettitt.

(83) "Molecular Dynamics on a Distributed-Memory Multiprocessor," J. Comp. Chem., 13, 1022-1035 (1992); S. L. Lin, J. Mellor-Crummey, B.M. Pettitt, and G.N. Phillips.

(84) "Stabilities of Double and Triple Strand Helical Nucleic Acids," Progress in Biophysics and Molecular Biology, 58, 225 - 257 (1992); Y.-K. Cheng and B.M. Pettitt.

(85) "A Site-site Theory for Finite Concentration Saline Solutions," J. Chem. Phys., 97 7656-7666 (1992); J.S. Perkyns and B.M. Pettitt.

(86) " Monte Carlo Evaluation of Real Time Feynman Path Integrals for Quantal Many Body Dynamics: Distributed Approximating Functions and Gaussian Sampling," J. Phys. Chem., 96, 9622-9630 (1992); D. J. Kouri, W. Zhu, X. Ma, B.M. Pettitt, and D. K. Hoffman.

(87) "Molecular Recognition of Watson-Crick Base pair Reversals in Triple Helix Forma- tion: Use of Nonnatural Oligonucleotide Bases," Biopolymers, 33, 1317-1325 (1993); V. Mohan, Y.-K. Cheng, G. Marlow, and B.M. Pettitt.

(88) "Grand Molecular Dynamics: An Application of Extended System Dynamics," in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, vol. 2, ed. W.F. van Gunsteren, P.K. Weiner, and A.J. Wilkinson (ES- COM, Leiden, 1993) pp 67-81; J. Ji and B.M. Pettitt.

(89) "Stochastic Dynamics Simulations of the Alanine Dipeptide Using a Solvent Modifed Potential Energy Surface," J. Phys. Chem, 97, 6907-6913 (1993); P. Smith, B.M. Pettitt and M. Karplus.

(90) "On the Mechanism of HRV-14 Antiviral Compounds: `Slow Growth' as a Conforma- tional Search Procedure," J. Med. Chem., 36 3489-3499 (1993); Michael Guha-Biswas, Michael Holder, and B.M. Pettitt.

(91) "Peptides in Ionic Solutions: A Simulation Study of a Bis-Penicillamine Enkephalin in Sodium Acetate Solution," J. Am. Chem. Soc., 115, 7493-7498 (1993); Paul E. Smith, Gail E. Marlow, and B. M. Pettitt.

(92) "Evidence for a New Spine of Hydration: Solvation of DNA Triple Helices," J. Am. Chem. Soc., 115, 9297-9298 (1993); V. Mohan, Paul E. Smith and B. M. Pettitt.

(93) "Molecular Dynamics Simulation of Ions and Water Around Triplex DNA," J. Phys. Chem., 97 12984-12990 (1993);V. Mohan, Paul E. Smith, and B. M. Pettitt.

(94) "Reply to: Comment on `Monte Carlo Evaluation of Real Time Feynman Path Integrals for Quantal Many Body Dynamics: Distributed Approximating Functions and Gaussian Sampling,' " J. Phys. Chem., 97 8107 (1993); D. J. Kouri, W. Zhu, X. Ma, B.M. Pettitt, and D. K. Hoffman.

(95) "Cooperative Triple Helix Formation at Distant Sites: The use of Hybrid Oligonu- cleotides Containing a Polymeric Linker," Nucleic Acids Research, 21 4810-4815 (1993); D. J. Kessler, B. M. Pettitt, Y.-K. Cheng, S. Smith, K. Jayaraman, and M. Hogan.

(96) "Salt Effects in Peptide Solutions: Theory and Simulations," Chemical Reviews, 93 2503-2521 (1993); Gail E. Marlow, John Perkyns and B.M. Pettitt.

(97) "Theoretical and Experimental Studies of Salt-Peptide Solutions," Adv. Comput. Biology, 1, 231-248 (1994); Gail E. Marlow and B.M. Pettitt.

(98) "The Relationship Between Mutation Rates for the (C
G) ! (T
A) Transition and Features of T.G Mispair Structures in Different Neighbor Environments, Determined by Free Energy Molecular Mechanics," Nucleic Acids Research, 21 6028-6037 (1994); Rahul Mitra, B.M. Pettitt, Graciela Rame' and R.D. Blake.

(99) "A Connected-Cluster of Hydration around Myoglobin: Correlation between Molec- ular Dynamics Simulations and Experiment," Proteins: Structure, Function and Genetics, 18 133-147 (1994); Valere Lounnas and B. M. Pettitt.

(100) "Distribution Function Implied Dynamics versus Residence Times and Correlations: Solvation Shells of Myoglobin," Proteins: Structure, Function and Genetics, 18 148- 160 (1994); Valere Lounnas and B. M. Pettitt.

(101) "A Global Model of the Protein-Solvent Interface," Biophysical J., 66, 601-614 (1994); Valere Lounnas, B. M. Pettitt and George N. Phillips.

(102) "A Structure Induced by 2S,3S-2,3- Methanomethionine," J. Am. Chem. Soc. 116 799-800 (1994); K. Burgess, K.-K. Ho and B.M. Pettitt.

(103) "On the Solubility of Aqueous 1-1 Electrolytes," J. Phys. Chem, 98 5147 - 5151 (1994); John Perkyns and B.M. Pettitt.

(104) "Phase Transitions of Water at Constant Chemical Potential," Mol. Phys., 82 67-83 (1994); J. Ji and B.M. Pettitt.

(105) "Sulfate Anion in Water: Model Structural, Thermodynamic and Dynamic Proper- ties," J. Phys. Chem, 98, 6225-6230 (1994); W.R. Cannon, B.M. Pettitt and J.A. McCammon.

(106) "Integral equation approaches to structure and thermodynamics of aqueous salt solu- tions," Biophysical Chemistry, 51, 129-146 (1994); John Perkyns and B.M. Pettitt.

(107) "Ideal Chemical Potential Contribution in Molecular Dynamics Simulations of the Grand Canonical Ensemble," Mol. Phys., 82 897-912 (1994); Samantha Weerasinghe and B.M. Pettitt.

(108) "Investigations into the Common Ion Effect," J. Chem. Phys., 101 5093-5109 (1994); Claudia Valdeavella, John Perkyns and B.M. Pettitt.

(109) "Modelling Solvation Effects in Biomolecules," J. Phys. Chem. 39 9700-9711 (1994); Paul Smith and B.M. Pettitt.

(110) "Molecular Dynamics at a Constant pH," Supercomputer Applications and High Per- formance Computing 8 47-53 (1994); John Mertz and B.M. Pettitt.

(111) "On the Conformational Effects of Substituting methionine with E-2,3-Methanome- thionine in Phe-Met-Arg-Phe-NH 2 ," J. Am. Chem. Soc. 117 54-65 (1995); K. - Burgess, K.-K. Ho and B.M. Pettitt.

(112) "Binary Solution Critical Opalescence: Mole Fraction vs. Temperature Phase Dia- gram," J. Chem. Ed., 72 560-564 (1995); Chris Stenland and B. M. Pettitt.

(113) "Ordinary Differential Equations of Molecular Dynamics," Comp. Math. Applic., 28 319-326 (1994); J. Andrew McCammon, Ridgway Scott and B. M. Pettitt.

(114) "Peptide Conformations Are Restricted by Solution Stability," J. Phys. Chem, 99 1-2 (1995); John Perkyns and B.M. Pettitt.

(115) "The Scaling of Molecular Dynamics On the KSR-1," I.E.E.E. Proceedings, Vol 5, 142-152 (1995); R. Haacke and B.M. Pettitt.

(116) "Structure and Dynamics of the Water Around Myoglobin," Protein Science 4, 149- 158 (1995); George N. Phillips and B.M. Pettitt.

(117) "Equilibrium Furanose Puckers in d(CG.G) 7 Triple-Strand Helical Nucleic Acids," J. Am. Chem. Soc. (submitted) Y.-K. Cheng, S. Weerasinghe, V. Mohan, P. Smith, G. Rame', B.M. Pettitt, K. Johnson, K. Dittrich, R. Tinder and M. Hogan.

(118) "Nanosecond Dynamics and Structure of a model DNA Triple Helix in Saltwater Solution," J. Am. Chem. Soc. 117 2147- 2158 (1995); S. Weerasinghe, P. Smith, V. Mohan, Y.-K. Cheng, B.M. Pettitt.

(119) "Non-isotropic Solutions of an OZ equation: Matrix Methods for Integral Equations," Comp. Phys. Comm. 85 239-250 (1995); Z.-M. Chen and B.M. Pettitt.

(120) "Conformational States Governing the Rates of Spontaneous Transition Mutations," Biopolymers 36 169-180 (1995); Rahul Mitra, B. M. Pettitt, and R. D. Blake.

(121) "Solvent Effects on Model d(CGG) 7 and d(TAT) 7 DNA Triple Helices," Biopolymers 35 457-473 (1995); Y.-K. Cheng and B.M. Pettitt.

(122) "A Sampling Problem in Molecular Dynamics Simulations of Macromolecules," Proc. Nat. Acad. Sci. USA 92 3288-92 (1995); James B. Clarage, Tod Romo, B. Kim Andrews, B. M. Pettitt and George N. Phillips Jr.

(123) "Effcient Ewald Electrostatic Calculations for Large Systems," Comp. Phys. Comm. 91 339-344 (1995); P.E. Smith and B.M. Pettitt.

(124) "Dielectric Response of Triplex DNA in Ionic Solution from Simulations," Biophys. J. 69 1519-1527 (1995); L. Yang, S. Weerasinghe, P. Smith and B.M. Pettitt.

(125) "Simulations of Conformations of Tuftsin and Cyclic Tuftsin Analogs," Int. J. Pep. Prot. Res. 46 372-380 (1995); C.V. Valdeavella, H. Blatt and B.M. Pettitt.

(126) "B to A transition of DNA on the Nanosecond Timescale," J. Phys. Chem 100, 2564- 2566 (1996); L. Yang and B. Montgomery Pettitt.

(127) " Salting in Peptides: Conformationally dependent solubilities and phase behavior of a tripeptide zwitterion in electrolyte solution," J. Am. Chem. Soc. 118, 1164-1172 (1996); John Perkyns, Y. Wang and B.M. Pettitt.

(128) "The dependence of hydration free energy on solute size," J. Phys. Chem. 100, 1323- 1329 (1996); John S. Perkyns and B.M. Pettitt.

(129) "Structure and Stability of a Model Pyrimidine-Purine-Purine DNA Triple Helix with a GC
T Mismatch by Simulation," Biochem. 34 16269-16278 (1996); S. Weerasinghe, P.E. Smith and B.M. Pettitt.

(130) "Tuftsin and Tuftsin Analogs: Biology, Synthesis and Design Theory," Curr. Med. Chem. 3 153{166 (1996); Kenji Nishioka, John McMurray, Fahad Al Obeidi and B.M. Pettitt.

(131) "Comparison of Protein Hydration Elucidated by Molecular Dynamics Simulations and X-ray Crystallography," Biophysical J. 74, 413 (1998); V.A. Makarov, B.A. An- drews and B.M. Pettitt.

(132) "Salt effects on peptide conformers: A dielectric study of tuftsin," Biophysical J. 71 3022-3029 (1996); L. Yang, C.V. Valdeavella, H.D. Blatt and B. M. Pettitt.

 (133) "Ewald Artifacts in Liquid State Molecular Dynamics Simulations," by J. Chem. Phys. 105 4289-4293 (1996); Paul E. Smith and B. M. Pettitt.

(134) "Modeling the DNA solvent Interface," Biopolymers 41 107-119 (1997); W. Rudnicki and B. M. Pettitt.

(135) "A Simple Two Dimensional Representation for the Common Secondary Structural Elements of Polypeptides and Proteins," Proteins: Structure, Function and Genetics 27 227-234(1997); Paul Smith, Herb Blatt and B. M. Pettitt.

(136) "Hydration effects on the electrostatic potential around tuftsin," Biopolymers 50 133- 143 (1999); C.V. Valdeavella, H.D. Blatt, L. Yang, and B. M. Pettitt.

(137) "Numerical considerations in the computation of the electrostatic free energy of inter- action within the Poisson-Boltzmann theory," J. Comp. Physics 136 263-271 (1997); A. M. Micu, B. Bagheri, A. V. Ilin, L. R. Scott and B. M. Pettitt.

(138) "Environmentally Dependent Conformational Preferences of Peptides," J. Am. Chem. Soc. 119 8714-8715 (1997); Paul Smith, Herb Blatt and B. M. Pettitt.

(139) "On the Presence of Rotational Ewald Artifacts in the Equilibrium and Dynamical Properties of a Zwitterionic Tetrapeptide in Solution," J. Phys. Chem. 101 3886-3890 (1997); Paul Smith, Herb Blatt and B. M. Pettitt.

(140) "Computationally useful bridge diagram series for the structure and thermodynamics of Lennard-Jones Theo. Chem. Accounts 96 61-70 (1997); John Perkyns, and B. M. Pettitt.

(141) "Experiment vs. Force Fields: DNA conformation from Molecular Dynamics Simula- tion," J. Phys. Chem. 101 7361-7363 (1997); Michael Feig and B. M. Pettitt.

(142) "Protonation effects on the Equilibrium and Dynamical Properties of the Alanine Tetrapeptide," J. Phys. Chem. 101 7628-7634 (1997); Herb Blatt, Paul Smith, and B. M. Pettitt.

(143) "Grand Canonical Ensemble Molecular Dynamics Simulations: Reformulation of Extended System Dynamics Approaches," J. Chem. Phys. 107 8594-8610 (1997); G. Lynch and B. M. Pettitt.

(144) " Structural Equilibrium of DNA Represented with Different Force Fields," Biophys. J. 75 (1998); Michael Feig and B. M. Pettitt.

(145) "Comparison of Simulated and Experimentally Determined Dynamics for a Variant of the LacI DNA-Binding Domain, Nlac-P," Biophysical J. 74 413-421 (1998); Liskin Swint-Kruse, K.S. Matthews, P.E. Smith, and B. M. Pettitt.

(146) "NMR and Quenched Molecular Dynamics Studies of Superpotent Linear and Cyclic alpha-Melanotropins", Int. J. Pep. Prot. Res. 51 420-431 (1998); F. Al-Obeidi, S. O'Connor, Constantin Job, V.J. Hruby and B. M. Pettitt.

(147) "Reconstructing the Protein-Water Interface," Biopolymers 45 469-478 (1998); Vladimir Makarov, K.A. Andrews, and B. M. Pettitt.

(148) "Protein Hydration Density: Theory, Simulation and Crystallography," Curr. Op. Struct. Bio. 8 218-221 (1998); Vladimir Makarov, K.A. Andrews, and B. M. Pettitt.

(149) "Erratum: Computationally useful bridge diagram series for the structure and ther- modynamics of Lennard-Jones Theo. Chem. Accounts 99 207-208 (1998); John Perkyns, and B. M. Pettitt.

 (150) "Diffusion of Solvent around Biomolecular Solutes: a Molecular Dynamics Simulation Study," Biophysical J. 75 1-9 (1998); Vladimir Makarov, M. Feig, K.A. Andrews, and B. M. Pettitt.

(151) "Characterizing Global Substates of Myoglobin" Structure 6 587-594 (1998); B. Kim Andrews, Tod Romo, James B. Clarage, B. M. Pettitt and George N. Phillips Jr.

(152) "A Reexamination of the Virial CoeÆcients of the Lennard-Jones Fluid," T. Chem. Acc. 105 244-251 (2001); Kippi Dyer, J.S. Perkyns and B. M. Pettitt.

(153) "Modeling Consistent with Experiment: High resolution Hydration patterns in Cor- relation with DNA Sequence and Conformation," Journal of Molecular Biology 286 1075-1095 (1999); M. Feig and B. M. Pettitt.

(154) "Comparison of the Potentials of Mean Force for Alanine Tetrapeptide between In- tegral Equation Theory and Simulation" Biophysical Chemistry 78 113-126 (1999); N. Prabhu, J. Perkyns, H. Blatt, P. Smith and B.M. Pettitt.

(155) "Structure and Dynamics of alpha -MSH using DRISM Integral Equation theory and Stochastic Dynamics" Biopolymers, 50, 255-272 (1999); N.V. Prabhu, J.S. Perkyns and B. M. Pettitt.

(156) "Modeling of alpha -MSH conformations with implicit solvent" Journal of Peptide Re- search, 54 394-407 (1999); N.V. Prabhu, J.S. Perkyns and B.M. Pettitt.

(157) "Kirkwood-Buff Thermodynamics Derived from Grand Canonical Molecular Dyna- mics and DRISM Calculations" Journal of Computational Physics, 151 , 135-145 (1999); G. Lynch, J.S. Perkyns and B.M. Pettitt.

(158) "Crystallographic Water Sites from a Theoretical Perspective" Structure, 6 1351-1354 (1998); M. Feig and B. M. Pettitt.

(159) "Large Scale Distributed Data Repository: Design of a Molecular Dynamics Trajec- tory Database" Future Generation Computer Systems, 16 101-110 (1999); Michael Feig, Matin Abdullah, Lennart Johnsson, and B. M. Pettitt.

(159) “Sodium and Chlorine Ions as Part of the DNA Solvation Shell Biophysical J. 77 1769-1781 (1999); Michael Feig, B. M. Pettitt.

(160) “perspective on ‘Volume and Heat of Hydration of Ions’, Born (1920) Z. Phys 1:45”, Theo. Chem. Accounts, 103 171-172 (2000); B. M. Pettitt.

(161) “Residence times of water molecules in the hydration sites of myoglobin” Biophysical J. 79 2966-2974 (2000); V. Makarov, K. Andrews, P. Smith, and B. M. Pettitt

(162) “comparison between simulation and Poisson-Boltzmann fields” Simulation and Theory of Electrostatic Interactions in Solution Eds. L.R. Pratt and G. Hummer, AIP Press, 411-416 (1999); B. M. Pettitt and C.V. Valdeavella.

(163) “Molecular Simulation Picture of DNA Hydration around A-and B-DNA” Biopoly­mers 48 199-209 (2000); Michael Feig and B. M. Pettitt.

(164) “SimDB: Problem Solving Environment for Molecular Dynamics Simulation and Analysis” 1st EGRID Forum (2000) L. Johnsson, Michael Feig and B.M. Pettitt.

(165) “Thermodynamics of Association to Molecule Immobilized in an Electric Double Layer” Chem. Phys. Let. 323 160-166 (2000); Arnold Vainrub and B.M. Pettitt.

(166) “New Boundary Condition for Computer Simulations of Interfacial Systems” Chem. Phys. Let. 326 193 -198 (2000); Ka-Yiu Wong and B.M. Pettitt.

(167) “Semi-grand canonical ensemble molecular dynamics simulation of BPTI” Chem. Phys. 258 405-413 (2000); G. Lynch and B.M. Pettitt.

(168) “Conformations of an Adenine Bulge in DNA Octamer and its Influence on DNA Structure from Molecular Dynamics Simulation”, Biophys. J. 81 352 -370 (2001); Michael Feig, Martin Zacharias and B. M. Pettitt.

(169) “Structural Basis for the Activity of pp60c?src Protein Tyrosine Kinase Inhibitors” Biopolymers, 59 167-179 (2001); N.V. Prabhu, S.A. Siddiqui, J.S. McMurray and B. M. Pettitt.

(170) “A Study of DNA tethered to Surface by an All-atom Molecular Dynamics Simula­tion” Theo. Chem. Accounts 106 233-235 (2001); Ka-Yiu Wong and B.M. Pettitt.

(171) “Numerical Simulation of the Sedimentation of Tripole-like body in an incompress­ible Viscous Fluid” Applied Math. Lett. 15 743-747 (2002); L. H. Juarez, R. Glowinski, B. M. Pettitt.

(172) “Simulations of the Bis-Penicillamine Enkephalin in Sodium Chloride Solution: Parameter Study” Biopolymers 60 134-152 (2001); Gail Marlow and B. M. Pettitt.

(173) “Fine tuning function: Correlation of hinge domain interactions with functional dis­tinctions between LacI and PurR Protein Science 11 778-794 (2002); Liskin Swint-Kruse, C. Larson, B. M. Pettitt and K.S. Matthews.

(174) “Computationally useful bridge diagram series II. Diagrams in h-bonds,” J. Chem. Phys. 116 9404-9413 (2002); John Perkyns, Kippi Dyer and B. M. Pettitt.

(175) “Computationally useful bridge diagram series III. Lennard-Jones mixtures,” J. Chem. Phys. 116 9413-9422 (2002); Kippi Dyer, John Perkyns, and B. M. Pettitt.

(176) “Solvation and Hydration of Proteins and Nucleic acids: Theoretical View of Simu­lation and Experiment” Accounts of Chemical Res. 35 376-384 (2002); V. Makarov, B.M. Pettitt and M. Feig.

(177) “Surface Electrostatic Effects in Oligonucleotide Microarrays: Control and Optimiza­tion of Binding Thermodynamics” Biopolymers 68,265-270 (2003); A. Vainrub and B.M. Pettitt.

(178) “Coulomb Blockage of Hybridization in Two-Dimensional DNA Arrays” Phys. Rev. 66, 41905 (2002); A. Vainrub and B.M. Pettitt.

(179) “Simulation of the Bis-Penicillamine Enkephalin in Ammonium Chloride Solution:comparison with Sodium Chloride” Biopolymers 68 192 -209 (2003); Gail E. Marlow and B. M. Pettitt.

(180) “Theoretical Considerations for the Efficient Design of DNA Arrays”, in Biomedical Technology and Devices Handbook, Eds. James E. Moore Jr. and George Zouri­dakis CRC Press,14:1-12, 2003; Arnold Vainrub, Tong Bin Li, Yuriy Fofanov and B. M. Pettitt.

(181) “Reconstruction of the genetic regulatory dynamics of the Rat spinal cord devel­opment: Local Invariants Approach” J. Biomed. Informatics 35 343-351(2003); Y. Fofanov and B.M. Pettitt.

(182) “non-Watson-Crick Motif of Base-pairing On Surfaces for Untethered Oligonu­cleotides”, Molecular Simulation 30, 121-129 (2004); Ka-Yiu Wong, Arnold Vainrub, Tom Powdrill, Michael Hogan, and B. M. Pettitt.

(183) “Microscopic DNA Fluctuations are in accord with macroscopic DNA stretching elas­ticity without strong dependence on force field choice” NATO ASI Series: Metal Ligand Interactions Kluwer Academic Press, ed. N. Russo 193-204 (2003); John Marko, Michael Feig and B. M. Pettitt.

(184) “Sensitive Quantitative Nucleic Acid Detection Using Oligonucleotide Microarrays”, J. Am. Chem. Soc., 125, 7798-7799 (2003); Arnold Vainrub and B. M. Pettitt.

(185) “Orientation of DNA on surface from simulation”, Biopolymers, 73, 570-578 (2004); Ka-Yiu Wong and B. M. Pettitt.

(186) “Theoretical aspects of genomic variation screening using DNA microarrays”, Biopoly­mers 73, 614-620 (2004); Arnold Vainrub and B. M. Pettitt.

(187) “A fast solver for the Ornstein-Zernike Equations”, J. Comp. Phys. 197/2 491-501 (2004); C.T. Kelly and B.M. Pettitt.

(188) “Statistical Thermodynamic Approach to the Chemical Activities in Two-Component Solutions”, J. Phys. Chem. 108, 2048-2055(2004); J. Roesgen, B. Montgomery Pettitt, John Perkyns, and David Wayne Bolen.

(189) “How correlated (independent) are appearances of n-mers in different genomes?” Bioinformatics 20(15), 2421-2428 (2004); Yi Luo, Charles Katili, Jim Wang, Yuri Y. Belosludtsev, Thomas F. Powdrill, Viacheslav Fofanov, Sergey Chumakov, Yuriy Fofanov, and B. M. Pettitt.

(190) “Communications Overlapping in Fast Multipole Particle Dynamics Methods”, J. Comp. Phys. (in press); Jakub Kurzak, B. M. Pettitt.

(191) “Short subsequences in genomes: How random are they?” Technical Report, Comp. Sci. of (2004); Yi Luo, Charles Katili, Jim Wang, Yuri Y. Belosludtsev, Thomas F. Powdrill, Viacheslav Fofanov, Sergey Chumakov, Yuriy Fofanov, and B. M. Pettitt.

(192) “Uncovering the basis of non-ideal behavior of biological molecules”, Biochemistry 43(45), 14472-14484 (2004); Joerg Roesgen, B. M. Pettitt, David Wayne Bolen.

(193) “Mutual Information for Continuous Variables and Analysis of Gene Expression Data”, Bull Math. Bio. (in press); Sergey Chumakov, Yuan Sun, Tongbin Li, Jorge Emmanuel Snchez Rodrguez, Arturo Chavez, B. Montgomery Pettitt, Yuriy Fofanov.

(194) “On the Mechanism of association of nanoscopic solutes” J. Am. Chem. Soc. (in press); Niharendu Choudhury and B.M. Pettitt.

(195) “Combined hopping-super exchange model of hole transfer in DNA” Chem. Phys. Lett. 400(1-3), 47-53 (2004); V. D. Lakhno, V. B. Sultanov, B.M. Pet­titt.

(196) “DNA Saline Solutions Near Surfaces: Design Parameters of DNA Arrays” NATO ASI Series Kluwer Academic Press, ed. Henderson (in press); B.M. Pettitt, Arnold Vainrub, and Ka-Yiu Wong.

"Uncovering the basis of non-ideal behavior of biological molecules", Biochemistry 43(45), 14472-14484 (2004); Joerg Roesgen, B. M. Pettitt, David Wayne Bolen.

"Using Statistical Properties of Short Subsequences in Microbial Identification", Proc. Int. Con. Math. Eng. Tech. Med. Bio. Sci. S. Chumakov, Catherine Putonti, B. M. Pettitt, George E. Fox, Richard C. Willson, Yuriy Fofanov, (Las Vegas, Nevada), 2004: 363-367.

"On the Mechanism of association of nanoscopic solutes" J. Am. Chem. Soc. 127, 3556-3567 (2005); Niharendu Choudhury and B.M. Pettitt.

"Combined hopping-super exchange model of a hole transfer in DNA" Chem. Phys. Lett. 400(1-3), 47-53 (2004); V. D. Lakhno, V. B. Sultanas, B.M. Pettitt.

"DNA Saline Solutions Near Surfaces: Design Parameters of DNA Arrays" NATO Sci- ence Series Kluwer Academic Press, ed. D Henderson, M. Holovko and A. Trokhymchuk 206, 381{393 (2005); B.M. Pettitt, Arnold Vainrub, and Ka-Yiu Wong.

"Dynamics of water trapped between hydrophobic solutes" J. Phys. Chem. B 109, 6422-6429 (2005); Niharendu Choudhury and B.M. Pettitt.

"Local Density Profiles are Coupled to Solute Size and Attractive Potential for Nanoscopic Hydrophobic Solutes" Molecular Simulations 31, 457-463 (2005); Ni- harendu Choudhury, B.M. Pettitt.

"Massively Parallel Implementation of a Fast Multipole Method for Distributed Mem- ory Machines" Journal of Parallel and Distributed Computing 65 870-881 (2005); Jakub Kurzak, B.M. Pettitt.

"Simple Bond Length Dependence: A Correspondence Between Reactive Fluid The- ories" J. Chem. Phys. 122 (23) 236101/1-236101/2 (2005); Kippi M. Dyer, John S. Perkyns and B.M. Pettitt.

"Solvent Participation in Serratia marcescens Endonuclease Complexes" Proteins: Structure, Function, Bioinformatics 62(4) 982-995 (2006); Chuanying Chen, Brian W. Beck, Kurt Krause and B.M. Pettitt.

"Protein Folding, Stability and Solvation Structure in Osmolal Solutions" Biophys. J. 89, 29882997 (2005); Joerg Roesgen, B. M. Pettitt, David Wayne Bolen.

"Effective Density Terms in Proper Integral Equations" J. Chem. Phys. 123(20), 204512/1-204512/11 (2005); Kippi M. Dyer, John S. Perkyns and B.M. Pettitt.

The role of attractive forces on the dewetting of large hydrophobic solutes", Mod- elling Molecular Structure and Reactivity in Biological Systems Ed: Naidoo, K.J. Royal Society of Chemistry, Cambridge, UK, 49-57 (2006); Niharendu Choudhury and B.M. Pettitt.

"Electrostatics of DNA-DNA juxtapositions: Consequences for type II topoisomerase function" J. Phys. Cond. Matter, 18(14), S173-S185 (2006); Graham L. Randall, B. M. Pettitt, Gregory R. Buck, E. Lynn Zechiedrich.

"The theoretical basis of universal identification systems for bacteria and viruses", The Journal of Biological Physics and Chemistry 5, 121-11128 (2005); S. Chumakov, C. Belapurkar, C. Putonti, T.-B. Li, B.M. Pettitt, G. E. Fox, R. C. Willson and Y. Fofanov.

"Enthalpy-Entropy contributions to the potential of mean force of nanoscopic hy- drophobic solutes" J. Phys. Chem. B, 110(16), 8459-8463(2006); Niharendu Choudhury and B.M. Pettitt.

"Fast Multipole Methods for Particle Dynamics" Molecular Simulations 32 1-17 (2006); Jakub Kurzak, B.M. Pettitt.

"Force Field Comparisons of the Heat Capacity of Carbon Nanotubes", Mol. Simulation 32 839-848 (2006); Cliff Y. Guo, B.M. Pettitt, Lewis T. Wheeler.

"Using Mutual Information to Discover Temporal Patterns in Gene Expression Data", Medical Physics: Ninth Mexican Symposium on Medical Physics, 854 25-30 (2006); Chumakov S., Ballesteros E., Snchez Rodrguez, J.E., Chvez, A., Zhang, M., Pettitt, B.M. and Fofanov, Y.

" A Systematic Investigation of Theories of Transport in the Lennard-Jones Fluid", J. Chem. Phys. 126, 034502-1:10 (2007); Kippi Dyer, B. M. Pettitt, George Stell.

"An Analysis of the Molecular Origin of Osmolyte-dependent Protein Stability" Prot. Sci. 16, 733-743 (2007); Joerg Roesgen, B. M. Pettitt, David Wayne Bolen.

" An optimized theory for simple and molecular °uids", J. Chem. Phys. 126 124107- 1:9 (2007); M. Marucho and B. M. Pettitt.

"The Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics", Biopolymers 85(3), 241-252 (2007); Chuanying Chen, Brian W. Beck, Kurt Krause, Tiffany E. Weksberg and B.M. Pettitt.

"The Dewetting transition and the Hydrophobic Effect" Journal of the American Chemical Society, 129(15), 4848-4852 (2007); Niharendu Choudhury and B.M. Pettitt.

"Preferential Solvation in Urea Solutions at Different Concentrations: Properties from Simulation Studies" J. Phys. Chem. 111(19), 5233-5242 (2007); H. Kokubo and B. M. Pettitt.

"Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin: Loop-Cap Transition May Explain Selective Activation of Metronidazole" Biophys. J. 92, 3337- 3345 (2007); Tiffany E Warth, Gillian C Lynch, Kurt L Krause, B.M. Pettitt.

"PIDA: A new algorithm for pattern identification", O. J. Bioinf. (in press) Catherine Putonti, B. M. Pettitt, Jeffrey Reid and Yuriy Fofanov.

"Generation of FFT's for Translations of Multipole Expansions in Spherical Harmonics" J. High Perf. Comp., (in press); Jakub Kurzak, Dragan Mirkovic, B.M. Pettitt and S. Lennart Johnsson.

"Message-Passing Implementation of the Data Diffusion Communication Model in Fast Multipole Methods: Large Scale Biomolecular Simulations" J. Algor. Comp. Tech., (in press); Jakub Kurzak, B.M. Pettitt

"A Site-Renormalized Molecular Fluid Theory" J. Chem. Phys. 127(19), 194506/1- 194506/14(2007); Kippi M. Dyer, John S. Perkyns and B.M. Pettitt.

"An Angle Dependent Site-Renormalized Theory for the Conformations of n-butane in a simple °uid"Cond. Mat. Phys. 10 331-342 (2007); Kippi M. Dyer, John S. Perkyns, B.M. Pettitt and George Stell.

"Molecular basis of the near ideality of urea solutions"Biophysical J. 93, 3392-3407 (2007); H. Kokubo, Joerg Roesgen, David Wayne Bolen and B.M. Pettitt.

"Peptide conformations of a microarray surface-tethered epitope of the tumor suppres- sor p53" J. Phys. Chem. , 111(49), 13797-13806 (2007); Jun Feng, Ka-Yiu Wong, Gillian Lynch, Xiaolian Gao and B.M. Pettitt.

"Free Energy Calculations for DNA near surfaces using an Ellipsoidal Geometry", Comm. Phys. Comm. 3, 1117-1131 (2008); J. Ambia-Garrido, and B.M. Pettitt

"Determination of the transition-state entropy for aggregation suggests how the growth of sickle cell hemoglobin polymers can be slowed", J. Mol. Biol. (2008); Peter G Vekilov, Nihar Choudhury, B.M. Pettitt, Ronald L Nagel