Publications


  • Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15
    Asthagiri D, Karandur D, Tomar DS, Pettitt BM.
    J Phys Chem B. 121(34), 8078-8084 (2017)
  • Influence of DNA sequence on the structure of minicircles under torsional stress.
    Wang Q, Irobalieva RN, Chiu W, Schmid MF, Fogg JM, Zechiedrich L, Pettitt BM.
    Nucleic Acids Res. 45(13), 7633-7642 (2017)
  • Phage-like packing structures with mean field sequence dependence.
    Myers CG, Pettitt BM.
    J Comput Chem. 38(15), 1191-1197 (2017)
  • Nonpolar Solvation Free Energy from Proximal Distribution Functions.
    Ou S, Drake JA, Pettitt BM.
    J Phys Chem B. 121(15), 3555-3564 (2017)
  • Importance of disentanglement and entanglement during DNA replication and segregation: Comment on: "Disentangling DNA molecules" by Alexander Vologodskii.
    Bates D, Pettitt BM, Buck GR, Zechiedrich L.
    Phys Life Rev., 18, 160-164 (2016)
  • Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility
    Drake JA, Harris RC, Pettitt BM
    Biophys J., 111(4), 756-67 (2016)
  • Dielectric behavior for saline solutions from renormalized diagrammatically proper interaction site model theory
    Dyer KM, Perkyns JS, Pettitt BM
    J Phys Condens Matter, 28(41), 414006 (2016)
  • Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace
    Zhang C, Lai CL, Pettitt BM
    Mol Simul., 42(13), 1079-89 (2016)
  • Changes in conformational dynamics of basic side chains upon protein-DNA association
    Esadze A, Chen C, Zandarashvili L, Roy S, Pettitt BM, Iwahara J
    Nucl. Acids Res., 44(14), 6961-70 (2016)
  • Solute-Solvent Energetics Based on Proximal Distribution Functions
    Ou SC, Pettitt BM
    J Phys Chem B, 120(33), 8230-7 (2016)
  • The Contribution of Electrostatic Interactions to the Collapse of Oligoglycine in Water
    Karandur D, Pettitt BM
    Condensed Matter Physics, 19(2), 23802 (2016)
  • Sequence Affects the Cyclization of DNA Minicircles
    Wang Q, Pettitt BM
    J Phys Chem Lett, 7, 1042-1046 (2016)
  • Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins
    Harris RC, Pettitt BM
    J Phys Condens Matter, 28(8), 083003 (2016)
  • DNA Shape versus Sequence Variations in the Protein Binding Process
    Chen C, Pettitt BM
    Biophys. J., 110(3), 534-44 (2016)
  • Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide
    Tomar DS, Weber V, Pettitt BM, Asthagiri D.
    J. Phys. Chem. B., 120(1), 69-76 (2016)
  • Protein collapse driven against solvation free energy without H-bonds
    Karandur D, Harris RC, Pettitt BM
    Protein Sci., 25(1), 103-10 (2016)
  • Examining the Assumptions Underlying Continuum-Solvent Models
    Robert C. Harris, B.M. Pettitt
    J. Chem. Theory Comput., 11(10), 4593-600 (2015)
  • Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins
    Nguyen BL, Pettitt BM.
    J. Chem. Theory Comput., 11(4), 1399-1409 (2015)
  • Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes
    Chen C, Esadze A, Zandarashvili L, Nguyen D, Pettitt BM, Iwahara J
    J Phys Chem Lett., 6(14), 2733-2737 (2015)
  • Computation of virial coefficients from integral equations
    Zhang C, Lai CL, Pettitt BM.
    J Chem Phys., 142(21), 214110 (2015)
  • Force field-dependent solution properties of glycine oligomers
    Drake JA, Pettitt BM
    J Comput Chem., 36(17), 1275-85 (2015)
  • Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines
    Rojas M, Golovko G, Khanipov K, Albayrak L, Chumakov S, Pettitt BM, Strongin AY, Fofanov Y.
    PLoS One, 10(6), e0127799 (2015)
  • Twist-Induced Defects of the P-SSP7 Genome Revealed by Modeling the Cryo-EM Density
    Wang Q, Myers CG, Pettitt BM
    J Phys Chem B., 119(15), 4937-43 (2015)
  • Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries
    Dyer KM, Perkyns JS, Pettitt BM
    J Phys Chem B., 119 (29), 9450-9459 (2015)
  • Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins
    Lichti CF, Mostovenko E, Wadsworth PA, Lynch GC, Pettitt BM, Sulman EP, Wang Q, Lang FF, Rezeli M, Marko-Varga G, Végvári A, Nilsson CL
    J Proteome Res., 14(2), 778-86 (2015)
  • Solvation and cavity occupation in biomolecules
    Lynch GC, Perkyns JS, Nguyen BL, Pettitt BM
    Biochim Biophys Acta., 1850(5), 923-31 (2015)
  • Multibody correlations in the hydrophobic solvation of glycine peptides
    Harris RC, Drake JA, Pettitt BM
    J Chem Phys., 141(22), 22D525 (2014)
  • Effects of geometry and chemistry on hydrophobic solvation
    Harris RC, Pettitt BM
    Proc Natl Acad Sci U S A, 111(41), 14681-6 (2014)
  • Solubility and aggregation of Gly(5) in water
    Karandur D, Wong KY, Pettitt BM
    J Phys Chem B, 118(32), 9565-72 (2014)
  • Computation of high-order virial coefficients in high-dimensional hard-sphere fluids by Mayer sampling
    C Zhang, BM Pettitt
    Molecular Physics, 112(9-10), 1427-47 (2014).
  • Conditional Solvation Thermodynamics of Isoleucine in Model Peptides and the Limitations of the Group-Transfer Model
    DS Tomar, V Weber, BM Pettitt, D. Asthagiri
    J Phys Chem B, 118(15), 4080-87 (2014).
  • Modeling DNA Thermodynamics under Torsional Stress
    Q Wang, BM Pettitt
    Biophysical Journal, 106(5), 1182-93 (2014).
  • A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies
    JF Truchon, BM Pettitt, P Labute
    J Chem Theory Comput, 10(3), 934-41 (2014).
  • Solvation Free Energies of Alanine Peptides: The Effect of Flexibility
    H Kokubo, RC Harris, D Asthagiri, BM Pettitt
    J Phys Chem B, 117(51), 16428-35 (2013).
  • Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence
    JA Theruvathu, YW Yin, BM Pettitt, LC Sowers
    Biochemistry, 52(47), 8590-8598 (2013).
  • Proximal distributions from angular correlations: A measure of the onset of coarse-graining
    KM Dyer, BM Pettitt
    J Chem Phys, 139(21), 214111 (2013).
  • Physico-chemical foundations underpinning microarray and next-generation sequencing experiments
    Andrew Harrison, Hans Binder, Arnaud Buhot, Conrad J. Burden, Enrico Carlon, Cynthia Gibas, Lara J. Gamble, Avraham Halperin, Jef Hooyberghs, David P. Kreil, Rastislav Levicky, Peter A. Noble, Albrecht Ott, B. Montgomery Pettitt, Diethard Tautz, Alexander E. Pozhitkov
    Nucleic Acids Research, 41, 2779-2796 (2013).
  • Domain organization of membrane-bound factor VIII
    Svetla Stoilova-McPhie, Gillian C. Lynch, Steven Ludtke, B. Montgomery Pettitt
    Biopolymers, 99, 448-459 (2013).
  • Osmophobics and Hydrophobics: The changing landscape of protein folding
    M.A. Auton and B.M. Pettitt
    Fluctuation Theory of Solutions: Applications in Chemistry, Chemical Engineering, and Biophysics, Taylor and Francis, eds. Paul E. Smith, Enrico Matteoli, John P. OConnell (2013).
  • The unsolved "solved-problem" of protein folding
    B. Montgomery Pettitt
    Journal of Biomolecular Structure & Dynamics, 31, 1024-1027 (2013).
  • Communication: Origin of the contributions to DNA structure in phages
    Christopher G. Myers, B. Montgomery Pettitt
    Journal of Chemical Physics, 138, 071103 (2013).
  • Studying proteins and peptides at material surfaces
    Jun Feng, Gillian C. Lynch, B. Montgomery Pettitt
    in Innovations in Biomolecular Modeling and Simulations; Tamar Schlick (eds.); The Royal Society of Chemistry, 293-320 (2012).
  • Bullied no more: when and how DNA shoves proteins around
    Jonathan M. Fogg, Graham L. Randall, B. Montgomery Pettitt, De Witt L. Sumners, Sarah A. Harris, Lynn Zechiedrich
    Quarterly Reviews of Biophysics, 45, 257-299 (2012).
  • Correction to "Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions"
    Bin Lin, Ka-Yiu Wong, Char Hu, Hironori Kokubo, B. Montgomery Pettitt
    The Journal of Physical Chemistry Letters, 3, 69-69 (2012).
  • Accurate prediction of binding thermodynamics for DNA on surfaces
    Arnold Vainrub, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 115, 13300-13303 (2011).
  • The binding process of a nonspecific enzyme with DNA
    Chuanying Chen, B. Montgomery Pettitt
    Biophysical Journal, 101, 1139-1147 (2011).
  • Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach
    J. Ambia-Garrido, Arnold Vainrub, B. Montgomery Pettitt
    Journal of Physics: Condensed Matter, 23, 325101 (2011).
  • Integral equations in the study of polar and ionic interaction site fluids
    Jesse J. Howard, B. Montgomery Pettitt
    Journal of Statistical Physics, 145, 441-466 (2011).
  • Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions
    Bin Lin, Ka-Yiu Wong, Char Hu, Hironori Kokubo, B. Montgomery Pettitt
    The Journal of Physical Chemistry Letters, 2, 1626-1632 (2011).
  • Peptide conformational preferences in osmolyte solutions: transfer free energies of decaalanine
    Hironori Kokubo, Char Y. Hu, B. Montgomery Pettitt
    Journal of the American Chemical Society, 133, 1849-1858 (2011).
  • Note: On the universality of proximal radial distribution functions of proteins
    Bin Lin, B. Montgomery Pettitt
    Journal of Chemical Physics, 134, 106101 (2011).
  • Ion and solvent density distributions around canonical B-DNA from integral equations
    Jesse J. Howard, Gillian C. Lynch, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 115, 547-556 (2011).
  • Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water
    Bin Lin, B. Montgomery Pettitt
    Journal of Computational Chemistry, 32, 878-885 (2011).
  • A model for structure and thermodynamics of ssDNA and dsDNA near a surface: a coarse grained approach
    J. Ambia-Garrido, Arnold Vainrub, B. Montgomery Pettitt
    Computer Physics Communications, 181, 2001-2007 (2010).
  • The behavior of ions near a charged wall-dependence on ion size, concentration, and surface charge
    Jesse J. Howard, John S. Perkyns, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 114, 6074-6083 (2010).
  • Backbone additivity in the transfer model of protein solvation
    Char Y. Hu, Hironori Kokubo, Gillian C. Lynch, D. Wayne Bolen, B. Montgomery Pettitt
    Protein Science, 19, 1011-1022 (2010).
  • Protein solvation from theory and simulation: exact treatment of coulomb interactions in three-dimensional theories
    John S. Perkyns, Gillian C. Lynch, Jesse J. Howard, B. Montgomery Pettitt
    The Journal of Chemical Physics, 132, 064106 (2010).
  • Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model
    Char Y. Hu, Gillian C. Lynch, Hironori Kokubo, B. Montgomery Pettitt
    Proteins: Structure, Function, and Bioinformatics, 78, 695-704 (2010).
  • Bullied no more : when DNA shoves proteins around (knots and soft-matter physics: topology of polymers and related topics in physics, mathematics and biology
    Graham L. Randall, DeWitt L. Summers, B. Montgomery Pettitt, Lynn Zechiedrich
    Bussei Kenkyu, 92, 80-83 (2009).
  • Transport properties of water at functionalized molecular interfaces
    Jun Feng, Ka-Yiu Wong, Kippi Dyer, B. Montgomery Pettitt
    The Journal of Chemical Physics, 131, 125102 (2009).
  • In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form
    Graham L. Randall, Lynn Zechiedrich, B. Montgomery Pettitt
    Nucleic Acids Research, 37, 5568-5577 (2009).
  • Site-renormalised molecular fluid theory: on the utility of a two-site model of water
    Kippi M. Dyer, John S. Perkyns, George Stell, B. Montgomery Pettitt
    Molecular Physics, 107, 423-431 (2009).
  • The melting mechanism of DNA tethered to a surface
    Khawla Qamhieh, Ka-Yiu Wong, Gillian C. Lynch, B. Montgomery Pettitt
    International Journal of Numerical Analysis and Modeling, 6, 474-488 (2009).
  • Osmolyte influence on protein stability: perspectives from theory and experiments
    Char Hu, Joerg Rosgen, and B.M. Pettitt
    in Modeling of Solvent Environments, ed. M. Feig, J Wiley, NY NY 77-92 (2009).
  • Salt effects on surface-tethered peptides in solution
    Jun Feng, Ka-Yiu Wong, Gillian C. Lynch, Xiaolian Gao, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 113, 9472-9478 (2009).
  • Osmolyte solutions and protein folding
    Char Y. Hu, B. Montgomery Pettitt, Joerg Roesgen
    F1000 Biology Reports, 1, (2009).
  • Advantage of being a dimer for Serratia marcescens endonuclease
    Chuanying Chen, Kurt Krause, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 113, 511-521 (2009).
  • An integral equation study of the hydrophobic interaction between graphene plates
    Jesse J. Howard, John S. . Perkyns, Niharendu Choudhury, B. Montgomery Pettitt
    Journal of Chemical Theory and Computation, 4, 1928-1939 (2008).
  • The pathway of oligomeric DNA melting investigated by molecular dynamics simulations
    Ka-Yiu Wong, B. Montgomery Pettitt
    Biophysical Journal, 95, 5618-5626 (2008).
  • A molecular site-site integral equation that yields the dielectric constant
    Kippi M. Dyer, John S. Perkyns, George Stell, B. Montgomery Pettitt
    The Journal of Chemical Physics, 129, 104512 (2008).
  • Solutions of the optimized closure integral equation theory: heteronuclear polyatomic fluids
    M. Marucho, C. T. Kelley, B. Montgomery Pettitt
    Journal of Chemical Theory and Computation, 4, 385-396 (2008).
  • Determination of the transition-state entropy for aggregation suggests how the growth of sickle cell hemoglobin polymers can be slowed
    Peter G. Vekilov, Oleg Galkin, B. Montgomery Pettitt, Nihar Choudhury, Ronald L. Nagel
    Journal of Molecular Biology, 377, 882-888 (2008).
  • Free energy calculations for DNA near surfaces using an ellipsoidal geometry
    J. Ambia-Garrido, B. Montgomery Pettitt
    Communications in Computational Physics, 3, 1117-1131 (2008).
  • Message-passing implementation of the data diffusion communication model in fast multipole methods: large scale biomolecular simulations
    Jakub Kurzak, B. Montgomery Pettitt
    Journal of Algorithms & Computational Technology, 2, 557-579 (2008).
  • Automatic generation of FFT for translations of multipole expansions in spherical harmonics
    Jakub Kurzak, Dragan Mirkovic, B. Montgomery Pettitt, S. Lennart Johnsson
    International Journal of High Performance Computing Applications, 22, 219-230 (2008).
  • Molecular basis of the apparent near ideality of urea solutions
    Hironori Kokubo, Jörg Rösgen, David Wayne Bolen, B. Montgomery Pettitt
    Biophysical Journal, 93, 3392-3407 (2007).
  • Peptide conformations for a microarray surface-tethered epitope of the tumor suppressor p53
    Jun Feng, Ka-Yiu Wong, Gillian C. Lynch, Xiaolian Gao, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 111, 13797-13806 (2007).
  • A site-renormalized molecular fluid theory
    Kippi M. Dyer, John S. Perkyns, B. Montgomery Pettitt
    The Journal of Chemical Physics, 127, 194506 (2007).
  • An angle dependent site-renormalized theory for the conformations of N-butane in a simple fluid
    K. Dyer, J. Perkyns, B. Pettitt, G. Stell
    Condensed Matter Physics, 10, 331-342 (2007).
  • PIDA: A new algorithm for pattern identification
    C. Putonti, B. M. Pettitt, J. G. Reid, Y. Fofanov
    Online Journal of Bioinformatics, 8, 30-40 (2007).
  • Molecular dynamics simulations of Trichomonas vaginalis ferredoxin show a loop-cap transition
    Tiffany E. Weksberg, Gillian C. Lynch, Kurt L. Krause, B. Montgomery Pettitt
    Biophysical Journal, 92, 3337-3345 (2007).
  • Preferential solvation in urea solutions at different concentrations: properties from simulation studies
    Hironori Kokubo, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 111, 5233-5242 (2007).
  • The dewetting transition and the hydrophobic effect
    Niharendu Choudhury, B. Montgomery Pettitt
    Journal of the American Chemical Society, 129, 4847-4852 (2007).
  • Effects of dimerization of Serratia marcescens endonuclease on water dynamics
    Chuanying Chen, Brian W. Beck, Kurt Krause, Tiffany E. Weksberg, B. Montgomery Pettitt
    Biopolymers, 85, 241-252 (2007).
  • Optimized theory for simple and molecular fluids
    M. Marucho, B. Montgomery Pettitt
    Journal of Chemical Physics, 126, 124107 (2007).
  • An analysis of the molecular origin of osmolyte-dependent protein stability
    Jörg Rösgen, B. Montgomery Pettitt, David Wayne Bolen
    Protein Science, 16, 733-743 (2007).
  • Systematic investigation of theories of transport in the Lennard-Jones fluid
    Kippi M. Dyer, B. M. Pettitt, George Stell
    Journal of Chemical Physics, 126, 034502 (2007).
  • Using Mutual Information to Discover Temporal Patterns in Gene Expression Data
    Chumakov S., Ballesteros E., Snchez Rodrguez, J.E., Chvez, A., Zhang, M., Pettitt, B.M. and Fofanov, Y.
    Medical Physics: Ninth Mexican Symposium on Medical Physics, 854 25-30 (2006).
  • Force field comparisons of the heat capacity of carbon nanotubes
    C. Y. Guo, B. Montgomery Pettitt, L. T. Wheeler
    Molecular Simulation, 32, 839-848 (2006).
  • Fast multipole methods for particle dynamics
    J. Kurzak, B. M. Pettitt
    Molecular Simulation, 32, 775-790 (2006).
  • Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes
    Niharendu Choudhury, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 110, 8459-8463 (2006).
  • Electrostatics of DNA-DNA juxtapositions: consequences for type II topoisomerase function
    Graham L. Randall, B. Montgomery Pettitt, Gregory R. Buck, E. Lynn Zechiedrich
    Journal of Physics: Condensed Matter, 18, S173-S185 (2006).
  • The role of attractive forces on the dewetting of large hydrophobic solutes
    Niharendu Choudhury and B.M. Pettitt
    Modelling Molecular Structure and Reactivity in Biological Systems , Ed: Naidoo, K.J. Royal Society of Chemistry, Cambridge, UK, 49-57 (2006).
  • Solvent participation in Serratia marcescens endonuclease complexes
    Chuanying Chen, Brian W. Beck, Kurt Krause, B. Montgomery Pettitt
    Proteins: Structure, Function, and Bioinformatics, 62, 982-995 (2006).
  • DNA saline solutions near surfaces - A few ideas towards design parameters of DNA arrays
    B. M. Pettitt, A. Vainrub, K.-Y. Wong
    in Ionic Soft Matter: Modern Trends in Theory and Applications; NATO Science Series; Douglas Henderson, Myroslav Holovko, Andrij Trokhymchuk (eds.); Springer, 381-393 (2005).
  • The theoretical basis of universal identification systems for bacteria and viruses
    S. Chumakov, C. Belapurkar, C. Putonti, T.-B. Li, B. M. Pettitt, G. E. Fox, R. C. Willson, Y. Fofanov
    Journal of Biological Physics and Chemistry, 5, 121-128 (2005).
  • Effective density terms in proper integral equations
    Kippi M. Dyer, John S. Perkyns, B. Montgomery Pettitt
    The Journal of Chemical Physics, 123, 204512 (2005).
  • Protein folding, stability, and solvation structure in osmolyte solutions
    Jörg Rösgen, B. Montgomery Pettitt, David Wayne Bolen
    Biophysical Journal, 89, 2988-2997 (2005).
  • Simple bond length dependence: a correspondence between reactive fluid theories
    Kippi M. Dyer, John S. Perkyns, B. M. Pettitt
    The Journal of Chemical Physics, 122, 236101 (2005).
  • Massively parallel implementation of a fast multipole method for distributed memory machines
    Jakub Kurzak, B. Montgomery Pettitt
    Journal of Parallel and Distributed Computing, 65, 870-881 (2005).
  • Local density profiles are coupled to solute size and attractive potential for nanoscopic hydrophobic solutes
    N. Choudhury, B. Montgomery Pettitt
    Molecular Simulation, 31, 457-463 (2005).
  • Dynamics of water trapped between hydrophobic solutes
    Niharendu Choudhury, B. Montgomery Pettitt
    The Journal of Physical Chemistry. B, 109, 6422-6429 (2005).
  • On the mechanism of hydrophobic association of nanoscopic solutes
    Niharendu Choudhury, B. Montgomery Pettitt
    Journal of the American Chemical Society, 127, 3556-3567 (2005).
  • Communications overlapping in fast multipole particle dynamics methods
    Jakub Kurzak, B. Montgomery Pettitt
    Journal of Computational Physics, 203, 731-743 (2005).
  • Short subsequences in genomes: How random are they?
    Yi Luo, Charles Katili, Jim Wang, Yuri Y. Belosludtsev, Thomas F. Powdrill, Viacheslav Fofanov, Sergey Chumakov, Yuriy Fofanov, and B. M. Pettitt
    Technical Report, Comp. Sci. U of H (2004).
  • Uncovering the basis for nonideal behavior of biological molecules
    Jörg Rösgen, Bernard Montgomery Pettitt, David Wayne Bolen
    Biochemistry, 43, 14472-14484 (2004).
  • Combined hopping–superexchange model of a hole transfer in DNA
    V. D. Lakhno, V. B. Sultanov, B. Montgomery Pettitt
    Chemical Physics Letters, 400, 47-53 (2004).
  • Using statistical properties of short subsequences in microbial identification
    Sergei Chumakov, Catherine Putonti, B. Montgomery Pettitt, George Fox, Richard C. Willson, Yuriy Fofanov
    in Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS '04; Faramarz Valafar, Homayoun Valafar (eds.); CSREA Press, 363-370 (2004).
  • How independent are the appearances of N-mers in different genomes?
    Yuriy Fofanov, Yi Luo, Charles Katili, Jim Wang, Yuri Belosludtsev, Thomas Powdrill, Chetan Belapurkar, Viacheslav Fofanov, Tong-Bin Li, Sergey Chumakov, B. Montgomery Pettitt
    Bioinformatics, 20, 2421-2428 (2004).
  • Statistical thermodynamic approach to the chemical activities in two-component solutions
    Jörg Rösgen, B. Montgomery Pettitt, John Perkyns, David Wayne Bolen
    The Journal of Physical Chemistry B, 108, 2048-2055 (2004).
  • A fast solver for the Ornstein–Zernike equations
    C. T. Kelley, B. Montgomery Pettitt
    Journal of Computational Physics, 197, 491-501 (2004).
  • Theoretical aspects of genomic variation screening using DNA microarrays
    Arnold Vainrub, B. Montgomery Pettitt
    Biopolymers, 73, 614-620 (2004).
  • Orientation of DNA on a surface from simulation
    Ka-Yiu Wong, B. Montgomery Pettitt
    Biopolymers, 73, 570-578 (2004).
  • A non-Watson–Crick motif of base-pairing on surfaces for untethered oligonucleotides
    Ka-Yiu Wong, Arnold Vainrub, Tom Powdrill, Michael Hogan, B. Montgomery Pettitt
    Molecular Simulation, 30, 121-129 (2004).
  • Sensitive quantitative nucleic acid detection using oligonucleotide microarrays
    Arnold Vainrub, B. Montgomery Pettitt
    Journal of the American Chemical Society, 125, 7798-7799 (2003).
  • Microscopic DNA Fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force field choice
    John Marko, Michael Feig and B. M. Pettitt
    NATO ASI Series: Metal Ligand Interactions Kluwer Academic Press, ed. N. Russo, 193-204 (2003).
  • Simulation of the bis-(penicillamine) enkephalin in ammonium chloride solution: a comparison with sodium chloride
    Gail E. Marlow, B. Montgomery Pettitt
    Biopolymers, 68, 192-209 (2003).
  • Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics
    Arnold Vainrub, B. Montgomery Pettitt
    Biopolymers, 68, 265-270 (2003).
  • Theoretical considerations for the efficient design of DNA arrays
    Arnold Vainrub, Tong-Bin Li, B. Montgomery Pettitt
    in Biomedical Technology and Devices Handbook; James E. Moore, George Zouridakis (eds.); CRC Press, (2003).
  • Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: local invariants approach
    Yuriy Fofanov, B. Montgomery Pettitt
    Journal of Biomedical Informatics, 35, 343-351 (2002).
  • Coulomb blockage of hybridization in two-dimensional DNA arrays
    Arnold Vainrub, B. Montgomery Pettitt
    Physical Review E, 66, 041905 (2002).
  • Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment
    Valdimir Makarov, B. Montgomery Pettitt, M. Feig
    Accounts of Chemical Research, 35, 376-384 (2002).
  • Computationally useful bridge diagram series. III. Lennard-Jones mixtures
    Kippi Dyer, John Perkyns, B. Montgomery Pettitt
    Journal of Chemical Physics, 116, 9413-9421 (2002).
  • Computationally useful bridge diagram series. II. Diagrams in h-bonds
    John S. Perkyns, Kippi M. Dyer, B. Montgomery Pettitt
    Journal of Chemical Physics, 116, 9404-9412 (2002).
  • Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR
    Liskin Swint-Kruse, Christopher Larson, B. Montgomery Pettitt, Kathleen Shive Matthews
    Protein Science, 11, 778-794 (2002).
  • Numerical simulation of the sedimentation of a tripole-like body in an incompressible viscous fluid
    L. H. Juárez, R. Glowinski, B. M. Pettitt
    Applied Mathematics Letters, 15, 743-747 (2002).
  • Simulations of the bis-penicillamine enkephalin in sodium chloride solution: a parameter study
    Gail E. Marlow, B. Montgomery Pettitt
    Biopolymers, 60, 134-152 (2001).
  • A reexamination of virial coefficients of the Lennard-Jones fluid
    Kippi M. Dyer, John S. Perkyns, B. Montgomery Pettitt
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 105, 244-251 (2001).
  • A study of DNA tethered to a surface by an all-atom molecular dynamics simulation
    Ka-Yiu Wong, B. Montgomery Pettitt
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 106, 233-235 (2001).
  • Structural basis for the activity of pp60c-src protein tyrosine kinase inhibitors
    Ninad V. Prabhu, Subeeh A. Siddiqui, John S. McMurray, B. Montgomery Pettitt
    Biopolymers, 59, 167-179 (2001).
  • Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations
    Michael Feig, Martin Zacharias, B. Montgomery Pettitt
    Biophysical Journal, 81, 352-370 (2001).
  • Semi-grand canonical molecular dynamics simulation of bovine pancreatic trypsin inhibitor
    Gillian C. Lynch, B. Montgomery Pettitt
    Chemical Physics, 258, 405-413 (2000).
  • A new boundary condition for computer simulations of interfacial systems
    Ka-Yiu Wong, B. Montgomery Pettitt
    Chemical Physics Letters, 326, 193-198 (2000).
  • Thermodynamics of association to a molecule immobilized in an electric double layer
    Arnold Vainrub, B. Montgomery Pettitt
    Chemical Physics Letters, 323, 160-166 (2000).
  • SimDB: a problem solving environment for molecular dynamics simulation and analysis
    Martin Abdullah, Michael Feig, Lennart Johnsson, B. Montgomery Pettitt, Zdenko Tomasic
    in Isthmus 2000: Research and Development for the Information Society : Conference Proceedings; Scientific Research Committee (Poland) and Politechnika Pozna (eds.); Instytut Informatyki Politechnika Pozna, 321-329 (2000).
  • Residence times of water molecules in the hydration sites of myoglobin
    Vladimir A. Makarov, B. Kim Andrews, Paul E. Smith, B. Montgomery Pettitt
    Biophysical Journal, 79, 2966-2974 (2000).
  • A perspective on “Volume and heat of hydration of ions”
    B. M. Pettitt
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 103, 171-172 (2000).
  • Hydration effects on the electrostatic potential around tuftsin
    C. V. Valdeavella, H. D. Blatt, Liqiu Yang, B. Montgomery Pettitt
    Biopolymers, 50, 133-143 (1999).
  • A comparison between simulation and Poisson-Boltzmann fields
    B. Montgomery Pettitt, C. V. Valdeavella
    in Simulation and Theory of Electrostatic Interactions in Solution: Computational Chemistry, Biophysics, and Aqueous Solutions: Santa Fe, New Mexico, June 1999; Lawrence Riley Pratt, Gerhard Hummer (eds.); American Institute of Physics, 411-416 (1999).
  • Sodium and chlorine ions as part of the DNA solvation shell
    Michael Feig, B. Montgomery Pettitt
    Biophysical Journal, 77, 1769-81 (1999).
  • Large scale distributed data repository: design of a molecular dynamics trajectory database
    Michael Feig, Matin Abdullah, Lennart Johnsson, B. Montgomery Pettitt
    Future Generation Computer Systems, 16, 101-110 (1999).
  • Kirkwood–Buff thermodynamics derived from grand canonical molecular dynamics and DRISM calculations
    Gillian C. Lynch, John S. Perkyns, B. Montgomery Pettitt
    Journal of Computational Physics, 151, 135-145 (1999).
  • Modeling of α-MSH conformations with implicit solvent
    N. V. Prabhu, J. S. Perkyns, B. M. Pettitt
    The Journal of Peptide Research, 54, 394-407 (1999).
  • Structure and dynamics of α-MSH using DRISM integral equation theory and stochastic dynamics
    Ninad V. Prabhu, John S. Perkyns, B. Montgomery Pettitt, Victor J. Hruby
    Biopolymers, 50, 255-72 (1999).
  • Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation
    Ninad V. Prabhu, John S. Perkyns, Herb D. Blatt, Paul E. Smith, B. Montgomery Pettitt
    Biophysical Chemistry, 78, 113-26 (1999).
  • Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation
    Michael Feig, B. Montgomery Pettitt
    Journal of Molecular Biology, 286, 1075-95 (1999).
  • Crystallographic water sites from a theoretical perspective
    Michael Feig, B. Montgomery Pettitt
    Structure, 6, 1351-4 (1998).
  • A molecular simulation picture of DNA hydration around A- and B-DNA
    Michael Feig, B. Montgomery Pettitt
    Biopolymers, 48, 199-209 (1998).
  • Characterizing global substates of myoglobin
    B. Kim Andrews, Tod Romo, James B. Clarage, B. Montgomery Pettitt, George N. Phillips Jr.
    Structure, 6, 587-94 (1998).
  • Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study
    Vladimir A. Makarov, Michael Feig, B. Kim Andrews, B. Montgomery Pettitt
    Biophysical Journal, 75, 150-8 (1998).
  • Erratum: computationally useful bridge diagram series for the structure and thermodynamics of Lennard-Jones fluids
    John Perkyns, B. Montgomery Pettitt
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 99, 207-208 (1998).
  • Protein hydration density: theory, simulations and crystallography
    B. Montgomery Pettitt, Valdimir A. Makarov, B. Kim Andrews
    Current Opinion in Structural Biology, 8, 218-21 (1998).
  • Reconstructing the protein-water interface
    Vladimir A. Makarov, B. Kim Andrews, B. Montgomery Pettitt
    Biopolymers, 45, 469-78 (1998).
  • NMR and quenched molecular dynamics studies of superpotent linear and cyclic α-melanotropins
    Fahad Al-Obeidi, Steven D. O'Connor, Constantin Job, Victor J. Hruby, B. Montgomery Pettitt
    The Journal of Peptide Research, 51, 420-431 (1998).
  • Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P
    Liskin Swint-Kruse, Kathleen Shive Matthews, Paul E. Smith, B. Montgomery Pettitt
    Biophysical Journal, 74, 413-21 (1998).
  • Structural equilibrium of DNA represented with different force fields
    Michael Feig, B. Montgomery Pettitt
    Biophysical Journal, 75, 134-49 (1998).
  • Computational challenges in theoretical chemistry
    B. M. Pettitt, P. E. Smith
    in Computational Science for the 21st Century; M.-O. Bristeau, G. Etgen, W. Fitzgibbon, J. L. Lions, J. Periaux, M. F. Wheeler (eds.); John Wiley & Sons Ltd, 432-446 (1997).
  • Grand canonical ensemble molecular dynamics simulations: reformulation of extended system dynamics approaches
    Gillian C. Lynch, B. Montgomery Pettitt
    Journal of Chemical Physics, 107, 8594-8610 (1997).
  • Protonation effects on the equilibrium and dynamical properties of the alanine tetrapeptide
    Herb D. Blatt, Paul E. Smith, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 101, 7628-7634 (1997).
  • Experiment vs force fields: DNA conformation from molecular dynamics simulations
    Michael Feig, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 101, 7361-7363 (1997).
  • Computationally useful bridge diagram series for the structure and thermodynamics of Lennard-Jones fluids
    John Perkyns, B. Montgomery Pettitt
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 96, 61-70 (1997).
  • On the presence of rotational Ewald artifacts in the equilibrium and dynamical properties of a zwitterionic tetrapeptide in aqueous solution
    Paul E. Smith, Herb D. Blatt, B. Montgomery Pettitt
    The Journal of Physical Chemistry B, 101, 3886-3890 (1997).
  • Environmentally dependent conformational preferences of peptides
    Paul E. Smith, Herb D. Blatt, B. Montgomery Pettitt
    Journal of the American Chemical Society, 119, 8714-8715 (1997).
  • Numerical considerations in the computation of the electrostatic free energy of interaction within the Poisson–Boltzmann theory
    Alexandru M. Micu, Babak Bagheri, Andrew V. Ilin, L. Ridgway Scott, B. Montgomery Pettitt
    Journal of Computational Physics, 136, 263-271 (1997).
  • A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins
    Paul E. Smith, Herb D. Blatt, B. Montgomery Pettitt
    Proteins: Structure, Function, and Bioinformatics, 27, 227-34 (1997).
  • Modeling the DNA-solvent interface
    Witold R. Rudnicki, B. Montgomery Pettitt
    Biopolymers, 41, 107-119 (1997).
  • Ewald artifacts in liquid state molecular dynamics simulations
    Paul E. Smith, B. Montgomery Pettitt
    Journal of Chemical Physics, 105, 4289-4293 (1996).
  • Salt effects on peptide conformers: a dielectric study of tuftsin
    Liqiu Yang, Claudia V. Valdeavella, Herb D. Blatt, B. Montgomery Pettitt
    Biophysical Journal, 71, 3022-9 (1996).
  • Tuftsin and tuftsin analogs: biology, synthesis and design theory
    Kenji Nishioka, John McMurray, Fahad Al Obeidi, B. Montgomery Pettitt
    Current Medicinal Chemistry, 3, 153-166 (1996).
  • Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GC•T mismatch by simulation
    Samantha Weerasinghe, Paul E. Smith, B. Montgomery Pettitt
    Biochemistry, 34, 16269-16278 (1995).
  • Dependence of hydration free energy on solute size
    John Perkyns, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 100, 1323-1329 (1996).
  • Salting in peptides: conformationally dependent solubilities and phase behavior of a tripeptide zwitterion in electrolyte solution
    John S. Perkyns, Yiyang Wang, B. Montgomery Pettitt
    Journal of the American Chemical Society, 118, 1164-1172 (1996).
  • B to A transition of DNA on the nanosecond time scale
    Liqiu Yang, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 100, 2564-2566 (1996).
  • Biomolecular Modeling
    B.M. Pettitt and J.C. Smith
    Computer Physics Communications: Special Issue, v. 91 ed.
  • Simulations of conformers of tuftsin and a cyclic tuftsin analog
    C. V. Valdeavella, H. D. Blatt, B. Montgomery Pettitt
    International Journal of Peptide and Protein Research, 46, 372-80 (1995).
  • Dielectric response of triplex DNA in ionic solution from simulations
    Liqiu Yang, Samantha Weerasinghe, Paul E. Smith, B. Montgomery Pettitt
    Biophysical Journal, 69, 1519-27 (1995).
  • Efficient Ewald electrostatic calculations for large systems
    Paul E. Smith, B. Montgomery Pettitt
    Computer Physics Communications, 91, 339-344 (1995).
  • A sampling problem in molecular dynamics simulations of macromolecules
    James B. Clarage, Tod Romo, B. Kim Andrews, B. Montgomery Pettitt, George N. Phillips Jr.
    Proceedings of the National Academy of Sciences of the United States of America, 92, 3288-3292 (1995).
  • Solvent effects on model d(CG•G)7 and d(TA•T)7 DNA triple helices
    Yuen-Kit Cheng, B. Montgomery Pettitt
    Biopolymers, 35, 457-73 (1995).
  • Conformational states governing the rates of spontaneous transition mutations
    Rahul Mitra, B. Montgomery Pettitt, R. D. Blake
    Biopolymers, 36, 169-179 (1995).
  • Non-isotropic solution of an OZ equation: matrix methods for integral equations
    Zhuo-Min Chen, B. Montgomery Pettitt
    Computer Physics Communications, 85, 239-250 (1995).
  • Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution
    Samantha Weerasinghe, Paul E. Smith, V. Mohan, Y.-K. Cheng, B. Montgomery Pettitt
    Journal of the American Chemical Society, 117, 2147-2158 (1995).
  • Structure and dynamics of the water around myoglobin
    George N. Phillips Jr., B. Montgomery Pettitt
    Protein Science, 4, 149-58 (1995).
  • The scaling of molecular dynamics on the KSR1
    Robert Haacke, B. Montgomery Pettitt
    in System Sciences, 1995. Vol. V. Proceedings of the Twenty-Eighth Hawaii International Conference on; IEEE, 142-152 (1995).
  • Peptide conformations are restricted by solution stability
    John S. Perkyns, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 99, 1-2 (1995).
  • Ordinary differential equations of molecular dynamics
    J. A. McCammon, B. M. Pettitt, L. R. Scott
    Computers & Mathematics with Applications, 28, 319-326 (1994).
  • Binary-solution critical opalescence: mole fraction versus temperature phase diagram
    Chris Stenland, B. Montgomery Pettitt
    Journal of Chemical Education, 72, 560-564 (1995).
  • On the conformational effects of substituting methionine with (2S,3S)-2,3-methanomethionine in Phe-Met-Arg-Phe-NH2
    Kevin Burgess, Kwok-Kan Ho, B. Montgomery Pettitt
    Journal of the American Chemical Society, 117, 54-65 (1995).
  • Molecular dynamics at a constant pH
    John E. Mertz, B. Montgomery Pettitt
    International Journal of High Performance Computing Applications, 8, 47-53 (1994).
  • Modeling solvent in biomolecular systems
    Paul E. Smith, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 98, 9700-9711 (1994).
  • Investigations into the common ion effect
    C. V. Valdeavella, John S. Perkyns, B. Montgomery Pettitt
    Journal of Chemical Physics, 101, 5093-5019 (1994).
  • Ideal chemical potential contribution in molecular dynamics simulations of the grand canonical ensemble
    Samantha Weerasinghe, B. Montgomery Pettitt
    Molecular Physics, 82, 897-912 (1994).
  • Erratum: a site–site theory for finite concentration saline solutions [J. Chem. Phys. 97, 7656 (1992)]
    John Perkyns, B. Montgomery Pettitt
    Journal of Chemical Physics, 100, 8556-8556 (1994).
  • Integral equation approaches to structure and thermodynamics of aqueous salt solutions
    John Perkyns, B. Montgomery Pettitt
    Biophysical Chemistry, 51, 129-42; discussion 142-6 (1994).
  • Sulfate anion in water: model structural, thermodynamic, and dynamic properties
    William R. Cannon, B. Montgomery Pettitt, J. Andrew McCammon
    The Journal of Physical Chemistry, 98, 6225-6230 (1994).
  • Phase transitions of water at constant excess chemical potential an application of grand molecular dynamics
    Jie Ji, B. Montgomery Pettitt
    Molecular Physics, 82, 67-83 (1994).
  • On the solubility of aqueous electrolytes
    John Perkyns, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 98, 5147-5151 (1994).
  • A γ-turn structure induced by 2S, 3S-2,3-methanomethionine
    Kevin Burgess, Kwok-Kan Ho, B. Montgomery Pettitt
    Journal of the American Chemical Society, 116, 799-800 (1994).
  • A global model of the protein-solvent interface
    Valère Lounnas, B. Montgomery Pettitt, George N. Phillips Jr.
    Biophysical Journal, 66, 601-14 (1994).
  • Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin
    Valère Lounnas, B. Montgomery Pettitt
    Proteins: Structure, Function, and Bioinformatics, 18, 148-160 (1994).
  • A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment
    Valère Lounnas, B. Montgomery Pettitt
    Proteins: Structure, Function, and Bioinformatics, 18, 133-147 (1994).
  • 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
    Rahul Mitra, B. Montgomery Pettitt, Graciela L. Ramé, R. D. Blake
    Nucleic Acids Research, 21, 6028-6037 (1993).
  • Studies of salt-peptide solutions: theoretical and experimental approaches
    Gail E. Marlow, B. Montgomery Pettitt
    in Advances in Computational Biology; Hugo O. Villar (eds.); JAI Press Inc, 231-249 (1994).
  • Salt effects in peptide solutions: theory and simulation
    Gail E. Marlow, John S. Perkyns, B. Montgomery Pettitt
    Chemical Reviews, 93, 2503-2521 (1993).
  • Cooperative triple helix formation at distant sites: hybrid oligonucleotides containing a polymeric linker
    Donald J. Kessler, B. Montgomery Pettitt, Yuen-Kit Cheng, Sean R. Smith, Krishna Jayaraman, Huynh M. Muv, Michael E. Hogan
    Nucleic Acids Research, 21, 4810-4815 (1993).
  • Reply to "Comment on 'Monte Carlo evaluation of real-time Feynman path integrals for quantal many-body dynamics: distributed approximating functions and Gaussian sampling'"
    Donald J. Kouri, Wei Zhu, Xin Ma, B. Montgomery Pettitt, David K. Hoffman
    The Journal of Physical Chemistry, 97, 8107-8107 (1993).
  • Molecular dynamics simulation of ions and water around triplex DNA
    V. Mohan, Paul E. Smith, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 97, 12984-12990 (1993).
  • Evidence for a new spine of hydration: solvation of DNA triple helixes
    V. Mohan, Paul E. Smith, B. Montgomery Pettitt
    Journal of the American Chemical Society, 115, 9297-9298 (1993).
  • Peptides in ionic solutions: a simulation study of a bis(penicillamine) enkephalin in sodium acetate solution
    Paul E. Smith, Gail E. Marlow, B. Montgomery Pettitt
    Journal of the American Chemical Society, 115, 7493-7498 (1993).
  • On the mechanism of HRV-14 antiviral compounds: "slow growth" as a conformational search procedure
    Michael Guha-Biswas, Michael Holder, B. Montgomery Pettitt
    Journal of Medicinal Chemistry, 36, 3489-95 (1993).
  • Stochastic dynamics simulations of the alanine dipeptide using a solvent-modified potential energy surface
    Paul E. Smith, B. Montgomery Pettitt, Martin Karplus
    The Journal of Physical Chemistry, 97, 6907-6913 (1993).
  • Grand molecular dynamics: an application of extended system dynamics
    Jie Ji, B. Montgomery Pettitt
    in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; Wilfred F. van Gunsteren, Paul K. Weiner, Anthony J. Wilkinson (eds.); ESCOM Science Publishers B. V., 67-81 (1993).
  • Molecular recognition of watson-crick base-pair reversals in triple-helix formation: use of nonnatural oligonucleotide bases
    V. Mohan, Y.-K. Cheng, Gail E. Marlow, B. Montgomery Pettitt
    Biopolymers, 33, 1317-25 (1993).
  • Monte Carlo evaluation of real-time Feynman path integrals for quantal many-body dynamics: distributed approximating functions and Gaussian sampling
    Donald J. Kouri, Wei Zhu, Xin Ma, B. Montgomery Pettitt, David K. Hoffman
    The Journal of Physical Chemistry, 96, 9622-9630 (1992).
  • A site-site theory for finite concentration saline solutions
    John Perkyns, B. Montgomery Pettitt
    Journal of Chemical Physics, 97, 7656-7666 (1992).
  • Stabilities of double- and triple-strand helical nucleic acids
    Yuen-Kit Cheng, B. Montgomery Pettitt
    Progress in Biophysics and Molecular Biology, 58, 225-57 (1992).
  • Molecular dynamics on a distributed-memory multiprocessor
    S. L. Lin, J. Mellor-Crummey, B. M. Pettitt, G. N. Phillips Jr.
    Journal of Computational Chemistry, 13, 1022-1035 (1992).
  • Amino acid side-chain populations in aqueous and saline solution: bis-penicillamine enkephalin
    Paul E. Smith, B. Montgomery Pettitt
    Biopolymers, 32, 1623-9 (1992).
  • A microscopic view of protein solvation
    Valère Lounnas, B. Montgomery Pettitt, L. Findsen, S. Subramaniam
    The Journal of Physical Chemistry, 96, 7157-7159 (1992).
  • Comparison of structural theories for graphite intercalation compounds
    Zhuo-Min Chen, B. Montgomery Pettitt, George Reiter, Simon C. Moss, Omar A. Karim
    Physical Review B, 46, 10476-10478 (1992).
  • Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions
    V. Mohan, M. E. Davis, J. A. McCammon, B. M. Pettitt
    The Journal of Physical Chemistry, 96, 6428-6431 (1992).
  • Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogues
    Stephen D. O'Connor, Paul E. Smith, Fahad Al-Obeidi, B. Montgomery Pettitt
    Journal of Medicinal Chemistry, 35, 2870-81 (1992).
  • Hoogsteen versus reversed-Hoogsteen base pairing: DNA triple helixes
    Yuen-Kit Cheng, B. Montgomery Pettitt
    Journal of the American Chemical Society, 114, 4465-4474 (1992).
  • A dielectrically consistent interaction site theory for solvent—electrolyte mixtures
    J. S. Perkyns, B. Montgomery Pettitt
    Chemical Physics Letters, 190, 626-630 (1992).
  • On the correlation between like ion pairs in water
    Liem X. Dang, B. Montgomery Pettitt, Peter J. Rossky
    Journal of Chemical Physics, 96, 4046-4047 (1992).
  • Dynamic simulations of water at constant chemical potential
    Jie Ji, Tahir Çağin, B. Montgomery Pettitt
    Journal of Chemical Physics, 96, 1333-1342 (1992).
  • Peptides in ionic solutions: a comparison of the Ewald and switching function techniques
    Paul E. Smith, B. Montgomery Pettitt
    Journal of Chemical Physics, 95, 8430-8441 (1991).
  • Dynamical search for bis-penicillamine enkephalin conformations
    B. M. Pettitt, T. Matsunaga, F. Al-Obeidi, C. Gehrig, V. J. Hruby, M. Karplus
    Biophysical Journal, 60, 1540-4 (1991).
  • Binding of triple helix forming oligonucleotides to sites in gene promoters
    Ross H. Durland, Donald J. Kessler, Sandy Gunnell, Madeleine Duvic, B. M. Pettitt, Michael E. Hogan
    Biochemistry, 30, 9246-9255 (1991).
  • Effects of salt on the structure and dynamics of the bis(penicillamine) enkephalin zwitterion: a simulation study
    Paul E. Smith, B. Montgomery Pettitt
    Journal of the American Chemical Society, 113, 6029-6037 (1991).
  • Aspects of the design of conformationally constrained peptides
    Paul E. Smith, Fahad Al-Obeidi, B. Montgomery Pettitt
    in Molecular Design and Modeling: Concepts and Applications Part A: Proteins, Peptides, and Enzymes; John J. Langone (eds.); Academic Press, 411-436 (1991).
  • A method for modeling icosahedral virions: rotational symmetry boundary conditions
    Tahir Çağin, Michael Holder, B. Montgomery Pettitt
    Journal of Computational Chemistry, 12, 627-634 (1991).
  • Aqueous solvation of N-methylacetamide conformers: comparison of simulations and integral equation theories
    Hsiang-Ai Yu, B. Montgomery Pettitt, Martin Karplus
    Journal of the American Chemical Society, 113, 2425-2434 (1991).
  • Time scales and fluctuations of protein dynamics: metmyoglobin in aqueous solution
    L. A. Findsen, S. Subramaniam, V. Lounnas, B. M. Pettitt
    in Principles of Molecular Recognition; A. D. Buckingham, A. C. Legon, S. M. Roberts (eds.); Blackie Academic & Professional, 168-193 (1993).
  • Convergence of the chemical potential in aqueous simulations
    Michael Mazor, B. Montgomery Pettitt
    Molecular Simulation, 6, 1-4 (1991).
  • Convergence of the chemical potential in aqueous simulations
    Michael Mazor, B. Montgomery Pettitt
    Molecular Simulation, 6, 1-4 (1991).
  • Molecular dynamics with a variable number of molecules
    Tahir Çağin, B. Montgomery Pettitt
    Molecular Physics, 72, 169-175 (1991).
  • Simulation of the structure and dynamics of the bis(penicillamine) enkephalin zwitterion
    Paul E. Smith, Liem X. Dang, B. Montgomery Pettitt
    Journal of the American Chemical Society, 113, 67-73 (1991).
  • Modeling of solvation effects in biopolymer solutions
    B. Montgomery Pettitt, Peter J. Rossky
    in Theoretical Biochemistry & Molecular Biophysics; David L. Beveridge, Richard Lavery (eds.); Adenine Press, 223-229 (1991).
  • A study of model energetics and conformational properties of polynucleotide triplexes
    Herman W. Th. van Vlijmen, Graciela L. Ramé, B. Montgomery Pettitt
    Biopolymers, 30, 517-32 (1990).
  • Diatomic intercalation in lamellar graphite compounds
    Zhuo-Min Chen, B. Montgomery Pettitt
    Physical Review B, 42, 8173-8178 (1990).
  • The free energy of intercalation: the structure of graphite intercalation compounds
    Zhuo-Min Chen, Omar A. Karim, B. Montgomery Pettitt
    in 44th International Meeting of Physical Chemistry on Modeling of Molecular Structures and Properties in Physical Chemistry and Biophysics; Jean Louis Rivail (eds.); 103-117 (1990).
  • A theoretical study of like ion pairs in solution
    Liem X. Dang, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 94, 4303-4308 (1990).
  • Flexibility of tripeptides in solution: free energy molecular mechanics
    Graciela L. Ramé, Wan F. Lau, B. Montgomery Pettitt
    International Journal of Peptide and Protein Research, 35, 315-327 (1990).
  • Selective elimination of interactions: a method for assessing thermodynamic contributions to ligand binding with application to rhinovirus antivirals
    Wan F. Lau, B. Montgomery Pettitt
    Journal of Medicinal Chemistry, 32, 2542-7 (1989).
  • Elastic constants of nickel: variations with respect to temperature and pressure
    Tahir Çağin, B. Montgomery Pettitt
    Physical Review B, 39, 12484-12491 (1989).
  • Dynamics of an oxazole compound bound to a common cold virus
    Wan F. Lau, B. Montgomery Pettitt
    Journal of the American Chemical Society, 111, 4111-4113 (1989).
  • Thermodynamics of diatomic guests in β-quinol clathrates
    Liem X. Dang, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 93, 3794-3799 (1989).
  • Design of a new class of superpotent cyclic α-melanotropins based on quenched dynamic simulations
    Fahad Al-Obeidi, Mac E. Hadley, B. Montgomery Pettitt, Victor J. Hruby
    Journal of the American Chemical Society, 111, 3413-3416 (1989).
  • Successes, failures and curiositites in free energy calculations
    B. Montgomery Pettitt
    in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; Wilfred F. van Gunsteren, Paul K. Weiner (eds.); ESCOM Science Publishers B. V., 94-100 (1989).
  • Conformation biological activity relationships for receptor-selective, conformationally constrained opioid peptides
    Victor J. Hruby, B. Montgomery Pettitt
    in Computer-Aided Drug Design: Methods and Applications; Thomas J. Perun, C. L. Propst (eds.); Marcel Dekker, Inc, 405-460 (1989).
  • Methods for calculating geometries of transition states in solution
    Jeffry D. Madura, B. Montgomery Pettitt, J. Andrew McCammon
    Chemical Physics, 129, 185-191 (1989).
  • Conformational constraints in the design of receptor selective peptides: conformational analysis and molecular dynamics
    V. J. Hruby, W. Kazmierski, B. M. Pettitt, Fahad Al-Obeidi
    in Molecular Biology of Brain and Endocrine Peptidergic Systems; Michel Chrétien, Kenneth W. McKerns (eds.); Plenum Press, 13-27 (1988).
  • Molecular dynamics of coat proteins of the human rhinovirus
    Wan F. Lau, B. Montgomery Pettitt, Terry P. Lybrand
    Molecular Simulation, 1, 385-398 (1988).
  • Proteins: A theoretical perspective on Structure, Dynamics and Thermodynamics
    C.L. Brooks, M. Karplus, and B.M. Pettitt
    Advances in Chemical Physics, vol. 71; Ilya Prigogine, Stuart A. Rice (eds.); John Wiley and Sons, 1-259 (1990).
  • Effects of truncating long-range interactions in aqueous ionic solution simulations
    Jeffry D. Madura, B. Montgomery Pettitt
    Chemical Physics Letters, 150, 105-108 (1988).
  • A theory of the interionic structure of graphite intercalation synthetic metals: variations with respect to interactions and state
    Zhuo-Min Chen, Omar A. Karim, B. Montgomery Pettitt
    Journal of Chemical Physics, 89, 1042-1048 (1988).
  • A theoretical study of the inclusion complexes of β-quinol
    Liem X. Dang, B. Montgomery Pettitt
    Journal of Chemical Physics, 89, 968-974 (1988).
  • Conformational free energy of hydration for the alanine dipeptide: thermodynamic analysis
    B. Montgomery Pettitt, Martin Karplus
    The Journal of Physical Chemistry, 92, 3994-3997 (1988).
  • Water under high pressure
    Jeffry D. Madura, B. Montgomery Pettitt, Daniel F. Calef
    Molecular Physics, 64, 325-336 (1988).
  • The conformational properties of the delta opioid peptide [cyclic][D-pen2,D-pen5]enkephalin in aqueous solution determined by NMR and energy minimization calculations
    Victor J. Hruby, Lung-Fa Kao, B. Montgomery Pettitt, Martin Karplus
    Journal of the American Chemical Society, 110, 3351-3359 (1988).
  • Configurational entropy of native proteins
    M. Karplus, T. Ichiye, B. M. Pettitt
    Biophysical Journal, 52, 1083-5 (1987).
  • Geometric considerations in the calculation of relative free energies of activation
    Jeffry D. Madura, B. Montgomery Pettitt, J. Andrew McCammon
    Chemical Physics Letters, 141, 83-87 (1987).
  • Conformations of the glycine dipeptide
    Wan F. Lau, B. Montgomery Pettitt
    Biopolymers, 26, 1817-1831 (1987).
  • Molecular dynamics studies on antiviral agents: thermodynamics of solvation and binding
    Terry P. Lybrand, Wan F. Lau, J. Andrew McCammon, B. Montgomery Pettitt
    in Protein Structure, Folding, and Design 2: Proceedings of a Dupont-UCLA Symposium held in Steamboat Springs, Colorado, April 4-11, 1987; Dale L. Oxender (eds.); Liss, 227-233 (1987).
  • Proteins
    B.M. Pettitt
    McGraw-Hill World Book Encyclopedia 1988 Yearbook of Science and Technology, ed. S. Parker, 360-362 (1987)
  • A theoretical study of the structure of shocked water
    Daniel F. Calef, B. Montgomery Pettitt
    Chemical Physics Letters, 139, 129-133 (1987).
  • Chloride ion pairs in water
    Liem X. Dang, B. Montgomery Pettitt
    Journal of the American Chemical Society, 109, 5531-5532 (1987).
  • Simple intramolecular model potentials for water
    Liem X. Dang, B. Montgomery Pettitt
    The Journal of Physical Chemistry, 91, 3349-3354 (1987).
  • Solvated chloride ions at contact
    L. X. Dang, B. M. Pettitt
    Journal of Chemical Physics, 86, 6560-6561 (1987).
  • Two-dimensional fluids in a periodic external potential: intercalation in graphite
    Omar A. Karim, B. Montgomery Pettitt
    Chemical Physics Letters, 137, 72-77 (1987).
  • The structure of water surrounding a peptide: a theoretical approach
    B. Montgomery Pettitt, Martin Karplus
    Chemical Physics Letters, 136, 383-386 (1987).
  • On the structure of high-density water at constant temperature
    B. Montgomery Pettitt, Daniel F. Calef
    The Journal of Physical Chemistry, 91, 1541-1545 (1987).
  • New approaches to solvent-mediated molecular interactions
    B. Montgomery Pettitt, Peter J. Rossky
    Israel Journal of Chemistry, 27, 156-62 (1986).
  • Integral equation model for aqueous solvation of polyatomic solutes: application to the determination of the free energy surface for the internal motion of biomolecules
    B. Montgomery Pettitt, Martin Karplus, Peter J. Rossky
    The Journal of Physical Chemistry, 90, 6335-6345 (1986).
  • Interaction energies: their role in drug design
    B. Montgomery Pettitt, Martin Karplus
    in Molecular Graphics and Drug Design; A. S. V. Burgen, Gordon Carl Kenmure Roberts, M. S. Tute (eds.); Elsevier, 75-113 (1986).
  • Alkali halides in water: ion–solvent correlations and ion–ion potentials of mean force at infinite dilution
    B. Montgomery Pettitt, Peter J. Rossky
    Journal of Chemical Physics, 84, 5836-5844 (1986).
  • The Structural and Energetic Effects of Terminating Long-ranged Forces in Fluids
    C.L. Brooks, B.M. Pettitt, and M. Karplus
    Journal of Chemical Physics, 83, 5897-5908 (1985).
  • The potential of mean force surface for the alanine dipeptide in aqueous solution: a theoretical approach
    B. Montgomery Pettitt, Martin Karplus
    Chemical Physics Letters, 121, 194-201 (1985).
  • The Intermolecular Potential of Mean Force Between Polyatomics in a Polar Molecular Solvent
    B. Montgomery Pettitt, Martin Karplus
    Journal of Chemical Physics, 83, 781-9 (1985).
  • Calculation of temperature-dependent multimode resonance Raman line shapes for harmonic potential surfaces
    Richard Friesner, Montgomery Pettitt, John M. Jean
    Journal of Chemical Physics, 82, 2918-2926 (1985).
  • The role of electrostatics in the structure, energy and dynamics of biomolecules: a model study of N-methylalanylacetamide
    B. Montgomery Pettitt, Martin Karplus
    Journal of the American Chemical Society, 107, 1166-73 (1985).
  • Entropy of macromolecules
    M. Karplus, J. Brady, B. Brooks, J. Kushick, M. Pettitt
    in Molecular Dynamics and Protein Structure : Proceedings of a workshop held 13-18 May 1984 at the University of North Carolina; Jan Hermans (eds.); Polycrystal Book Service, 47-49 (1985).
  • The coupling of long and short range correlations in ISM liquids
    Peter J. Rossky, B. Montgomery Pettitt, George Stell
    Molecular Physics, 50, 1263-1271 (1983).
  • Theoretical Compton profile anisotropies in molecules and solids. IX. Chemical bonding and 0-90 anisotropies in the first-row diatomic hydrides AH
    B. M. Pettitt, Robert L. Matcha, B. I. Ramirez
    Journal of Chemical Physics, 79, 2913-17 (1983).
  • The contribution of hydrogen bonding to the structure of liquid methanol
    B. Montgomery Pettitt, Peter J. Rossky
    Journal of Chemical Physics, 78, 7296-9 (1983).
  • The interionic potential of mean force in a molecular polar solvent from an extended RISM equation
    Fumio Hirata, Peter J. Rossky, B. Montgomery Pettitt
    Journal of Chemical Physics, 78, 4133-44 (1983).
  • Integral equation predictions of liquid state structure for waterlike intermolecular potentials
    B. Montgomery Pettitt, Peter J. Rossky
    Journal of Chemical Physics, 77, 1451-7 (1982).
  • Application of an extended RISM equation to dipolar and quadrupolar fluids
    Fumio Hirata, B. Montgomery Pettitt, Peter J. Rossky
    Journal of Chemical Physics, 77, 509-20 (1982).
  • Theoretical Compton profile anisotropics in molecules and solids. VIII. Vibrational, rotational, and temperature-dependent diatomic alkali halide anisotropics
    B. Montgomery Pettitt, Shridhar R. Gadre, Robert L. Matcha
    International Journal of Quantum Chemistry, 18, 697-706 (1980).
  • Theoretical Compton profile anisotropies in molecules and solids. VII. Zero point Compton profile anisotropies and bond polarities in alkali halide diatomic molecules
    Robert L. Matcha, Bernard M. Pettitt
    Journal of Chemical Physics, 72, 4588-90 (1980).
  • Theory of the chemical bond. V. Bond polarities of post-transition hydrides
    Robert L. Matcha, Stephen C. King Jr., B. M. Pettitt
    Journal of Chemical Physics, 73, 3944-6 (1980).
  • Collinear reaction surface for He and ArH+
    B. M. Pettitt, Kent Jacobson, R. L. Matcha
    Journal of Chemical Physics, 72, 2892-4 (1980).
  • Theoretical Compton profile anisotropies in molecules and solids. IV. Parallel-perpendicular anisotropies in alkali fluoride molecules
    Robert L. Matcha, Bernard M. Pettitt, B. I. Ramirez, William R. McIntire
    Journal of Chemical Physics, 71, 991-6 (1979).
  • Theoretical Compton profile anisotropies in molecules and solids. VI. Compton profile anisotropies and chemical binding
    Robert L. Matcha, Bernard M. Pettitt
    Journal of Chemical Physics, 70, 3130-2 (1979).
  • Theoretical Compton profile anisotropies in molecules and solids. V. Lithium and sodium bromide diatomics
    Robert L. Matcha, Bernard M. Pettitt, B. I. Ramirez, William R. McIntire
    Journal of Chemical Physics, 70, 558-64 (1979).
  • Theoretical Compton profile anisotropies in molecules and solids. III. Relationship of parallel-perpendicular anisotropies to charge distributions in alkali chloride molecules
    R. L. Matcha, B. M. Pettitt, B. I. Ramirez, W. R. McIntire
    Journal of Chemical Physics, 69, 3025-33 (1978).
  • Potential energy surface for the collinear reaction of Ne and HeH+
    Robert L. Matcha, Bernard M. Pettitt, Paul F. Meier, Phil Pendergast
    Journal of Chemical Physics, 69, 2264-5 (1978).