Bernard Pettitt, PhD

Director, Sealy Center for Structural Biology

  • 12189 Citations
  • 62 h-Index
1978 …2021

Research output per year

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Research Output

2007

Systematic investigation of theories of transport in the Lennard-Jones fluid

Dyer, K. M., Pettitt, B. M. & Stell, G., Jan 29 2007, In : Journal of Chemical Physics. 126, 3, 034502.

Research output: Contribution to journalArticle

29 Scopus citations

The dewetting transition and the hydrophobic effect

Choudhury, N. & Pettitt, B. M., Apr 18 2007, In : Journal of the American Chemical Society. 129, 15, p. 4847-4852 6 p.

Research output: Contribution to journalArticle

115 Scopus citations
2006
4 Scopus citations

Electrostatics of DNA-DNA juxtapositions: Consequences for type II topoisomerase function

Randall, G. L., Pettitt, B. M., Buck, G. R. & Zechiedrich, E. L., Apr 12 2006, In : Journal of Physics Condensed Matter. 18, 14, p. S173-S185

Research output: Contribution to journalArticle

20 Scopus citations

Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes

Choudhury, N. & Montgomery Pettitt, B., Apr 27 2006, In : Journal of Physical Chemistry B. 110, 16, p. 8459-8463 5 p.

Research output: Contribution to journalArticle

101 Scopus citations

Fast multipole methods for particle dynamics

Kurzak, J. & Pettitt, B. M., Aug 1 2006, In : Molecular Simulation. 32, 10-11, p. 775-790 16 p.

Research output: Contribution to journalArticle

21 Scopus citations

Force field comparisons of the heat capacity of carbon nanotubes

Guo, C. Y., Pettitt, B. M. & Wheeler, L. T., Aug 1 2006, In : Molecular Simulation. 32, 10-11, p. 839-848 10 p.

Research output: Contribution to journalArticle

15 Scopus citations

Guest editorial: Nanobiology

Pettitt, B. M., Aug 1 2006, In : Molecular Simulation. 32, 10-11, 1 p.

Research output: Contribution to journalEditorial

Solvent participation in Serratia marcescens endonuclease complexes

Chen, C., Beck, B. W., Krause, K. & Pettitt, B. M., Mar 1 2006, In : Proteins: Structure, Function and Genetics. 62, 4, p. 982-995 14 p.

Research output: Contribution to journalArticle

10 Scopus citations

Using mutual information to discover temporal patterns in gene expression data

Chumakov, S., Ballesteros, E., Rodriguez Sanchez, J. E., Chavez, A., Zhang, M., Pettit, B. M. & Fofanov, Y., Dec 1 2006, In : AIP Conference Proceedings. 854, p. 25-30 6 p.

Research output: Contribution to journalConference article

3 Scopus citations
2005

Communications overlapping in fast multipole particle dynamics methods

Kurzak, J. & Pettitt, B. M., Mar 1 2005, In : Journal of Computational Physics. 203, 2, p. 731-743 13 p.

Research output: Contribution to journalArticle

12 Scopus citations

Dynamics of water trapped between hydrophobic solutes

Choudhury, N. & Pettitt, B. M., Apr 7 2005, In : Journal of Physical Chemistry B. 109, 13, p. 6422-6429 8 p.

Research output: Contribution to journalArticle

137 Scopus citations

Effective density terms in proper integral equations

Dyer, K. M., Perkyns, J. S. & Pettitt, B. M., Dec 9 2005, In : Journal of Chemical Physics. 123, 20, 204512.

Research output: Contribution to journalArticle

9 Scopus citations

Local density profiles are coupled to solute size and attractive potential for nanoscopic hydrophobic solutes

Choudhury, N. & Pettitt, B. M., May 15 2005, In : Molecular Simulation. 31, 6-7, p. 457-463 7 p.

Research output: Contribution to journalArticle

35 Scopus citations

Massively parallel implementation of a fast multipole method for distributed memory machines

Kurzak, J. & Pettitt, B. M., Jul 1 2005, In : Journal of Parallel and Distributed Computing. 65, 7, p. 870-881 12 p.

Research output: Contribution to journalArticle

32 Scopus citations

On the mechanism of hydrophobic association of nanoscopic solutes

Choudhury, N. & Pettitt, B. M., Mar 16 2005, In : Journal of the American Chemical Society. 127, 10, p. 3556-3567 12 p.

Research output: Contribution to journalArticle

248 Scopus citations

Protein folding, stability, and solvation structure in osmolyte solutions

Rösgen, J., Pettitt, B. M. & Bolen, D. W., Nov 2005, In : Biophysical Journal. 89, 5, p. 2988-2997 10 p.

Research output: Contribution to journalArticle

116 Scopus citations

Simple bond length dependence: A correspondence between reactive fluid theories

Dyer, K. M., Perkyns, J. S. & Pettitt, B. M., Jun 15 2005, In : Journal of Chemical Physics. 122, 23, 236101.

Research output: Contribution to journalArticle

5 Scopus citations
2004

A fast solver for the Ornstein-Zernike equations

Kelley, C. T. & Pettitt, B. M., Jul 1 2004, In : Journal of Computational Physics. 197, 2, p. 491-501 11 p.

Research output: Contribution to journalArticle

17 Scopus citations

A non-Watson-Crick motif of base-pairing on surfaces for untethered oligonucleotides

Wong, K. Y., Vainrub, A., Powdrill, T., Hogan, M. & Pettitt, B. M., Feb 15 2004, In : Molecular Simulation. 30, 2-3, p. 121-129 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

Biopolymers: Preface

Pettitt, M., Apr 5 2004, In : Biopolymers. 73, 5, 1 p.

Research output: Contribution to journalEditorial

Combined hopping-superexchange model of a hole transfer in DNA

Lakhno, V. D., Sultanov, V. B. & Pettitt, B. M., Dec 11 2004, In : Chemical Physics Letters. 400, 1-3, p. 47-53 7 p.

Research output: Contribution to journalArticle

21 Scopus citations

How independent are the appearances of n-mers in different genomes?

Fofanov, Y., Luo, Y., Katili, C., Wang, J., Belosludtsev, Y., Powdrill, T., Belapurkar, C., Fofanov, V., Li, T. B., Chumakov, S. & Pettitt, B. M., Oct 12 2004, In : Bioinformatics. 20, 15, p. 2421-2428 8 p.

Research output: Contribution to journalArticle

43 Scopus citations

Orientation of DNA on a Surface from Simulation

Wong, K. Y. & Pettitt, B. M., Apr 5 2004, In : Biopolymers. 73, 5, p. 570-578 9 p.

Research output: Contribution to journalArticle

54 Scopus citations

Statistical Thermodynamic Approach to the Chemical Activities in Two-Component Solutions

Rösgen, J., Pettitt, B. M., Perkyns, J. & Bolen, D. W., Feb 12 2004, In : Journal of Physical Chemistry B. 108, 6, p. 2048-2055 8 p.

Research output: Contribution to journalArticle

28 Scopus citations

Theoretical Aspects of Genomic Variation Screening Using DNA Microarrays

Vainrub, A. & Pettitt, B. M., Apr 5 2004, In : Biopolymers. 73, 5, p. 614-620 7 p.

Research output: Contribution to journalArticle

19 Scopus citations

Uncovering the basis for nonideal behavior of biological molecules

Rösgen, J., Pettitt, B. M. & Bolen, D. W., Nov 16 2004, In : Biochemistry. 43, 45, p. 14472-14484 13 p.

Research output: Contribution to journalArticle

50 Scopus citations

Using statistical properties of short subsequences in microbial identification

Chumakov, S., Putonti, C., Pettitt, B. M., Fox, G., Willson, R. C. & Fofanov, Y., Dec 1 2004, Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04. Valafar, F. & Valafar, H. (eds.). p. 363-367 5 p. (Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'04).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations
2003

Sensitive quantitative nucleic acid detection using oligonucleotide microarrays

Vainrub, A. & Pettitt, B. M., Jul 2 2003, In : Journal of the American Chemical Society. 125, 26, p. 7798-7799 2 p.

Research output: Contribution to journalArticle

64 Scopus citations

Simulation of the bis-(penicillamine) enkephalin in ammonium chloride solution: A comparison with sodium chloride

Marlow, G. E. & Pettitt, B. M., Feb 1 2003, In : Biopolymers. 68, 2, p. 192-209 18 p.

Research output: Contribution to journalArticle

6 Scopus citations

Surface electrostatic effects in oligonucleotide microarrays: Control and optimization of binding thermodynamics

Vainrub, A. & Pettitt, B. M., Feb 1 2003, In : Biopolymers. 68, 2, p. 265-270 6 p.

Research output: Contribution to journalArticle

103 Scopus citations

Theoretical considerations for the efficient design of dna arrays

Vainrub, A., Li, T. B., Fofanov, Y. & Pettitt, B. M., Jan 1 2003, Biomedical Technology and Devices Handbook. CRC Press, p. 14-1-14-14

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations
2002

Computationally useful bridge diagram series. II. Diagrams in h-bonds

Perkyns, J. S., Dyer, K. M. & Pettitt, B. M., Jun 1 2002, In : Journal of Chemical Physics. 116, 21, p. 9404-9412 9 p.

Research output: Contribution to journalArticle

22 Scopus citations

Computationally useful bridge diagram series. III. Lennard-Jones mixtures

Dyer, K., Perkyns, J. & Pettitt, B. M., Jun 1 2002, In : Journal of Chemical Physics. 116, 21, p. 9413-9421 9 p.

Research output: Contribution to journalArticle

13 Scopus citations
122 Scopus citations

Fine-tuning function: Correlation of hinge domain interactions with functional distinctions between LacI and PurR

Swint-Kruse, L., Larson, C., Montgomery Pettitt, B. & Matthews, K. S., Apr 3 2002, In : Protein Science. 11, 4, p. 778-794 17 p.

Research output: Contribution to journalArticle

29 Scopus citations

Numerical simulation of the sedimentation of a tripole-like body in an incompressible viscous fluid

Juárez, L. H., Glowinski, R. & Pettitt, B. M., Aug 2002, In : Applied Mathematics Letters. 15, 6, p. 743-747 5 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: Local Invariants approach

Fofanov, Y. & Pettitt, B. M., Oct 2002, In : Journal of Biomedical Informatics. 35, 5-6, p. 343-351 9 p.

Research output: Contribution to journalArticle

4 Scopus citations

Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment

Makarov, V., Pettitt, B. M. & Feig, M., Jul 6 2002, In : Accounts of Chemical Research. 35, 6, p. 376-384 9 p.

Research output: Contribution to journalArticle

272 Scopus citations
2001

A reexamination of virial coefficients of the Lennard-Jones fluid

Dyer, K. M., Perkyns, J. S. & Pettitt, B. M., Jan 1 2001, In : Theoretical Chemistry Accounts. 105, 3, p. 244-251 8 p.

Research output: Contribution to journalArticle

14 Scopus citations

A study of DNA tethered to a surface by an all-atom molecular dynamics simulation

Wong, K. Y. & Pettitt, B. M., Jul 1 2001, In : Theoretical Chemistry Accounts. 106, 3, p. 233-235 3 p.

Research output: Contribution to journalArticle

42 Scopus citations

Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations

Feig, M., Zacharias, M. & Montgomery Pettitt, B., Jan 1 2001, In : Biophysical Journal. 81, 1, p. 352-370 19 p.

Research output: Contribution to journalArticle

Open Access
28 Scopus citations

Simulations of the bis-penicillamine enkephalin in sodium chloride solution: A parameter study

Marlow, G. E. & Montgomery Pettitt, B., Aug 23 2001, In : Biopolymers - Peptide Science Section. 60, 2, p. 134-152 19 p.

Research output: Contribution to journalArticle

9 Scopus citations

Structural basis for the activity of pp60c-src protein tyrosine kinase inhibitors

Prabhu, N. V., Siddiqui, S. A., McMurray, J. S. & Montgomery Pettitt, B., Aug 11 2001, In : Biopolymers. 59, 3, p. 167-179 13 p.

Research output: Contribution to journalArticle

3 Scopus citations
2000

A new boundary condition for computer simulations of interfacial systems

Wong, K. Y. & Pettitt, B. M., Aug 18 2000, In : Chemical Physics Letters. 326, 3-4, p. 193-198 6 p.

Research output: Contribution to journalArticle

14 Scopus citations

A Perspective on "volume and heat of hydration of ions"

Pettitt, B. M., Feb 2000, In : Theoretical Chemistry Accounts. 103, 3-4, p. 171-172 2 p.

Research output: Contribution to journalReview article

8 Scopus citations

Residence times of water molecules in the hydration sites of myoglobin

Makarov, V. A., Andrews, B. K., Smith, P. E. & Pettitt, B. M., Dec 2000, In : Biophysical Journal. 79, 6, p. 2966-2974 9 p.

Research output: Contribution to journalArticle

Open Access
214 Scopus citations

Semi-grand canonical molecular dynamics simulation of bovine pancreatic trypsin inhibitor

Lynch, G. C. & Pettitt, B. M., Aug 15 2000, In : Chemical Physics. 258, 2-3, p. 405-413 9 p.

Research output: Contribution to journalArticle

10 Scopus citations

Thermodynamics of association to a molecule immobilized in an electric double layer

Vainrub, A. & Pettitt, B. M., Jun 9 2000, In : Chemical Physics Letters. 323, 1-2, p. 160-166 7 p.

Research output: Contribution to journalArticle

59 Scopus citations
1999

Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation

Prabhu, N. V., Perkyns, J. S., Blatt, H. D., Smith, P. E. & Pettitt, B. M., Apr 5 1999, In : Biophysical Chemistry. 78, 1-2, p. 113-126 14 p.

Research output: Contribution to journalArticle

11 Scopus citations