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

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2013

Proximal distributions from angular correlations: A measure of the onset of coarse-graining

Dyer, K. M. & Pettitt, B. M., Dec 7 2013, In : Journal of Chemical Physics. 139, 21, 214111.

Research output: Contribution to journalArticle

3 Scopus citations

Solvation free energies of alanine peptides: The effect of flexibility

Kokubo, H., Harris, R. C., Asthagiri, D. & Pettitt, B. M., Dec 27 2013, In : Journal of Physical Chemistry B. 117, 51, p. 16428-16435 8 p.

Research output: Contribution to journalArticle

21 Scopus citations
2011

Accurate prediction of binding thermodynamics for DNA on surfaces

Vainrub, A. & Pettitt, B. M., Nov 17 2011, In : Journal of Physical Chemistry B. 115, 45, p. 13300-13303 4 p.

Research output: Contribution to journalArticle

19 Scopus citations
25 Scopus citations

Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions

Lin, B., Wong, K. Y., Hu, C., Kokubo, H. & Pettitt, B. M., Jul 7 2011, In : Journal of Physical Chemistry Letters. 2, 13, p. 1626-1632 7 p.

Research output: Contribution to journalArticle

16 Scopus citations

Free energy considerations for nucleic acids with dangling ends near a surface: Acoarse grained approach

Ambia-Garrido, J., Vainrub, A. & Montgomery Pettitt, B., Aug 17 2011, In : Journal of Physics Condensed Matter. 23, 32, 325101.

Research output: Contribution to journalArticle

5 Scopus citations

Integral Equations in the Study of Polar and Ionic Interaction Site Fluids

Howard, J. J. & Pettitt, B. M., Oct 1 2011, In : Journal of Statistical Physics. 145, 2, p. 441-466 26 p.

Research output: Contribution to journalArticle

14 Scopus citations

Ion and solvent density distributions around canonical B-DNA from integral equations

Howard, J. J., Lynch, G. C. & Pettitt, B. M., Jan 27 2011, In : Journal of Physical Chemistry B. 115, 3, p. 547-556 10 p.

Research output: Contribution to journalArticle

29 Scopus citations

Note: On the universality of proximal radial distribution functions of proteins

Lin, B. & Pettitt, B. M., Mar 14 2011, In : Journal of Chemical Physics. 134, 10, 106101.

Research output: Contribution to journalArticle

14 Scopus citations

Peptide conformational preferences in osmolyte solutions: Transfer free energies of decaalanine

Kokubo, H., Hu, C. Y. & Pettitt, B. M., Feb 16 2011, In : Journal of the American Chemical Society. 133, 6, p. 1849-1858 10 p.

Research output: Contribution to journalArticle

95 Scopus citations

The binding process of a nonspecific enzyme with DNA

Chen, C. & Pettitt, B. M., Sep 7 2011, In : Biophysical Journal. 101, 5, p. 1139-1147 9 p.

Research output: Contribution to journalArticle

21 Scopus citations
2010

A model for structure and thermodynamics of ssDNA and dsDNA near a surface: A coarse grained approach

Ambia-Garrido, J., Vainrub, A. & Pettitt, B. M., Dec 1 2010, In : Computer Physics Communications. 181, 12, p. 2001-2007 7 p.

Research output: Contribution to journalArticle

36 Scopus citations

Backbone additivity in the transfer model of protein solvation

Hu, C. Y., Kokubo, H., Lynch, G. C., Bolen, D. W. & Pettitt, B. M., May 1 2010, In : Protein Science. 19, 5, p. 1011-1022 12 p.

Research output: Contribution to journalArticle

64 Scopus citations

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories

Perkyns, J. S., Lynch, G. C., Howard, J. J. & Pettitt, B. M., Feb 22 2010, In : Journal of Chemical Physics. 132, 6, 064106.

Research output: Contribution to journalArticle

61 Scopus citations

The behavior of ions near a charged wall-dependence on ion size, concentration, and surface charge.

Howard, J. J., Perkyns, J. S. & Pettitt, B. M., May 13 2010, In : Journal of Physical Chemistry B. 114, 18, p. 6074-6083 10 p.

Research output: Contribution to journalArticle

40 Scopus citations

Trimethylamine N-oxide influence on the backbone of proteins: An oligoglycine model

Hu, C. Y., Lynch, G. C., Kokubo, H. & Montgomery Pettitt, B., Apr 28 2010, In : Proteins: Structure, Function and Bioinformatics. 78, 3, p. 695-704 10 p.

Research output: Contribution to journalArticle

73 Scopus citations
2009

Advantage of being a dimer for Serratia marcescens endonuclease

Chen, C., Krause, K. & Pettitt, B. M., Jan 15 2009, In : Journal of Physical Chemistry B. 113, 2, p. 511-521 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form

Randall, G. L., Zechiedrich, L. & Pettitt, B. M., Jul 8 2009, In : Nucleic acids research. 37, 16, p. 5568-5577 10 p., gkp556.

Research output: Contribution to journalArticle

44 Scopus citations

Salt effects on surface-tethered peptides in solution

Feng, J., Wong, K. Y., Lynch, G. C., Gao, X. & Pettitt, B. M., Jul 16 2009, In : Journal of Physical Chemistry B. 113, 28, p. 9472-9478 7 p.

Research output: Contribution to journalArticle

13 Scopus citations

Site-renormalised molecular fluid theory: On the utility of a two-site model of water

Dyer, K. M., Perkyns, J. S., Stell, G. & Montgomery Pettitt, B., Feb 1 2009, In : Molecular Physics. 107, 4-6, p. 423-431 9 p.

Research output: Contribution to journalArticle

24 Scopus citations

The melting mechanism of DNA tethered to a surface

Qamhieh, K., Wong, K. Y., Lynch, G. C. & Pettitt, B. M., Mar 26 2009, In : International Journal of Numerical Analysis and Modeling. 6, 3, p. 474-488 15 p.

Research output: Contribution to journalArticle

24 Scopus citations

Transport properties of water at functionalized molecular interfaces

Feng, J., Wong, K. Y., Dyer, K. & Pettitt, B. M., Oct 8 2009, In : Journal of Chemical Physics. 131, 12, 125102.

Research output: Contribution to journalArticle

6 Scopus citations
2008

A molecular site-site integral equation that yields the dielectric constant

Dyer, K. M., Perkyns, J. S., Stell, G. & Pettitt, B. M., Sep 19 2008, In : Journal of Chemical Physics. 129, 10, 104512.

Research output: Contribution to journalArticle

21 Scopus citations

Automatic generation of FFT for translations of multipole expansions in spherical harmonics

Kurzak, J., Mirkovic, D., Pettitt B., M. B. & Johnsson S., L. S., Jun 1 2008, In : International Journal of High Performance Computing Applications. 22, 2, p. 219-230 12 p.

Research output: Contribution to journalArticle

2 Scopus citations

Determination of the Transition-State Entropy for Aggregation Suggests How the Growth of Sickle Cell Hemoglobin Polymers can be Slowed

Vekilov, P. G., Galkin, O., Pettitt, B. M., Choudhury, N. & Nagel, R. L., Mar 28 2008, In : Journal of Molecular Biology. 377, 3, p. 882-888 7 p.

Research output: Contribution to journalArticle

6 Scopus citations

Free energy calculations for DNA near surfaces using an ellipsoidal geometry

Ambia-Garrido, J. & Pettitt, B. M., May 2008, In : Communications in Computational Physics. 3, 5, p. 1117-1131 15 p.

Research output: Contribution to journalArticle

8 Scopus citations

Integral equation study of the hydrophobic interaction between graphene plates

Howard, J. J., Perkyns, J. S., Choudhury, N. & Pettitt, B. M., Nov 11 2008, In : Journal of Chemical Theory and Computation. 4, 11, p. 1928-1939 12 p.

Research output: Contribution to journalArticle

20 Scopus citations

Solutions of the optimized closure integral equation theory: Heteronuclear polyatomic fluids

Marucho, M., Kelley, C. T. & Pettitt, B. M., Mar 1 2008, In : Journal of Chemical Theory and Computation. 4, 3, p. 385-396 12 p.

Research output: Contribution to journalArticle

8 Scopus citations

The pathway of oligomeric DNA melting investigated by molecular dynamics simulations

Wong, K. Y. & Pettitt, B. M., Dec 15 2008, In : Biophysical Journal. 95, 12, p. 5618-5626 9 p.

Research output: Contribution to journalArticle

37 Scopus citations
2007

An analysis of the molecular origin of osmolyte-dependent protein stability

Rösgen, J., Pettitt, B. M. & Bolen, D. W., Apr 1 2007, In : Protein Science. 16, 4, p. 733-743 11 p.

Research output: Contribution to journalArticle

75 Scopus citations

An angle dependent site-renormalized theory for the conformations of n-butane in a simple fluid

Dyer, K., Perkyns, J., Pettitt, B. & Steli, G., Jan 1 2007, In : Condensed Matter Physics. 10, 3, p. 331-342 12 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

A site-renormalized molecular fluid theory

Dyer, K. M., Perkyns, J. S. & Pettitt, B. M., Nov 29 2007, In : Journal of Chemical Physics. 127, 19, 194506.

Research output: Contribution to journalArticle

19 Scopus citations

Effects of dimerization of Serratia marcescens endonuclease on water dynamics

Chen, C., Beck, B. W., Krause, K., Weksberg, T. E. & Pettitt, B. M., Feb 15 2007, In : Biopolymers. 85, 3, p. 241-252 12 p.

Research output: Contribution to journalArticle

2 Scopus citations

Molecular basis of the apparent near ideality of urea solutions

Kokubo, H., Rösgen, J., Bolen, D. W. & Pettitt, B. M., Nov 2007, In : Biophysical Journal. 93, 10, p. 3392-3407 16 p.

Research output: Contribution to journalArticle

52 Scopus citations

Molecular dynamics simulations of Trichomonas vaginalis ferredoxin show a loop-cap transition

Weksberg, T. E., Lynch, G. C., Krause, K. L. & Pettitt, B. M., May 2007, In : Biophysical Journal. 92, 10, p. 3337-3345 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Optimized theory for simple and molecular fluids

Marucho, M. & Pettitt, B. M., Apr 8 2007, In : Journal of Chemical Physics. 126, 12, 124107.

Research output: Contribution to journalArticle

12 Scopus citations

Peptide conformations for a microarray surface-tethered epitope of the tumor suppressor p53

Feng, J., Wong, K. Y., Lynch, G. C., Gao, X. & Pettitt, B. M., Dec 13 2007, In : Journal of Physical Chemistry B. 111, 49, p. 13797-13806 10 p.

Research output: Contribution to journalArticle

11 Scopus citations

Preferential solvation in urea solutions at different concentrations: Properties from simulation studies

Kokubo, H. & Pettitt, B. M., May 17 2007, In : Journal of Physical Chemistry B. 111, 19, p. 5233-5242 10 p.

Research output: Contribution to journalArticle

77 Scopus citations

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

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

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
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