Find Research Outputs

Search in all content

Filters for Publications

Search concepts
Selected Filters

Publication Year

  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011

Author

  • Bernard Pettitt

A cavity corrected 3D-RISM functional for accurate solvation free energies

Truchon, J. F., Pettitt, B. M. & Labute, P., Mar 11 2014, In : Journal of Chemical Theory and Computation. 10, 3, p. 934-941 8 p.

Research output: Contribution to journalArticle

85 Scopus citations

Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace

Zhang, C., Lai, C. L. & Pettitt, B., Sep 1 2016, In : Molecular Simulation. 42, 13, p. 1079-1089 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

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

20 Scopus citations

Allosteric discrimination at the NADH/ADP regulatory site of glutamate dehydrogenase

Nassar, O. M., Wong, K. Y., Lynch, G. C., Smith, T. J. & Pettitt, B. M., Dec 1 2019, In : Protein Science. 28, 12, p. 2080-2088 9 p.

Research output: Contribution to journalArticle

Bullied no more: When and how DNA shoves proteins around

Fogg, J. M., Randall, G. L., Pettitt, B. M., Sumners, D. W. L., Harris, S. A. & Zechiedrich, L., Aug 1 2012, In : Quarterly Reviews of Biophysics. 45, 3, p. 257-299 43 p.

Research output: Contribution to journalReview article

39 Scopus citations

Changes in conformational dynamics of basic side chains upon protein-DNA association

Esadze, A., Chen, C., Zandarashvili, L., Roy, S., Pettitt, B. M. & Iwahara, J., Aug 19 2016, In : Nucleic acids research. 44, 14, p. 6961-6970 10 p.

Research output: Contribution to journalArticle

37 Scopus citations

Communication: Origin of the contributions to DNA structure in phages

Myers, C. G. & Pettitt, B. M., Feb 21 2013, In : Journal of Chemical Physics. 138, 7, 071103.

Research output: Contribution to journalArticle

5 Scopus citations

Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence

Theruvathu, J. A., Yin, Y. W., Pettitt, B. M. & Sowers, L. C., Nov 26 2013, In : Biochemistry. 52, 47, p. 8590-8598 9 p.

Research output: Contribution to journalArticle

7 Scopus citations

Computation of high-order virial coefficients in high-dimensional hard-sphere fluids by Mayer sampling

Zhang, C. & Pettitt, B. M., May 19 2014, In : Molecular Physics. 112, 9-10, p. 1427-1447 21 p.

Research output: Contribution to journalArticle

20 Scopus citations

Computation of virial coefficients from integral equations

Zhang, C., Lai, C. L. & Pettitt, B., Jun 5 2015, In : Journal of Chemical Physics. 142, 21, 214110.

Research output: Contribution to journalArticle

2 Scopus citations

Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model

Tomar, D. S., Weber, V., Pettitt, B. M. & Asthagiri, D., Apr 17 2014, In : Journal of Physical Chemistry B. 118, 15, p. 4080-4087 8 p.

Research output: Contribution to journalArticle

9 Scopus citations

Controlling microarray DNA hybridization efficiency by probe-surface distance and external surface electrostatics

Qamhieh, K. & Pettitt, B., Mar 30 2015, 4th International Congress in Advances in Applied Physics and Materials Science, APMAS 2014. American Institute of Physics Inc., Vol. 1653. 020090

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

1 Scopus citations

Dielectric behavior for saline solutions from renormalized diagrammatically proper interaction site model theory

Dyer, K. M., Perkyns, J. S. & Pettitt, B. M., Aug 22 2016, In : Journal of Physics Condensed Matter. 28, 41, 414006.

Research output: Contribution to journalArticle

1 Scopus citations

DNA Shape versus Sequence Variations in the Protein Binding Process

Chen, C. & Pettitt, B., Feb 2 2016, In : Biophysical Journal. 110, 3, p. 534-544 11 p.

Research output: Contribution to journalArticle

3 Scopus citations

Domain organization of membrane-bound factor VIII

Stoilova-Mcphie, S., Lynch, G. C., Ludtke, S. & Pettitt, B. M., Jul 2013, In : Biopolymers. 99, 7, p. 448-459 12 p.

Research output: Contribution to journalArticle

18 Scopus citations

Dynamic equilibria of short-range electrostatic interactions at molecular interfaces of protein-DNA complexes

Chen, C., Esadze, A., Zandarashvili, L., Nguyen, D., Pettitt, B. & Iwahara, J., Jul 16 2015, In : Journal of Physical Chemistry Letters. 6, 14, p. 2733-2737 5 p.

Research output: Contribution to journalArticle

29 Scopus citations

Effects of acids, bases, and heteroatoms on proximal radial distribution functions for proteins

Nguyen, B. L. & Pettitt, B. M., Apr 14 2015, In : Journal of Chemical Theory and Computation. 11, 4, p. 1399-1409 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Effects of geometry and chemistry on hydrophobic salvation

Harris, R. C., Pettitt, B. M. & Debenedetti, P. G., Oct 14 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 41, p. 14681-14686 6 p.

Research output: Contribution to journalArticle

40 Scopus citations
25 Scopus citations

Erratum: Computation of virial coefficients from integral equations (Journal of Chemical Physics (2015) 142 (214110))

Zhang, C., Lai, C. L. & Pettitt, B., Jun 14 2016, In : Journal of Chemical Physics. 144, 22, 229901.

Research output: Contribution to journalComment/debate

Examining the Assumptions Underlying Continuum-Solvent Models

Harris, R. C. & Pettitt, B., Sep 1 2015, In : Journal of Chemical Theory and Computation. 11, 10, p. 4593-4600 8 p.

Research output: Contribution to journalArticle

14 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

Force field-dependent solution properties of glycine oligomers

Drake, J. A. & Pettitt, B. M., Jun 1 2015, In : Journal of Computational Chemistry. 36, 17, p. 1275-1285 11 p.

Research output: Contribution to journalArticle

20 Scopus citations

Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles

Ou, S. C. & Pettitt, B. M., Apr 9 2019, In : Journal of Chemical Theory and Computation. 15, 4, p. 2649-2658 10 p.

Research output: Contribution to journalArticle

1 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
3 Scopus citations

Importance of disentanglement and entanglement during DNA replication and segregation: Comment on: “Disentangling DNA molecules” by Alexander Vologodskii

Bates, D., Pettitt, B. M., Buck, G. R. & Zechiedrich, L., Sep 1 2016, In : Physics of Life Reviews. 18, p. 160-164 5 p.

Research output: Contribution to journalComment/debate

1 Scopus citations
15 Scopus citations

Influence of DNA sequence on the structure of minicircles under torsional stress

Wang, Q., Irobalieva, R. N., Chiu, W., Schmid, M. F., Fogg, J. M., Zechiedrich, L. & Pettitt, B. M., Jul 1 2017, In : Nucleic acids research. 45, 13, p. 7633-7642 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

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

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

Research output: Contribution to journalArticle

14 Scopus citations

Interactions between identical DNA double helices

Lai, C. L., Chen, C., Ou, S. C., Prentiss, M. & Pettitt, B. M., Mar 2020, In : Physical Review E. 101, 3, 032414.

Research output: Contribution to journalArticle

1 Scopus citations

Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15

Asthagiri, D., Karandur, D., Tomar, D. S. & Pettitt, B. M., Aug 31 2017, In : Journal of Physical Chemistry B. 121, 34, p. 8078-8084 7 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

30 Scopus citations

Mobility of Histidine Side Chains Analyzed with 15 N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions

Kemme, C. A., Luu, R. H., Chen, C., Pletka, C. C., Pettitt, B. M. & Iwahara, J., May 2 2019, In : Journal of Physical Chemistry B. 123, 17, p. 3706-3710 5 p.

Research output: Contribution to journalArticle

Modeling DNA thermodynamics under torsional stress

Wang, Q. & Pettitt, B. M., Mar 4 2014, In : Biophysical journal. 106, 5, p. 1182-1193 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

Multibody correlations in the hydrophobic solvation of glycine peptides

Harris, R. C., Drake, J. A. & Pettitt, B. M., Dec 14 2014, In : Journal of Chemical Physics. 141, 22, 22D525.

Research output: Contribution to journalArticle

11 Scopus citations
3 Scopus citations

Nonpolar Solvation Free Energy from Proximal Distribution Functions

Ou, S. C., Drake, J. A. & Pettitt, B. M., Apr 20 2017, In : Journal of Physical Chemistry B. 121, 15, p. 3555-3564 10 p.

Research output: Contribution to journalArticle

4 Scopus citations

Norovirus escape from broadly neutralizing antibodies is limited to allostery-like mechanisms

Kolawole, A. O., Smith, H. Q., Svoboda, S. A., Lewis, M. S., Sherman, M. B., Lynch, G. C., Pettitt, B. M., Smith, T. J. & Wobus, C. E., Sep 1 2017, In : mSphere. 2, 5, e00334-17.

Research output: Contribution to journalArticle

16 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

15 Scopus citations

Optimal updating magnitude in adaptive flat-distribution sampling

Zhang, C., Drake, J. A., Ma, J. & Pettitt, B., Nov 7 2017, In : Journal of Chemical Physics. 147, 17, 174105.

Research output: Contribution to journalArticle

Osmophobics and hydrophobics: The changing landscape of protein folding

Auton, M. & Pettitt, B., Apr 19 2016, Fluctuation Theory of Solutions: Applications in Chemistry, Chemical Engineering, and Biophysics. CRC Press, p. 309-323 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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

98 Scopus citations

Peptide Solubility Limits: Backbone and Side-Chain Interactions

Sarma, R., Wong, K. Y., Lynch, G. C. & Pettitt, B. M., Apr 5 2018, In : Journal of Physical Chemistry B. 122, 13, p. 3528-3539 12 p.

Research output: Contribution to journalArticle

1 Scopus citations

Phage-like packing structures with mean field sequence dependence

Myers, C. G. & Pettitt, B. M., Jun 5 2017, In : Journal of Computational Chemistry. 38, 15, p. 1191-1197 7 p.

Research output: Contribution to journalArticle

6 Scopus citations

Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder

Drake, J. A., Drake, J. A. & Pettitt, B. M., Jun 4 2020, In : Journal of Physical Chemistry B. 124, 22, p. 4379-4390 12 p.

Research output: Contribution to journalArticle

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Harrison, A., Binder, H., Buhot, A., Burden, C. J., Carlon, E., Gibas, C., Gamble, L. J., Halperin, A., Hooyberghs, J., Kreil, D. P., Levicky, R., Noble, P. A., Ott, A., Pettitt, B. M., Tautz, D. & Pozhitkov, A. E., Mar 2013, In : Nucleic acids research. 41, 5, p. 2779-2796 18 p.

Research output: Contribution to journalReview article

43 Scopus citations