Find Research Outputs

Search concepts
Selected Filters

Publication Year

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

Author

  • Bernard Pettitt
2020

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

Structure and the role of filling rate on model dsDNA packed in a phage capsid

Bores, C. & Pettitt, B. M., Jan 13 2020, In : Physical Review E. 101, 1, 012406.

Research output: Contribution to journalArticle

The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry

Seckfort, D., Lynch, G. C. & Pettitt, B. M., Apr 2020, In : Biochimica et Biophysica Acta - General Subjects. 1864, 4, 129538.

Research output: Contribution to journalArticle

2019

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

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
3 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

Price of disorder in the lac repressor hinge helix

Seckfort, D. & Montgomery Pettitt, B., Jan 2019, In : Biopolymers. 110, 1, e23239.

Research output: Contribution to journalArticle

1 Scopus citations
2018
2 Scopus citations

Peptide Solubility Limits: Backbone and Side-Chain Interactions

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

Research output: Contribution to journalArticle

Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model

Drake, J. A. & Pettitt, B., Jun 19 2018, In : Biophysical Journal. 114, 12, p. 2799-2810 12 p.

Research output: Contribution to journalArticle

4 Scopus citations

Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography

Dai, W., Chen, M., Myers, C., Ludtke, S. J., Pettitt, B., King, J. A., Schmid, M. F. & Chiu, W., Jan 1 2018, (Accepted/In press) In : Journal of Molecular Biology.

Research output: Contribution to journalArticle

3 Scopus citations
2017

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., Jul 1 2017, In : Nucleic Acids Research. 45, 13, p. 7633-7642 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15

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

Research output: Contribution to journalArticle

12 Scopus citations

Nonpolar Solvation Free Energy from Proximal Distribution Functions

Ou, S. C., Drake, J. A. & Pettitt, B., 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., Lynch, G. C., Pettitt, B., Smith, T. & Wobus, C. E., Sep 1 2017, In : mSphere. 2, 5, e00334-17.

Research output: Contribution to journalArticle

13 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

Phage-like packing structures with mean field sequence dependence

Myers, C. G. & Pettitt, B., 2017, (Accepted/In press) In : Journal of Computational Chemistry.

Research output: Contribution to journalArticle

6 Scopus citations
2016

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

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

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

Research output: Contribution to journalArticle

35 Scopus citations

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

Dyer, K. M., Perkyns, J. S. & Pettitt, B., 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

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

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

Bates, D., Pettitt, B., 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

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

Protein collapse driven against solvation free energy without H-bonds

Karandur, D., Harris, R. C. & Pettitt, B., Jan 1 2016, In : Protein Science. 25, 1, p. 103-110 8 p.

Research output: Contribution to journalArticle

10 Scopus citations

Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins

Harris, R. C. & Pettitt, B., Feb 2 2016, In : Journal of Physics Condensed Matter. 28, 8, 083003.

Research output: Contribution to journalArticle

11 Scopus citations

Sequence Affects the Cyclization of DNA Minicircles

Wang, Q. & Pettitt, B., Mar 17 2016, In : Journal of Physical Chemistry Letters. 7, 6, p. 1045-1046 2 p.

Research output: Contribution to journalArticle

6 Scopus citations

Solute-Solvent Energetics Based on Proximal Distribution Functions

Ou, S. C. & Pettitt, B., Aug 25 2016, In : Journal of Physical Chemistry B. 120, 33, p. 8230-8237 8 p.

Research output: Contribution to journalArticle

7 Scopus citations

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility

Drake, J. A., Harris, R. C. & Pettitt, B., Aug 23 2016, In : Biophysical Journal. 111, 4, p. 756-767 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

The contribution of electrostatic interactions to the collapse of oligoglycine in water

Karandur, D. & Pettitt, B., 2016, In : Condensed Matter Physics. 19, 2, 23802.

Research output: Contribution to journalArticle

1 Scopus citations
2015

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

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

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

27 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

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

Force field-dependent solution properties of glycine oligomers

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

Research output: Contribution to journalArticle

18 Scopus citations
2 Scopus citations

Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries

Dyer, K. M., Perkyns, J. S. & Pettitt, B., Jul 23 2015, In : Journal of Physical Chemistry B. 119, 29, p. 9450-9459 10 p.

Research output: Contribution to journalArticle

1 Scopus citations

Solvation and cavity occupation in biomolecules

Lynch, G. C., Perkyns, J. S., Nguyen, B. L. & Pettitt, B. M., May 2015, In : Biochimica et Biophysica Acta - General Subjects. 1850, 5, p. 923-931 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins

Lichti, C. F., Mostovenko, E., Wadsworth, P. A., Lynch, G. C., Pettitt, B. M., Sulman, E. P., Wang, Q., Lang, F. F., Rezeli, M., Marko-Varga, G., Végvári, Á. & Nilsson, C. L., Feb 6 2015, In : Journal of Proteome Research. 14, 2, p. 778-786 9 p.

Research output: Contribution to journalArticle

16 Scopus citations

Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density

Wang, Q., Myers, C. G. & Pettitt, B. M., Apr 16 2015, In : Journal of Physical Chemistry B. 119, 15, p. 4937-4943 7 p.

Research output: Contribution to journalArticle

4 Scopus citations
2014

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

82 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

18 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

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

39 Scopus citations

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