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Author

  • Bernard Pettitt
2015

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
2011

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
2018

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. M., King, J. A., Schmid, M. F. & Chiu, W., Oct 19 2018, In : Journal of Molecular Biology. 430, 21, p. 4156-4167 12 p.

Research output: Contribution to journalArticle

6 Scopus citations
2015

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
2011

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
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

85 Scopus citations
2015

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

4 Scopus citations
2014

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
2019
2020

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

2018

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
2016

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

2012

Studying proteins and peptides at material surfaces

Feng, J., Lynch, G. C. & Pettitt, B. M., 2012, RSC Biomolecular Sciences. Royal Society of Chemistry, p. 293-320 28 p. (RSC Biomolecular Sciences; vol. 1).

Research output: Chapter in Book/Report/Conference proceedingChapter

2017

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

2016

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
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

2015

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
2016

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility

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

Research output: Contribution to journalArticle

8 Scopus citations
2019
2016

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
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

20 Scopus citations
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

1 Scopus citations
2011

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

22 Scopus citations
2015

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

Solubility and aggregation of Gly5 in water

Karandur, D., Wong, K. Y. & Pettitt, B. M., Aug 14 2014, In : Journal of Physical Chemistry B. 118, 32, p. 9565-9572 8 p.

Research output: Contribution to journalArticle

21 Scopus citations
2016

Solute-Solvent Energetics Based on Proximal Distribution Functions

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

Research output: Contribution to journalArticle

7 Scopus citations
2017

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
2014

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
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
2017

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
2011
25 Scopus citations
2015
2 Scopus citations
2016

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

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

2015

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
2019

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

Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model

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

Research output: Contribution to journalArticle

5 Scopus citations
3 Scopus citations
2019

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

3 Scopus citations
2015

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
2016

Protein collapse driven against solvation free energy without H-bonds

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

Research output: Contribution to journalArticle

11 Scopus citations

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

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

Research output: Contribution to journalReview article

12 Scopus citations
2019

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
2015

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
2016

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
2011

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
2014

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
2016

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