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  • Bernard Pettitt
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
2013

The unsolved "solved-problem" of protein folding

Montgomery Pettitt, B., Sep 1 2013, In : Journal of Biomolecular Structure and Dynamics. 31, 9, p. 1024-1027 4 p.

Research output: Contribution to journalComment/debate

10 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
2013

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 1 2013, In : Nucleic acids research. 41, 5, p. 2779-2796 18 p.

Research output: Contribution to journalReview article

43 Scopus citations
2015

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
2020

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

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

18 Scopus citations
2013

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
2020

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

2018

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
2013

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
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

27 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
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

3 Scopus citations
2017

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
2014

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
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
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
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., Jun 1 2015, In : Journal of Computational Chemistry. 36, 17, p. 1275-1285 11 p.

Research output: Contribution to journalArticle

18 Scopus citations
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
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

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

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
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., 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
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

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
2016

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

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
2018

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

2 Scopus citations
2014

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
2011

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
2016

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
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

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
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

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
2017

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
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
2019
2017

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

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
2013

Domain organization of membrane-bound factor VIII

Stoilova-Mcphie, S., Lynch, G. C., Ludtke, S. & Pettitt, B. M., Jul 1 2013, In : Biopolymers. 99, 7, p. 448-459 12 p.

Research output: Contribution to journalArticle

18 Scopus citations
2011

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
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., 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
2016

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
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

19 Scopus citations
2019
3 Scopus citations