Members

Education

University of British Columbia, Vancouver, Canada, Ph.D., 1990 in Physical (Theoretical) Chemistry
University of British Columbia, Vancouver, Canada, M.Sc., 1985
Dalhousie University, Halifax, Nova Scotia, Canada, B.Sc., 1983; B.A., 1981

Selected Recent Publications

• Dyer KM, Perkyns JS, Pettitt BM. Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries. J Phys Chem B., 119 (29), 9450-9459 (2015)
• Lynch GC, Perkyns JS, Nguyen BL, Pettitt BM. Solvation and cavity occupation in biomolecules. Biochim Biophys Acta., 1850(5), 923-31 (2015)
• Howard JJ, Perkyns JS, Pettitt BM. The behavior of ions near a charged wall-dependence on ion size, concentration, and surface charge. J Phys Chem B, 114, 6074-6083 (2010)
• Perkyns JS, Lynch GC, Howard JJ, Pettitt BM. Protein solvation from theory and simulation: exact treatment of coulomb interactions in three-dimensional theories. J Chemi Phys, 132, 064106 (2010)
• Dyer KM, Perkyns JS, Stell G, Pettitt BM. Site-renormalised molecular fluid theory: on the utility of a two-site model of water. Mol Phys, 107, 423-431 (2009)
• Howard JJ, Perkyns JS, Choudhury N, Pettitt BM. An integral equation study of the hydrophobic interaction between graphene plates. J Chem Theo Comput, 4, 1928-1939 (2008)
• Dyer KM, Perkyns JS, Stell G, Pettitt BM. A molecular site-site integral equation that yields the dielectric constant. J Chem Phys, 129, 104512 (2008)
• Dyer KM, Perkyns JS, Pettitt BM. A site-renormalized molecular fluid theory. Condensed Matter Physics, 10, 331-342 (2007)

Education

Texas A&M University, College Station, Ph.D.
The Chinese University of Hong Kong, Hong Kong, B.Sc.

Research Interests

Modeling of nucleic acids in salt solutions.

Selected Publications

• Nassar OM, Wong KY, Lynch GC, Smith TJ, Pettitt BM. Allosteric discrimination at the NADH/ADP regulatory site of glutamate dehydrogenase. Protein Sci. 12, 2080-2088 (2019)
• Sarma R, Wong KY, Lynch GC, Pettitt BM. Peptide Solubility Limits: Backbone and Side-Chain Interactions. J Phys Chem B. 122(13), 3528-3539 (2018)
• Karandur D, Wong KY, Pettitt BM. Solubility and aggregation of Gly(5) in water. J Phys Chem B, 118(32), 9565-72 (2014)
• Lin B, Wong KY, Hu C, Kokubo H, Pettitt BM. Correction to "Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions". The Journal of Physical Chemistry Letters, 3, 69-69 (2012)
• Lin B, Wong KY, Hu C, Kokubo H, Pettitt BM. Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions. The Journal of Physical Chemistry Letters, 2, 1626-1632 (2011)
• Feng J, Wong KY, Dyer K, PettittBM. Transport Properties of Water at Functionalized Molecular Interfaces. J. Chem. Phys., 131:125102 (2009)
• Qamhieh K, Wong KY, Lynch GC, Pettitt BM. The melting mechanism of DNA tethered to a surface. International Journal of Numerical Analysis and Modeling, 6, 474-488 (2009)
• Feng J, Wong KY, Lynch GC, Gao X, Pettitt BM. Salt effects on surface-tethered peptides in solution. J Phys. Chem. B, 113, 9472-9478 (2009)
• Wong KY, Pettitt BM. The pathway of oligomeric DNA melting investigated by molecular dynamics simulations. Biophys J, 95, 5618-5626 (2008)
• Feng J, Wong KY, Lynch GC, Gao X, Pettitt BM. Peptide conformations for a microarray surface-tethered epitope of the tumor suppressor p53. J Phys Chem B, 111, 13797-13806 (2007)
• Pettitt BM, Vainrub A, Wong KY. DNA saline solutions near surfaces - A few ideas towards design parameters of DNA arrays. In Ionic Soft Matter: Modern Trends in Theory and Applications; NATO Science Series; Douglas Henderson, Myroslav Holovko, Andrij Trokhymchuk (eds.); Springer, 381-393 (2005)
• Wong KY, Pettitt BM. Orientation of DNA on a surface from simulation. Biopolymers, 73, 570-578 (2004)
• Wong KY, Vainrub A, Powdrill T, Hogan M, Pettitt BM. A non-Watson-Crick motif of base-pairing on surfaces for untethered oligonucleotides. Molecular Simulation, 30, 121-129 (2004)

Education

Georgia State University, Ph.D., 2003 in Biophysical Chemistry
Lanzhou University, China, M.Sc., 1998 in Physical Chemistry
Lanzhou University, China, B.Sc., 1995 in Physical Chemistry

Research Interests

In all biological processes, molecular recognition plays a central role in the assembly of biological structures and cellular events. A better understanding of molecular recognition is essential to the development of new drugs and biomaterials and of the design of novel molecular devices for catalysts and drug delivery. Currently I work on the topics of molecular recognition and solvation effects on biological processes using molecular modeling and simulation. I try to gain molecular descriptions of the free energy surface that govern these interactions and the corresponding mechanism that are consistent with known biological, thermodynamic, kinetic, and structural data.

Selected Publications

• Chen C, Pettitt BM. The Effects of Flexibility on dsDNA–dsDNA Interactions. Life (Basel) 12(5), 699 (2022)
• Lai CL, Chen C, Ou SC, Prentiss M, Pettitt BM. Interactions between identical DNA double helices. Physical Review E 101, 032414 (2020) (Featured in Editors' Suggestion)
• Esadze A, Chen C, Zandarashvili L, Roy S, Pettitt BM, Iwahara J. Changes in conformational dynamics of basic side chains upon protein-DNA association. Nucl. Acids Res., 44(14), 6961-70 (2016).
• Chen C, Pettitt BM. DNA shape versus sequence variations in the protein binding process. Biophys. J., 110(3), 534-44 (2016)
• Chen C, Esadze A, Zandarashvili L, Nguyen D, Pettitt BM, Iwahara J. Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes. J Phys Chem Lett., 6(14), 2733-2737 (2015)
• Chen C, Pettitt BM. The binding process of a nonspecific enzyme with DNA. Biophys. J., 101, 1139-1147 (2011)
• Chen C, Krause K, Pettitt BM. Advantage of being a dimer for Serratia marcescens endonuclease? J. Phys. Chem. B., 113, 395-588 (2009). (Figure featured on journal cover)
• Chen C, Beck BW, Krause K, Warth T E, Pettitt BM. The effects of dimerization of Serratia marcescens endonuclease on water dynamics. Biopolymers, 85, 241-252 (2007). (Figure featured on journal cover)
• Chen C, Beck BW, Krause K, Pettitt BM. Solvent participation in Serratia marcescens endonuclease complexes with DNA. Proteins: Structure, Function and Bioinformatics, 62, 982-995 (2006). (Figure featured on journal cover)