Pharmacology and Toxicology - Research

B. Montgomery Pettitt, Ph.D.

Professor

  • group web page

  • Research Interests

    The research in my laboratory involves work in the areas of Biochemistry, Chemical Physics/Physical Chemistry and Computer Science. I am interested in:
    1. Effects of anisotropic environments on DNA and Proteins: Tethering biomolecules to surfaces characterizes a wide variety of biotechnological devices including microarrays, nano beads, next generation sequencing etc. However the effects of electric fields, solvent gradients and density waves near surfaces has a profound effect on conformation and binding. Both theoretical and simulation methods are being developed to address these problems.
    2. Computational theory of exotic statistical ensembles and sampling methods. In particular the use of chemical potential to calculate phase related behavior requires sampling tricks. Application to systems at constant activity to explore phase transitions in saline solution and protein folding in multicomponent systems is of interest.
    3. Forces and structures governing thermodynamics and kinetics in liquid solutions especially aqueous systems. Most difficult is the question of how multicomposnent systems including cosolvents and ions affect the structure of proteins and nucleic acids in solution. Given correlations and statistical thermodynamics the relations to experimental observables on the effects ions and osmolytes have on biomacromolecules in solution should then be understandable. At the technical level we are working on activity models, diagramatic expansion techniques, and simulation algorithms.
    4. Theory and computational methods to investigate solution systems with couplings and correlations at many disparate length and time scales. There are many problems for which atomic correlations do not provide a direct link to macroscopic properties. Connecting meso scale averaging procedures to the atomic and macro levels via multiscale methods is important for biological/materials applications. For additional information: group web page

  • Selected Publications

    A. Vainrub; B. M. Pettitt The Journal of Physical Chemistry B 2011, 115, 13300-13303.

    B. Lin; K.-Y. Wong; C. Hu; H. Kokubo; B. M. Pettitt The journal of physical chemistry letters 2011, 2, 1626-1632.

    B. Lin; B. M. Pettitt Journal of Chemical Physics 2011, 134, 106101.

    B. Lin; B. M. Pettitt Journal of computational chemistry 2011, 32, 878-885.

    H. Kokubo; C. Y. Hu; B. M. Pettitt Journal of the American Chemical Society 2011, 133, 1849-1858.

    J. J. Howard; B. M. Pettitt Journal of Statistical Physics 2011, 1-26.

    J. J. Howard; G. C. Lynch; B. M. Pettitt The Journal of Physical Chemistry B 2011, 115, 547-556.

    C. Chen; B. M. Pettitt Biophysical journal 2011, 101, 1139-1147.

    J. Ambia-Garrido; A. Vainrub; B. M. Pettitt Journal of Physics: Condensed Matter 2011, 23, 325101.

    J. S. Perkyns; G. C. Lynch; J. J. Howard; B. M. Pettitt The Journal of chemical physics 2010, 132, 064106.

    C. Y. Hu; G. C. Lynch; H. Kokubo; B. M. Pettitt Proteins: Structure, Function, and Bioinformatics 2010, 78, 695-704.

    C. Y. Hu; H. Kokubo; G. C. Lynch; D. W. Bolen; B. M. Pettitt Protein Science 2010, 19, 1011-1022.

    J. J. Howard; J. S. Perkyns; B. M. Pettitt The Journal of Physical Chemistry B 2010, 114, 6074-6083.

    J. Ambia-Garrido; A. Vainrub; B. M. Pettitt Computer physics communications 2010, 181, 2001-2007.

    G. L. Randall; L. Zechiedrich; B. M. Pettitt Nucleic acids research 2009, 37, 5568-5577.

    G. L. Randall; D. L. Summers; B. M. Pettitt; L. Zechiedrich Bussei Kenkyu 2009, 92, 80-83.

    K. Qamhieh; K.-Y. Wong; G. C. Lynch; B. M. Pettitt International Journal of Numerical Analysis & Modeling 2009, 6, 474-488

    C. Y. Hu; B. M. Pettitt; J. Roesgen F1000 biology reports 2009, 1.

    J. Feng; K.-Y. Wong; G. C. Lynch; X. Gao; B. M. Pettitt The Journal of Physical Chemistry B 2009, 113, 9472-9478.

    J. Feng; K.-Y. Wong; K. Dyer; B. M. Pettitt The Journal of chemical physics 2009, 131, 125102.

    K. M. Dyer; J. S. Perkyns; G. Stell; B. M. Pettitt Molecular physics 2009, 107, 423-431.

    C. Chen; K. Krause; B. M. Pettitt The Journal of Physical Chemistry B 2009, 113, 511-521.