Interaction of bacteria with antimicrobial agents:

I am currently involved with the Canadian Advanced Food and Biomaterials Network, a consortium of food scientists, microbiologists and physicists, including scientists from the Centre for Food and Soft Materials Science (FSM) at University of Guelph. I interact with scientists from varied backgrounds on such topics as protein and nutraceutical purification, protein food interaction, and structural properties of molecules in food. A primary goal of my research is an atomic level understanding of the interaction of antimicrobial polypeptides such as protamine and lactoferricin with the outer lipopolysaccharide (LPS) membrane of various strains of gram-negative bacteria. In particular I am studying the reason for the polypeptide’s antimicrobial efficacy. Detailed simulation studies are underway using the CHARMM software package on a multi- university BEOWOLF cluster of parallel processors (SHARC-Net) to determine the structure of the lipopolysaccharide outer membrane and the mechanism by which the polypeptide penetrates the LPS and causes cellular death. Simulations studying different strains and species of bacteria and using other antimicrobial polypeptides will explore differences in susceptibility between different bacterial strains, and why certain proteins are particularly effective at inhibiting bacterial growth.

Local solvent structure and solubility in supercritical solvents:

The strongly state-dependent solvent power of a supercritical fluid (SCF) can be applied to the extraction of flavouring and pharmaceutical agents. I have a long term interest in studying the supercritical fluid extraction and properties of carotenoid anti-oxidants such as lycopene. There is great current interest in the documented cancer-preventing properties of lycopene, and in addition to using statistical mechanics to explore economically feasible ways of extracting lycopene from vegetables (lycopene is the chemical responsible for the red colour of a tomato), I also use simulations to study the electron transfer reaction by which the organism-damaging properties of free radicals such as singlet O 2 and singlet NO 2 are strongly quenched by carotenoids. Studies are being carried out using both computer-based quantum chemistry (i.e. GAUSSIAN) to directly study the electron transfer, and classical simulations to study the mediating effect of classical thermal fluctuations in the solvent.

Quantum mechanical effects in liquids and glasses:

These manifest themselves as isotopic differences in the structure of matter. For example, quantum effects account for the two percent difference between the structure of heavy and light water at 25 °C. Therefore accurate measurements must include quantum mechanical corrections. In collaboration with colleagues at the American Photon Source, high precision X-ray diffraction is used to measure isotopic differences in structure for liquids and glasses, and in the correction of quantum effects to neutron scattering data. In addition to elucidating the role of quantum mechanics in intermolecular forces, the glassy states of water studied in this project contribute to the fundamental understating of crystal formation and have potential applications in the field of tissue cryopreservation.

B. Tomberli, S. Goldman, C.G. Gray, M. Saldaña and F. Temelli, Using solute structure to predict solubility of organic molecules in supercritical carbon dioxide, J. Supercrit. Fl., in press (2005).

R.T. Hart, C. J. Benmore, J. Neuefeind, S. Kohara, B. Tomberli and P.A. Egelstaff, Temperature dependence of isotopic quantum effects in water, Physical Review Letters, 94, 047801 (2005) - selected for the February 15, 2005 issue of Virtual Journal of Biological Physics Research.

B . Tomberli, V. Vivcharuk, C.G. Gray and S. Goldman, Simulation studies of peptide-membrane interaction, Proceedings of the 2005 Chemical Biophysics Symposium, 2005146 (2005).

J. Urquidi, C.J. Benmore, J. Neuefeind, B. Tomberli, C.A. Tulk, M. Guthrie, P.A. Egelstaff and D.D. Klug, Isotopic quantum effects on the structure of low density amorphous ice, J. Phys., Cond. Mat., 15, 3657-3664 (2003). 

C.A. Tulk, C.J. Benmore, J. Urquidi, D.D. Klug, J. Neuefeind, B. Tomberli and P.A. Egelstaff, Structural studies of several distinct meta-stable forms of amorphous ice, Science, 297, 1320-1323 (2002).