Michael A. Ewing
We investigate new instrument designs by simulation of the instruments we have built or of those we propose. We use SIMION for calculation of the electric field and a separate program written in-house to simulate ion trajectories in the gas phase. This program adds the motion due to the electric field to a diffusive motion approximated as Brownian motion. These simulations have been helpful in understanding a variety of instruments from tandem IMS to OMS instruments, with recent work also aiding in the understanding of the kinetics of structural transitions in the gas phase. Current work in our lab uses instrumental simulations to understand new instruments we are developing and to assist in the design process.
Jonathan M. Dilger
The cross section of an ion is a measure of its overall shape and thus is related to its structure. The relative contribution to cross section for an individual amino acid residue within a peptide sequence can be derived with intrinsic size parameters (ISPs).1 These ISPs are derived with each residue as a separate variable from the large number of measurements contained within the cross section database. The utility of ISPs are demonstrated with respect to prediction of cross section,2, 3 extraction of average volumes of amino acid residues,4 and sequence specificity.5 Current work with ISPs focuses on the structural analysis of metalated tryptic peptides.6 Comparisons of these metal-coordinated ISPs with protonated ISPs can display general trends in metal interactions with a given peptide sequence.
Nicholas A. Pierson
Ion mobility analyses are often combined with computational modeling approaches to aid in the interpretation of experimental data. Molecular dynamics (MD) simulations use Newtonian physics to theoretically model the structure and dynamics of molecules in a given system over time. Our group utilizes these methods to model biomolecules both in solution and in vacuo. Energy-minimized structures can be related to IMS data by submitting atomic coordinates to a program called MOBCAL, developed by Martin F. Jarrold. MOBCAL (freely available online from the Jarrold Group at Indiana University) calculates theoretical collision cross sections for the submitted molecular structures.7 These theoretical cross section values are then compared with calculated experimental cross sections from IMS to match the data with tentative low-energy structures.
Full-text formats for many of these references can be found on the Publications page. External links are provided as necessary and available.