61st Annual Report on Research 2016

The initial undergraduate student on this project, Jacob Palumbo, applied his modeling experience to the project he presented at the iGEM Jamboree in Boston in September 2015. His travel expenses were covered by a NASA grant and fundraising for his iGEM submission. Mr. Palumbo graduated from Pacific University in May 2016 with a major in Bioinformatics. He plans to pursue graduate education and a career in computational/synthetic biology.

For summer 2016, two students were hired each for 10 weeks of work. Kjersti Chippendale is a senior chemistry major planning on pursuing chemical education as a career. This was Ms. Chippendale’s first intensive research experience outside of class activities. She became familiar with the programming interface for the OpenMM package we use for dynamics modeling of surfactants at water/organic interfaces. She also became quite familiar with the detailed AMOEBA parameterization of molecular properties required for our simulations. A good deal of her summer work involved validation of our methods in comparison to previous computational work in this group using AMBER parameters. Ms. Chippendale will start in the Fall semester on her Chemistry Capstone project investigating the effects of aqueous dissolved divalent cations on the structure of dodeconate surfactants following the work in the Richmond lab at the University of Oregon. (Robertson, E. J., Beaman, D. K., & Richmond, G. L. (2013). Designated Drivers: The Differing Roles of Divalent Metal Ions in Surfactant Adsorption at the Oil–Water Interface. Langmuir, 29(50), 15511–15520.) Ms. Chippendale is planning on attending the Spring 2017 ACS meeting.

Chris McCormick joined the project for summer 2016. Mr. McCormick is a senior computer science major at Pacific University. He developed a new Python based set of analysis tools that quantitatively describe interface structure. His programming effort has created opportunities to take the project forward in new analysis methods that characterize localized interface structure, whereas previously we have been limited to averaged properties of interfaces. Mr. McCormick has elected to pursue a senior project more closely aligned to his major field, and will not be actively working on the project in the upcoming year.

For the PI, the initial investment in computational hardware made possible by the ACS-PRF grant will allow for his continued research productivity in using classical molecular dynamics to investigate molecular scale cooperative interactions of surfactants at interfaces. Reviewers of paper submissions for purely computational projects expect validation studies. The work this past summer is the prelude to new studies of divalent cations, and a new approach of characterizing local surface structures.

Scientific progress:

Interface sensitive spectroscopic techniques measure average structural characteristics. Our MD modeling approach combined with analysis tools that quantify both depth and lateral structural characteristics of interfaces will allow us to more completely characterize water/organic interfaces as modulated by surfactants and the ions in solution in the aqueous layer. We expect to characterize the interface width and lateral distribution of carboxylate surfactant molecules and the effects of added divalent cations. Literature suggests that the surfactant molecules are drawn further into the aqueous layer even at low concentrations of the divalent cation. We will be able to characterize both the average depth profile, and the lateral length scale associated with any localized effects from the presence of the divalent cations.