60th Annual Report on Research 2015

This report covers two summers work, and therefore only one student was engaged on the project each summer. The same student, Jacob Palumbo, was hired both summers. Mr. Palumbo is a bioinformatics major at Pacific University, and started the summer following his first year of college. For Mr. Palumbo the experience has been transformative in that he has not only been able to apply his skills in computer programming toward scientific modeling, but it helped him in applying for a scholarship/grant through the Oregon NASA Space Grant Consortium. He was successful and received $12,000 toward computer equipment to be used in this project and scholarships. Mr. Palumbo will continue working on the project for his final two years of college culminating in a research-based senior project.

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. In particular, the opportunity to purchase GPU processors has allowed our research to move from software that required CPU processing (AMBER) to software that takes advantage of GPU multi-tasking (OpenMM) while preserving the critical force modeling components of the dynamics simulation. This software and hardware 'retooling' of our research methods will greatly increase the productivity of our project going into the final two years, when two students will be employed during the summers research season.

Scientific progress:

Our initial modeling plan is to investigate the structural effects on interface organization of two similar surfactant molecules at the interface of water and immiscible organic liquids. Specifically, we are modeling sodium dodecylsulfonate and sodium dodecylbenzenesulfonate. We hypothesize the additional benzene ring between the surfactant head-group and hydrophobic tail will disrupt the ordering of the surfactant at the interface. We successfully modeled the aqueous and organic layers and interface with published molecular dynamics parameters, including importantly molecular polarizabilities. We also used published parameters for sodium ions in aqueous solution. Our own previous work on dodecanoic acid and sodium dodecanonate provided parameters for the surfactant tail groups. In the first summer of work, we successfully parameterized the sulfonate head-group and benzenesulfonate combination.

The second summer of work was focused on converting our hardware to GPU processing and establishing procedures for using the new OpenMM software for our simulations.

Our goals are to transition from AMBER software and parameters to OpenMM software and Amoeba parameters for all simulations. Amoeba parameters better calculate the effect of polarizability in classical molecular dynamics simulations, and offers the additional advantage of GPU processing.