05.20.13 - Permalink
The two winners of the 2012 Graduate Student Award in Computational Physical Chemistry, given by the American Chemical Society’s Theoretical Subdivision, will receive 100,000 service units (3,125 node hours) on the Blue Waters supercomputer to accelerate their research.
Scott Carmichael, a graduate student in the Department of Chemical Engineering at the University of California Santa Barbara, will use Blue Waters to conduct molecular dynamics simulations of the structural and thermodynamic behavior of polymer brush conjugated peptide micelle systems. Understanding such systems is a key step in designing targeted drug therapies. (See project abstract below)
“Blue Waters will enable me to explore in great detail the complex driving forces underlying molecular self-assembly,” says Carmichael. “This computational resource will allow me to really push the envelope with my graduate research.”
Matthew Hermes, a graduate student in the Department of Chemistry at the University of Illinois at Urbana-Champaign, plans to use Blue Waters to perform groundbreaking ab initio vibrational structure calculations on ice Ih—the common form of solid water with which we are all familiar. (See abstract below)
“The Blue Waters project is dedicated to scientific and engineering excellence at scale in all disciplines. This means fostering young investigators such as Scott and Matthew who have demonstrated their potential by providing them the unique petascale resources to accelerate their education and development,” said deputy project director Bill Kramer.
The Blue Waters project sets aside compute cycles exclusively for educational use and plans to extend this type of allocation to other professional societies.
For more information about the Blue Waters supercomputer and the science and engineering work supported by the project, visit bluewaters.ncsa.illinois.edu.
Self-assembly and phase behavior of surface-tethered peptide/polymer-brush conjugates
The latest generation of rationally designed and targeted drug therapies are currently revolutionizing medicine. There has been recent success in utilizing self-assembled peptide micelles as targeted drug delivery vehicles. These novel agents offer the ability to safely transport and deliver drugs to a disease site, and maintain long circulation times in the bloodstream. A major challenge for designing peptide based drug delivery systems is that the peptide domains can assemble to form so-called β-sheet structures that drive a spherical micelle into a cylindrical form, the latter which is less suitable for drug delivery and storage. However, the addition of polymer brushes to the midpoints of the peptides has recently been shown to hinder the formation of β-sheet structures and promote spherical micellization.
In our work, we will use molecular dynamics simulations to elucidate the structural and thermodynamic behavior of such polymer brush conjugated peptide micelle systems. In particular we will focus on the effects of varying the polymer-brush length and peptide density to map out the structures that are formed by the complex interplay of different driving forces universally at play in such systems. An understanding of the structural effects of polymer-brush conjugation is crucial to improving drug targeting propensities and micellar stability.
Anharmonic calculation on Ice Ih
The use of embedded fragmentation techniques, which are trivially and extremely parallelizable, to perform sophisticated ab initio electronic structure calculations on systems which were considered intractably large just a few years ago is currently a hot topic of research. However, anharmonic vibrational structure calculations lag behind their electronic counterparts because phonons are fundamentally delocalized, and hence it is difficult to apply fragmentation techniques to solving the vibrational structure problem. Our lab has developed novel anharmonic vibrational structure methods, which render such calculations possible. I will use Blue Waters to perform completely ab initio anharmonic vibrational structure calculations on ice as a paradigm for simulations in which all electronic and vibrational properties are computed by members of systematic hierarchies of methods which converge to the exact limit. Blue Waters’ large parallel capacity will allow me to take full advantage of the parallelizability of the necessary electronic structure calculations using embedded fragmentation methods, permitting much more sophisticated calculations closer to convergence.