David A. Bruce, Ph.D. -- Research Activities

Molecular Modeling of Polymers
Molecular dynamics (MD), replica exchange MD, and parallel replica MD techniques are powerful tools for describing complex chemical systems at the atomic scale. These force field-based techniques provide an effective means for understanding and predicting macroscopic behavior that develops at time scales beyond those easily sampled by quantum computational methods (e.g., density functional theory) and include atomic level interactions and symmetry information that are not present in more coarse grained (e.g., bead and spring or lattice) models. We currently use the parallelized GROMACS MD simulation code and the OPLS force field (with parameters optimized for each polymer system) to examine polymer systems by MD and parallel MD techniques.

In an effort to better understand the nature of helices formation, which is one of several conformations that are commonly adopted by bio-based polymers and protein segments, we have chosen to study meta poly(phenyleneethynylene)s or m-PPEs. These oligomers undergo a solvent-driven transition from a random conformation in nonpolar solvents to an ?-helix conformation in polar solvents. Both experimental and modeling studies have indicated that solvophobic interactions are the dominant force in helices stabilization, and modeling studies by our group have shown that the helix conformation is maintained at temperatures as high as 523 K. We have used all-atom and united-atom molecular dynamics simulations as well as replica exchange MD simulations to examine the folding behavior of several amine-functionalized m-PPE oligomers in aqueous environment.

We have also begun modeling the transport properties of poly(lactic acid) or PLA, which is a biodegradable polymer that has received widespread attention due to its physical properties, ease of synthesis, and formation from low cost agricultural products, such as corn. PLA has begun to be used for commercial applications, such as food packaging and apparel, in addition to its more traditional uses in medical applications. Despite having these advantageous physical properties, single enantiomer PLA is not ideal for all commercial applications; hence, the creation of copolymers or PLA blends is required to achieve the desired polymer properties. Synthesis and testing of all of the possible copolymers and polymer blends would be prohibitively time consuming and expensive. Therefore, a promising alternative is to use molecular modeling to predict the physical and transport properties of the proposed polymer systems. We are currently using nonequilibrium and equilibrium MD techniques to predict the rheological and small molecule diffusion properties of single enantiomer PLA. Upon completion of these studies, we will then extend this work to homogeneous blends of PLA and related polymers.

Last Updated:April 18, 2009 -- Site Maintained by: Donna Kilbourne
Department of Chemical and Biomolecular Engineering
Clemson University, 127 Earle Hall, Clemson, SC 29634-0909
Phone: (864) 656-3055 -- FAX: (864) 656-0784

Clemson Home -- College Home -- Department Home
calendars -- campus map -- campus tour -- phonebook -- search -- webmail

Copyright © 2002-2006, Clemson University. All rights reserved.
Clemson University, Clemson, South Carolina 29634 -- Area Code: 864, Information: 656-3311