Thom Dunning, Todd Martinez, and Robert Pennington of the University of Illinois, Michael Klein of the University of Pennsylvania, and Robert Harrison, Robert Hinde, and Gregory Peterson of the University of Tennessee are supported by the NSF Division of Chemistry under the Cyberinfrastructure and Research Facilities Program. This collaborative project will examine the application of new computing technologies--those most likely to be found in the petascale computers of tomorrow--to the chemical sciences, through a multidisciplinary team with expertise in chemistry, computer science and technology, and computer engineering. The initial focus will be on chemical applications that are known to make heavy use of existing supercomputing facilities. These span a broad range of computational chemistry and, thus, can be viewed as prototypes for a larger class of applications. The goal is to assess the performance of these applications on the technologies expected to be the basis for future petascale computers, identify the bottlenecks limiting the performance of the applications on the new technologies, and seek solutions to the problems.
This project has the potential to extend chemical simulations to the petascale level, which will result in breakthroughs in understanding of molecular structure, energetics, and dynamics. Many of the results on chemical applications will be applicable to related activities in other fields of science--materials science, condensed matter physics, and molecular biology. Workshops, tailored to expert code developers as well as to users of standard chemistry codes, will be offered along with a dedicated website for dissemination and interactive environments.
PI: Michael L. Klein, Temple University One of the main achievements of work supported by this grant was to develop a set of tools to enable the use of graphics processing units—commonly referred to as GPUs—to be used to solve real world problems. GPUs are advanced computer hardware called coprocessors designed to speed up the rendering of images on screens such as needed in animation applications found in computer games. Specifically, the software tools we have developed leverage the GPU high-performance floating-point math, low power consumption, and low cost to allow the computer simulation of chemical systems at a fraction of the cost and environmental impact of previous computer chips. Importantly, our additions to the community computer codes: HOOMD and VMD have resulted in software packages that allow highly efficient computer simulation of a broad range of physical systems relevant to the design of consumer products such as soaps and detergents, as well as novel applications in nanotechnology, and biology. In our initial applications, we applied the HOOMD code to carry out computer simulations of dilute surfactant solutions. Our findings have provided the scientific community with the knowledge necessary to develop more accurate simulation protocols, which in turn can be used to understand, for example, protein aggregation, biological membrane structure and function, and the structure of polymer membranes relevant to fuel cell development. The broader impact of this work involves the training of post-doctoral researchers in advanced computer simulation methodologies, which in turn has resulted in the placement of five of them into research and teaching positions at City University of New York (Arben Jusufi), Yeshiva University (David LeBard), Michigan State University (Ben Levine), Procter and Gamble (Russell DeVane), and the International Center for Theoretical Physics in Trieste, Italy (Axel Kohlmeyer). Publications resulting from this grant: Surfactant concentration effects on micellar properties, Jusufi, A; LeBard, DN; Levine, BG; Klein, ML, Journal of Physical Chemistry B 116 (3): 987-991 (2012), DOI: 10.1021/jp2102989. Premicelles and monomer exchange in aqueous surfactant solutions above and below the critical micelle concentration, LeBard, DN; Levine, BG; DeVane, R; Shinoda, W; Klein, ML, Chemical Physics Letters 522: 38-42 (2012) , DOI: 10.1016/j.cplett.2011.11.075. Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing units, LeBard, DN; Levine, BG; Mertmann, P; Barr, SA; Jusufi, A; Sanders, S; Klein, ML; Panagiotopoulos, A, Soft Matter 8 (8): 2385-2397 (2012), DOI: 10.1039/c1sm06787g. Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics Levine, BG; LeBard, DN; DeVane, R; Shinoda, W; Kohlmeyer, A; Klein, ML, Journal of Chemical Theory and Computation 7 (12): 4135-4145 (2011), DOI: 10.1021/ct2005193. Fast Analysis of Molecular Dynamics Trajectories with graphics processing units: Radial distribution function histogramming, Levine, B. G., Stone, J. E., Kohlmeyer, A., J. Comput Phys. 230(9), 3556-3569 (2011).
