A novel MD/BD model for the simulation of multi-scale

COMP 171

Peter E Krouskop, krouskop@duq.edu, Department of Chemistry and Biochemistry, Duquesne University, 308 Mellon Hall, 600 Forbes Ave., Pittsburgh, PA 15282 and Jeffry D. Madura, madura@duq.edu, Department of Chemistry & Biochemistry, Center for Computational Sciences and Duquesne University, 308 Mellon Hall, 600 Forbes Ave., Pittsburgh, PA 15282.
Quantum dots (QDs) are being used in the development of new biosensors. During the fabrication of these sensors, the size and shape of groups of QDs on the substrate surface have been observed to be solvent dependent. We wish to illucidate the physical and chemical interactions important in the development of the observed secondary, QD structures. The size scales of the biosensors and QDs make this a good platform from which we are developing multiscale simulation methods. To this end, we have begun to develop a novel combination of molecular dynamics (MD) and Brownian dynamics (BD) in a single, multi-scale simulation. The model allows for simulation of system that range in size from atoms to groups of proteins. The methodology for this hybrid technique and the results of preliminary simulations will be presented.