Robert M. Wellek
CBET Division of Chemical, Bioengineering, Environmental, and Transport Systems
ENG Directorate for Engineering
Start Date:
September 1, 2002
Expires:
August 31, 2007 (Estimated)
Awarded Amount to Date:
$499117
Investigator(s):
David Kofke kofke@buffalo.edu (Principal Investigator)
Sponsor:
SUNY at Buffalo
501 Capen Hall
Buffalo, NY 14260 716/645-5000
NSF Program(s):
ITR SMALL GRANTS, INTERFAC PROCESSES & THERMODYN
Field Application(s):
0308000 Industrial Technology
Program Reference Code(s):
OTHR, 1686, 1660, 0000
Program Element Code(s):
1686, 1414
ABSTRACT
This Information Technology Research (ITR) project aims to apply state-of-the-art software tools and methods to develop an advanced computational environment for molecular and mesoscale modeling. This work is performed to address specific, well-documented needs that block the broader adoption of molecular and multiscale modeling tools to solve practical problems. The environment is designed to be extensible (accommodates easily new methods and models), computationally efficient, and easy to use. It aims to be platform independent yet configurable to exploit features of different computing environments, including parallel and grid architectures. It is developed using the Java programming language, and consists of two distinct parts. First is an Application Programming Interface (API) that can be used to construct a wide variety of simulations from a common set of building blocks; the API can be used, for example, by programming in a text editor. Second is an Integrated Development Environment (IDE), which provides an alternative graphical environment for the development and application of complex molecular simulations. The work performed here consists of designing, developing and testing the API and IDE, researching how they can be best implemented on a wide variety of single and multiprocessor computing architectures, disseminating them, and conducting activities to promote understanding and use of them. A range of experts are consulted to assist in the detailed implementation of the best simulation methods and models in current use; this practice serves the dual purpose of speeding the development as well as broadening the interest in it. The focus of the development is to facilitate use in research applications, but there are significant educational components to the activity: (1) the tools are used to produce aids for teaching molecular phenomena and its role in producing macroscopic behaviors; (2) the development environment is used as a basis to teach ideas about molecular simulation to students from Buffalo-area high schools and freshman- through senior-level undergraduates at the University; (3) undergraduates contribute through tightly-focused development activities. Further, the object-oriented structure of the API provides a sound pedagogical basis for teaching molecular simulation in a way that promotes broader use. Accordingly the codes and concepts developed in this work are used as a central component in a regular series of national workshops in molecular simulation offered by the newly created Nanomaterials Theory Institute at Oak Ridge National Laboratory.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Bucher, HK; Schultz, AJ; Kofke, DA. "An Eclipse-Based Environment for Molecular Simulation," Proceedings of the 2005 Object oriented programming systems languages and applications (OOPSLA) workshop on Eclipse technology eXchange, San Diego, CA, 2005, p. 130.
Singh, JK; Kofke, DA. "Molecular simulation study of effect of molecular association on vapor-liquid interfacial properties," JOURNAL OF CHEMICAL PHYSICS, v.121, 2004, p. 9574-9580.
Singh, JK; Kofke, DA. "Molecular simulation study of the effect of pressure on the vapor-liquid interface of the square-well fluid," LANGMUIR, v.21, 2005, p. 4218-4226.
Singh, JK; Kofke, DA; Errington, JR. "Surface tension and vapor-liquid phase coexistence of the square-well fluid," JOURNAL OF CHEMICAL PHYSICS, v.119, 2003, p. 3405-3412.
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