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A Parallel Simulation Environment for Studying Programmed Self-Assembly Systems

R. Stevens* and I.R. Judson

Argonne National Laboratory
Office A-119, Bldg. 221
Argonne, IL 60441
This is an abstract for a poster to be presented at the Fifth Foresight Conference on Molecular Nanotechnology. There will be a link from here to the full article when it is available on the web.
Of the many possible paths to constructing engineered nanosystems, "programmed self-assembly" has a number of advantages. It requires only global resources and control, it scales to large numbers of objects or entities, it has many biological models and existence proofs, and it is an active area of research by the mathematics, computer science and molecular communities. We will describe a parallel simulation system under development at Argonne that is designed to support a variety of investigations in the area of programmed self-assembly and self-assembly dynamics. The system we call ORIGIN is aimed at enabling the investigation of both two and three-dimensional systems. It supports flexible user defined object geometry's (e.g. nodes, surfaces, vertices, edges), user defined interaction models (e.g. magnetic, sticky, surface and edge encoded, etc.), multiple models of object transport (e.g. diffusion, elastic, planar, self- gravity), user defined global or transport media (e.g. gas, liquid, vacuum) and multiple global communications modalities (e.g. acoustic, temperature, ion, electromagnetic, subparticles, etc.). The system is designed to scale to hundreds of processors and to handle billions of objects, thereby covering and extending the range of desktop experimental systems. We are targeting ORIGIN to enable the computational study of a range of self-assembly model systems, including macro-scale desktop experiments and some molecular systems. ORIGIN is designed as meso-scale simulation environment that doesn't directly model molecular properties, however ORIGIN's object interaction mechanisms can use parameters derived from molecular simulations and measurements. Ultimately we wish to interface ORIGIN with a goal oriented back-chaining system to derive self-assembly programs for given structures however that is not a goal for the current implementation of ORIGIN. One objective for our discussion of ORIGIN at the Foresight meeting is to collect classes of self-assembly problems that can be used to test and validate ORIGIN's design.

*Corresponding Address:
Rick Stevens, Argonne National Laboratory, Office A-119 Bldg. 221, Argonne, IL 60441, ph: 630-252-3378, fax: 630-252-5986, email:
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