A Parallel Simulation Environment
for Studying Programmed
Self-Assembly Systems
Argonne
National Laboratory
Office A-119, Bldg. 221
Argonne, IL 60441
email: [email protected]
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: [email protected]
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