This page provides a simple graphical toolkit for generating icosahedrally-symmetric local rule sets for the DESSA discrete-event self-assembly simulator. It is designed to make the simulator more accessible to new users by eliminating the need to directly write XML specifications of new particle systems. The code is written in Java, like the DESSA simulator itself, to support widespread portability. The code was developed on a Windows system and so far has seen only limited use beyond that on Linux and Macintosh. Feedback would therefore be appreciated.
The XML Generator creates a graphical environment in which users can add assembly subunits to an icosahedron and create binding sites between them in order to specify particular icosahedral geometries. The generator displays all of the symmetric particles and interactions and generates XML defining the particle types for the DESSA simulator. This XML can be directly loaded into the DESSA simulator for self-assembly simulations with default rate constants and starting conditions or can be modified as needed.
The following figure shows the XML Generator during the process of specifying a T=1 rule set:
The following figure shows the results of a simulation run from rules generated from the above configuration, creating model T=1 virus capsids:
See the README file, provided in the archive, for further details. The code can be downloaded from the following link:
Questions or comments can be emailed to Russell Schwartz at
russells (at) andrew (dot) cmu (dot) edu
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.