RodSim

Name

RodSim: An Optimized Simulator for the aSAM and kSAM

Description

RodSim is an abstract Slat Assembly Model (aSAM) and kinetic Slat Assembly Model (kSAM) simulator written in C++ that is optimized to allow for much faster simulation than SlatTAS. However, it has no graphical user interface and no way of visualizing assemblies. Instead, they can be opened and inspected using SlatTAS.

RodSim is freely released and its source code is freely available, along with a README file explaining its dependencies and how to build it.

Beta Release

This is a beta release - there are still surely plenty of bugs and inconveniences. Use at your own risk! Please feel free to email tas@self-assembly.net with any questions, comments, etc. We hope that you enjoy this software and find it useful!

RodSim Beta Release (C++ code) Note that the latest version can be found at the bottom of the list.

Slat Generator API: Utility Scripts

The Slat Generator API is a set of Python scripts and functions designed to facilitate the generation, simulation, viewing, and analysis of slat assembly systems. It is evolving, and therefore changing, extremely quickly so it is likely to have many bugs and broken pieces of functionality. Its main components are the following:

• slat_generator.py: A set of classes and functions shared by most scripts and used to abstractly represent, generate, manipulate, and output slats, gadgets, etc.

• SlatSystem.py, SlatAssembly.py, SlatType.py, PyTASTileTypeLight.py: A set of classes to represent slat systems, assemblies, and types

• slat_ribbon_generator.py: A script for generating slat systems that self-assemble ``ribbons, allowing for the setting of parameters such as cooperativity, slat count, motifs, etc.

• slat_simulator_wrapper.py: A script that can be used to drive the RodSim simulator by setting all necessary input parameters via the command line. It allows for batches of simulations to be run and performs tasks such as pattern matching of input file names.

• slat-assembly-drawer.py: A script that can read xml files containing slat assemblies (e.g. those output by RodSim) and output PDF and/or SVG files showing images of the assemblies.

• slat-Sierpinski-triangle-generator.py: A script for generating slat systems that self-assemble the Sierpinski triangle pattern, allowing for the setting of parameters such as cooperativity, slat count, motifs, etc.

Slat Generator API files Note that the latest version can be found at the bottom of the list.