BONSAI (Bio-Organic Nucleation and Self-Assembly at Interfaces) is an ambitious research project in which we investigate folding and aggregation of small proteins, as well as the adsorption of peptides to crystalline materials as, e.g., metals and semiconductors. These studies are based on semiclassical all-atom force-field models for proteins and simplified hybrid models for the interaction of organic with inorganic matter.

The main tool for these analyses is a newly developed computer simulation package, also called bonsai. It is written in C/C++ and its inherent modularity allows for simple extension and adaptation.

Scope and main features:

Monte Carlo simulation package for folding, aggregation, and adsorption of small proteins
Two implicit-solvent protein force fields incorporated
Metal and semiconductor substrate materials with arbitrary surface orientations
Monte Carlo methods: Metropolis, multicanonical sampling, multi-core multicanonical sampling, multi-core parallel tempering, Wang-Landau sampling
Simple minimization algorithms: simulated annealing, two variants of energy-landscape paving
Visualization interface based on the OpenInventor™ graphics library; current implementation is based on Coin3D™; quadbuffer stereo mode included, i.e., NVIDIA® 3D Vision™ capable

bonsai package details:
Language: C/C++
Libraries: OpenInventor™, OpenGL™, Motif™ (visualization interface)
Version: 0.9, "alpha" (as of July 2014)
OS: Linux
Release: currently not scheduled
Developed by: M. Bachmann (Soft Matter Systems Research Group)

Two synthetic peptides near a bare, etched Si(100) substrate.