2007/07/17 by Kerson Huang, Huang, Kerson
Physics and Astronomy · #FOS: Physical sciences #Soft Condensed Matter (cond-mat.soft) #cond-mat.soft
paper · pdf · doi:10.48550/arxiv.0707.2388
20 pages, 15 figures, Keynote talk at BIOMAT2007, 24th-29th Nov, 2007, Brazil
arxiv created 2007/07/17 · arxiv updated 2009/12/01
We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as hydrogen bonding, which can be taken into account by imposing conditions on SAW. The resulting model is termed CSAW (conditioned self-avoiding walk. Conceptually, the mathematical basis is a generalized Langevin equation. In practice, the model is implemented on a computer by combining SAW and Monte Carlo. To illustrate the flexibility and capabilities of the model, we consider a number of examples, including folding pathways, elastic properties, helix formation, and collective modes.