Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

Details Monte Carlo simulations of the HP model (the "Ising model" of protein folding) Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

2011-02-01

arxiv.org/abs/1102.0308v1

Physics

Condensed Matter

Soft Condensed Matter

6 pages, 6 figures. Article in press. To be published in Computer Physics Communications (2011)

Scientific paper

10.1016/j.cpc.2010.12.049

Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse "transition" to a globule state followed by a second "transition" into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of "transitions". These transitions depend upon the relative interaction strengths and are largely inaccessible to "standard" Monte Carlo methods.

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