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arXiv · 1607.03253

A Parallel Trajectory Swapping Wang - Landau Study Of The HP Protein Model

Luke Kristopher Davis
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Abstract

The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica -exchange scheme between individual Wang- Landau samplers, the problem of dynamical trapping (spiking in the density of states) was avoided and an enhancement in the efficiency of traversing configuration space was obtained. Highlighting dynamical trapping as an issue for lattice polymer simulations for increasing lengths is explicitly done here for the first time. The 1/t scheme is also integrated within this sophisticated Monte Carlo methodology. A trial move set was developed which includes pull, bond re-bridging, pivot, kink-flip and a newly invented and implemented fragment random walk move which allowed rapid exploration of high and low temperature configurations. A native state search was conducted leading to the attainment of the native states of the benchmark sequences of 2D50 (-21), 2D60 (-36)and 2D64 (-42), whilst attaining minimum energies close to the native state for 2D85(-52 NATIVE= -53), 2D100a (-47 NATIVE= -48) and 2D100b (-49 NATIVE=-50). Thermodynamic observables such as the specific heat, internal energy, entropy and free energy were computed for 2D benchmark sequences at varying temperatures and folding and unfolding behaviour was investigated. Lattice polymers with monomeric hydrophobic structure were also studied in the same manner with the recording of minimum energy values and thermodynamic behaviour. The native results for the benchmark sequences and lattice polymers were compared with varying computational methods.

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Luke Kristopher Davis. 2016-07-12. A Parallel Trajectory Swapping Wang - Landau Study Of The HP Protein Model. https://arxiv.org/abs/1607.03253

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