6,134 research outputs found
A Hybrid Monte Carlo Ant Colony Optimization Approach for Protein Structure Prediction in the HP Model
The hydrophobic-polar (HP) model has been widely studied in the field of
protein structure prediction (PSP) both for theoretical purposes and as a
benchmark for new optimization strategies. In this work we introduce a new
heuristics based on Ant Colony Optimization (ACO) and Markov Chain Monte Carlo
(MCMC) that we called Hybrid Monte Carlo Ant Colony Optimization (HMCACO). We
describe this method and compare results obtained on well known HP instances in
the 3 dimensional cubic lattice to those obtained with standard ACO and
Simulated Annealing (SA). All methods were implemented using an unconstrained
neighborhood and a modified objective function to prevent the creation of
overlapping walks. Results show that our methods perform better than the other
heuristics in all benchmark instances.Comment: In Proceedings Wivace 2013, arXiv:1309.712
All-electron magnetic response with pseudopotentials: NMR chemical shifts
A theory for the ab initio calculation of all-electron NMR chemical shifts in
insulators using pseudopotentials is presented. It is formulated for both
finite and infinitely periodic systems and is based on an extension to the
Projector Augmented Wave approach of Bloechl [P. E. Bloechl, Phys. Rev. B 50,
17953 (1994)] and the method of Mauri et al [F. Mauri, B.G. Pfrommer, and S.G.
Louie, Phys. Rev. Lett. 77, 5300 (1996)]. The theory is successfully validated
for molecules by comparison with a selection of quantum chemical results, and
in periodic systems by comparison with plane-wave all-electron results for
diamond.Comment: 25 pages, 4 tables, submitted to Physical Review
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