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The permeation free-energy profile and maximum ion conductance of proton transport along the channel of three aquaporin-1 (AQP1) mutants (H180A/R195V, H180A, and R195V) are calculated via molecular dynamics simulations and Poisson-Nernst-Planck theory. The proton dynamics was described by the multistate empirical valence bond (MS-EVB) model. The results(More)
Keywords: Symbiosis Multi-species coevolution Species extinction and speciation PSO PS 2 O a b s t r a c t This paper presents a general optimization model gleaned ideas from the coevolution of symbiotic species in natural ecosystems. Species extinction and speciation events are also considered in this model to tie it closer to natural evolution, as well as(More)
Conditional and time-dependent radial distribution functions reveal the details of the water structure surrounding the hydronium during the proton mobility process. Using this methodology for classical multistate empirical valence bond (MS-EVB) and ab initio molecular dynamics trajectories, as well as quantal MS-EVB trajectories, we supply statistical proof(More)
The explicit contribution to the free energy barrier and proton conductance from the delocalized nature of the excess proton is examined in aquaporin channels using an accurate all-atom molecular dynamics computer simulation model. In particular, the channel permeation free energy profiles are calculated and compared for both a delocalized (fully Grotthuss(More)
Artificial Bee Colony (ABC) algorithm is one of the most recently introduced swarm intelligence algorithms which inspired by the foraging behavior of honey bee swarms. It has been widely used in numerical and engineering optimization problems. This paper presents a hybrid artificial bee colony (HABC) model to improve the canonical ABC algorithm. The main(More)