Flexible protein folding by ant colony optimization

Protein structure prediction is one of the most challenging topics in bioinformatics. As the protein structure is found to be closely related to its functions, predicting the folding structure of a protein to judge its functions is meaningful to the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice model. Different from the previous ant algorithms for PFPs, the pheromones in the proposed algorithm are placed on the arcs connecting adjacent squares in the lattice. Such pheromone placement model is similar to the one used in the traveling salesmen problems (TSPs), where pheromones are released on the arcs connecting the cities. Moreover, the collaboration of effective heuristic and pheromone strategies greatly enhances the performance of the algorithm so that the algorithm can achieve good results without local search methods. By testing some benchmark two-dimensional hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed algorithm is quite competitive compared with some other well-known methods for solving the same protein folding problems

Protein folding in hydrophobic-polar lattice model: a flexible ant colony optimization approach

This paper proposes a flexible ant colony (FAC) algorithm for solving protein folding problems based on the hydrophobic-polar square lattice model. Collaborations of novel pheromone and heuristic strategies in the proposed algorithm make it more effective in predicting structures of proteins compared with other state-of-the-art algorithms

Coherent population trapping in a dressed two-level atom via a bichromatic field

We show theoretically that by applying a bichromatic electromagnetic field, the dressed states of a monochromatically driven two-level atom can be pumped into a coherent superposition termed as dressed-state coherent population trapping. Such effect can be viewed as a new doorknob to manipulate a two-level system via its control over dressed-state populations. Application of this effect in the precision measurement of Rabi frequency, the unexpected population inversion and lasing without inversion are discussed to demonstrate such controllability.Comment: 14 pages, 6 figure

Relativistic description of magnetic moments in nuclei with doubly closed shells plus or minus one nucleon

Using the relativistic point-coupling model with density functional PC-PK1, the magnetic moments of the nuclei $^{207}$Pb, $^{209}$Pb, $^{207}$Tl and $^{209}$Bi with a $jj$ closed-shell core $^{208}$Pb are studied on the basis of relativistic mean field (RMF) theory. The corresponding time-odd fields, the one-pion exchange currents, and the first- and second-order corrections are taken into account. The present relativistic results reproduce the data well. The relative deviation between theory and experiment for these four nuclei is 6.1% for the relativistic calculations and somewhat smaller than the value of 13.2% found in earlier non-relativistic investigations. It turns out that the $\pi$ meson is important for the description of magnetic moments, first by means of one-pion exchange currents and second by the residual interaction provided by the $\pi$ exchange.Comment: 11 pages, 7 figure

Phonon Squeezed States Generated by Second Order Raman Scattering

We study squeezed states of phonons, which allow a reduction in the quantum fluctuations of the atomic displacements to below the zero-point quantum noise level of coherent phonon states. We investigate the generation of squeezed phonon states using a second order Raman scattering process. We calculate the expectation values and fluctuations of both the atomic displacement and the lattice amplitude operators, as well as the effects of the phonon squeezed states on macroscopically measurable quantities, such as changes in the dielectric constant. These results are compared with recent experiments.Comment: 4 pages, REVTE

Structure-Induced Reversible Anionic Redox Activity in Na Layered Oxide Cathode

Anionic redox reaction (ARR) in lithium- and sodium-ion batteries is under hot discussion, mainly regarding how oxygen anion participates and to what extent oxygen can be reversibly oxidized and reduced. Here, a P3-type Na0.6[Li0.2Mn0.8]O2 with reversible capacity from pure ARR was studied. The interlayer O-O distance (peroxo-like O-O dimer, 2.506(3) Å), associated with oxidization of oxygen anions, was directly detected by using a neutron total scattering technique. Different from Li2RuO3 or Li2IrO3 with strong metal-oxygen (M-O) bonding, for P3-type Na0.6[Li0.2Mn0.8]O2 with relatively weak Mn-O covalent bonding, crystal structure factors might play an even more important role in stabilizing the oxidized species, as both Li and Mn ions are immobile in the structure and thus may inhibit the irreversible transformation of the oxidized species to O2 gas. Utilization of anionic redox reaction (ARR) on oxygen has been considered as an effective way to promote the charge-discharge capacity of the layered oxide cathodes for lithium- or sodium-ion batteries. The detailed mechanism of ARR, in particular how crystal structure affects and coordinates with the ARR, is not yet well understood. In the present work, a combination of X-ray and neutron total scattering measurements has been performed to study the structure of the prototype P3-type layered Na0.6[Li0.2Mn0.8]O2 with pure ARR. Unique structural characteristics, rather than prevailing knowledge of covalency of metal-oxygen, enable the stabilization of the crystal structure of Na0.6[Li0.2Mn0.8]O2 along with the ARR. This work suggests that reversible ARR can be manipulated by proper structure designs, thus to achieve high lithium or sodium storage in layered oxide cathodes. For P3-type Na0.6[Li0.2Mn0.8]O2 with relatively weak Mn-O covalent bonding, crystal structure factors play an important role in stabilizing the oxidized species, inhibiting the irreversible transformation of the oxidized species to O2 gas. The finding is important for better design of layered oxide positive materials with higher reversible capacity via the introduction of a reversible anionic redox reaction

SamACO: variable sampling ant colony optimization algorithm for continuous optimization

An ant colony optimization (ACO) algorithm offers algorithmic techniques for optimization by simulating the foraging behavior of a group of ants to perform incremental solution constructions and to realize a pheromone laying-and-following mechanism. Although ACO is first designed for solving discrete (combinatorial) optimization problems, the ACO procedure is also applicable to continuous optimization. This paper presents a new way of extending ACO to solving continuous optimization problems by focusing on continuous variable sampling as a key to transforming ACO from discrete optimization to continuous optimization. The proposed SamACO algorithm consists of three major steps, i.e., the generation of candidate variable values for selection, the ants’ solution construction, and the pheromone update process. The distinct characteristics of SamACO are the cooperation of a novel sampling method for discretizing the continuous search space and an efficient incremental solution construction method based on the sampled values. The performance of SamACO is tested using continuous numerical functions with unimodal and multimodal features. Compared with some state-of-the-art algorithms, including traditional ant-based algorithms and representative computational intelligence algorithms for continuous optimization, the performance of SamACO is seen competitive and promising

Nonequilibrium Phase Transitions of Vortex Matter in Three-Dimensional Layered Superconductors

Large-scale simulations on three-dimensional (3D) frustrated anisotropic XY model have been performed to study the nonequilibrium phase transitions of vortex matter in weak random pinning potential in layered superconductors. The first-order phase transition from the moving Bragg glass to the moving smectic is clarified, based on thermodynamic quantities. A washboard noise is observed in the moving Bragg glass in 3D simulations for the first time. It is found that the activation of the vortex loops play the dominant role in the dynamical melting at high drive.Comment: 3 pages,5 figure