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Geometric methods for the construction of three structural motifs, the icosahedron, Ino's decahedron, and the complete octahedron, are proposed. On the basis of the constructed lattices and the genetic algorithm, a method for optimization of large size Lennard-Jones (LJ) clusters is presented. Initially, the proposed method is validated by optimization of(More)
A parallel fast annealing evolutionary algorithm (PFAEA) was presented and applied to optimize Lennard-Jones (LJ) clusters. All the lowest known minima up to LJ(116) with both icosahedral and nonicosahedral structure, including the truncated octahedron of LJ(38), central fcc tetrahedron of LJ(98), the Marks' decahedron of LJ(75)(-)(77), and LJ(102)(-)(104),(More)
SHEF (spherical harmonic coefficient filter), a geometrical matching procedure constituting a preliminary step in the virtual high throughput screening of large databases of small drug-like molecules, is demonstrated. This filter uses a description of both the binding site of the target and the ligand surfaces using spherical harmonic polynomial expansions.(More)
Molecular surfaces are important because surface-shape complementarity is often a necessary condition in protein-ligand interactions and docking studies. We have previously described a fast and efficient method to obtain triangulated surface-meshes by topologically mapping ellipsoids on molecular surfaces. In this paper, we present an extension of our work(More)
Based on independent component analysis (ICA), a new regression method, independent component regression (ICR), was developed to build the model of NIR spectra and the routine components of plant samples. It is found that ICR and principal component regression (PCR) are completely equivalent when they are applied in quantitative prediction. However,(More)
An adaptive immune algorithm (AIA) was proposed for resolution of the overlapping GC/MS signal with background. By using AIA, the chromatographic profiles corresponding to the independent components (ICs) in the overlapping signal are calculated with the mass spectra extracted by means of independent component analysis (ICA). The number of the ICs in the(More)
Boosting partial least squares (PLS) has been used for regression to improve the predictive accuracy of PLS models, however, there are still problems when the outliers exist in the calibration dataset. To make the method robust and enhance its prediction ability, an improved boosting PLS is proposed and applied in quantitative analysis of near-infrared(More)
On the basis of the icosahedral and decahedral lattices, the lowest energies of the Lennard-Jones (LJ) clusters containing 562-1000 atoms with the two motifs are obtained by using a greedy search method (GSM). Energy comparison between the decahedra and icosahedra shows that icosahedral structures are predominant. However, most of the icosahedral structures(More)
The inclusion of hydrocortisone, progesterone, and testosterone into the cavity of beta-cyclodextrin (beta-CD) following two possible orientations was investigated using molecular dynamics simulations and free-energy calculations. The free-energy profiles that delineate the inclusion process were determined using an adaptive biasing force. The present(More)
Near-infrared (NIR) spectrometry will present a more promising tool for quantitative measurement if the robustness and predictive ability of the partial least square (PLS) model are improved. In order to achieve the purpose, we present a new algorithm for simultaneous wavelength selection and outlier detection; at the same time, the problems of background(More)