A theoretical investigation on optimal structures of ethane clusters (C2H6)n with n ≤ 25 and their building-up principle

Geometry optimization of ethane clusters (C(2)H(6))(n) in the range of n ≤ 25 is carried out with a Morse potential. A heuristic method based on perturbations of geometries is used to locate global minima of the clusters. The following perturbations are carried out: (1) the molecule or group with the highest energy is moved to the interior of a cluster, (2) it is moved to stable positions on the surface of a cluster, and (3) orientations of one and two molecules are randomly modified. The geometry obtained after each perturbation is optimized by a quasi-Newton method. The global minimum of the dimer is consistent with that previously reported. The putative global minima of the clusters with 3 ≤ n ≤ 25 are first proposed and their building-up principle is discussed.     

A versatile method for systematic conformational searches: application to CheY

A novel molecular structure prediction method, the Z Method, is described. It provides a versatile platform for the development and use of systematic, grid‐based conformational search protocols, in which statistical information (i.e., rotamers) can also be included. The Z Method generates trial structures by applying many changes of the same type to a single starting structure, thereby sampling the conformation space in an unbiased way. The method, implemented in the CHARMM program as the Z Module, is applied here to an illustrative model problem in which rigid, systematic searches are performed in a 36‐dimensional conformational space that describes the relative positions of the 10 secondary structural elements of the protein CheY. A polar hydrogen representation with an implicit solvation term (EEF1) is used to evaluate successively larger fragments of the protein generated in a hierarchical build‐up procedure. After a final refinement stage, and a total computational time of about two‐and‐a‐half CPU days on AMD Opteron processors, the prediction is within 1.56 Å of the native structure. The errors in the predicted backbone dihedral angles are found to approximately cancel. Monte Carlo and simulated annealing trials on the same or smaller versions of the problem, using the same atomic model and energy terms, are shown to result in less accurate predictions. Although the problem solved here is a limited one, the findings illustrate the utility of systematic searches with atom‐based models for macromolecular structure prediction and the importance of unbiased sampling in structure prediction methods. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

A comparison of neighbor search algorithms for large rigid molecules

Fast determination of neighboring atoms is an essential step in molecular dynamics simulations or Monte Carlo computations, and there exists a variety of algorithms to efficiently compute neighbor lists. However, most of these algorithms are general, and not specifically designed for a given type of application. As a result, although their average performance is satisfactory, they might be inappropriate in some specific application domains. In this article, we study the case of detecting neighbors between large rigid molecules, which has applications in, e.g., rigid body molecular docking, Monte Carlo simulations of molecular self-assembly or diffusion, and rigid body molecular dynamics simulations. More precisely, we compare the traditional grid-based algorithm to a series of hierarchy-based algorithms that use bounding volumes to rapidly eliminate large groups of irrelevant pairs of atoms during the neighbor search. We compare the performance of these algorithms based on several parameters: the size of the molecules, the average distance between them, the cutoff distance, as well as the type of bounding volume used in the culling hierarchy (AABB, OBB, wrapped, or layered spheres). We demonstrate that for relatively large systems (> 100,000 atoms) the algorithm based on the hierarchy of wrapped spheres shows the best results and the traditional grid-based algorithm gives the worst timings. For small systems, however, the grid-based algorithm and the one based on the wrapped sphere hierarchy are beneficial.     

A modification of the successive projections algorithm for spectral variable selection in the presence of unknown interferents

This work proposes a modification to the successive projections algorithm (SPA) aimed at selecting spectral variables for multiple linear regression (MLR) in the presence of unknown interferents not included in the calibration data set. The modified algorithm favours the selection of variables in which the effect of the interferent is less pronounced. The proposed procedure can be regarded as an adaptive modelling technique, because the spectral features of the samples to be analyzed are considered in the variable selection process. The advantages of this new approach are demonstrated in two analytical problems, namely (1) ultraviolet–visible spectrometric determination of tartrazine, allure red and sunset yellow in aqueous solutions under the interference of erythrosine, and (2) near-infrared spectrometric determination of ethanol in gasoline under the interference of toluene. In these case studies, the performance of conventional MLR-SPA models is substantially degraded by the presence of the interferent. This problem is circumvented by applying the proposed Adaptive MLR-SPA approach, which results in prediction errors smaller than those obtained by three other multivariate calibration techniques, namely stepwise regression, full-spectrum partial-least-squares (PLS) and PLS with variables selected by a genetic algorithm. An inspection of the variable selection results reveals that the Adaptive approach successfully avoids spectral regions in which the interference is more intense.     

Kinetic study of oxidative coupling of methane over Mn and/or W promoted Na_2SO_4/SiO_2 catalysts

A comprehensive kinetic model for oxidative coupling of methane(OCM)over Mn and/or W promoted Na2SO4/SiO2 catalysts was developed based on a micro-catalytic reactor data.The methane conversion and ethylene,ethane,carbon monoxide and carbon dioxide selectivities were obtained in a wide operating condition range of 750 - 825-C,CH4/O2=2.5 - 10 and contact time=267 - 472 kg s m-3.Reaction networks of six models with different rate equation types were compared together.The kinetic rate parameters of each reaction network were estimated using linear regression or genetic algorithm optimization method(GA).A reaction network suggested by Stansch et al.for OCM was found to be the best one and was further used in this work.The suggested model could predict the experimental results of OCM reaction within a deviation range of ± 20%.     

Multiobjective optimization scheme for industrial synthesis gas sweetening plant in GTL process

In industrial amine plants the optimized operating conditions are obtained from the conclusion of occurred events and challenges that are normal in the working units. For the sake of reducing the costs, time consuming, and preventing unsuitable accidents, the optimization could be performed by a computer program. In this paper, simulation and parameter analysis of amine plant is performed at first. The optimization of this unit is studied using Non-Dominated Sorting Genetic Algorithm-II in order to produce sweet gas with CO 2 mole percentage less than 2.0% and H 2 S concentration less than 10 ppm for application in Fischer-Tropsch synthesis. The simulation of the plant in HYSYS v.3.1 software has been linked with MATLAB code for real-parameter NSGA-II to simulate and optimize the amine process. Three scenarios are selected to cover the effect of (DEA/MDEA) mass composition percent ratio at amine solution on objective functions. Results show that sour gas temperature and pressure of 33.98 ? C and 14.96 bar, DEA/CO 2 molar flow ratio of 12.58, regeneration gas temperature and pressure of 94.92 ? C and 3.0 bar, regenerator pressure of 1.53 bar, and ratio of DEA/MDEA = 20%/10% are the best values for minimizing plant energy consumption, amine circulation rate, and carbon dioxide recovery.     

三维荧光二阶校正法用于复杂基体样中川芎嗪和替米沙坦的快速定量分析

采用三维荧光光谱法,结合化学计量学中基于交替归一加权残差(ANWE)算法的二阶校正方法,实现了人血浆样品中川芎嗪和替米沙坦的同时快速定量分析.当组分数N取4时,ANWE算法解析获得的川芎嗪和替米沙坦的平均回收率分别为99.3士3.5%和96.8±2.0%.本文同时给出了此方法的检测限(LOD)与定量下限(LOQ),获得...     

Study on tribological behaviors of short glass fiber and polytetrafluoroethylene reinforced polycarbonate composites via a d‐optimal mixture design

This study analyzed variations of tribological behaviors that depend on the injection molding techniques during the blending of short glass fiber (SGF) and polytetrafluoroethylene (PTFE) reinforced polycarbonate (PC) composites. The proposed planning of blending experiments is to use a D‐optimal mixture design (DMD). The tribological behaviors of friction coefficient and wear mass loss were selected for discussion. Nine experimental runs, based on a DMD method, utilized to train the back‐propagation neural network (BPNN) and then the simulated annealing algorithm (SAA) approach is applied to search for an optimal mixture ratio setting. In addition, the result of BPNN integrating SAA was also compared with response surface methodology (RSM) approach. The results of confirmation experiment show that DMD, RSM, and BPNN integrating SAA method are effective tools for the optimization of reinforced process. Furthermore, the scanning electron microscope (SEM) images show that the abundant debris are peeled off from the matrix materials and predominant delamination mechanisms and plastic deformation are shown on the worn surface after tribological behavior tests. Copyright © 2010 John Wiley & Sons, Ltd.     

A hybrid shuffled complex evolution approach based on differential evolution for unconstrained optimization

Numerous optimization methods have been proposed for the solution of the unconstrained optimization problems, such as mathematical programming methods, stochastic global optimization approaches, and metaheuristics. In this paper, a metaheuristic algorithm called Modified Shuffled Complex Evolution (MSCE) is proposed, where an adaptation of the Downhill Simplex search strategy combined with the differential evolution method is proposed. The efficiency of the new method is analyzed in terms of the mean performance and computational time, in comparison with the genetic algorithm using floating-point representation (GAF) and the classical shuffled complex evolution (SCE-UA) algorithm using six benchmark optimization functions. Simulation results and the comparisons with SCE-UA and GAF indicate that the MSCE improves the search performance on the five benchmark functions of six tested functions.     

Finding the shortest paths by node combination

By repeatedly combining the source node’s nearest neighbor, we propose a node combination (NC) method to implement the Dijkstra’s algorithm. The NC algorithm finds the shortest paths with three simple iterative steps: find the nearest neighbor of the source node, combine that node with the source node, and modify the weights on edges that connect to the nearest neighbor. The NC algorithm is more comprehensible and convenient for programming as there is no need to maintain a set with the nodes’ distances. Experimental evaluations on various networks reveal that the NC algorithm is as efficient as Dijkstra’s algorithm. As the whole process of the NC algorithm can be implemented with vectors, we also show how to find the shortest paths on a weight matrix.