Density functional studies of molecular structures of N-methyl formamide, N,N-dimethyl formamide, and N,N-dimethyl acetamide

Density functional theory was applied to the calculation of molecular structures of N-methyl formamide (NMF), N,N-dimethyl formamide (DMF), and N,N-dimethyl acetamide (DMA). DFT calculations on NMF, DMF, and DMA were performed using a combination of the local functional of Vosko, Wilk, and Nusair (VWN) with the nonlocal exchange functional of Becke and the nonlocal correlational functional of Lee, Yang, and Parr (BLYP). The adiabatic connection method (ACM) of Becke has also been used, for the first time, for the calculation of molecular structures of NMF, DMF, and DMA. The calculated molecular structures are in excellent agreement with the experimental geometries of NMF and DMA derived from gas-phase electron-diffraction studies. Sparse experimental data on the gas-phase geometry of DMF reported in the literature compares well with the DFT results on DMF. DFT emerges as a powerful method to calculate molecular structures.     

Project Scheduling with Multiple Modes: A Genetic Algorithm

In this paper we consider the resource-constrained project scheduling problem with multiple execution modes for each activity and makespan minimization as objective. We present a new genetic algorithm approach to solve this problem. The genetic encoding is based on a precedence feasible list of activities and a mode assignment. After defining the related crossover, mutation, and selection operators, we describe a local search extension which is employed to improve the schedules found by the basic genetic algorithm. Finally, we present the results of our thorough computational study. We determine the best among several different variants of our genetic algorithm and compare it to four other heuristics that have recently been proposed in the literature. The results that have been obtained using a standard set of instances show that the new genetic algorithm outperforms the other heuristic procedures with regard to a lower average deviation from the optimal makespan.     

On the numerical solution of the linear complementarity problem

The well-known linear complementarity problem with definite matrices is considered. It is proposed to solve it using a global optimization algorithm in which one of the basic stages is a special local search. The proposed global search algorithm is tested using a variety of randomly generated problems; a detailed analysis of the computational experiment is given.     

Lower bounds on the pathwidth of some grid-like graphs

We present proofs of lower bounds on the node search number of some grid-like graphs including two-dimensional grids, cylinders, tori and a variation we call “orb-webs”. Node search number is equivalent to pathwidth and vertex separation, which are all important graph parameters. Since matching upper bounds are not difficult to obtain, this implies that the pathwidth of these graphs is easily computed, because the bounds are simple functions of the graph dimensions. We also show matching upper and lower bounds on the node search number of equidimensional tori which are one less than the obvious upper bound.     

Effects of initial states on the quantum correlations in the generalized Grover search algorithm

We investigate the correlations between two qubits in the Grover search algorithm with arbitrary initial states by numerical simulation. Using a set of suitable bases, we construct the reduced density matrix and give the numerical expression of correlations relating to the iterations. For different initial states, we obtain the concurrence and quantum discord compared with the success probability in the algorithm. The results show that the initial states affect the correlations and the limit point of the correlations in the searching process. However, the initial states do not influence the whole cyclical trend.     

A UNIVERSAL APPROACH FOR CONTINUOUS OR DISCRETE NONLINEAR PROGRAMMINGS WITH MULTIPLE VARIABLES AND CONSTRAINTS

IntroductionExtensive research works have been published for solving nonlinear mathematicprogramming problems.Nonetheless,it is still difficult to find an effective and universalapproach for general programming problems with multiple design variables and …     

双相介质参数反演的混沌搜索方法

混沌运动能在一定的范围内按自身的规律不重复地遍历所有状态。利用这个特点 ,本文将混沌运动引入到双相介质参数反问题的研究中。首先利用边界元方法实现了由介质参数到地表位移的非线性映射 ,然后通过建立合成位移与实测位移的相关函数将参数识别问题归结为优化问题 ,最后利用混沌运动指导优化搜索求得介质参数。算例结果表明了混沌搜索方法用于双相介质参数反演问题的可行性和有效性     

SKATE: A docking program that decouples systematic sampling from scoring

SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in‐house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross‐docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin‐dependent kinase. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing data

DNA methylation is one of the most important epigenetic modification types, which plays a critical role in gene expression. High efficient surveying of whole genome DNA methylation has been aims of many researchers for long. Recently, the rapidly developed massively parallel DNA‐sequencing technologies open the floodgates to vast volumes of sequence data, enabling a paradigm shift in profiling the whole genome methylation. Here, we describe a strategy, combining methylated DNA immunoprecipitation sequencing with peak search to identify methylated regions on a whole‐genome scale. Massively parallel methylated DNA immunoprecipitation sequencing combined with methylation DNA immunoprecipitation was adopted to obtain methylated DNA sequence data from human leukemia cell line K562, and the methylated regions were identified by peak search based on Poison model. From our result, 140 958 non‐overlapping methylated regions have been identified in the whole genome. Also, the credibility of result has been proved by its strong correlation with bisulfite‐sequencing data (Pearson R²=0.92). It suggests that this method provides a reliable and high‐throughput strategy for whole genome methylation identification.     

Precise and global identification of phospholipid molecular species by an Orbitrap mass spectrometer and automated search engine Lipid Search

In the present research, we have established a new lipidomics approach for the comprehensive and precise identification of molecular species in a crude lipid mixture using a LTQ Orbitrap mass spectrometer (MS) and reverse-phase liquid chromatography (RPLC) combination with our newly developed lipid search engine “Lipid Search”. LTQ Orbitrap provides high mass accuracy MS spectra by Fourier-transform (FT) mass spectrometer mode and can perform rapid MSⁿ by ion trap (IT) mass spectrometer mode. In this study, the negative ion mode was selected to detect fragment ions from phospholipids, such as fatty acid anions, by MS2 or MS3. We selected the specific detection approach by neutral loss survey-dependent MS3, for the identification of molecular species of phosphatidylcholine, sphingomyelin and phosphatidylserine. Identification of molecular species was performed by using both the high mass accuracy of the mass spectrometric data obtained from FT mode and structural data obtained from fragments in IT mode. Some alkylacyl and alkenylacyl species have the same m/z value as molecular-related ions and fragment ions, thus, direct acid hydrolysis analysis was performed to identify alkylacyl and alkenylacyl species, and then the RPLC–LTQ Orbitrap method was applied. As a result, 290 species from mouse liver and 248 species from mouse brain were identified within six different classes of phospholipid, only those in manually detected and confirmed. Most of all manually detected mass peaks were also automatically detected by “Lipid Search”. Adding to differences in molecular species in different classes of phospholipids, many characteristic differences in molecular species were detected in mouse liver and brain. More variable number of saturated and monounsaturated fatty acid-containing molecular species were detected in mouse brain than liver.