Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein

Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein–ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl‐xL complex with ABT‐737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single‐ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X‐ray crystallographic maps, and aiding fragment‐based drug design, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Quantum control implemented as combinatorial optimization

Optimal control theory provides a general means for designing controls to manipulate quantum phenomena. Traditional implementation requires solving coupled nonlinear equations to obtain the optimal control solution, whereas this work introduces a combinatorial quantum control (CQC) algorithm to avoid this complexity. The CQC technique uses a predetermined toolkit of small time step propagators in conjunction with combinatorial optimization to identify a proper sequence for the toolkit members. Results indicate that the CQC technique exhibits invariance of search effort to the number of system states and very favorable scaling upon comparison to a standard gradient algorithm, taking into consideration that CQC is easily parallelizable. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Generation and characterization of low‐energy structures in atomic clusters

Factors relevant for controlling the structures determined in the local optimization of argon clusters are investigated. In particular, the role of volume and shape for the box where initial structures are generated is assessed. A thorough characterization of the optimization is also presented, based on a nearest‐neighbor analysis, in clusters ranging from 30 to 55 atoms. This includes the assessment of the degree of preservation of aspects of the initial randomly generated structure in the final optimized counterpart, and the correlation between optimized energy and the number of nearest neighbors and average departure from the diatomic reference distance. The usefulness of this analysis to explore the energy landscape of atomic clusters is also highlighted. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Sorbent trapping solid-phase microextraction of fragrance allergens in indoor air

Exposure to fragrance substances is exponentially increasing in our daily life due to the enhanced use of scented products. Some fragrances are known to be important sensitizers, inhalation being an important exposure pathway in indoor environments. A simple and sensitive method based on solid-phase enrichment and solid-phase microextraction (SPME) followed by gas chromatography–mass spectrometry (GC–MS) has been developed for the analysis of 24 volatile fragrance allergens in indoor air. Suspected allergens present in the air (0.2 m³) were adsorbed onto a very small quantity of florisil (25 mg) and then transferred to a SPME fiber in the headspace mode (HS). To the best of our knowledge, this paper describes the first application of SPME for the determination of these compounds in air samples. The experimental parameters affecting the microextraction process have been optimized using a multifactor experimental design strategy. Accuracy, linearity, precision and detection limits (LODs) were evaluated to assess the performance of the proposed method. External calibration, using spiked sorbent standards, and not requiring the complete sampling process (only the SPME step), demonstrated to be suitable for the quantification of all suspected allergens. Recovery studies were performed at three concentration levels (0.04, 1.00 and 50 μg m⁻³), obtaining quantitative recoveries (≥85%) in most cases. LOD values at the low ng m⁻³ level were achieved for all the target compounds. The application of the method to daily home air samples demonstrated the ubiquity of this kind of fragrance ingredients in quotidian indoor environments, finding 18 of the 24 considered compounds in concentrations ranging from 0.01 to 56 μg m⁻³. Benzyl alcohol, linalool, citronellol, ionone and lilial were found in most analyzed samples.     

基于遗传优化SVM的通信信号的分类

为了充分利用遗传算法的全局寻优能力和SVM（支持向量机）的分类能力,文章设计了遗传优化SVM的分类算法。用遗传算法优化SVM中核函数的两个参数,再利用优化后的SVM进行分类。通过对方波和白噪声两种信号的分类仿真,证明了其优越性,同时也展现了遗传优化SVM在通信领域很好的应用前景。     

基于混沌优化的无线定位算法研究

本文提出一种抗NLOS干扰的TDOA定位算法。基于混沌优化算法对TDOA算法做了改进,采用混沌优化算法计算初值,再利用Taylor级数展开法进行定位。根据产生混沌序列的两种映射Logistic映射和Kent映射的特点,提出了Kent-Logistic模型修正Logistic映射用于定位。在移动台距服务基站较近时,直接采用该模型进行定位。通过和传统蜂窝定位算法的仿真结果进行比较,表明提出的算法能够提高NLOS传播环境下的定位精度。     

认知无线电系统中基于量子粒子群算法的PHY层及MAC层决策优化

认知无线电技术是下一代通信发展的方向和趋势,同时也是目前通信研究中的热点问题。针对认知无线电系统中,在某一信道条件下其通信系统的物理层（PHY）和媒体链路层（MAC）的基于多个目标来实现优化的问题,基于量子粒子群算法的基本思想,把量子粒子群算法引入认知无线电系统中,并对该算法进行适当的改进,最后基于WSGA控制对电台优化问题进行了仿真,通过仿真证明了其有效性。     

一种改进的全四边形网格生成方法及优化

在任意二维区域的全四边形网格生成方法中,铺砌法是目前较好的一种方法。但是当边界出现不规则区域时,网格生成完毕后内部会产生一些质量较差的单元,且判断网格交叉现象是否发生和解决网格交叉问题比较困难。为了提高该方法的适应性和可靠性,提出一种新的改进算法,它对边界不规则区域网格生成和解决网格交叉问题等关键技术进行改进,并加入四边形网格优化方法。将改进后的铺砌法应用于船舶有限元网格划分中,取得了较好的应用效果,最后给出算例进行了验证。     

一种基于PSO的改进型多智能体遗传算法

通过将多智能体系统加入基本的粒子群算法（PSO）,提出了一种新的函数优化方法——多智能体遗传PSO算法（MAGPA）。该方法将智能体固定在网格上,而每个智能体通过邻域的竞争和合作,随机交叉操作,变异操作,再联合PSO的进化机制,不断地感受局部环境,逐步影响整个智能体网格,以增强对环境的适应度。该算法可以有效地保持智能体的多样性,提高优化的准确性。     

基于SOM和PSO的聚类组合算法

自组织映射（SOM）算法和粒子群优化（PSO）算法拥有概念简明、实现方便、收敛速度快、参数设置少,自组织自适应的特点。为了提高聚类效果,提出一种基于SOM和PSO的聚类组合算法SOM／PSO算法。先用SOM算法对UCI数据集中的数据进行聚类,然后以SOM的输出权值初始化PSO的粒子位置,再用PSO聚类算法进行聚类。实验结果表明所提出算法能够改进聚类性能,有很好的全局收敛性,不易陷入局部最优,也不会出现空簇现象。