Batch tautomer generation with MolTPC

Besides all their conformational degrees of freedom, drug‐like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of ring‐chain tautomerism. Here, we describe an adjustable fully automatic tautomer enumeration approach, which is freely available and also incorporates the detection of ring‐chain variants. The algorithm is implemented in the MolTPC framework and accessible on SourceForge. © 2013 Wiley Periodicals, Inc.     

Raman Optical Activity of N-Acetyl-L-Cysteine in Water and in Methanol: The “Clusters-in-a-Liquid” Model and ab Initio Molecular Dynamics Simulations

Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, that is, the DFT based “clusters-in-a-liquid” solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP−D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations, which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.     

基于麻雀搜索算法结合深度前馈神经网络的近红外模型转移方法研究

该文提出了一种基于麻雀搜索算法结合深度前馈神经网络（SSA－DFN）的近红外光谱模型转移方法。使用深度前馈神经网络拟合不同仪器采集到的光谱之间的非线性函数映射,并将麻雀搜索算法用于网络各层连接权值和阈值的初始化,通过种群中个体位置的迭代更新,求得连接权值和阈值的最优初始值;通过多次调整深度前馈神经网络模型的超参数,使网络拟合效果趋于最优,最终确定转移函数。为验证方法的有效性,分别从烟叶近红外光谱谱图、主成分投影和预测结果的角度,将SSA－DFN方法与分段直接校正算法（PDS）、典型相关性分析算法（CCA）转移前后的效果进行了对比。结果表明SSA－DFN方法转移后的从机光谱与原主机光谱重合度最高,转移后主、从机总糖、烟碱含量的预测结果差异不显著,预测平均误差从8.32%、9.15%分别降至4.65%、4.82%,预测均方根误差（RMSEP）和决定系数（R2）等指标均优于PDS和CCA,取得了最佳的转移效果,可满足企业需求。结果表明该方法是一种有效的模型转移方法。     

二冷配水优化建模与混合自适应PSO算法求解

针对连铸二冷区生产环境复杂且存在着大量水雾干扰的情况,建立了连铸水量优化模型并提出了一种混合的自适应粒子群算法来求解连铸二冷水优化问题。依据冶金过程中的工艺要求建立了二冷水量优化模型,并在经典的PSO算法基础上提出了适合该问题求解了混合自适应PSO算法。由于连铸过程存在着偏微分方程约束,传统的优化方法容易陷入局部最优解,不能达到很好的动态优化效果。研究了粒子群算法,基于种群的多样性,不断的自适应的更新粒子群算法中参数,将禁忌搜索的方法和传统的粒子群算法结合,增强了算法的局部搜索能力和全局寻找全局最优的能力。将该算法应用到连铸二冷水动态优化中,实验结果表面该算法能够快速有效的求解该优化问题。该方法用于连铸二冷水优化是可行的、有效的。     

An energy-based microstructure model to account for fatigue scatter in polycrystals

Scatter observed in the fatigue response of a nickel-based superalloy, U720, is linked to the variability in the microstructure. Our approach is to model the energy of a persistent slip band (PSB) structure and use its stability with respect to dislocation motion as our failure criterion for fatigue crack initiation. The components that contribute to the energy of the PSB are identified, namely, the stress field resulting from the applied external forces, dislocation pile-ups, and work-hardening of the material is calculated at the continuum scale. Further, energies for dislocations creating slip in the matrix/precipitates, interacting with the GBs, and nucleating/agglomerating within the PSB are computed via molecular dynamics simulations. Through this methodology, fatigue life is predicted based on the energy of the PSB, which inherently accounts for the microstructure of the material. The present approach circumvents the introduction of uncertainty principles in material properties. It builds a framework based on mechanics of microstructure, and from this framework, we construct simulated microstructures based on the measured distributions of grain size, orientation, neighbor information, and grain boundary character, which allows us to calculate fatigue scatter using a deterministic approach. The uniqueness of the approach is that it avoids the large number of parameters prevalent in previous fatigue models. The predicted lives are in excellent agreement with the experimental data validating the model capabilities.     

闪光照相中源尺寸和散射对成像的影响

 利用Monte Carlo(MC)模拟技术解释实验中心线灰度曲线的各部分波形。结果发现，系统中的散射照射量、光源的尺寸和H-D特征曲线的形状对实验灰度曲线的各部分波形均有影响：散射量越大，中心信号幅度越低;H-D曲线趾部的非线性越严重，中心信号幅度也越低;光源尺寸造成图像越模糊。指出了用实验波形可以半定量确定系统散射程度和光源尺寸。在测量照射量时，应该尽可能避免散射的干扰,用台阶法测量H-D曲线时，应使台阶远离剂量片而前移。     

Completeness and Admissibility for General Heuristic Search Algorithms—A Theoretical Study: Basic Concepts and Proofs

We propose a formal generalization for various works dealing with Heuristic Search in State Graphs. This generalization focuses on the properties of the evaluation functions, on the characteristics of the state graphs, on the notion of path length, on the procedures that control the node expansions, on the rules that govern the update operations. Consequently, we present the algorithm family and the sub-family Ã, which include Nilsson's A or A_* and many of their successors such as HPA, B, A ^* , A, C, BF^*, B, IDA^*, D, A^**, SDW. We prove general theorems about the completeness and the sub-admissibility that widely extend the previous results and provide a theoretical support for using diverse kinds of Heuristic Search algorithms in enlarged contexts, specially when the state graphs and the evaluation functions are less constrained than ordinarily.     

Parallelization of a Two-Phase Metaheuristic for Routing Problems with Time Windows

This paper describes the parallelization of a two-phase metaheuristic for the vehicle routing problem with time windows and a central depot (VRPTW). The underlying objective function combines the minimization of the number of vehicles in the first search phase of the metaheuristic with the minimization of the total travel distance in the second search phase. The parallelization of the metaheuristic follows a type 3 parallelization strategy (cf. Crainic and Toulouse (2001). In F. Glover and G. Kochenberger (eds.). State-of-the-Art Handbook in Metaheuristics. Norwell, MA: Kluwer Academic Publishers), i.e. several concurrent searches of the solution space are carried out with a differently configured metaheuristic. The concurrently executed processes cooperate through the exchange of solutions. The parallelized two-phase metaheuristic was subjected to a comparative test on the basis of 358 problems from the literature with sizes varying from 100 to 1000 customers. The derived results seem to justify the proposed parallelization concept.     

Parallelizing Tabu Search on a Cluster of Heterogeneous Workstations

In this paper, we present the parallelization of tabu search on a network of workstations using PVM. Two parallelization strategies are integrated: functional decomposition strategy and multi-search threads strategy. In addition, domain decomposition strategy is implemented probabilistically. The performance of each strategy is observed and analyzed. The goal of parallelization is to speedup the search in finding better quality solutions. Observations support that both parallelization strategies are beneficial, with functional decomposition producing slightly better results. Experiments were conducted for the VLSI cell placement, an NP-hard problem, and the objective was to achieve the best possible solution in terms of interconnection length, timing performance (circuit speed), and area. The multiobjective nature of this problem is addressed using a fuzzy goal-based cost computation.