Feature vector clustering molecular pairs in computer simulations

A clustering framework is introduced to analyze the microscopic structural organization of molecular pairs in liquids and solutions. A molecular pair is represented by a representative vector (RV). To obtain RV, intermolecular atom distances in the pair are extracted from simulation trajectory as components of the key feature vector (KFV). A specific scheme is then suggested to transform KFV to RV by removing the influence of permutational molecular symmetry on the KFV as the predicted clusters should be independent of possible permutations of identical atoms in the pair. After RVs of pairs are obtained, a clustering analysis technique is finally used to classify all the RVs of molecular pairs into the clusters. The framework is applied to analyze trajectory from molecular dynamics simulations of an ionic liquid (trihexyltetradecylphosphonium bis(oxalato)borate ([P_6,6,6,14][BOB])). The molecular pairs are successfully categorized into physically meaningful clusters, and their effectiveness is evaluated by computing the product moment correlation coefficient (PMCC). (Willett, Winterman, and Bawden, J. Chem. Inf. Comput. Sci. 1986, 26, 109–118; Downs, Willett, and Fisanick, J. Chem. Inf. Comput. Sci. 1994, 34, 1094–1102) It is observed that representative configurations of two clusters are related to two energy local minimum structures optimized by density functional theory (DFT) calculation, respectively. Several widely used clustering analysis techniques of both nonhierarchical (k-means) and hierarchical clustering algorithms are also evaluated and compared with each other. The proposed KFV technique efficiently reveals local molecular pair structures in the simulated complex liquid. It is a method, which is highly useful for liquids and solutions in particular with strong intermolecular interactions. © 2019 Wiley Periodicals, Inc.     

Anisotropy Effects and Observational Data on the Constraints of Evolution Dark Energy Models

We investigate cosmological dark energy models where the accelerated expansion of the universe is driven by a field with an anisotropic universe. The constraints on the parameters are obtained by maximum likelihood analysis using observational of 194 Type Ia supernovae(SNIa) and the most recent joint light-curve analysis(JLA) sample. In particular we reconstruct the dark energy equation of state parameter w(z) and the deceleration parameter q(z). We find that the best fit dynamical w(z) obtained from the 194 SNIa dataset does not cross the phantom divide line w(z) =-1 and remains above and close to w(z)≈-0.92 line for the whole redshift range 0 ≤ z ≤ 1.75 showing no evidence for phantom behavior. By applying the anisotropy effect on the ΛCDM model, the joint analysis indicates that ?_(σ0)= 0.0163 ± 0.03,with 194 SNIa, ?_(σ0)=-0.0032 ± 0.032 with 238 the SiFTO sample of JLA and ?_(σ0)= 0.011 ± 0.0117 with 1048 the SALT2 sample of Pantheon at 1σ′confidence interval. The analysis shows that by considering the anisotropy, it leads to more best fit parameters in all models with JLA SNe datasets. Furthermore, we use two statistical tests such as the usual χ_(min)~2/dof and p-test to compare two dark energy models with ΛCDM model. Finally we show that the presence of anisotropy is confirmed in mentioned models via SNIa dataset.     

利用带无标签数据的双支持向量机对恒星光谱分类

恒星光谱分类是天文技术与方法领域一直关注的热点问题之一。随着观测设备持续运行和不断改进，人类获得的光谱数量与日俱增。这些海量光谱为人工处理带来了极大挑战。鉴于此，研究人员开始关注数据挖掘算法，并尝试对这些光谱进行数据挖掘。近年来，神经网络、自组织映射、关联规则等数据挖掘方法广泛应用于恒星光谱分类。在这些方法中，支持向量机(SVM)以其强大的学习能力和高效的分类性能而备受推崇。SVM的基本思想是试图在两类样本之间找到一个最优分类面将两类分开。SVM在求解时，通过将其最优化问题转化为具有(QP)形式的凸问题，进而得到全局最优解。尽管该方法在实际应用中表现优良，但为了进一步提高其分类能力，有的学者提出双支持向量机(TSVM)。该方法通过构造两个非平行的分类面将两类分开，每一类靠近某个分类面，而远离另一个分类面。TSVM的计算效率较之传统SVM提高近4倍，因此，自TSVM提出后便受到研究人员的持续关注，并出现若干改进算法。在恒星光谱分类中，一般分类算法都是根据历史观测光谱来建立分类模型，其中最关键的是对光谱进行人工标注，这项工作极为繁琐，且容易犯错。如何利用已标记的光谱以及部分无标签的光谱来建立分类模型显得尤为重要。因此，提出带无标签数据的双支持向量机(TSVMUD)用以实现对恒星光谱智能分类的目的。该方法首先将光谱分为训练数据集和测试数据集两部分；然后，在训练集上进行学习，得到分类依据；最后利用分类依据对测试集上的光谱进行验证。继承了双支持向量机的优势，更重要的是，在训练集上学习分类模型过程中，不仅考虑有标记的训练样本，也考虑部分未标记的样本。一方面提高了学习效率，另一方面得到更优的分类模型。在SDSS DR8恒星光谱数据集上的比较实验表明，与支持向量机SVM、双支持向量机TSVM以及K近邻(KNN)等传统分类方法相比，带无标签数据的双支持向量机TSVMUD具有更优的分类能力。然而，该方法亦存在一定的局限性，其中一大难题是其无法处理海量光谱数据。该工作将借鉴海量数据随机采样思想，利用大数据处理技术，来对所提方法在大数据环境下的适应性展开进一步研究。     

An efficient edge based data structure for the compressible Reynolds-averaged Navier–Stokes equations on hybrid unstructured meshes

An efficient edge based data structure has been developed in order to implement an unstructured vertex based finite volume algorithm for the Reynolds-averaged Navier–Stokes equations on hybrid meshes. In the present approach, the data structure is tailored to meet the requirements of the vertex based algorithm by considering data access patterns and cache efficiency. The required data are packed and allocated in a way that they are close to each other in the physical memory. Therefore, the proposed data structure increases cache performance and improves computation time. As a result, the explicit flow solver indicates a significant speed up compared to other open-source solvers in terms of CPU time. A fully implicit version has also been implemented based on the PETSc library in order to improve the robustness of the algorithm. The resulting algebraic equations due to the compressible Navier–Stokes and the one equation Spalart–Allmaras turbulence equations are solved in a monolithic manner using the restricted additive Schwarz preconditioner combined with the FGMRES Krylov subspace algorithm. In order to further improve the computational accuracy, the multiscale metric based anisotropic mesh refinement library PyAMG is used for mesh adaptation. The numerical algorithm is validated for the classical benchmark problems such as the transonic turbulent flow around a supercritical RAE2822 airfoil and DLR-F6 wing-body-nacelle-pylon configuration. The efficiency of the data structure is demonstrated by achieving up to an order of magnitude speed up in CPU times.     

Nanoscale C‐Rich SixC1−x Bus/Ring Waveguide Based Cross‐Wavelength Data Converter

The carbon‐rich silicon carbide (C‐rich Si_xC_1?x) micro‐ring channel waveguide with asymmetric core aspect is demonstrated for all‐optical cross‐wavelength pulsed return‐to‐zero on‐off keying (PRZ‐OOK) data conversion. Enhanced nonlinear optical Kerr switching enables 12‐Gbit per second data processing with optimized modulation depth. The inverse tapered waveguide at end‐face further enlarges the edge‐coupling efficiency, and the asymmetric channel waveguide distinguishes the polarization modes. To prevent data shape distortion, the bus/ring gap spacing is adjusted to control the quality factor (Q‐factor) of the micro‐ring. Designing the waveguide cross section at 500 × 350 nm² provides the C‐rich Si_xC_1?x channel waveguide to induce strong transverse electric mode (TE‐mode) confinement with a large Kerr nonlinearity of 2.44 × 10^?12 cm² W^?1. Owing to the trade‐off between the Q‐factor and the on/off extinction ratio, the optimized bus/ring gap spacing of 1400 nm is selected to provide a coupling ratio at 5–6% for compromising the modulation depth and the switching throughput. Such a C‐rich Si_xC_1?x micro‐ring with asymmetric channel waveguide greatly enhances the cross‐wavelength data conversion efficiency to favor its on‐chip all‐optical data processing applications for future optoelectronic interconnect circuits.     

Qualitative and quantitative determination of Atractylodes rhizome using ultra‐performance liquid chromatography coupled with linear ion trap–Orbitrap mass spectrometry with data‐dependent processing

A quick and effective workflow based on ultra‐performance liquid chromatography coupled with electron spray ionization and LTQ‐Orbitrap mass spectrometry (UPLC‐LTQ‐Orbitrap MS) was established for compositional analysis and screening of the characteristic compounds of three species of Atractylodes rhizome for quality evaluation. This technique was employed to determine the seven main components in Atractylodes rhizome samples. Ultimately, 78 constituents were identified; of these, seven characteristic compounds were selected for species discrimination, comprising atractylodin (63), atractylenolide I (43), atractylenolide II (49), atractylenolide III (53), atractylon (69), methyl‐atractylenolide II (54) and (4E,6E,12E)‐tetradecadecatriene‐8,10‐diyne‐1,3‐diacetate (59). The seven main compounds, including six characteristic compounds, were simultaneously determined in 29 batches of Atractylodes rhizome samples. Thus, the method validation showed acceptable results. Quantitative analysis showed significantly different contents of the seven main components among the three species of Atractylodes rhizome, which indicates possible distinctions in the pharmacological effects. This established method can simultaneously provide qualitative and quantitative results for compositional characterization of Atractylodes rhizomes and for quality control.     

Enhancing signal-to-noise ratio and resolution in low-field NMR relaxation measurements using post-acquisition digital filters

The traditional way to enhance signal-to-noise ratio (SNR) of nuclear magnetic resonance (NMR) signals is to increase the number of scans. However, this procedure increases the measuring time that can be prohibitive for some applications. Therefore, we have tested the use of several post-acquisition digital filters to enhance SNR up to one order of magnitude in time domain NMR (TD-NMR) relaxation measurements. The procedures were studied using continuous wave free precession (CWFP-T₁) signals, acquired with very low flip angles that contain six times more noise than the Carr–Purcell–Meiboom–Gill (CPMG) signal of the same sample and experimental time. Linear (LI) and logarithmic (LO) data compression, low-pass infinity impulse response (LP), Savitzky–Golay (SG), and wavelet transform (WA) post-acquisition filters enhanced the SNR of the CWFP-T₁ signals by at least six times. The best filters were LO, SG, and WA that have high enhancement in SNR without significant distortions in the ILT relaxation distribution data. Therefore, it was demonstrated that these post-acquisition digital filters could be a useful way to denoise CWFP-T₁, as well as CPMG noisy signals, and consequently reducing the experimental time. It was also demonstrated that filtered CWFP-T₁ method has the potential to be a rapid and nondestructive method to measure fat content in beef and certainly in other meat samples.     

Code2vect: An efficient heterogenous data classifier and nonlinear regression technique

The aim of this paper is to present a new classification and regression algorithm based on Artificial Intelligence. The main feature of this algorithm, which will be called Code2Vect, is the nature of the data to treat: qualitative or quantitative and continuous or discrete. Contrary to other artificial intelligence techniques based on the “Big-Data,” this new approach will enable working with a reduced amount of data, within the so-called “Smart Data” paradigm. Moreover, the main purpose of this algorithm is to enable the representation of high-dimensional data and more specifically grouping and visualizing this data according to a given target. For that purpose, the data will be projected into a vectorial space equipped with an appropriate metric, able to group data according to their affinity (with respect to a given output of interest). Furthermore, another application of this algorithm lies on its prediction capability. As it occurs with most common data-mining techniques such as regression trees, by giving an input the output will be inferred, in this case considering the nature of the data formerly described. In order to illustrate its potentialities, two different applications will be addressed, one concerning the representation of high-dimensional and categorical data and another featuring the prediction capabilities of the algorithm.