Solitons in a generalized space- and time-variable coefficients nonlinear Schrödinger equation with higher-order terms

We introduce an approach that combines a similarity method with several transformations to find analytical solitary wave solutions for a generalized space- and time-variable coefficients of nonlinear Schrödinger equation with higher-order terms with consideration of varying dispersion, higher nonlinearities, gain/loss and external potential. One of these transformations is constructed in such a way that allows study of the width of localized solutions. Solitary-like wave solutions for front, bright and dark are given. The precise expressions of the soliton?s width, peak, and the trajectory of its mass center and the external potential which are symbol of dynamic behavior of these solutions, are investigated analytically. In addition, the dynamical behavior of moving, periodic, quasi-periodic of breathing, and resonant are discussed. Stability of the obtained solutions is analyzed both analytically and numerically.     

Exploring structure–selectivity relationships of biogenic amine GPCR antagonists using similarity searching and dynamic compound mapping

We design and analyze compound selectivity sets of antagonists with differential selectivity against seven biogenic amine G-protein coupled receptors. The selectivity sets consist of a total of 267 antagonists and contain a spectrum of in part closely related molecular scaffolds. Each set represents a different selectivity profile. Using these com- pound sets, a systematic computational analysis of structure-selectivity relationships is carried out with different 2D similarity methods including fingerprints, recursive partitioning, clustering, and dynamic compound mapping. Screening calculations are performed in a background database containing nearly four million molecules. Fingerprint searching and compound mapping are found to enrich target-selective antagonists over family-selective ones. Dynamic compound mapping effectively discriminates database compounds from GPCR antagonists and consistently retains target-selective antagonists during the final dimension extension levels. Furthermore, the widely used MACCS key fingerprint displays a strong tendency to distinguish between target- and family-selective GPCR antagonists. Taken together, the results indicate that different types of 2D similarity methods are capable of distinguishing closely related molecules having different selectivity. The reported compound benchmark system is made freely available in order to enable selectivity-oriented analyses using other computational approaches.     

A Construction of Subsets of the Reals which have a Similarity Decomposition

We construct a subset of the set R of real numbers of cardinality |R| which has a similarity decomposition, and which has an ordertype < that of R. Seymour Ginsburg had posed the question whether there exist sets with another ordertype than that of R which also have a similarity decomposition.      

Characterizing vibrational motion beyond internal coordinates

We present a procedure for the decomposition of the normal modes of a composite system, including its rotations and translations, into those of fragments. The method permits—by the cross-contraction of dyads of mass-weighted displacement vectors, without recourse to valence coordinates—the direct comparison of nuclear motions of structurally similar but otherwise arbitrary fragments of molecules, and it leads to a quantitative definition of the similarity and the overlap of nuclear motions. We illustrate its usefulness by the quantification of the mixing of the normal modes of formic acid monomers upon the formation of a dimer, by the comparison of the overlap of the intermolecular normal vibrations of the water dimer computed with different ab initio schemes, and by the comparison of similarity and overlap of vibrations of (4S,7R)-galaxolide and (4S)-4-methylisochromane. The approach is expected to become a standard tool in vibrational analysis.     

A computational model for predicting fusion peptide of retroviruses

As a pivotal domain within envelope protein, fusion peptide (FP) plays a crucial role in pathogenicity and therapeutic intervention. Taken into account the limited FP annotations in NCBI database and absence of FP prediction software, it is urgent and desirable to develop a bioinformatics tool to predict new putative FPs (np-FPs) in retroviruses. In this work, a sequence-based FP model was proposed by combining Hidden Markov Method with similarity comparison. The classification accuracies are 91.97% and 92.31% corresponding to 10-fold and leave-one-out cross-validation. After scanning sequences without FP annotations, this model discovered 53,946 np-FPs. The statistical results on FPs or np-FPs reveal that FP is a conserved and hydrophobic domain. The FP software programmed for windows environment is available at https://sourceforge.net/projects/fptool/files/?source=navbar.     

一种识别病毒和蠕虫的算法

对现有的恶意软件检测算法进行研究之后发现,某些检测算法只能检测一种恶意软件,并且部分传统的检测算法在检测恶意程序时漏检率偏高。针对目前现有的检测算法缺乏综合性检测能力的短板,在此文中提出了一种新的检测算法,该检测算法具有一定的综合检测能力。新算法的思路如下：第一步区分某种软件是恶意软件还是非恶意软件,如果是恶意软件则提取其特征码,然后使用决策树根据恶意软件的特征码对恶意软件进行识别和分类,如果存在特征码不能识别的恶意软件,那么再根据病毒和蠕虫的特征使用相似性计算算法对未知的恶意软件进行相似性计算,最后使用决策系统对相似性算法计算的结果进行决策,该恶意软件是病毒还是蠕虫。将相似性计算算法,决策树和决策系统在检测恶意软件算法中进行应用是本文的创新之处。     

人工神经网络法鉴别红外光谱

本文将反向传播人工神经网络（ＢＰ－ＡＮＮ）用于ＦＴＩＲ,鉴别未知化合物。结果表明,当训练集样本不含噪声时,纯光谱的预测结果很好。而当训练集样本有少量噪声干扰时,预测结果随预测集样本的不同,而得到不同的改善。     

Analysis and use of fragment-occurrence data in similarity-based virtual screening

Current systems for similarity-based virtual screening use similarity measures in which all the fragments in a fingerprint contribute equally to the calculation of structural similarity. This paper discusses the weighting of fragments on the basis of their frequencies of occurrence in molecules. Extensive experiments with sets of active molecules from the MDL Drug Data Report and the World of Molecular Bioactivity databases, using fingerprints encoding Tripos holograms, Pipeline Pilot ECFC_4 circular substructures and Sunset Molecular keys, demonstrate clearly that frequency-based screening is generally more effective than conventional, unweighted screening. The results suggest that standardising the raw occurrence frequencies by taking the square root of the frequencies will maximise the effectiveness of virtual screening. An upper-bound analysis shows the complex interactions that can take place between representations, weighting schemes and similarity coefficients when similarity measures are computed, and provides a rationalisation of the relative performance of the various weighting schemes.     

Influence of temperature-dependent viscosity and thermal radiation on MHD forced convection over a non-isothermal wedge

An analysis has been carried out to study heat transfer characteristics of an incompressible Newtonian electrically conducting and heat generating/absorbing fluid having temperature-dependent viscosity over a non-isothermal wedge in the presence of thermal radiation. The Rosseland approximation is used to describe the radiative heat flux in the energy equation. The wedge surface is assumed to be permeable so as to allow for possible wall suction or injection. The effects of viscous dissipation, Joule heating, stress work and thermal radiation are included in the model. The governing differential equations are derived and transformed using a non-similarity transformation. The transformed equations are solved numerically by applying a fifth-order Runge-Kutta-Fehlberg scheme with shooting technique. Favorable comparisons with previously published work on various special cases of the problem are obtained. Numerical results for the velocity and temperature profiles for a prescribed magnetic field parameter as well as the development of the local skin-friction coefficient and local Nusselt number with the magnetic field and radiation parameters are presented graphically and in tabulated form to elucidate the influence of the various physical parameters.