Blind separation of fluorescence spectra using sparse non‐negative matrix factorization on right hand factor

Sparse non‐negative matrix factorization on right side factor (SNMF/R) has better performance in feature extraction than non‐negative matrix factorization. In this work, SNMF/R was first used to separate the overlapped three‐dimensional fluorescence spectra of polycyclic aromatic hydrocarbons mixtures in pure water, lake water, and river water, respectively. It is found that the similarity coefficients between the acquired three‐dimensional spectra and the corresponding reference spectra with random initials are all above 0.80; the recognition rate of SNMF/R is higher than that of PARAFAC and non‐negative matrix factorization algorithms, especially in the case of lake water and river water samples. In addition, SNMF/R does not need any initialization scheme designing during spectra separation. These results demonstrate that SNMF/R is an appropriate algorithm to separate the overlapped fluorescence spectra of polycyclic aromatic hydrocarbons in aquatic environment accurately and effectively. Copyright © 2015 John Wiley & Sons, Ltd.     

Recovery performance and characteristics in shape memory effects of aliphatic polyether urethane

The analysis on the recovery performance and characteristics in shape memory effects is helpful for the optimal design and engineering applications of shape memory polymers and their composites. To investigate the relationships among recovery performance, material parameters, and loading conditions, by taking aliphatic polyether urethane as an example, the researchers simulate the shape memory behaviors numerically using a three‐dimensional viscoelastic model. The material parameters for this model are taken from stress relaxation tests, rather than dynamic mechanical analysis tests. Both the unconstrained and the constrained recovery behaviors during strain‐controlled shape memory processes are analyzed. The results reveal that the unconstrained recovery occurs at the same temperature regardless of the applied strain values. Another interesting result is that the shape recovery temperature in unconstrained recovery situations increases and the maximum recovery stress under constrained recovery conditions decreases with the increase of heating rates. Copyright © 2013 John Wiley & Sons, Ltd.     

Stabilization of Large Adsorbates by Rotational Entropy: A Time‐Resolved Variable‐Temperature STM Study

Investigating the dynamics in an adlayer of the oligopyridine derivative 2‐phenyl‐4,6‐bis(6‐(pyridine‐2‐yl)‐4‐(pyridine‐4‐yl)pyridine‐2‐yl)pyrimidine (2,4′‐BTP) on Ag(111) by fast scanning tunneling microscopy (video‐STM), we found that rotating 2,4′‐BTP adsorbates coexist in a two‐dimensional (2D) liquid phase (β‐phase) in a dynamic equilibrium with static adsorbate molecules. Furthermore, exchange between an ordered phase (α‐phase) and β‐phase leads to fluctuations of the domain boundary on a time scale of seconds. Quantitative evaluation of the temperature‐dependent equilibrium between rotating and static adsorbates, evaluated from a large number of STM images, gains insight into energetic and entropic stabilization and underlines that the rotating adsorbate molecules are stabilized by an entropy contribution, which is compatible with that derived by using statistical mechanics. The general validity of the concept of entropic stabilization of rotating admolecules, favoring rotation already at room temperature, is tested for other typical small, mid‐size and large adsorbates.     

CuI‐Catalyzed Multicomponent Synthesis of Aminoindolizines from Aldehydes,Amines, and Alkynes under Solvent‐Free Conditions

A direct and efficient approach to 1‐aminoindolizines through three‐component one‐pot reaction of heteroaryl aldehydes, secondary amines and terminal alkynes catalyzed by CuI under solvent‐free conditions has been developed. This methodology provides a rapid access to substituted aminoindolizines with good yields (up to 97%).     

Water PMF for predicting the properties of water molecules in protein binding site

Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer‐aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non‐redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D‐RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid‐based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than ?4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc.     

聚合物单晶生长的三维相场模拟研究

利用元胞自动机方法与相场模型的结合建立新型三维模拟相场模型.同时,为模拟真实的、三维的高分子结晶的过程,采用元胞自动机方法离散方程,且元胞几何形状的选取符合真实聚合物晶格扩散方式的物理规律,以及新建立的相场模型套用间规聚丙烯的实验参数.利用该模型模拟了多种三维立方体或者薄层的晶体形貌及其相互之间的演化过程,包括正方形、长方形、菱形、六边形、多层单晶等.通过模拟结果与真实形貌作对比来证明所建立的相场模型真实可靠性.     

Efficient algorithms for three‐dimensional axial and planar random assignment problems

Beautiful formulas are known for the expected cost of random two‐dimensional assignment problems, but in higher dimensions even the scaling is not known. In three dimensions and above, the problem has natural “Axial” and “Planar” versions, both of which are NP‐hard. For 3‐dimensional Axial random assignment instances of size n, the cost scales as Ω(1/ n), and a main result of the present paper is a linear‐time algorithm that, with high probability, finds a solution of cost O(n^–1+o(1)). For 3‐dimensional Planar assignment, the lower bound is Ω(n), and we give a new efficient matching‐based algorithm that with high probability returns a solution with cost O(n log n). © 2013 Wiley Periodicals, Inc. Random Struct. Alg., 46, 160–196, 2015     

A new two‐dimensional manganese(II) coordination polymer based on thiophene‐3,4‐dicarboxylic acid

A novel manganese coordination polymer, poly[(μ₅‐thiophene‐3,4‐dicarboxylato)manganese(II)], [Mn(C₆H₂O₄S)]_n, was synthesized hydrothermally using 3,4‐thiophenedicarboxylate (3,4‐tdc²⁻) as the organic linker. The asymmetric unit of the complex contains an Mn²⁺ cation and one half of a deprotonated 3,4‐tdc²⁻ anion, both residing on a twofold axis. Each Mn²⁺ centre is six‐coordinated by O atoms of bridging/chelating carboxylate groups from five 3,4‐tdc²⁻ anions, forming a slightly distorted octahedron. The Mn²⁺ centres are bridged by 3,4‐tdc²⁻ anions to give an infinite two‐dimensional layer which incorporates one‐dimensional Mn–O gridlike chains, and in which the 3,4‐tdc²⁻ anion adopts a novel hexadentate chelating and μ₅‐bridging coordination mode. The fully deprotonated 3,4‐tdc²⁻ anion exhibits unexpected efficiency as a ligand towards the Mn²⁺ centres, which it coordinates through all of its carboxylate O atoms to provide the novel coordination mode. The IR spectrum of the complex is also reported.     

A three‐dimensional CdII coordination framework: poly[di‐μ2‐aqua‐{μ2‐1,4‐bis[(1H‐1,2,4‐triazol‐1‐yl)methyl]benzene‐κ2N4:N4′}di‐μ3‐terephthalato‐κ3O:O′:O′′‐dicadmium(II)]

The title Cd^II coordination polymer, [Cd(C₁₀H₈O₄)(C₁₂H₁₂N₆)_0.5(H₂O)]_n, has been obtained by the hydrothermal method and studied by single‐crystal X‐ray diffraction, elemental analysis, thermogravimetric analysis, IR spectroscopy and fluorescence spectroscopy. The compound forms a novel three‐dimensional framework with 3,8‐connected three‐dimensional binodal {4.5²}₂{4².5¹⁰.6¹².7.8³} topology. An investigation of its photoluminescence properties shows that the compound exhibits a strong fluorescence emission in the solid state at room temperature.