A fast parallel clustering algorithm for molecular simulation trajectories

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.     

TargetATPsite: A template‐free method for ATP‐binding sites prediction with residue evolution image sparse representation and classifier ensemble

Understanding the interactions between proteins and ligands is critical for protein function annotations and drug discovery. We report a new sequence‐based template‐free predictor (TargetATPsite) to identify the Adenosine‐5′‐triphosphate (ATP) binding sites with machine‐learning approaches. Two steps are implemented in TargetATPsite: binding residues and pockets predictions, respectively. To predict the binding residues, a novel image sparse representation technique is proposed to encode residue evolution information treated as the input features. An ensemble classifier constructed based on support vector machines (SVM) from multiple random under‐samplings is used as the prediction model, which is effective for dealing with imbalance phenomenon between the positive and negative training samples. Compared with the existing ATP‐specific sequence‐based predictors, TargetATPsite is featured by the second step of possessing the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm. Experimental results on three benchmark datasets demonstrate the efficacy of TargetATPsite. © 2013 Wiley Periodicals, Inc.     

The Effects of Alcohol with Different Chain Length on the Phase Equilibria of Nonionic Surfactant System

Addition of alcohol with longer chain length (C₆H₁₃OH, C₈H₁₇OH, and C₁₂H₂₁OH) caused a reduction the cloud point of a commercial nonionic surfactant, Tesgitol (T_15-s-9). The formation of lamellar liquid crystal (LLC) was favored so that isotropic liquid (L₁)-LLC two-phase region became wider with increasing temperature at an appropriate weight ratio of surfactant to alcohol. The isotropic liquid phase/liquid two phase transformation was replaced by a two-phase transformation to isotropic liquid/lamellar liquid crystal at the cloud point for the system without alcohol.     

Experimental Validation of the Temperature-Resistant and Salt-Tolerant Xanthan Enhanced Foam for Enhancing Oil Recovery

Xanthan enhanced foam (XGF) is a newly developed chemical agent for enhanced oil recovery in high-temperature and high-salinity reservoirs. In this paper, laboratory experiments were performed to characterize the morphology and foam properties of XGF, to study its performance under different temperature and different salinity conditions, respectively. Based on simulate reservoir formation conditions of Xidaliya field, a series of research on XGF were conducted. The experimental results showed that the scanning electron microscopy of XGF reflected a more viscoelastic and stable nature of the foam system. High temperature had a great adverse impact upon the stability of XGF, and the increase of salinity in the solution helped to improve the stability of foam. The foam stability increased remarkably when XG4 is added, and an increase in ambient pressure made enhancement of foam stability became more noticeable. In the presence of crude oil, Xanthan could enhance the stability of emulsions and was more favorable to stabilize foam. XG4 enhanced foam had dramatic properties for mobility controlling and oil displacement in the porous media.     

The Influences of Polymers and Temperature on the Foam Properties of 3‐Dodecylalkoxyl‐2‐hydroxylpropyl Trimethylammonium Chloride

The foam performances of 3‐dodecoxy‐2‐hydroxypropyl trimethylammonium chloride (C₁₂TAC) have been determined in the existence of different relative amount of polymer. The experimental results show that the foaming ability of the mixture systems of the C₁₂TAC/PEG and C₁₂TAC/PVP is stronger than that of the surfactant solutions in the absence of polymer, and with the increase of relative amount of polymer both foaming efficiency and foam stability of the surfactant solutions are evidently enhanced. For the aqueous solution of the surfactant, effect of temperature on foaming properties has also been examined. The results show that both the foaming ability and stability of the foams of the surfactant solutions are highest (or strongest) at 30°C.     

奎宁-杂多酸杂化催化剂催化H2O2为氧源的苯羟基化反应

将奎宁与Keggin结构磷钼钒杂多酸结合制备出一种新颖的多相苯羟基化杂化催化剂, 采用傅里叶变换红外光谱、紫外-可见光谱、X射线衍射、扫描电镜、热重、N₂吸附-脱附和CHN元素分析等表征手段对催化剂进行了分析. 结果表明, 该催化剂是一种具有较高比表面积和孔体积的半无定形有机杂多酸盐. 在H₂O₂为氧源的苯羟基化反应中, 杂化催化剂引导了液-固两相催化体系, 表现出较高催化活性和重复使用稳定性. 催化剂中奎宁与杂多阴离子间的氢键和电子相互作用赋予了其高熔点和难溶性, 而高比表面积和因奎宁而改善的杂多阴离子的氧化还原性是其获得优异催化性能的主要原因. 这为多相苯羟基化反应提供了一种新的且制备便捷的基于多金属氧酸盐的高效催化剂.     

Synthesis and characterization of biodegradable polyesteramides constructed mainly by alternating diesterdiamide units from N,N′-bis(2-hydroxyethyl)-adipamide and diacids

Two kinds of aliphatic alternating polyesteramide prepolymers were prepared through melt polycondensation from N,N’-bis(2-hydroxyethyl)-adipamide and adipic acid or sebacic acid. Chain extension of them was conducted with 2,2′-(1,4-phenylene)-bis(2-oxazoline) and adipoyl biscaprolactamate as combined chain extenders. The chain extended polyesteramides (ExtPEAs) were characterized by IR, 1 H-NMR, differential scanning calorimetry, thermogravimetric analysis, wide angle X-ray scattering, tensile test and enzymatic degradation. The results showed that the ExtPEA(4,m)s were mainly constituted with the diester adipamide alternating units. ExtPEA(4,4) and ExtPEA(4,8) had Tm of 83.8℃ and 85.8℃ and initial decomposition temperature above 310.0℃. They crystallized similarly as Nylon-66 did and were flexible thermoplastic materials with tensile strength up to 25.64 MPa and strain at break up to 737%.     

Halonickel 2,4-di-t-butyl-6-(quinolin-8-yliminomethyl)phenolates: Synthesis, characterization and ethylene reactivity

A series of nickel halides bearing 2,4-di-t-butyl-6-(quinolin-8-yliminomethyl) phenolate ligands was synthesized and characterized by IR spectroscopy and elemental analysis.Molecular structures of C1(R = H,X = Br) and C2(R = H,X = Cl) were further confirmed by single-crystal X-ray crystallographic studies,and revealed a distorted square planar geometry at nickel.Upon activation with diethylaluminum chloride(Et 2 AlCl),all nickel pre-catalysts displayed good catalytic activity [up to 9.3 × 10 5 g mol 1(Ni) h 1 ] for ethylene oligomerization with major dimerization.In the presence of methylaluminoxane(MAO),the nickel complex C1 was capable of ethylene polymerization under 3 MPa,and produced polyethylene products with narrow polydispersity(1.16 1.73) and molecular weights in the range of 2.6 4.95 kg/mol.     

Fast switching beam steering based on ferroelectric liquid crystal phase shutter and polarisation grating

We report on fast-switching and high-efficient optical beam steering based on a polymerisable liquid crystal polarisation grating (PG) in combination with ferroelectric liquid crystal (FLC) phase shutter. The PG was fabricated in a convenient single-step holographic exposure process using photo-sensitive azo-dye material as alignment layer for liquid crystal (LC) director. A binary electro-optical FLC was employed for circular polarisation selection, which enables the electro-tunable steering of the combined system. The efficiency of 95.7% with 82 μs switching time is obtained for 1064 nm laser. This work provides a versatile candidate for non-mechanical beam steering devices.     

Orientational ordering in the nematic phase of 4-alkyl-4'-cyanobicyclohexanes

The orientational ordering of three liquid crystals (trans,trans-4-n-alkyl-4'-cyanobicyclohexanes) has been investigated using ¹³C NMR. 2D proton-encoded local field spectroscopy was used to determine the ¹³C-¹H dipolar coupling constants, from which the order parameters were calculated. Semi-empirical linear relations between the obtained order parameters and anisotropic ¹³C chemical shifts were established. It was found that the order parameters of the major axis of the cyclohexane rings are smaller than those of liquid crystals with phenyl rings, and the order parameters of the C-H bonds in the aliphatic chains also behave differently.