FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.     

The study of the stability of aqueous three-phase fire-resistant foam in typical liquidus hydrocarbons

The utilization of solid particles in aqueous foam has a great potential in improving fire fighting efficiency. In this study, aqueous foam supported by micro fly-ash (FA) was prepared and its stability in a specific type of oil was characterized. Firstly, different amount of FA was added to study the influence of FA concentration on foamability. It showed that within a specific extent, foam expansion ratio increased with the increasing of FA concentration. And compared with conventional foams, oil resistance of FA stabilized foams, which was investigated by analyzing drainage rate and evolution process with a self-made apparatus, was remarkably improved when FA concentration exceed 4.8wt.%. Secondly, SiO₂ and Al₂O₃ particles with different median sizes were used to study the effect of particle size on stability. However, the smaller hydrophilic particles didn’t behave better as expected. Moreover, the foam stability in three hydrocarbons was evaluated in the same way. The results indicated that the short chain hydrocarbons had much stronger detrimental effect to both two-phase foam and three-phase foam. But overall, the three-phase foam stabilized by FA exhibited much better oil resistance, so it can be used as a promising material for pool fire extinguishing and prevention.GRAPHICAL ABSTRACT     

Effect of Demulsifiers on Dilatational Properties of Crude Oil–Water Interfaces

The dilatational properties of polyether demulsifiers PEA, PEB, PEC, PED, PEF, and PEG at the decane-water interface were investigated. Meanwhile, the effect of demulsifiers with different structures on interfacial dilatational modulus of diluted crude oil also was explored. The properties of demulsifiers are compared and analyzed in combine with the dilatational parameters at decane-water interface and at 5% crude oil-water interface. The results show that interfacial dilatational viscoelasticity could characterize the interfacial behavior of demulsifiers. The demulsifiers, which have different kinds or structures, have different effects on destroying the interfacial film of crude oil with increasing bulk concentration. Therefore, the dosage of demulsifier is a very important role in controlling nature of crude oil film.     

The Hydrotrope Action of Vitamin C

The effects of vitamin C are determined in the oil-in-water(0/ W) and water-in-oil(W/ 0) microemulsion regions of CTAB/ pentanol/ p-xylene/ H20 system. The addition of Vc joins the O/ W and W/ O areas in the phase diagram and expands the bicontinous region by reducing the lamellar liquid crystal one. The results show that the “ coupling action” of Vc is in fact a structural transition from lamellar crystal to isotropic phase with W/ O, O/ W and bicontinous structure.     

Surface-Modified Sb2S3 Nanoparticles and Their Tribological Behaviors in Liquid Paraffin

Sb₂S₃ nanoparticles surface-modified with S-tetradecyl N, N-dihydroxyethyl dithiocarbamate (C₁₄DTC-Sb₂S₃) have been synthesized via extraction of Sb₂S₃ colloidal particles from ethylene glycol into toluene in the presence of C₁₄DTC. The obtained products were characterized by high-resolution transmission electron microscope (HRTEM) and Fourier transformation infrared (FTIR), and their tribological behaviors as an additive in liquid paraffin were investigated using a four-ball tribometer. The results show that C₁₄DTC-Sb₂S₃ nanoparticles can significantly improve the friction reduction, anti-wear, and load-carrying properties of base oils. The preliminary lubrication mechanism was discussed based on the SEM and XPS investigation of the rubbed surfaces.     

Fabrication and characterization of an irradiation facility for large-sample geometry

An irradiation facility consisting of a modified beam port shielding plug has been designed, fabricated built and characterized for use in irradiating non-standard sample geometries. The shielding plug features a graphite moderator at the core end with a hole, or “well” drilled of sufficient diameter and depth to accommodate an eight ounce (227 gram) sample bottle. Added shielding behind the graphite consists of castable neutron- and -gamma-ray shielding. The modified shielding plug can be removed relatively quickly from its irradiation position to minimize personnel exposures. It is mounted in close proximity to the Ohio State University Research Reactor reactor core to allow performance of high-sensitivity neutron activation analysis studies. Using the SAND-II unfolding code, the energy-dependent neutron flux has been measured in the sample irradiation position. When operating at 100 % power, the total flux is 3.9 × 10¹² n/cm²/s. Of this, 55 % is thermal (<0.5 eV), 23 % is epithermal (>0.5 eV, <0.5 MeV), and 22 % is “fast” (>0.5 MeV). This makes the facility suitable for neutron activation studies. Recently it has been used for irradiation of filter papers collected in a study of particulate air pollution in the form of atmospheric particulate matter in an urban environment.     

高温高压Li3N-hBN体系cBN转变的热力学分析

以经典热力学第二定律ΔG<0为依据,分析了静态高温高压触媒法合成立方氮化硼(cBN)过程中发生的可能反应.考虑温度和压强对反应物相体积的影响,计算了六方氮化硼(Li3N-hBN)体系中hBN+Li3N→Li3BN2,h BN→cBN及Li3BN2→Li3N+cBN反应在高温高压条件下的ΔG.结果证实,Li3BN2由Li3N与hBN在高温高压(T>1300 K,P>3.0 GPa)条件下反应得到,在cBN的合成(T=1600～1800 K,P=4.6～6.0 GPa)条件下,hBN和Li3BN2都有向cBN转化的倾向,但由hBN向cBN直接转变的反应自由能比Li3BN2分解生成cBN的反应自由能更负,反应的可能性更大.探讨了高温高压条件下立方氮化硼的转变机理。     

纳米金标记抗体增强SPR检测大肠杆菌O157∶H7

将金纳米粒子(AuNPs)标记的大肠杆菌O157∶H7(E.coli O157∶H7)的多克隆抗体(PAb)作为二抗,采用氨基偶联法将PAb固定在传感器表面作为一抗,通过三明治方法用双通道表面等离子体子共振(SPR)传感器对E.coli O157∶H7进行检测,并与SPR直接法检测进行了比较.结果表明,直接法的检出限为103cfu/mL,线性范围为103～109cfu/mL;AuNPs增强三明治法的检出限为10 cfu/mL,线性范围为10～1010cfu/mL,灵敏度比直接法提高了100倍,且具有更宽的检测范围.本方法不仅检测时间短,而且具有良好的选择性和重现性.     

小球藻热裂解油催化加氢精制研究

以Ni-Co-Pd/γ-Al₂O₃为催化剂,在固定床反应器中研究了小球藻热裂解油的催化加氢精制。在较低加氢压力(2×10⁶ Pa)下考察了加氢温度和氢油比(体积比)对精制生物油的含水率、热值、运动黏度和十六烷值等参数的影响,并对加氢前后油品进行了元素分析和GC-MS分析。结果表明,在2×10⁶ Pa压力下,氢油比为120:1,温度为300 ℃时,精制油收率达89.6%,热值和十六烷值较加氢前分别增加了17.94%和71.2%,黏度下降66.32%。元素分析和GC-MS分析表明,精制生物油的H/C原子比由1.55提高至1.97,氧、氮、硫含量明显降低,脱氧率达到80.46%。精制油中的有机酸、酯、酮、醛的含量明显降低,烷烃和醇醚含量明显增加。     

两相流中煤粉的燃烧机理及动力学特征

利用微型流化床动力学分析仪研究了两相流条件下无烟煤粉的燃烧反应机理和动力学特征,并与热重法所得结果进行比较分析。结果表明,当温度大于850℃时,煤粉燃烧机理发生了变化,燃烧气态产物的生成比例也随之改变;当气速大于0.10 m/s时,气体扩散限制基本被消除,煤粉燃烧反应速率主要受界面化学反应控制;煤粉燃烧反应速率随着氧气分压的增大呈幂函数形式增长,且氧气分压对煤粉静置燃烧的影响更加显著。煤氧两相流燃烧的表观活化能与静置燃烧相比降低了49 kJ/mol,相同温度条件下两相流燃烧的界面化学反应阻力也明显小于热重法测试结果。