Influence of Mg²⁺, Ni²⁺, and Cu²⁺ on DNA assembly on HOPG surfaces: atomic force microscopy study

Adsorption of circular DNA onto bare highly oriented pyrolytic graphite (HOPG) surfaces by the addition of Mg²⁺, Ni²⁺, and Cu²⁺ has been investigated by atomic force microscopy (AFM). AFM results revealed that the topography and height of DNA on HOPG surface by the addition of different metal ions are quite different. After the addition of Mg²⁺ for incubation, DNA molecules tend to form many loops on HOPG surfaces, which are derived from the crossover of intramolecular and intermolecular chains. After the addition of Ni²⁺, DNA molecules can form network on HOPG surfaces, and the density of DNA network was significantly increased with increasing DNA concentration. Consequently, dense DNA network can be obtained by using relatively low concentration of DNA and Ni²⁺. As for the addition of Cu²⁺, angular DNA loops composed of flat chains were observed. The observed flat DNA chains with an average height of 0.52 nm can be ascribed to Cu²⁺ insert into the site between bases and phosphate group of DNA inducing denaturation of DNA molecules. This study is very helpful for understanding the interactions of metal ions and DNA molecules, and for constructing various DNA structures on the carbonaceous surfaces. SCANNING 34: 68–75, 2012. © 2011 Wiley Periodicals, Inc.     

Cooperativity and intermediate structures of single-stranded DNA binding-assisted RecA-single-stranded DNA complex formation studied by atomic force microscopy

The formation of a complex between RecA protein and single-stranded (ss) DNA was studied systematically by atomic force microscopy (AFM) by varying incubation time and the molecular ratio of RecA protein to single-stranded DNA binding (SSB) protein. New intermediate structures, such as small circular, tangled, and protruded structures in the absence of SSB and sharply turned structures in the presence of SSB, were clearly identified at the early stage of complex formation. These structures have probably resulted from competitive binding of RecA and SSB to DNA. After long incubation, only fully covered RecA-ssDNA and totally RecA-free SSB-ssDNA complexes were present regardless of RecA concentrations. Together with intermediate structures which consisted of only two parts, that is, ssDNA covered by SSB and by RecA proteins, the observation suggested strong neighbor cooperative binding of RecA to ssDNA assisted by SSB.     

Hybridisation of short DNA molecules investigated with in situ atomic force microscopy

By introducing the complementary DNA (cDNA) strand to a molecular layer of short single stranded DNA (ssDNA), immobilised on a gold surface, we have investigated hybridisation between the two DNA strands through the technique of in situ atomic force microscopy (AFM). Before introduction of cDNA, the ssDNA molecular layer was modulated with the spacer molecule mercaptohexanol (MCH), which makes the ssDNA molecules more accessible for hybridisation.With in situ AFM, we have monitored the formation of a smooth, mixed molecular layer containing ssDNA and MCH. Furthermore, the hybridisation between the two DNA strands has been studied. Introduction of the cDNA strand resulted in an increase in smoothness and thickness of the molecular layer. Both the increase in order and thickness of the molecular layer can be expected if hybridisation occurs, since double stranded DNA molecules have a more rigid and elongated structure than ssDNA molecules.     

A comparative study on the self‐assembly of an amyloid‐like peptide at water–solid interfaces and in bulk solutions

In the past years the self‐assembly of amyloid‐like peptides has attracted increasing attentions, because it is highly related to neurodegenerative diseases and has a potential for serving as nanomaterial to fabricate novel and useful nanostructures. In this paper, we focused on the role of interfacial conditions in the self‐assembly of an amyloid‐like peptide, termed Pep11. It was found that, when dissolved in bulk solutions, Pep11 formed into β‐sheet structures and assembled into long filaments in several hours, as revealed by Thioflavin T fluorescence and transmission electron microscopy (TEM) morphology characterization, respectively. When the peptide solution was added onto a mica/HOPG substrate, peptide filaments with three preferred orientations with an angle of 60° to each other were formed immediately, as imaged in situ by atomic force microscopy (AFM). However, the kinetics in filament formation and the morphologies of the formed beta sheet either on HOPG and mica or in bulk solutions were quite different. These results indicate that the interfacial properties dramatically affect the peptide self‐assembly process. Microsc. Res. Tech. 78:375–381, 2015. © 2015 Wiley Periodicals, Inc.     

Effect of Zn doping on the sublimation rate of pentaerythritol tetranitrate using atomic force microscopy

A series of Zn ion‐doped pentaerythritol tetranitrate (PETN) nanoislands in the form of thin films were prepared on Si substrates using spin coating. The effect of Zn concentrations on the sublimation energy was investigated by atomic force microscopy (AFM). The pure and Zn‐doped nanoislands are imaged by AFM in contact mode at room temperature after annealing isothermally for a given time. The volume of the islands starts to decrease after annealing at 45°C for pure PETN, whereas Zn‐doped nanoislands start to decrease in height and volume after annealing at 55–58°C. The minimum activation energy is found to be 29.7 Kcal/mol for 1,000 ppm Zn concentration. These studies are important for the long‐term stabilization of PETN. SCANNING 31: 181–187, 2009. © 2009 Wiley Periodicals, Inc.     

Transmission electron microscopy characterization of the erbium silicide formation process using a Pt/Er stack on a silicon-on-insulator substrate

Very thin erbium silicide layers have been used as source and drain contacts to n‐type Si in low Schottky barrier MOSFETs on silicon‐on‐insulator substrates. Erbium silicide is formed by a solid‐state reaction between the metal and silicon during annealing. The influence of annealing temperature (450 °C, 525 °C and 600 °C) on the formation of an erbium silicide layer in the Pt/Er/Si/SiO₂/Si structure was analysed by means of cross‐sectional transmission electron microscopy. The Si grains/interlayer formed at the interface and the presence of Si grains within the Er‐related layer constitute proof that Si reacts with Er in the presence of a Pt top layer in the temperature range 450–600 °C. The process of silicide formation in the Pt/Er/Si structure differs from that in the Er/Si structure. At 600 °C, the Pt top layer vanishes and a (Pt–Er)Si_x system is formed.     

Chemical reactions and morphological stability at the Cu/Al2O3 interface

The microstructures of diffusion‐bonded Cu/(0001)Al₂O₃ bicrystals annealed at 1000 °C at oxygen partial pressures of 0.02 or 32 Pa have been studied with various microscopy techniques ranging from optical microscopy to high‐resolution transmission electron microscopy. The studies revealed that for both oxygen partial pressures a 20–35 nm thick interfacial CuAlO₂ layer formed, which crystallises in the rhombohedral structure. However, the CuAlO₂ layer is not continuous, but interrupted by many pores. In the samples annealed in the higher oxygen partial pressure an additional reaction phase with a needle‐like structure was observed. The needles are several millimetres long, ～10 µm wide and ～1 µm thick. They consist of CuAlO₂ with alternating rhombohedral and hexagonal structures. Solid‐state contact angle measurements were performed to derive values for the work of adhesion. The results show that the adhesion is twice as good for the annealed specimen compared to the as‐bonded sample.     

The effect of surface treatments on the microroughness of laser-sintered and vacuum-cast base metal alloys for dental prosthetic frameworks

This study aimed to evaluate the effect of four chemomechanical surface treatments on the surface average microroughness and profile of laser‐sintered and vacuum‐cast dental prosthetic structures. Square‐shaped blocks (10 mm × 10 mm × 1.5 mm) were prepared as follows: (1) laser‐sintered Co? Cr (L) (ST2724G); (2) cast Co? Cr (C) (Gemium‐cn); and (3) cast Ni? Cr? Ti (T) (Tilite). Specimens of each alloy group were randomly divided into five subgroups (n = 10 each), depending on the conditioning method used: (1) no treatment (control); (2) sandblasting (125 μm Al₂O₃‐particles); (3) silica coating (50 μm silica‐modified Al₂O₃‐particles); (4) oxidation; and (5) oxidation plus opacification. Subgroups 2 and 3 represent “inner” pretreatments proposed for ceramometal restorations to improve the metal surface area available for luting cements. Subgroups 4 and 5 are the “outer” pretreatments required for bonding the aesthetic veneering ceramics to the underlying metal frameworks. Average surface roughness (Ra/μm) was determined using a surface profilometer. Data were analyzed by two‐way ANOVA and Student–Newman–Keuls tests (α = 0.05). Metal surface topography was SEM‐analyzed. Despite the inner pretreatment applied, L samples resulted in the highest microroughness (P < 0.001), whereas sandblasting produced a surface‐smoothing effect in cast specimens. After oxidation, a significant increase in surface roughness occurred in all groups compared with controls, L specimens being the roughest (P < 0.001). Opacification caused a flattening effect of all oxidized structures; all opacified groups resulting in similar microroughness. Laser sintering of Co? Cr enhances the roughness of metal structures, which may improve the frameworks' microretention of the cements, and of the opaquer before the copings are veneered with the aesthetic ceramics. Microsc. Res. Tech. 75:1206–1212, 2012. © 2012 Wiley Periodicals, Inc.     

The low‐temperature method for study of coniferous tissues in the environmental scanning electron microscope

The use of non‐standard low‐temperature conditions in environmental scanning electron microscopy might be promising for the observation of coniferous tissues in their native state. This study is aimed to analyse and evaluate the method based on the principle of low‐temperature sample stabilization. We demonstrate that the upper mucous layer is sublimed and a microstructure of the sample surface can be observed with higher resolution at lower gas pressure conditions, thanks to a low‐temperature method. An influence of the low‐temperature method on sample stability was also studied. The results indicate that high‐moisture conditions are not suitable for this method and often cause the collapse of samples. The potential improvement of stability to beam damage has been demonstrated by long‐time observation at different operation parameters. We finally show high applicability of the low‐temperature method on different types of conifers and Oxalis acetosella. Microsc. Res. Tech., 78:13–21, 2015. © 2014 Wiley Periodicals, Inc.     

Infrared consequence spectroscopy of gaseous protonated and metal ion cationized complexes

In this article, the new and exciting techniques of infrared consequence spectroscopy (sometimes called action spectroscopy) of gaseous ions are reviewed. These techniques include vibrational predissociation spectroscopy and infrared multiple photon dissociation spectroscopy and they typically complement one another in the systems studied and the information gained. In recent years infrared consequence spectroscopy has provided long‐awaited direct evidence into the structures of gaseous ions from organometallic species to strong ionic hydrogen bonded structures to large biomolecules. Much is being learned with respect to the structures of ions without their stabilizing solvent which can be used to better understand the effect of solvent on their structures. This review mainly covers the topics with which the author has been directly involved in research: structures of proton‐bound dimers, protonated amino acids and DNA bases, amino acid and DNA bases bound to metal ions and, more recently, solvated ionic complexes. It is hoped that this review reveals the impact that infrared consequence spectroscopy has had on the field of gaseous ion chemistry. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:586–607, 2009     

Interfacial reactions and silicate formation in highly dispersed Lu2O3– SiO2 system

Solid state interface reactions in highly dispersed Lu₂O₃– SiO₂ binary oxide system were studied at 600–1100 °C with X‐ray powder diffraction (XRD), high‐resolution transmission electron microscopy (HRTEM) and Fourier Transform Infrared spectroscopy (FTIR). The results show that at 600–900 °C an amorphous, nanometer thick Lu‐O‐Si layer covering SiO₂ particles exists in the system. At higher temperatures the breakage of the layer into amorphous islands occurs and crystalline silicates with various structures are formed. In particular, Lu₄[Si₃O₁₀][SiO₄] silicate, analogue of B‐type Dy – Tm disilicates, forms at 1000 °C.     

Design and construction of a new temperature-controlled chamber for light and confocal microscopy under monitored conditions: biological application for plant samples

A new light microscope–temperature‐controlled chamber (LM–TCC) has been constructed. The special feature of the light microscope–temperature‐controlled chamber is the Peltier‐element temperature control of a specimen holder for biological samples, with a volume capacity of 1 mL. This system has marked advantages when compared to other approaches for temperature‐controlled microscopy. It works in a temperature range of −10°C to +95°C with an accuracy of ±0.1°C in the stationary phase. The light microscope–temperature‐controlled chamber allows rapid temperature shift rates. A maximum heating rate of 12.9°C min⁻¹ and a maximum cooling rate of 6.0°C min⁻¹ are achieved with minimized overshoots (≤1.9°C). This machinery operates at low cost and external coolants are not required. Especially with samples absorbing irradiation strongly, temperature control during microscopy is necessary to avoid overheating of samples. For example, leaf segments of Ficaria verna exposed to 4500 μmol photons m⁻² s⁻¹ in a standard microscopic preparation show a temperature increase (δT) of 18.0°C, whereas in the light microscope–temperature‐controlled chamber this is reduced to 4°C. The kinetics of microscope‐light induced δT are described and infrared thermography demonstrates the dissipation of the temperature. Chloroplasts of the cold adapted plant Ranunculus glacialis show the tendency to form stroma‐filled protrusions in relation to the exposure temperature. The relative number of chloroplasts with protrusions is reduced at 5°C when compared to 25°C. This effect is reversible. The new light microscope–temperature‐controlled chamber will be useful in a wide range of biological applications where a rapid change of temperature during microscopic observations is necessary or has to be avoided allowing a simulation of ecologically relevant temperature scenarios.     

Tribological performance of distilled biomass oil from rice straw by pyrolysis process

The biomass oil pyrolysed from rice straw was refined through distillation process under one atmosphere pressure. Four distilled fractions were obtained in the temperature ranges of 54–64, 72–80, 84–92 and 96–100 °C respectively. Their chemical components and special group structures were analysed by gas chromatography‐mass spectrometry (GC‐MS) and Fourier transform infrared spectroscopy. The tribological performances of the prepared fractions were evaluated by MQ‐800 four‐ball tribometer as well. The results showed that both density and acid number of the biomass oil increased with the distillation temperature and that the total distillation yield was 55.7%. Every distillation fraction had different anti‐wear and friction reduction. Their average friction coefficients were 0.185, 0.227, 0.179 and 0.293 in 30 minutes, and the average wear scar diameters were 1.035, 0.958, 0.870 and 0.983 mm under a rotation speed of 1450 rpm respectively. It was found that the fraction distilled in the temperature range of 84–92 °C showed better friction reduction and wear resistance. Copyright © 2008 John Wiley & Sons, Ltd.     

Application of mixed self-assembled monolayers (Mixed SAMs) for nucleic acid detection

Mixed self-assembled monolayers (Mixed SAMs) consisting of 8-Ferrocenyl-1-octanethiol and 6-Mercapto-1-hexanol (FcOT:MCH) with probe PNA on gold electrodes were fabricated by using two-step after the optimization of immobilization temperature of FcOT:MCH SAMs. Using AC voltammetry, a novel nucleic acid detection platform, with mixed SAMs, was proposed. A negative formal potential shift was observed after complementary ssDNA hybridization while there was no significant difference after non-complementary ssDNA hybridization. Compatible results were obtained with the measurement of formal potential differences between mixed SAMs and target DNA (complementary and non-complementary DNA) in different target DNA concentrations. The formal potential difference between mixed SAMs immobilization and complementary ssDNA hybridization was measured in different ionic strength concentrations.     

Correlation of structure and properties of groups I to III base oils

The understanding of the relationship between molecular structure and viscosity–temperature behaviour of a lubricant system is a subject of considerable importance. The quantitative distribution and types of different classes of hydrocarbons such as aromatics, paraffins (normal and iso) and naphthenes determine the physico‐chemical behaviour of a lubricant system. The study of molecular structure and molecular alignment of hydrocarbons constituting a lubricant helps in the development of lubricating oil with desired physico‐chemical properties. The present study highlights the application of nuclear magnetic resonance spectroscopic technique for deriving detailed hydrocarbon structural features present in API groups II and III base oils produced through catalytic hydrocracking/isodewaxing processes. The viscosity–temperature and viscosity–pressure properties, such as viscosity index, pour point, elastohydrodynamic film thickness and cold cranking simulator viscosity, were determined. The structural features of these base oils such as various methyl branched structures of isoparaffins and branching index, which are characteristics of high performance molecules, were correlated with the above‐mentioned properties to explain their physico‐chemical properties, particularly low temperature properties. The molecular dynamics parameters such as diffusion coefficient and T₁ relaxation times estimated from the nuclear magnetic resonance spectral studies have provided sufficient evidence for the dependence of these properties on these high performance molecules present in various types of methyl structures of isoparaffins of groups II and III base oils compared with conventional group I base oils. Results are explained on the basis of molecular structural differences of hydrocarbons present in these base oils and diffusion measurement studies. On the basis of the studies, molecular engineering concept for the designing of a high performance base oil molecule is proposed. Copyright © 2012 John Wiley & Sons, Ltd.     

Effect of surface roughness on magneto‐hydrodynamic couple‐stress squeeze film lubrication between circular stepped plates

In this paper, a theoretical analysis of the problem of magneto‐hydrodynamic couple‐stress squeeze film lubrication between rough circular stepped plates is presented. The modified averaged Reynolds equation is derived for the two types of one‐dimensional roughness structures, namely the radial roughness pattern and the azimuthal roughness pattern. The closed‐form expressions are obtained for the mean squeeze film pressure, load‐carrying capacity and squeeze film time. The results are presented for different operating parameters. It is observed that the effect of azimuthal (radial) roughness pattern on the bearing surface is to increase (decrease) the mean load‐carrying capacity and squeeze film time. The applied magnetic field increases the load‐carrying capacity and lengthens the squeezing time. Copyright © 2012 John Wiley & Sons, Ltd.     

Evaluation of tribological behavior of Al-co-cr-fe-ni high entropy alloy using molecular dynamics simulation

High‐entropy alloys have been studied extensively for their excellent properties and performance, including outstanding strength and resistance to oxidation at high temperatures. This study employed molecular dynamics simulation to produce a high‐entropy alloy containing an equal molar ratio of Al, Co, Cr, Fe, and Ni and investigated the tribological behavior of the material using a diamond tool in a vacuum environment. We also simulated a AlCoCrFeNi high‐entropy alloy cooled from a high temperature molten state to 300 K in a high‐speed quenching process to produce an amorphous microstructure. In a simulation of nanoscratching, the cutting force–distance curve of high‐entropy alloys was used to evaluate work hardening and stick–slip. An increase in temperature was shown to reduce the scratching force and scratching resistance. Nanoscratching the high‐entropy alloy at elevated temperatures provided evidence of work hardening; however, the degree of work hardening decreased with an increase in temperature. And it can also be found that when the temperature is higher, the fluctuation of the cutting force curve is greater. SCANNING 34: 325–331, 2012. © 2012 Wiley Periodicals, Inc.     

Studies of thick boundary lubrication — influence of zddp and oxidized hexadecane

The requirements of a test machine to simulate asperity lubrication are discussed. It is shown that if one test specimen is reciprocated against the other at a realistic rate (50 Hz) over a small stroke (±0.5 mm) and at a suitable temperature, the necessary requirements are fulfilled. Electrical resistance is found to be important. The reproducibility of the results is excellent. A thick boundary layer was formed when zinc dialkyl dithiophosphate was added to hexadecane and it was found that there was a considerable improvement in lubrication when the hexadecane was oxidized. The temperature of formation of the thick boundary layer was strongly dependant on the alkyl group and fell with increasing number of carbon atoms. Straight chains were more effective than branched chains     

Self‐assembled monolayers of DNA on cysteamine modified Au(111) surface: Atomic force microscopy study

The λ‐DNA molecules self‐assemble on cysteamine‐modified gold (111) surface to form flat‐lying self‐assembled monolayers (SAMs). The formation kinetics of such DNA SAMs is studied by atomic force microscopy (AFM). AFM results show that DNA molecules do not arrange themselves on cysteamine‐modified gold (111) surface into a well‐ordered monolayer. It is also found that the surface density of DNA monolayer does not increase as the DNA concentration increases. The high temperature of DNA solution and the immersing in ultrapure water produce some obvious DNA bundles. Whereas divalent cations in DNA solution result in the formation of more compact DNA films. The obtained information may be useful for practical application of the DNA films and further theoretical studies. Microsc. Res. Tech., 2009. © 2009 Wiley‐Liss, Inc.     

Terminal protein-induced stretching of bacteriophage φ29 DNA

Stretching of DNA molecules helps to resolve detail during the fluorescence microscopy of both single DNA molecules and single DNA–protein complexes. To make stretching occur, intricate procedures of specimen preparation and manipulation have been developed in previous studies. By contrast, the present study demonstrates that conventional procedures of specimen preparation cause DNA stretching to occur, if the specimen is the double‐stranded DNA genome of bacteriophage φ29. Necessary for this stretching is a protein covalently bound at both 5′ termini of φ29 DNA molecules. Some DNA molecules are attached to a cover glass only at the two ends. Others are attached at one end only with the other end free in solution. The extent of stretching varies from ～50% overstretched to ～50% understretched. The understretched DNA molecules are internally mobile to a variable extent. In addition to stretching, some φ29 DNA molecules also undergo assembly to form both linear and branched concatemers observed by single‐molecule fluorescence microscopy. The assembly also requires the terminal protein. The stretched DNA molecules are potentially useful for observing DNA biochemistry at the single molecule level.