Physical methods of analysis

The choice of analytical techniques for the solution of real analytical problems is governed not only by the characteristics of the individual methods, but also by the alternatives available. The capabilities of some methods of elemental analysis are considered and compared with those of selected techniques based upon sample irradiation with charged particles.     

Self-assembly of nanometer-scale magnetic dots with narrow size distributions on an insulating substrate

The self-assembly of iron dots on the insulating surface of NaCl(001) is investigated experimentally and theoretically. Under proper growth conditions, nanometer-scale magnetic iron dots with remarkably narrow size distributions can be achieved in the absence of a wetting layer. Furthermore, both the vertical and lateral sizes of the dots can be tuned with the iron dosage without introducing apparent size broadening, even though the clustering is clearly in the strong coarsening regime. These observations are interpreted using a phenomenological mean-field theory, in which a coverage-dependent optimal dot size is selected by strain-mediated dot-dot interactions.     

High-avidity,low-affinity multivalent interactions and the block to polyspermy in Xenopus laevis

The interaction of the lectin XL35 with the jelly coat protein (JCP) surrounding oocytes in Xenopus laevis is essential for the block to polyspermy. The molecular details of this event are poorly understood, and the present study has been undertaken with a view to delineating the mechanism of formation of the fertilization envelope. A range of JCP-derived oligosaccharides were synthesized, and all were installed with an artificial aminopropyl arm. This arm allowed the preparation of monovalent derivatives by acetylation of the amino group or the synthesis of polyvalent compounds by attachment to an activated polyacrylamide polymer. A number of analytical techniques, including enzyme-linked lectin assays and surface plasmon resonance, have been developed and utilized to study the interactions of the mono- and polyvalent compounds with XL35. The results reveal that the lectin XL35 has remarkably broad specificity for galactose-containing saccharides and the affinities are only slightly modulated by secondary features, such as anomeric configuration of the terminal sugar or the identity and linkage pattern of branching sugars. Broad specificity was also observed when the saccharides were presented in a polyvalent fashion. The glycopolymers displayed 10-20-fold increases in valency-corrected affinities compared to the corresponding monovalent counterparts. Although the synthetic polymers are not as potent as the JCP, the kinetics of their interactions mirror closely those of the native ligand, and in each case extremely long-lived interactions were observed. The results of this study indicate that, in X. laevis, the true biological function of multivalency is not to create an extremely tightly binding complex between XL35 and its natural ligand but, instead, to create a very stable protective layer that will not dissociate and is yet flexible enough to encapsulate the developing embryo. It is postulated that, even if these partners are unable to attain true equilibrium on the time scale of the biological event, their mode of interaction would, nevertheless, be expected to guarantee an insurmountable physical block to polyspermy. This study has also highlighted that multivalent interactions require a very long time to achieve equilibrium, and this feature may well be the origin of several of the ambiguities reported in the literature when multivalent ligands have been evaluated.     

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots

Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure.     

A synthetic DNA walker for molecular transport

Inspired by kinesin movement along a microtubule, we demonstrate a processive bipedal DNA walker. Powered by externally controlled DNA fuel strands, the walker locomotes with a 5 nm stride by advancing the trailing foot to the lead at each step. Real-time monitoring of specific bidirectional walker movement is achieved via multiplexed fluorescence quenching.     

Quasistatic x-ray speckle metrology of microscopic magnetic return-point memory

We have used coherent, resonant, x-ray magnetic speckle patterns to measure the statistical evolution of the microscopic magnetic domains in perpendicular magnetic films as a function of the applied magnetic field. Our work constitutes the first direct, ensemble-averaged study of microscopic magnetic return-point memory, and demonstrates the profound impact of interfacial roughness on this phenomenon. At low fields, the microscopic magnetic domains forget their past history with an exponential field dependence.     

Stresses around elliptic holes in circular cylindrical shells

The stress state around an elliptic hole in a circular cylindrical shell under axial loads is measured. The test cylinders which are made of aluminum are loaded both in tension and compression. Stress-concentration factors around the hole for different eccentricities of the ellipse and different curvature parameters are evaluated. Stress-concentration factors away from the edge of the hole are also determined. The results obtained are compared with theoretical results available in the literature. The effect of bending on the stress concentration as related to the eccentricity of the elliptic hole and to the curvature parameters of the shell is discussed. The results from tension test and those from compression test are also compared, and the sensitivity of the shell to any imperfection and possible local buckling at the hole in the case of compression test are demonstrated.     

Low resolution and high resolution MS for studies on the metabolism and toxicological detection of the new psychoactive substance methoxypiperamide (MeOP)

In 2013, the new psychoactive substance methoxypiperamide (MeOP) was first reported to the European Monitoring Centre for Drug and Drug Addiction. Its structural similarity to already controlled piperazine designer drugs might have contributed to the decision to offer MeOP for online purchase. The aims of this work were to identify the phase I/II metabolites of MeOP in rat urine and the human cytochrome P450 (CYP) isoenzymes responsible for the initial metabolic steps. Finally, the detectability of MeOP in rat urine by gas chromatography–mass spectrometry (GC‐MS) and liquid chromatography coupled with multistage mass spectrometry (LC‐MSⁿ) standard urine screening approaches (SUSAs) was evaluated. After sample preparation by cleavage of conjugates followed by extraction for elucidating phase I metabolites, the analytes were separated and identified by GC‐MS as well as liquid chromatography‐high resolution‐tandem mass spectrometry (LC‐HR‐MS/MS). For detection of phase II metabolites, the analytes were separated and identified after urine precipitation followed by LC‐HR‐MS/MS. The following metabolic steps could be postulated: hydrolysis of the amide, N‐oxide formation, N‐ and/or O‐demethylation, oxidation of the piperazine ring to the corresponding keto‐piperazine, piperazine ring opening followed by oxidation of a methylene group to the corresponding imide, and hydroxylation of the phenyl group. Furthermore, N‐acetylation, glucuronidation and sulfation were observed. Using human CYPs, CYP1A2, CYP2C19, CYP2D6, and/or CYP3A4 were found to catalyze N‐oxide formation and N‐, O‐demethylation and/or oxidation. Mostly MeOP and N‐oxide‐MeOP but to a minor degree also other metabolites could be detected in the GC‐MS and LC‐MSⁿ SUSAs. Copyright © 2015 John Wiley & Sons, Ltd.