Towards biochips using microstructured optical fiber sensors

In this paper we present the first incorporation of a microstructured optical fiber (MOF) into biochip applications. A 16-mm-long piece of MOF is incorporated into an optic-fluidic coupler chip, which is fabricated in PMMA polymer using a CO₂ laser. The developed chip configuration allows the continuous control of liquid flow through the MOF and simultaneous optical characterization. While integrated in the chip, the MOF is functionalized towards the capture of a specific single-stranded DNA string by immobilizing a sensing layer on the microstructured internal surfaces of the fiber. The sensing layer contains the DNA string complementary to the target DNA sequence and thus operates through the highly selective DNA hybridization process. Optical detection of the captured DNA was carried out using the evanescent-wave-sensing principle. Owing to the small size of the chip, the presented technique allows for analysis of sample volumes down to 300 nL and the fabrication of miniaturized portable devices.      

In situ surface x-ray diffraction studies of homoepitaxial electrochemical growth on Au(100)

Direct in situ x-ray surface scattering studies of growth at a solid-liquid interface are demonstrated using the homoepitaxial electrodeposition on Au(100) as an example. With decreasing potential transitions from step-flow to layer-by-layer growth, manifested by layering oscillations in the x-ray intensity, then to multilayer growth, and finally back to layer-by-layer growth were observed. This complex growth behavior can be explained by the effect of anion coadsorbates and the potential-dependent Au surface reconstruction on the Au surface mobility.     

An implicit box scheme for subsonic compressible flow with dissipative source term

We investigate the stability and convergence of an implicit box scheme for subsonic flows modelled by scalar conservation laws with dissipative and possibly stiff source terms. The scheme is proposed for solving transient gas flow problems in pipeline networks. Such networks are operated in the subsonic flow region and are characterized by pressure losses due to dissipative friction terms. We verify the properties stated by Kru?kov’s theorem (Kru?kov, Math. USSR-Sb. 10:217–243, 1970) for the approximate solution and prove its convergence to the entropy solution.     

Carnap,Goguen, and the Hyperontologies: Logical Pluralism and Heterogeneous Structuring in Ontology Design

This paper addresses questions of universality related to ontological engineering, namely aims at substantiating (negative) answers to the following three basic questions: (i) Is there a ‘universal ontology’?, (ii) Is there a ‘universal formal ontology language’?, and (iii) Is there a universally applicable ‘mode of reasoning’ for formal ontologies? To support our answers in a principled way, we present a general framework for the design of formal ontologies resting on two main principles: firstly, we endorse Rudolf Carnap’s principle of logical tolerance by giving central stage to the concept of logical heterogeneity, i.e. the use of a plurality of logical languages within one ontology design. Secondly, to structure and combine heterogeneous ontologies in a semantically well-founded way, we base our work on abstract model theory in the form of institutional semantics, as forcefully put forward by Joseph Goguen and Rod Burstall. In particular, we employ the structuring mechanisms of the heterogeneous algebraic specification language HetCasl for defining a general concept of heterogeneous, distributed, highly modular and structured ontologies, called hyperontologies. Moreover, we distinguish, on a structural and semantic level, several different kinds of combining and aligning heterogeneous ontologies, namely integration, connection, and refinement. We show how the notion of heterogeneous refinement can be used to provide both a general notion of sub-ontology as well as a notion of heterogeneous equivalence of ontologies, and finally sketch how different modes of reasoning over ontologies are related to these different structuring aspects.     

Iterated local search with Powell’s method: a memetic algorithm for continuous global optimization

In combinatorial solution spaces Iterated Local Search (ILS) turns out to be exceptionally successful. The question arises: is ILS also capable of improving the optimization process in continuous solution spaces? To demonstrate that hybridization leads to powerful techniques in continuous domains, we introduce a hybrid meta-heuristic that integrates Powell’s direct search method. It combines direct search with elements from population based evolutionary optimization. The approach is analyzed experimentally on a set of well known test problems and compared to a state-of-the-art technique, i.e., a restart variant of the Covariance Matrix Adaptation Evolution Strategy with increasing population sizes (G-CMA-ES). It turns out that the population-based Powell-ILS is competitive to the CMA-ES, in some cases even significantly faster and behaves more robust than the pure strategy of Powell in multimodal fitness landscapes. Further experiments on the perturbation mechanism, population sizes, and problems with noise complete the analysis of the hybrid methodology and lead to parameter recommendations.     

The ultraviolet photodissociation of axial and equatorial conformers of 3-pyrroline

Resolved sets of photoproducts arising from the photodissociation of axial and equatorial conformers of 3-pyrroline have been observed using H(Rydberg) atom photofragment translational spectroscopy following excitation in the wavelength range of 250-213 nm. 3-pyrroline (alternatively 2,5-dihydropyrrole) is a five membered partially saturated heterocycle in which the bonding around the N atom is pyramidal (sp(3) hybridized) and the N-H bond can lie either axial or equatorial to the ring. Careful analysis of total kinetic energy release data derived from H atom time-of-flight measurements reveals excitation of the 3-pyrrolinyl cofragment consistent with N-H bond fission in both the axial and equatorial conformers. This allows determination of the energy difference between the ground state conformers to be 340±50 cm(-1) and the N-H bond strength for axial and equatorial conformers as 31,610±50 and 31,270±50 cm(-1), respectively.     

Methyl 4‐O‐β‐d‐galactopyranosyl α‐d‐mannopyranoside methanol 0.375‐solvate

Methyl β‐d ‐galactopyranosyl‐(1→4)‐α‐d ‐mannopyranoside methanol 0.375‐solvate, C₁₃H₂₄O₁₁·0.375CH₃OH, (I), was crystallized from a methanol–ethanol solvent system in a glycosidic linkage conformation, with ϕ′ (O5_Gal—C1_Gal—O1_Gal—C4_Man) = −68.2 (3)° and ψ′ (C1_Gal—O1_Gal—C4_Man—C5_Man) = −123.9 (2)°, where the ring is defined by atoms O5/C1–C5 (monosaccharide numbering); C1 denotes the anomeric C atom and C6 the exocyclic hydroxymethyl C atom in the βGalp and αManp residues, respectively. The linkage conformation in (I) differs from that in crystalline methyl α‐lactoside [methyl β‐d ‐galactopyranosyl‐(1→4)‐α‐d ‐glucopyranoside], (II) [Pan, Noll & Serianni (2005). Acta Cryst. C 61 , o674–o677], where ϕ′ is −93.6° and ψ′ is −144.8°. An intermolecular hydrogen bond exists between O3_Man and O5_Gal in (I), similar to that between O3_Glc and O5_Gal in (II). The structures of (I) and (II) are also compared with those of their constituent residues, viz. methyl α‐d ‐mannopyranoside, methyl α‐d ‐glucopyranoside and methyl β‐d ‐galactopyranoside, revealing significant differences in the Cremer–Pople puckering parameters, exocyclic hydroxymethyl group conformations and intermolecular hydrogen‐bonding patterns.     

A new structure type of RE4B4O11F2: High-pressure synthesis and crystal structure of La4B4O11F2

The first lanthanum fluoride borate La₄B₄O₁₁F₂ was obtained in a Walker-type multianvil apparatus at 6 GPa and 1300 °C. La₄B₄O₁₁F₂ crystallizes in the monoclinic space group P2₁/c with the lattice parameters a=778.1(2) pm, b=3573.3(7) pm, c=765.7(2) pm, β=113.92(3)° (Z=8), and represents a new structure type in the class of compounds with the composition RE₄B₄O₁₁F₂. The crystal structure contains BO₄-tetrahedra interconnected with two BO₃-groups via common vertices, B₂O₅-pyroborate units, and isolated BO₃-groups. The structure shows a wave-like modulation along the b-axis. The crystal structure and properties of La₄B₄O₁₁F₂ are discussed and compared to Gd₄B₄O₁₁F₂.