Neutron-mapping polymer flow: Scattering, flow visualization, and molecular theory

Flows of complex fluids need to be understood at both macroscopic and molecular scales, because it is the macroscopic response that controls the fluid behavior, but the molecular scale that ultimately gives rise to rheological and solid-state properties. Here the flow field of an entangled polymer melt through an extended contraction, typical of many polymer processes, is imaged optically and by small-angle neutron scattering. The dual-probe technique samples both the macroscopic stress field in the flow and the microscopic configuration of the polymer molecules at selected points. The results are compared with a recent tube model molecular theory of entangled melt flow that is able to calculate both the stress and the single-chain structure factor from first principles. The combined action of the three fundamental entangled processes of reptation, contour length fluctuation, and convective constraint release is essential to account quantitatively for the rich rheological behavior. The multiscale approach unearths a new feature: Orientation at the length scale of the entire chain decays considerably more slowly than at the smaller entanglement length.

Characterization of carbon molecular sieves using methane and carbon dioxide as adsorptive probes

Nitrogen adsorption at 77 K is the current standard means for pore size determination of adsorbent materials. However, nitrogen adsorption reaches limitations when dealing with materials such as molecular sieving carbon with a high degree of ultramicroporosity. In this investigation, methane and carbon dioxide adsorption is explored as a possible alternative to the standard nitrogen probe. Methane and carbon dioxide adsorption equilibria and kinetics are measured in a commercially derived carbon molecular sieve over a range of temperatures. The pore size distribution is determined from the adsorption equilibrium, and the kinetics of adsorption is shown to be Fickian for carbon dioxide and non-Fickian for methane. The non-Fickian response is attributed to transport resistance at the pore mouth experienced by the methane molecules but not by the carbon dioxide molecules. Additionally, the change in the rate of adsorption with loading is characterized by the Darken relation in the case of carbon dioxide diffusion but is greater than that predicted by the Darken relation for methane transport. Furthermore, the proposition of inkbottle-shaped micropores in molecular sieving carbon is supported by the determination of the activation energy for the transport of methane and subsequent sizing of the pore-mouth barrier by molecular potential calculations.

Unlocking pathology archives for molecular genetic studies: a reliable method to generate probes for chromogenic and fluorescent in situ hybridization

Chromogenic (CISH) and fluorescent ( FISH) in situ hybridization have emerged as reliable techniques to identify amplifications and chromosomal translocations. CISH provides a spatial distribution of gene copy number changes in tumour tissue and allows a direct correlation between copy number changes and the morphological features of neoplastic cells. However, the limited number of commercially available gene probes has hindered the use of this technique. We have devised a protocol to generate probes for CISH that can be applied to formalin-fixed, paraffin-embedded tissue sections (FFPETS). Bacterial artificial chromosomes ( BACs) containing fragments of human DNA which map to specific genomic regions of interest are amplified with phi 29 polymerase and random primer labelled with biotin. The genomic location of these can be readily confirmed by BAC end pair sequencing and FISH mapping on normal lymphocyte metaphase spreads. To demonstrate the reliability of the probes generated with this protocol, four strategies were employed: (i) probes mapping to cyclin D1 (CCND1) were generated and their performance was compared with that of a commercially available probe for the same gene in a series of 10 FFPETS of breast cancer samples of which five harboured CCND1 amplification; (ii) probes targeting cyclin-dependent kinase 4 were used to validate an amplification identified by microarray-based comparative genomic hybridization (aCGH) in a pleomorphic adenoma; (iii) probes targeting fibroblast growth factor receptor 1 and CCND1 were used to validate amplifications mapping to these regions, as defined by aCGH, in an invasive lobular breast carcinoma with FISH and CISH; and (iv) gene-specific probes for ETV6 and NTRK3 were used to demonstrate the presence of t(12; 15)(p12; q25) translocation in a case of breast secretory carcinoma with dual colour FISH. In summary, this protocol enables the generation of probes mapping to any gene of interest that can be applied to FFPETS, allowing correlation of morphological features with gene copy number.