A device for extraction, manipulation and stretching of DNA from single human chromosomes

We describe the structure and operation of a micro/nanofluidic device in which individual metaphase chromosomes can be isolated and processed without being displaced during exchange of reagents. The change in chromosome morphology as a result of introducing protease into the device was observed by time-lapse imaging; pressure-driven flow was then used to shunt the chromosomal DNA package into a nanoslit. A long linear DNA strand (>1.3 Mbp) was seen to stretch out from the DNA package and along the length of the nanoslit. Delivery of DNA in its native metaphase chromosome package as well as the microfluidic environment prevented DNA from shearing and will be important for preparing ultra-long lengths of DNA for nanofluidic analysis.     

Bias-corrected Pearson estimating functions for Taylor’s power law applied to benthic macrofauna data

Estimation of Taylor’s power law for species abundance data may be performed by linear regression of the log empirical variances on the log means, but this method suffers from a problem of bias for sparse data. We show that the bias may be reduced by using a bias-corrected Pearson estimating function. Furthermore, we investigate a more general regression model allowing for site-specific covariates. This method may be efficiently implemented using a Newton scoring algorithm, with standard errors calculated from the inverse Godambe information matrix. The method is applied to a set of biomass data for benthic macrofauna from two Danish estuaries.     

Nanofiltering via integrated liquid core waveguides

We demonstrate and describe how nanoporous liquid core waveguides can exclude scattering particles, making them an ideal integrated platform for analysis of turbid solutions. Milk with 0.5% fat showed an optical propagation loss of 0.05?dB/mm at 633?nm in nanoporous waveguides compared to the 10.6?dB/mm loss in standard cuvette measurements. To examine the nanofiltering effect, waveguides were infiltrated with solutions containing Rhodamine B molecules (1?nm) and 22?nm red fluorescing polystyrene beads. With fluorescence spectroscopy we show that 22?nm beads are excluded, while Rhodamine B molecules penetrate the waveguides. This is further confirmed by fluorescence microscopy, also revealing a homogenous distribution of Rhodamine in the waveguide volume.     

Nanoimprinted distributed feedback lasers comprising TiO2 thin films: Design guidelines for high performance sensing

Design guidelines for optimizing the sensing performance of nanoimprinted second order distributed feedback dye lasers are presented. The guidelines are verified by experiments and simulations. The lasers, fabricated by UV‐nanoimprint lithography into Pyrromethene doped Ormocomp thin films on glass, have their sensor sensitivity enhanced by a factor of up to five via the evaporation of a titanium dioxide (TiO₂) waveguiding layer. The influence of the TiO₂ layer thickness on the device sensitivity is analyzed with a simple model that accurately predicts experimentally measured wavelength shifts induced by varied superstrate refractive indices. The superstrate refractive index is additionally shown to determine which of the possible waveguiding modes dominates for lasing, indicating a method to flexibly select the polarization of the laser. The detection limit of the sensor system is further discussed, finding an optimum at 7.5· 10⁻⁶ RIU. Wavelength changes caused by dye bleaching must be taken into account for long‐term measurements.     

Characterization of Generalized Gradient Young Measures Generated by Sequences in W1,1 and BV

Generalized Young measures as introduced by DiPerna and Majda (Commun Math Phys 108:667–689, 1987) provide a quantitative tool for studying the one-point statistics of oscillation and concentration in sequences of functions. In this work, after developing a functional-analytic framework for such measures, including a compactness theorem and results on the generation of such Young measures by L¹-bounded sequences (or even by sequences of bounded Radon measures), we turn to investigation of those Young measures that are generated by bounded sequences of W^1,1-gradients or BV-derivatives. We provide several techniques to manipulate such measures (including shifting, averaging and approximation by piecewise-homogeneous Young measures) and then establish the main new result of this work, the duality characterization of the set of (BV- or W^1,1-)gradient Young measures in terms of Jensen-type inequalities for quasiconvex functions with linear growth at infinity. This result is the natural generalization of the Kinderlehrer–Pedregal Theorem (Arch Ration Mech Anal 115:329–365, 1991; J Geom Anal 4:59–90, 1994) for classical Young measures to the W^1,1- and BV-case and contains its version for weakly converging sequences in W^1,1 as a special case. Finally, we give an application to a new lower semicontinuity theorem in BV.     

Fractional decay of quantum dots in real photonic crystals

We show that fractional decay may be observable in experiments using quantum dots and photonic crystals with parameters that are currently achievable. We focus on the case of inverse opal photonic crystals and locate the position in the crystal where the effect is most pronounced. Furthermore, we quantify the influence of absorptive loss and show that it is a limiting but not prohibitive effect.     

Investigating porcine pancreatic phospholipase A2 action on vesicles and supported planar bilayers using a quartz crystal microbalance with dissipation

We present an investigation of the activity of porcine pancreatic phospholipase A2 towards phospholipids. The phospholipids are presented in three different ways, namely as tethered vesicles, intact surface-bound vesicles, and supported planar bilayers (SPBs). The process is followed using a quartz crystal microbalance which measures both the frequency shift and the energy dissipation factor. This technique is very sensitive not only to the mass of the material deposited on the crystal, but also to its viscoelasticity. The breakdown of the phospholipid vesicles and bilayers consequently gives rise to very large signal changes. Enzyme binding is separated from vesicle hydrolysis using nonhydrolyzable ether lipids. Intact and tethered vesicles give rise to the same profile, indicating that direct immobilization of the vesicles does not affect hydrolysis significantly. The data fit well to a Voight-based model describing the change in film structure with time. Initial enzyme binding to intact vesicles is accompanied by a significant increase in layer thickness as well as a decrease in viscosity and shear modulus. This effect, which is less pronounced in SPBs, is probably mainly due to the accumulation of hydrolysis products in the vesicle prior to rupture of the vesicles and release of bound water, since it disappears when lysolipid is included in the vesicles prior to hydrolysis.     

High resolution inductively coupled plasma mass spectrometry (HR-ICPMS) determination and multivariate evaluation of 10 trace elements in mussels from 7 sites in Limfjorden, Denmark

The contents of V, Cr, Co, Ni, Cu, Ga, Rb, Cd, Ba, and Pb in the soft tissue of blue mussel (Mytilus edulis) were determined by a high resolution inductively coupled plasma mass spectrometry (HR-ICPMS) method. Sample digestions were performed in closed microwave vessels using nitric acid and hydrogen peroxide. Using HR-ICPMS it is possible to resolve the analytical peaks from otherwise interfering polyatomic ions with a mass resolution setting of 4,000 (Cr, Ni, Cu). The proposed method was validated using a mussel tissue reference material (NIST SRM 2974). The proposed method was applied to real samples of blue mussel from seven sites in the inlet "Limfjorden", Denmark, and the levels of trace elements found were compared with the levels found in an earlier study. For the mussel samples large inter-regional differences in trace element concentrations in the tissues were recorded. The mussels from the different sites could be separated using principal component analysis (PCA). Comparison with the levels of trace elements in mussels found in 1982 showed that the trace elemental contamination has increased during the last 15 years. From the data obtained, mussel tissue appears to be good bio-indicator for identification of coastal areas exposed to metallic contaminants.     

Efficient integration of stiff kinetics with phase change detection for reactive reservoir processes

We propose the use of implicit one-step Explicit Singly Diagonal Implicit Runge–Kutta (ESDIRK) methods for integration of the stiff kinetics in reactive, compositional and thermal processes that are solved using operator-splitting type approaches. To facilitate the algorithmic development we construct a virtual kinetic cell model. The model serves both as a tool for the development and testing of tailored solvers as well as a testbed for studying the interactions between chemical kinetics and phase behavior. As case study, two chemical kinetics models with 6 and 14 components, respectively, are implemented for in situ combustion, a thermal oil recovery process. Through benchmark studies using the 14 component reaction model the new ESDIRK solvers are shown to improve computational speed when compared to the widely used multi-step BDF methods DASSL and LSODE. Phase changes are known to cause convergence problems for the integration method. We propose an algorithm for detection and location of phase changes based on discrete event system theory. Experiments show that the algorithm improves the robustness of the integration process near phase boundaries by lowering the number convergence and error test failures by more than 50% compared to direct integration without the new algorithm.