Modulation-frequency encoded multi-color fluorescent DNA analysis in an optofluidic chip

We introduce a principle of parallel optical processing to an optofluidic lab-on-a-chip. During electrophoretic separation, the ultra-low limit of detection achieved with our set-up allows us to record fluorescence from covalently end-labeled DNA molecules. Different sets of exclusively color-labeled DNA fragments-otherwise rendered indistinguishable by spatio-temporal coincidence-are traced back to their origin by modulation-frequency-encoded multi-wavelength laser excitation, fluorescence detection with a single ultrasensitive, albeit color-blind photomultiplier, and Fourier analysis decoding. As a proof of principle, fragments obtained by multiplex ligation-dependent probe amplification from independent human genomic segments, associated with genetic predispositions to breast cancer and anemia, are simultaneously analyzed.     

All-numerical noise filtering of fluorescence signals for achieving ultra-low limit of detection in biomedical applications

We present an all-numerical method for post-processing of the fluorescent signal as obtained from labeled molecules by capillary electrophoresis (CE) in an optofluidic chip, on the basis of data filtering in the Fourier domain. It is shown that the method outperforms the well-known lock-in amplification during experiments in the reduction of noise by a factor of (square root)2. The method is illustrated using experimental data obtained during CE separation of molecules from a commercial DNA ladder with 17 fluorescently labeled molecules having different base-pair sizes. An improvement in signal-to-noise ratio by a factor of ～10 is achieved, resulting in a record-low limit of detection of 210 fM.     

The discrete-dipole-approximation code ADDA: Capabilities and known limitations

The open-source code ADDA is described, which implements the discrete dipole approximation (DDA), a method to simulate light scattering by finite 3D objects of arbitrary shape and composition. Besides standard sequential execution, ADDA can run on a multiprocessor distributed-memory system, parallelizing a single DDA calculation. Hence the size parameter of the scatterer is in principle limited only by total available memory and computational speed. ADDA is written in C99 and is highly portable. It provides full control over the scattering geometry (particle morphology and orientation, and incident beam) and allows one to calculate a wide variety of integral and angle-resolved scattering quantities (cross sections, the Mueller matrix, etc.). Moreover, ADDA incorporates a range of state-of-the-art DDA improvements, aimed at increasing the accuracy and computational speed of the method. We discuss both physical and computational aspects of the DDA simulations and provide a practical introduction into performing such simulations with the ADDA code. We also present several simulation results, in particular, for a sphere with size parameter 320 (100-wavelength diameter) and refractive index 1.05.     

Heavy ion induced damage to plasmid DNA: plateau region vs. spread out Bragg-peak

We have investigated the damage of synthetic plasmid pBR322 DNA in dilute aqueous solutions induced by fast carbon ions. The relative contribution of indirect damage and direct damage to the DNA itself is expected to vary with linear energy transfer along the ion track, with the direct damage contribution increasing towards the Bragg peak. Therefore, ¹²C ions at the spread-out Bragg peak (dose averaged LET_∞ = 189 ± 15 keV/μm) and in the plateau region of the Bragg curve (LET = 40 keV/μm) were employed and the radical scavenger concentration in the plasmid solution was varied to quantify the indirect effect. In order to minimize the influence of ¹²C break-up fragments, a relatively low initial energy of 90 MeV/nucleon was employed for the carbon ions. DNA damage has been quantified by subsequent electrophoresis on agarose gels. We find that strand breaks due to both indirect and direct effects are systematically higher in the plateau region as compared to the Bragg peak region with the difference being smallest at high scavenging capacities. In view of the fact that the relative biological effectiveness for many biological endpoints is maximum at the Bragg peak our findings imply that DNA damage at the Bragg peak is qualitatively most severe.     

Pulsed EPR spin-probe study of intracellular glasses in seed and pollen

EPR spectra of 3-carboxy-proxyl (CP) in dry biological tissues exhibited a temperature-dependent change in the principal value A'(zz) of the hyperfine interaction tensor. The A'(zz) value changed sharply at a particular temperature that was dependent on water content. At elevated water contents, the break occurred at lower temperatures and appeared to be associated with the melting of the cytoplasmic glassy state. To investigate the reason for the change in A'(zz), we employed echo-detected EPR (ED EPR) spectroscopy. The shape of the ED EPR spectrum revealed the presence of librational motion of the spin probe, a motion typically present in glassy materials. The similarities in temperature dependency of A'(zz) and librational motion of CP in pea seed axes indicated that the change in A'(zz) arose from librational motion. ED EPR measurements of CP as a function of water content in Typha latifolia pollen showed that librational motion decreased with decreasing water contents until a plateau or minimum was reached. ED EPR spectroscopy is a valuable technique for characterizing the relation between molecular motion and storage kinetics of dry seed and pollen.     

A manufactured solution for a two-dimensional steady wall-bounded incompressible turbulent flow

This paper presents a manufactured solution (MS), resembling a two-dimensional, steady, wall-bounded, incompressible, turbulent flow for RANS codes verification. The specified flow field satisfies mass conservation, but requires additional source terms in the momentum equations. To also allow verification of the correct implementation of the turbulence models transport equations, the proposed MS exhibits most features of a true near-wall turbulent flow. The model is suited for testing six eddy-viscosity turbulence models: the one-equation models of Spalart and Allmaras and Menter; the standard two-equation k–ε model and the low-Reynolds version proposed by Chien; the TNT and BSL versions of the k–ω model.     

纳米SiO2在钧瓷釉料中的应用及对釉料性质的影响

在钧瓷基础釉中加入过渡金属氧化物可以使钧瓷呈现出丰富多彩的釉色,但同时也会造成严重的流釉现象.在传统钧瓷中,适当的流釉可以给瓷器带来艺术的美感,严重的流釉反而影响钧瓷的艺术效果和产品质量.通过在钧瓷釉料中添加纳米SiO2,并控制其质量比例在2wt;和4wt;,研究纳米SiO2对钧瓷釉料性质的影响.添加纳米SiO2前后的钧瓷釉料的结构和性质通过X-射线衍射仪、扫面电子显微镜和X-射线电子能谱仪进行表征分析.对比发现,纳米SiO2的添加可提高釉的化学稳定性和热稳定性,有效地改善钧瓷制品的流釉现象,并且能够提高釉层的亮度.     

Performance of a parallel algebraic multilevel preconditioner for stabilized finite element semiconductor device modeling

In this study results are presented for the large-scale parallel performance of an algebraic multilevel preconditioner for solution of the drift-diffusion model for semiconductor devices. The preconditioner is the key numerical procedure determining the robustness, efficiency and scalability of the fully-coupled Newton–Krylov based, nonlinear solution method that is employed for this system of equations. The coupled system is comprised of a source term dominated Poisson equation for the electric potential, and two convection–diffusion-reaction type equations for the electron and hole concentration. The governing PDEs are discretized in space by a stabilized finite element method. Solution of the discrete system is obtained through a fully-implicit time integrator, a fully-coupled Newton-based nonlinear solver, and a restarted GMRES Krylov linear system solver. The algebraic multilevel preconditioner is based on an aggressive coarsening graph partitioning of the nonzero block structure of the Jacobian matrix. Representative performance results are presented for various choices of multigrid V-cycles and W-cycles and parameter variations for smoothers based on incomplete factorizations. Parallel scalability results are presented for solution of up to 10⁸${10}^8$ unknowns on 4096 processors of a Cray XT3/4 and an IBM POWER eServer system.     

Reflection of Electromagnetic Waves by a Nonuniform Plasma Layer Covering a Metal Surface

Reflection coefficients of electromagnetic waves in a nonuniform plasma layer with electrons, positive ions and negative ions, covering a metal surface are investigated by using the finite-difference-time-domMn method. It is shown that the reflection coemcients are influenced greatly by the density gradient on the layer edge, layer thickness and electron proportion, i.e., the effect of the negative ions. It is also found that low reflection or high attenuation can be reached by properly choosing high electron proportion, thick plasma layer, and smooth density gradient in the low frequency regime, but sharp density gradient in the high frequency regime.     

Pseudo-Zeeman splitting of excited states in MnI2: Cu+

MnI₂ doped with CuI shows extra absorption lines in the spectral region between 24000 and 30000 cm^-1. At low temperature these lines have an anomalously large Zeeman splitting in an applied magnetic field, with apparent g values as large as 150. This effect is attributed to exchange coupling of an electron (or hole) in the excited state with the spins of the surrounding Mn²⁺ ions. The applied magnetic field partly aligns the Mn²⁺ ion spins and this causes the observed very large pseudo-Zeeman splitting of the absorption lines.