Selective trapping of DNA using glass microcapillaries

We show experimentally that a cheap glass microcapillary can accumulate {\lambda}-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop an efficient simulation model for this phenomenon based on the electrokinetic equations and the finite-element method. Using our model, we explore the large parameter space of the trapping mechanism by varying the salt concentration, the capillary surface charge, the applied voltage, the pressure difference, and the mobility of the analyte molecules. Our simulation results show that this system can be tuned to capture a wide range of analyte molecules, such as DNA or proteins, based on their electrophoretic mobility. Our method for separation and pre-concentration of analytes has implications for the development of low-cost lab-on-a-chip devices.Comment: 9 pages, 4 figure

Reducing spurious flow in simulations of electrokinetic phenomena

Electrokinetic transport phenomena can strongly influence the behaviour of macromolecules and colloidal particles in solution, with applications in, e.g., DNA translocation through nanopores, electro-osmotic flow in nanocapillaries, and electrophoresis of charged macromolecules. Numerical simulations are an important tool to investigate these electrokinetic phenomena, but are often plagued by spurious fluxes and spurious flows that can easily exceed physical fluxes and flows. Here, we present a method that reduces one of these spurious currents, spurious flow, by several orders of magnitude. We demonstrate the effectiveness and generality of our method for both electrokinetic lattice-Boltzmann and finite-element-method based algorithms by simulating a charged sphere in an electrolyte solution, and flow through a nanopore. We also show that previous attempts to suppress these spurious currents introduce other sources of error.Comment: 13 pages, 7 figure

Non-linearly stable reduced-order models for incompressible flow with energy-conserving finite volume methods

A novel reduced-order model (ROM) formulation for incompressible flows is presented with the key property that it exhibits non-linearly stability, independent of the mesh (of the full order model), the time step, the viscosity, and the number of modes. The two essential elements to non-linear stability are: (1) first discretise the full order model, and then project the discretised equations, and (2) use spatial and temporal discretisation schemes for the full order model that are globally energy-conserving (in the limit of vanishing viscosity). For this purpose, as full order model a staggered-grid finite volume method in conjunction with an implicit Runge-Kutta method is employed. In addition, a constrained singular value decomposition is employed which enforces global momentum conservation. The resulting `velocity-only' ROM is thus globally conserving mass, momentum and kinetic energy. For non-homogeneous boundary conditions, a (one-time) Poisson equation is solved that accounts for the boundary contribution. The stability of the proposed ROM is demonstrated in several test cases. Furthermore, it is shown that explicit Runge-Kutta methods can be used as a practical alternative to implicit time integration at a slight loss in energy conservation

Planktonic events may cause polymictic-dimictic regime shifts in temperate lakes

Water transparency affects the thermal structure of lakes, and within certain lake depth ranges, it can determine whether a lake mixes regularly (polymictic regime) or stratifies continuously (dimictic regime) from spring through summer. Phytoplankton biomass can influence transparency but the effect of its seasonal pattern on stratification is unknown. Therefore we analysed long term field data from two lakes of similar depth, transparency and climate but one polymictic and one dimictic, and simulated a conceptual lake with a hydrodynamic model. Transparency in the study lakes was typically low during spring and summer blooms and high in between during the clear water phase (CWP), caused when zooplankton graze the spring bloom. The effect of variability of transparency on thermal structure was stronger at intermediate transparency and stronger during a critical window in spring when the rate of lake warming is highest. Whereas the spring bloom strengthened stratification in spring, the CWP weakened it in summer. The presence or absence of the CWP influenced stratification duration and under some conditions determined the mixing regime. Therefore seasonal plankton dynamics, including biotic interactions that suppress the CWP, can influence lake temperatures, stratification duration, and potentially also the mixing regime

Charging phenomena in PEEM imaging and spectroscopy

Spectromicroscopy with the imaging technique of X-ray photoelectron emission microscopy (X-PEEM) is a microchemical analytical tool installed in many synchrotron radiation laboratories, and which is finding application in diverse fields of research. The method of sample analysis, X-ray absorption spectroscopy, does not encounter the same problems as X-ray photoemission spectroscopy when sample charging occurs, hence even good insulators may often be analyzed without any apparent artifacts in images or spectra, We show, however, that charging effects cannot be neglected. We model the effect of surface charge formation on the secondary electron yield from uniform samples to demonstrate that surface charge primarily reduces the yield of electrons which may contribute to the detected signal. We illustrate that on non-uniform insulating samples, localized centers of charge may substantially affect microscope imaging and resolution as the electrostatic held close to the surface is distorted. Finally, in certain circumstances non-uniform surface charge may lead to unexpected lineshapes in X-fay absorption spectra causing, in some extreme cases, negative spectra, These negative spectra are explained, and several strategies are reviewed to minimize the impact of sample charging when analyzing poorly conducting samples of any nature. (C) 2000 Elsevier Science B.V. All rights reserved

Electron optical benches for in-line and branched systems. A new bench designed for mirror-based aberration correction and low energy electron microscopy

6 pagesA review of electron optical bench literature is presented, and the designs of two optical benches used by the authors are described. One bench was designed for testing individual electrostatic electron lenses and in-line optical systems, for example, emission electron microscopes and transmission electron microscopes. It has been in operation for many years. The second electron optical bench is new. It is a branched system designed for several purposes: to study correction of spherical and chromatic aberration with an electron mirror, and to gain experience with low energy electron microscopy (LEEM) optics. The alignment of the electron optical support structure is independent of the vacuum housing, and the bench is designed to be operated either horizontally or vertically. As a demonstration of the performance of the new bench in the horizontal mode, a test pattern on a silicon surface was imaged with LEEM optics

Photoelectron imaging of cells: photoconductivity extends the range of applicability.

Photoelectron imaging is a sensitive surface technique in which photons are used to excite electron emission. This novel method has been applied successfully in studies of relatively flat cultured cells, viruses, and protein-DNA complexes. However, rounded-up cell types such as tumor cells frequently are more difficult to image. By comparing photoelectron images of uncoated and metal-coated MCF-7 human breast carcinoma cells, it is shown that the problem is specimen charging rather than a fundamental limitation of the electron imaging process. This is confirmed by emission current measurements on uncoated monolayers of MCF-7 carcinoma cells and flatter, normal Wi-38 fibroblasts. We report here that sample charging in photoelectron microscopy can be eliminated in most specimens by simultaneous use of two light sources--the standard UV excitation source (e.g., 254 nm) and a longer wavelength light source (e.g., 325 nm). The reduction in sample charging results largely from enhanced photoconduction in the bulk sample and greatly extends the range of cells that can be examined by photoelectron imaging. The contributions of photoconductivity, the electric field of the imaging system, and the short escape depths of the photoelectrons combine to make photoelectron imaging a uniquely sensitive technique for the study of biological surfaces