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

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

Coherent deglacial changes in western Atlantic Ocean circulation

Abrupt climate changes in the past have been attributed to variations in Atlantic Meridional Overturning Circulation (AMOC) strength. However, the exact timing and magnitude of past AMOC shifts remain elusive, which continues to limit our understanding of the driving mechanisms of such climate variability. Here we show a consistent signal of the 231Pa/230Th proxy that reveals a spatially coherent picture of western Atlantic circulation changes over the last deglaciation, during abrupt millennial-scale climate transitions. At the onset of deglaciation, we observe an early slowdown of circulation in the western Atlantic from around 19 to 16.5 thousand years ago (ka), consistent with the timing of accelerated Eurasian ice melting. The subsequent weakened AMOC state persists for over a millennium (~16.5–15 ka), during which time there is substantial ice rafting from the Laurentide ice sheet. This timing indicates a role for melting ice in driving a two-step AMOC slowdown, with a positive feedback sustaining continued iceberg calving and climate change during Heinrich Stadial 1

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Sensitivity of Nd isotopic composition in seawater to changes in Nd sources and paleoceanographic implications

It has been argued that past changes in the sources of Nd could hamper the use of the Nd isotopic composition (ϵNd) as a proxy for past changes in the overturning of deep water masses. Here we reconsider uncertainties associated with ϵNd in seawater due to potential regional to global scale changes in the sources of Nd by applying a modeling approach. For illustrative purposes we describe rather extreme changes in the magnitude of source fluxes, their isotopic composition or both. We find that the largest effects on ϵNd result from changes in the boundary source. Considerable changes also result from variations in the magnitude or ϵNd of dust and rivers but are largely constrained to depths shallower than 1 km, except if they occur in or upstream of regions where deep water masses are formed. From these results we conclude that changes in Nd sources have the potential to affect ϵNd. However, substantial changes are required to generate large-scale changes inϵNd in deep water that are similar in magnitude to those that have been reconstructed from sediment cores or result from changes in meridional overturning circulation in model experiments. Hence, it appears that a shift in ϵNdcomparable to glacial-interglacial variations is difficult to obtain by changes in Nd sources alone, but that more subtle variations can be caused by such changes and must be interpreted with caution

<Poster Presentation 4>Tracking chaotic behavior in environmental hydraulics. Measurement models for the temporal coefficients of Proper Orthogonal Decomposition of free-surface flows

[Date] November 28 (Mon) - December 2 (Fri), 2011: [Place] Kyoto University Clock Tower Centennial Hall, Kyoto, JAPA

Photoelectron microscopy of organic surfaces: The effect of substrate reflectivity

5 pagesPhotoelectron measurements of thin organic films deposited on a metal substrate may contain information from deep within the sample, derived from reflected ultraviolet light. This effect depends on the reflectivity of the substrate, the sample thickness and optical absorption coefficient, and the photoelectron escape depth. Calculations are given for phthalocyanine as a specific example. Contrast reversal and apparent seethrough effects resulting from reflection are predicted in overlapping thin films. Photoelectron micrographs of thin films and grid patterns of phthalocyanine show that the reflection model is essentially correct. This effect can be substantially reduced by using a nitrocellulose-coated carbon substrate

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