Dynamic Stern layers in charge-regulating electrokinetic systems: three regimes from an analytical approach

We present analytical solutions for the electrokinetics at a charged surface with both non-zero Stern-layer conductance and finite chemical reaction rates. We have recently studied the same system numerically [Werkhoven {\em et al.}, Phys. Rev. Lett. {\bf 120}, 264502 (2018)], and have shown that an applied pressure drop across the surface leads to a non-trivial, laterally heterogeneous surface charge distribution at steady state. In this work, we linearise the governing electrokinetic equations to find closed expressions for the surface charge profile and the generated streaming electric field. The main results of our calculations are the identification of three important length and time scales that govern the charge distribution, and consequently the classification of electrokinetic systems into three distinct regimes. The three governing time scales can be associated to (i) the chemical reaction, (ii) diffusion in the Stern layer, and (iii) conduction in the Stern layer, where the dominating (smallest) time scale characterises the regime. In the reaction-dominated regime we find a constant surface charge with an edge effect, and recover the Helmholtz-Smoluchowski equation. In the other two regimes, we find that the surface charge heterogeneity extends over the entire surface, either linearly (diffusion-dominated regime) or nonlinearly (conduction-dominated regime).Comment: Accepted for publication in European Physical Journal: Special Topic

Coupled water, charge and salt transport in heterogeneous nano-fluidic systems

We theoretically study the electrokinetic transport properties of nano-fluidic devices under the influence of a pressure, voltage or salinity gradient. On a microscopic level the behaviour of the device is quantified by the Onsager matrix ${\bf L}$, a generalised conductivity matrix relating the local driving forces and the induced volume, charge and salt flux. Extending ${\bf L}$ from a local to a global linear-response relation is trivial for homogeneous electrokinetic systems, but in this manuscript we derive a generalised conductivity matrix ${\bf G}$ from ${\bf L}$ that applies also to heterogeneous electrokinetic systems. This extension is especially important in the case of an imposed salinity gradient, which gives necessarily rise to heterogeneous devices. Within this formalism we can also incorporate a heterogeneous surface charge due to, for instance, a charge regulating boundary condition, which we show to have a significant impact on the resulting fluxes. The predictions of the Poisson-Nernst-Planck-Stokes theory show good agreement with exact solutions of the governing equations determined using the Finite Element Method under a wide variety of parameters. Having established the validity of the theory, it provides an accessible method to analyse electrokinetic systems in general without the need of extensive numerical methods. As an example, we analyse a Reverse Electrodialysis "blue energy" system, and analyse how the many parameters that characterise such a system affect the generated electrical power and efficiency

Lessons learned in a decade of research software engineering gpu applications

After years of using Graphics Processing Units (GPUs) to accelerate scientific applications in fields as varied as tomography, computer vision, climate modeling, digital forensics, geospatial databases, particle physics, radio astronomy, and localization microscopy, we noticed a number of technical, socio-technical, and non-technical challenges that Research Software Engineers (RSEs) may run into. While some of these challenges, such as managing different programming languages within a project, or having to deal with different memory spaces, are common to all software projects involving GPUs, others are more typical of scientific software projects. Among these challenges we include changing resolutions or scales, maintaining an application over time and making it sustainable, and evaluating both the obtained results and the achieved performance

S-DIMM+ height characterization of day-time seeing using solar granulation

To evaluate site quality and to develop multi-conjugative adaptive optics systems for future large solar telescopes, characterization of contributions to seeing from heights up to at least 12 km above the telescope is needed. We describe a method for evaluating contributions to seeing from different layers along the line-of-sight to the Sun. The method is based on Shack Hartmann wavefront sensor data recorded over a large field-of-view with solar granulation and uses only measurements of differential image displacements from individual exposures, such that the measurements are not degraded by residual tip-tilt errors. We conclude that the proposed method allows good measurements when Fried's parameter r_0 is larger than about 7.5 cm for the ground layer and that these measurements should provide valuable information for site selection and multi-conjugate development for the future European Solar Telescope. A major limitation is the large field of view presently used for wavefront sensing, leading to uncomfortably large uncertainties in r_0 at 30 km distance.Comment: Accepted by AA 22/01/2010 (12 pages, 11 figures

High-order aberration compensation with Multi-frame Blind Deconvolution and Phase Diversity image restoration techniques

Context. For accurately measuring intensities and determining magnetic field strengths of small-scale solar (magnetic) structure, knowledge of and compensation for the point spread function is crucial. For images recorded with the Swedish 1-meter Solar Telescope, restoration with Multi-Frame Blind Deconvolution and Joint Phase Diverse Speckle methods lead to remarkable improvements in image quality but granulation contrasts that are too low, indicating additional stray light. Aims. We propose a method to compensate for stray light from high-order atmospheric aberrations not included in MFBD and JPDS processing. Methods. To compensate for uncorrected aberrations, a reformulation of the image restoration process is proposed that allows the average effect of hundreds of high-order modes to be compensated for by relying on Kolmogorov statistics for these modes. The applicability of the method requires simultaneous measurements of Fried's parameter r0. The method is tested with simulations as well as real data and extended to include compensation for conventional stray light. Results. We find that only part of the reduction of granulation contrast in SST images is due to uncompensated high-order aberrations. The remainder is still unaccounted for and attributed to stray light from the atmosphere, the telescope with its re-imaging system and to various high-altitude seeing effects. Conclusions. We conclude that statistical compensation of high-order modes is a viable method to reduce the loss of contrast occurring when a limited number of aberrations is explicitly compensated for with MFBD and JPDS processing. We show that good such compensation is possible with only 10 recorded frames. The main limitation of the method is that already MFBD and JPDS processing introduces high-order compensation that, if not taken into account, can lead to over-compensation.Comment: in press in Astronomy & Astrophysic

Square root singularity in the viscosity of neutral colloidal suspensions at large frequencies

The asymptotic frequency $\omega$, dependence of the dynamic viscosity of neutral hard sphere colloidal suspensions is shown to be of the form $\eta_0 A(\phi) (\omega \tau_P)^{-1/2}$, where $A(\phi)$ has been determined as a function of the volume fraction $\phi$, for all concentrations in the fluid range, $\eta_0$ is the solvent viscosity and $\tau_P$ the P\'{e}clet time. For a soft potential it is shown that, to leading order steepness, the asymptotic behavior is the same as that for the hard sphere potential and a condition for the cross-over behavior to $1/\omega \tau_P$ is given. Our result for the hard sphere potential generalizes a result of Cichocki and Felderhof obtained at low concentrations and agrees well with the experiments of van der Werff et al, if the usual Stokes-Einstein diffusion coefficient $D_0$ in the Smoluchowski operator is consistently replaced by the short-time self diffusion coefficient $D_s(\phi)$ for non-dilute colloidal suspensions.Comment: 18 pages LaTeX, 1 postscript figur

The Oceanographic Multipurpose Software Environment (OMUSE v1.0)

In this paper we present the Oceanographic Multipurpose Software Environment (OMUSE). OMUSE aims to provide a homogeneous environment for existing or newly developed numerical ocean simulation codes, simplifying their use and deployment. In this way, numerical experiments that combine ocean models representing different physics or spanning different ranges of physical scales can be easily designed. Rapid development of simulation models is made possible through the creation of simple high-level scripts. The low-level core of the abstraction in OMUSE is designed to deploy these simulations efficiently on heterogeneous high-performance computing resources. Cross-verification of simulation models with different codes and numerical methods is facilitated by the unified interface that OMUSE provides. Reproducibility in numerical experiments is fostered by allowing complex numerical experiments to be expressed in portable scripts that conform to a common OMUSE interface. Here, we present the design of OMUSE as well as the modules and model components currently included, which range from a simple conceptual quasi-geostrophic solver to the global circulation model POP (Parallel Ocean Program). The uniform access to the codes' simulation state and the extensive automation of data transfer and conversion operations aids the implementation of model couplings. We discuss the types of couplings that can be implemented using OMUSE. We also present example applications that demonstrate the straightforward model initialization and the concurrent use of data analysis tools on a running model. We give examples of multiscale and multiphysics simulations by embedding a regional ocean model into a global ocean model and by coupling a surface wave propagation model with a coastal circulation model

A spatial column-store to triangulate the Netherlands on the fly

3D digital city models, important for urban planning, are currently constructed from massive point clouds obtained through airborne LiDAR (Light Detection and Ranging). They are semantically enriched with information obtained from auxiliary GIS data like Cadastral data which contains information about the boundaries of properties, road networks, rivers, lakes etc. Technical advances in the LiDAR data acquisition systems made possible the rapid acquisition of high resolution topographical information for an entire country. Such data sets are now reaching the trillion points barrier. To cope with this data deluge and provide up-to-date 3D digital city models on demand current geospatial management strategies should be re-thought. This work presents a column-oriented Spatial Database Management System which provides in-situ data access, effective data skipping, efficient spatial operations, and interactive data visualization. Its efficiency and scalability is demonstrated using a dense LiDAR scan of The Netherlands consisting of 640 billion points and the latest Cadastral information, and compared with PostGIS

Creating a reusable cross-disciplinary multi-scale and multi-physics framework: From AMUSE to OMUSE and beyond

Here, we describe our efforts to create a multi-scale and multi-physics framework that can be retargeted across different disciplines. Currently we have implemented our approach in the astrophysical domain, for which we developed AMUSE (github.com/amusecode/amuse ), and generalized this to the oceanographic and climate sciences, which led to the development of OMUSE (bitbucket.org/omuse ). The objective of this paper is to document the design choices that led to the successful implementation of these frameworks as well as the future challenges in applying this approach to other domains