Microfluidic multipoles: theory and applications

Microfluidic multipoles (MFMs) have been realized experimentally and hold promise for "open-space" biological and chemical surface processing. Whereas convective flow can readily be predicted using hydraulic-electrical analogies, the design of advanced MFMs is constrained by the lack of simple, accurate models to predict mass transport within them. In this work, we introduce the first exact solutions to mass transport in multipolar microfluidics based on the iterative conformal mapping of 2D advection-diffusion around a simple edge into dipoles and multipolar geometries, revealing a rich landscape of transport modes. The models were validated experimentally with a library of 3D printed MFM devices and found in excellent agreement. Following a theory-guided design approach, we further ideated and fabricated two new classes of spatiotemporally reconfigurable MFM devices that are used for processing surfaces with time-varying reagent streams, and to realize a multistep automated immunoassay. Overall, the results set the foundations for exploring, developing, and applying open-space MFMs.Comment: 16 pages, 5 figure

Improvements to the APBS biomolecular solvation software suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining p$K_a$ values, and an improved web-based visualization tool for viewing electrostatics

Fast integral equation methods for the Laplace-Beltrami equation on the sphere

Integral equation methods for solving the Laplace-Beltrami equation on the unit sphere in the presence of multiple "islands" are presented. The surface of the sphere is first mapped to a multiply-connected region in the complex plane via a stereographic projection. After discretizing the integral equation, the resulting dense linear system is solved iteratively using the fast multipole method for the 2D Coulomb potential in order to calculate the matrix-vector products. This numerical scheme requires only O(N) operations, where $N$ is the number of nodes in the discretization of the boundary. The performance of the method is demonstrated on several examples

Computation of Electromagnetic Fields Scattered From Objects With Uncertain Shapes Using Multilevel Monte Carlo Method

Computational tools for characterizing electromagnetic scattering from objects with uncertain shapes are needed in various applications ranging from remote sensing at microwave frequencies to Raman spectroscopy at optical frequencies. Often, such computational tools use the Monte Carlo (MC) method to sample a parametric space describing geometric uncertainties. For each sample, which corresponds to a realization of the geometry, a deterministic electromagnetic solver computes the scattered fields. However, for an accurate statistical characterization the number of MC samples has to be large. In this work, to address this challenge, the continuation multilevel Monte Carlo (CMLMC) method is used together with a surface integral equation solver. The CMLMC method optimally balances statistical errors due to sampling of the parametric space, and numerical errors due to the discretization of the geometry using a hierarchy of discretizations, from coarse to fine. The number of realizations of finer discretizations can be kept low, with most samples computed on coarser discretizations to minimize computational cost. Consequently, the total execution time is significantly reduced, in comparison to the standard MC scheme.Comment: 25 pages, 10 Figure

Detecting chaos in particle accelerators through the frequency map analysis method

The motion of beams in particle accelerators is dominated by a plethora of non-linear effects which can enhance chaotic motion and limit their performance. The application of advanced non-linear dynamics methods for detecting and correcting these effects and thereby increasing the region of beam stability plays an essential role during the accelerator design phase but also their operation. After describing the nature of non-linear effects and their impact on performance parameters of different particle accelerator categories, the theory of non-linear particle motion is outlined. The recent developments on the methods employed for the analysis of chaotic beam motion are detailed. In particular, the ability of the frequency map analysis method to detect chaotic motion and guide the correction of non-linear effects is demonstrated in particle tracking simulations but also experimental data.Comment: Submitted for publication in Chaos, Focus Issue: Chaos Detection Methods and Predictabilit

Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis

Given the piecewise approach to modeling intermolecular interactions for force fields, they can be difficult to parameterize since they are fit to data like total energies that only indirectly connect to their separable functional forms. Furthermore, by neglecting certain types of molecular interactions such as charge penetration and charge transfer, most classical force fields must rely on, but do not always demonstrate, how cancellation of errors occurs among the remaining molecular interactions accounted for such as exchange repulsion, electrostatics, and polarization. In this work we present the first generation of the (many-body) MB-UCB force field that explicitly accounts for the decomposed molecular interactions commensurate with a variational energy decomposition analysis, including charge transfer, with force field design choices that reduce the computational expense of the MB-UCB potential while remaining accurate. We optimize parameters using only single water molecule and water cluster data up through pentamers, with no fitting to condensed phase data, and we demonstrate that high accuracy is maintained when the force field is subsequently validated against conformational energies of larger water cluster data sets, radial distribution functions of the liquid phase, and the temperature dependence of thermodynamic and transport water properties. We conclude that MB-UCB is comparable in performance to MB-Pol, but is less expensive and more transferable by eliminating the need to represent short-ranged interactions through large parameter fits to high order polynomials

Using global interpolation to evaluate the Biot-Savart integral for deformable elliptical Gaussian vortex elements

This paper introduces a new method for approximating the Biot-Savart integral for elliptical Gaussian functions using high-order interpolation and compares it to an existing method based on small aspect ratio asymptotics. The new evaluation technique uses polynomials to approximate the kernel corresponding to the integral representation of the streamfunction. We determine the polynomial coefficients by interpolating precomputed values from look-up tables over a wide range of aspect ratios. When implemented in a full nonlinear vortex method, we find that the new technique is almost three times faster and unlike the asymptotic method, provides uniform accuracy over the full range of aspect ratios. As a proof-of-concept for large scale computations, we use the new technique to calculate inviscid axisymmetrization and filamentation of a two-dimensional elliptical fluid vortex. We compare our results with those from a pseudo-spectral computation and from electron vortex experiments, and find good agreement between the three approaches

Analysis and Visualization of Higher-Order Tensors: Using the Multipole Representation

Materialien wie Kristalle, biologisches Gewebe oder elektroaktive Polymere kommen häufig in verschiedenen Anwendung, wie dem Prothesenbau oder der Simulation von künstlicher Muskulatur vor. Diese und viele weitere Materialien haben gemeinsam, dass sie unter gewissen Umständen ihre Form und andere Materialeigenschaften ändern. Um diese Veränderung beschreiben zu können, werden, abhängig von der Anwendung, verschiedene Tensoren unterschiedlicher Ordnung benutzt. Durch die Komplexität und die starke Abhängigkeit der Tensorbedeutung von der Anwendung, gibt es bisher kein Verfahren Tensoren höherer Ordnung darzustellen, welches standardmäßig benutzt wird. Auch bezogen auf einzelne Anwendungen gibt es nur sehr wenig Arbeiten, die sich mit der visuellen Darstellung dieser Tensoren auseinandersetzt. Diese Arbeit beschäftigt sich mit diesem Problem. Es werden drei verschiedene Methoden präsentiert, Tensoren höherer Ordnung zu analysieren und zu visualisieren. Alle drei Methoden basieren auf der sogenannte deviatorischen Zerlegung und der Multipoldarstellung. Mit Hilfe der Multipole können die Symmetrien des Tensors und damit des beschriebenen Materials bestimmt werden. Diese Eigenschaft wird in für die Visualisierung des Steifigkeitstensors benutzt. Die zweite Methode basiert direkt auf den Multipolen und kann damit beliebige Tensoren in drei Dimensionen darstellen. Dieses Verfahren wird anhand des Kopplungs Tensors, ein Tensor dritter Ordnung, vorgestellt. Die ersten zwei Verfahren sind lokale Glyph-basierte Verfahren. Das dritte Verfahren ist ein erstes globales Tensorvisualisierungsverfahren, welches Tensoren beliebiger Ordnung und Symmetry in drei Dimensionen mit Hilfe eines linienbasierten Verfahrens darstellt.Materials like crystals, biological tissue or electroactive polymers are frequently used in applications like prosthesis construction or the simulation of artificial musculature. These and many other materials have in common that they change their shape and other material properties under certain circumstances. To describe these changes, different tensors of different order, dependent of the application, are used. Due to the complexity and the strong dependency of the tensor meaning of the application, there is, by now, no visualization method that is used by default. Also for specific applications there are only a few methods that address the visual analysis of higher-order tensors. This work adresses this problem. Three different methods to analyse and visualize tensors of higher order will be provided. All three methods are based on the so called deviatoric decomposition and the multipole representation. Using the multipoles the symmetries of a tensor and, therefore, of the described material, can be calculated. This property is used to visualize the stiffness tensor. The second method uses the multipoles directly and can be used for each tensor of any order in three dimensions. This method is presented by analysing the third-order coupling tensor. These two techniques are glyph-based visualization methods. The third one, a line-based method, is, according to our knowledge, a first global visualization method that can be used for an arbitrary tensor in three dimensions

Self-induced decoherence in dense neutrino gases

Dense neutrino gases exhibit collective oscillations where "self-maintained coherence" is a characteristic feature, i.e., neutrinos of different energies oscillate with the same frequency. In a non-isotropic gas, however, the flux term of the neutrino-neutrino interaction has the opposite effect of causing kinematical decoherence of neutrinos propagating in different directions, an effect that is at the origin of the "multi-angle behavior" of neutrinos streaming off a supernova core. We cast the equations of motion in a form where the role of the flux term is manifest. We study in detail the symmetric case of equal neutrino and antineutrino densities where the evolution consists of collective pair conversions ("bipolar oscillations"). A gas of this sort is unstable in that an infinitesimal anisotropy is enough to trigger a run-away towards flavor equipartition. The "self-maintained coherence" of a perfectly isotropic gas gives way to "self-induced decoherence."Comment: Revtex, 16 pages, 12 figure