A new level‐dependent coarse grid correction scheme for indefinite Helmholtz problems

In this paper, we construct and analyze a level‐dependent coarse grid correction scheme for indefinite Helmholtz problems. This adapted multigrid (MG) method is capable of solving the Helmholtz equation on the finest grid using a series of MG cycles with a grid‐dependent complex shift, leading to a stable correction scheme on all levels. It is rigorously shown that the adaptation of the complex shift throughout the MG cycle maintains the functionality of the two‐grid correction scheme, as no smooth modes are amplified in or added to the error. In addition, a sufficiently smoothing relaxation scheme should be applied to ensure damping of the oscillatory error components. Numerical experiments on various benchmark problems show the method to be competitive with or even outperform the current state‐of‐the‐art MG‐preconditioned Krylov methods, for example, complex shifted Laplacian preconditioned flexible GMRES. Copyright © 2013 John Wiley & Sons, Ltd.     

Quantum chemical electron impact mass spectrum prediction for de novo structure elucidation: Assessment against experimental reference data and comparison to competitive fragmentation modeling

We investigate the success of the quantum chemical electron impact mass spectrum (QCEIMS) method in predicting the electron impact mass spectra of a diverse test set of 61 small molecules selected to be representative of common fragmentations and reactions in electron impact mass spectra. Comparison with experimental spectra is performed using the standard matching algorithms, and the relative ranking position of the actual molecule matching the spectra within the NIST‐11 library is examined. We find that the correct spectrum is ranked in the top two matches from structural isomers in more than 50% of the cases. QCEIMS, thus, reproduces the distribution of peaks sufficiently well to identify the compounds, with the RMSD and mean absolute difference between appropriately normalized predicted and experimental spectra being at most 9% and 3% respectively, even though the most intense peaks are often qualitatively poorly reproduced. We also compare the QCEIMS method to competitive fragmentation modeling for electron ionization, a training‐based mass spectrum prediction method, and remarkably we find the QCEIMS performs equivalently or better. We conclude that QCEIMS will be very useful for those who wish to identify new compounds which are not well represented in the mass spectral databases.     

An anti‐diffusive volume of fluid method for interfacial fluid flows

A volume of fluid (VOF) method is developed combining a first‐order limited downwind scheme with higher order accurate schemes. The method is characterized by retaining a sharp fluid interface and a reduction in numerical diffusion near the interface, but avoids complicated geometrical reconstruction as occurs in most volume tracing algorithms. To demonstrate the accuracy and robustness of the method, a selection of numerical experiments are presented involving a pure advection problem, a water wave impact caused by a dam breaking and liquid sloshing in a partially filled tank. Copyright © 2011 John Wiley & Sons, Ltd.     

A simplified adaptive Cartesian grid system for solving the 2D shallow water equations

This paper presents a new simplified grid system that provides local refinement and dynamic adaptation for solving the 2D shallow water equations (SWEs). Local refinement is realized by simply specifying different subdivision levels to the cells on a background uniform coarse grid that covers the computational domain. On such a non‐uniform grid, the structured property of a regular Cartesian mesh is maintained and neighbor information is determined by simple algebraic relationships, i.e. data structure becomes unnecessary. Dynamic grid adaptation is achieved by changing the subdivision level of a background cell. Therefore, grid generation and adaptation is greatly simplified and straightforward to implement. The new adaptive grid‐based SWE solver is tested by applying it to simulate three idealized test cases and promising results are obtained. The new grid system offers a simplified alternative to the existing approaches for providing adaptive mesh refinement in computational fluid dynamics. Copyright © 2011 John Wiley & Sons, Ltd.     

Distance versus Capillary Flow Dynamics-Based Detection Methods on a Microfluidic Paper-Based Analytical Device (μPAD)

In recent years, there has been high interest in paper-based microfluidic sensors or microfluidic paper-based analytical devices (μPADs) towards low-cost, portable, and easy-to-use sensing for chemical and biological targets. μPAD allows spontaneous liquid flow without any external or internal pumping, as well as an innate filtration capability. Although both optical (colorimetric and fluorescent) and electrochemical detection have been demonstrated on μPADs, several limitations still remain, such as the need for additional equipment, vulnerability to ambient lighting perturbation, and inferior sensitivity. Herein, alternative detection methods on μPADs are reviewed to resolve these issues, including relatively well studied distance-based measurements and the newer capillary flow dynamics-based method. Detection principles, assay performance, strengths, and weaknesses are explained for these methods, along with their potential future applications towards point-of-care medical diagnostics and other field-based applications.     

A class of finite difference schemes for interface problems with an HOC approach

In this paper, we propose a new methodology for numerically solving elliptic and parabolic equations with discontinuous coefficients and singular source terms. This new scheme is obtained by clubbing a recently developed higher‐order compact methodology with special interface treatment for the points just next to the points of discontinuity. The overall order of accuracy of the scheme is at least second. We first formulate the scheme for one‐dimensional (1D) problems, and then extend it directly to two‐dimensional (2D) problems in polar coordinates. In the process, we also perform convergence and related analysis for both the cases. Finally, we show a new direction of implementing the methodology to 2D problems in cartesian coordinates. We then conduct numerous numerical studies on a number of problems, both for 1D and 2D cases, including the flow past circular cylinder governed by the incompressible Navier–Stokes equations. We compare our results with existing numerical and experimental results. In all the cases, our formulation is found to produce better results on coarser grids. For the circular cylinder problem, the scheme used is seen to capture all the flow characteristics including the famous von Kármán vortex street. Copyright © 2016 John Wiley & Sons, Ltd.     

FFLUX: Transferability of polarizable machine‐learned electrostatics in peptide chains

The fully polarizable, multipolar, and atomistic force field protein FFLUX is being built from machine learning (i.e., kriging) models, each of which predicts an atomic property. Each atom of a given protein geometry needs to be assigned such a kriging model. Such a knowledgeable atom needs to be informed about a sufficiently large environment around it. The resulting complexity can be tackled by collecting the 20 natural amino acids into a few groups. Using substituted deca‐alanines, we present the proof‐of‐concept that a given atom's charge can be modeled by a few kriging models only. © 2017 Wiley Periodicals, Inc.     

Complex dynamics in equilibrium asset pricing models with boundedly rational,heterogeneous agents

We study a simple model based upon the Lucas framework where heterogeneous agents behave rationally in a fully intertemporal setting but do not know other investors' personal preferences, wealth or investment portfolios. As a consequence, agents initially do not know the equilibrium asset pricing function and must make guesses, which they update via adaptive learning with constant gain. We demonstrate that even in this simple environment the economy can, depending on parameters, exhibit either stable convergence to equilibrium, or chaotic dynamical behavior of asset prices and trading volume without converging to the rational expectations equilibrium of the Lucas model. This contradicts the assertion that the Lucas model is stable in the face of modest deviations from the strong assumptions required to compute the equilibrium. © 2013 Wiley Periodicals, Inc. Complexity 19: 38–55, 2014     

Evolving a three-world framework for solving algebraic equations in the light of what a student has met before

In this paper we consider data from a study in which students shift from linear to quadratic equations in ways that do not conform to established theoretical frameworks. In solving linear equations, the students did not exhibit the ‘didactic cut’ of Filloy and Rojano (1989) or the subtleties arising from conceiving an equation as a balance (Vlassis, 2002). Instead they used ‘procedural embodiments’, shifting terms around with added ‘rules’ to obtain the correct answer (Lima & Tall, 2008). Faced with quadratic equations, the students learn to apply the formula with little success. The interpretation of this data requires earlier theories to be seen within a more comprehensive framework that places them in an evolving context. We use the developing framework of three worlds of mathematics (Tall, 2004, Tall, 2013), based fundamentally on human perceptions and actions and their consequences, at each stage taking into account the experiences that students have ‘met-before’ (Lima and Tall, 2008, McGowen and Tall, 2010). These experiences may be supportive in new contexts, encouraging pleasurable generalization, or problematic, causing confusion and even mathematical anxiety. We consider how this framework explains and predicts the observed data, how it evolves from earlier theories, and how it gives insights that have both theoretical and practical consequences.