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The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by the mesh, and the point charges are accounted for explicitly. In fact, there are several well-known boundary integral formulations available in the literature. This work presents a generalized expression of the boundary integral representation of the implicit solvent model, giving rise to new forms to compute the electrostatic potential. Moreover, it proposes a strategy to build efficient preconditioners for any of the resulting systems, improving the convergence of the linear solver. We perform systematic benchmarking of a set of formulations and preconditioners, focusing on the time to solution, matrix conditioning, and eigenvalue spectrum. We see that the eigenvalue clustering is a good indicator of the matrix conditioning, and show that they can be easily manipulated by scaling the preconditioner. Our results suggest that the optimal choice is problem-size dependent, where a simpler direct formulation is the fastest for small molecules, but more involved second-kind equations are better for larger problems. We also present a fast Calderón preconditioner for first-kind formulations, which shows promising behavior for future analysis. This work sets the basis towards choosing the most convenient boundary integral formulation of the Poisson-Boltzmann equation for a given problem.

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The Poisson-Boltzmann equation is a widely used model to study electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate representations of the solute, which is usually a complicated geometry. Here, we utilize adjoint-based analyses to form two goal-oriented error estimates that allow us to determine the contribution of each discretization element (panel) to the numerical error in the solvation free energy. This information is useful to identify high-error panels to then refine them adaptively to find optimal surface meshes. We present results for spheres and real molecular geometries, and see that elements with large error tend to be in regions where there is a high electrostatic potential. We also find that even though both estimates predict different total errors, they have similar performance as part of an adaptive mesh refinement scheme. Our test cases suggest that the adaptive mesh refinement scheme is very effective, as we are able to reduce the error one order of magnitude by increasing the mesh size less than 20% and come out to be more efficient than uniform refinement when computing error estimations. This result sets the basis toward efficient automatic mesh refinement schemes that produce optimal meshes for solvation energy calculations.

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Implicit-solvent models are widely used to study the electrostatics in dissolved biomolecules, which are parameterized using force fields. Standard force fields treat the charge distribution with point charges; however, other force fields have emerged which offer a more realistic description by considering polarizability. In this work, we present the implementation of the polarizable and multipolar force field atomic multipole optimized energetics for biomolecular applications (AMOEBA), in the boundary integral Poisson-Boltzmann solver PyGBe. Previous work from other researchers coupled AMOEBA with the finite-difference solver APBS, and found difficulties to effectively transfer the multipolar charge description to the mesh. A boundary integral formulation treats the charge distribution analytically, overlooking such limitations. This becomes particularly important in simulations that need high accuracy, for example, when the quantity of interest is the difference between solvation energies obtained from separate calculations, like happens for binding energy. We present verification and validation results of our software, compare it with the implementation on APBS, and assess the efficiency of AMOEBA and classical point-charge force fields in a Poisson-Boltzmann solver. We found that a boundary integral approach performs similarly to a volumetric method on CPU. Also, we present a GPU implementation of our solver. Moreover, with a boundary element method, the mesh density to correctly resolve the electrostatic potential is the same for standard point-charge and multipolar force fields. Finally, we saw that for binding energy calculations, a boundary integral approach presents more consistent results than a finite difference approximation for multipolar force fields. © 2019 Wiley Periodicals, Inc.

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It is well established that the parasites of the genus Leishmania exhibit complex surface interactions with the sandfly vector midgut epithelium, but no prior study has considered the details of their hydrodynamics. Here, the boundary behaviours of motile Leishmania mexicana promastigotes are explored in a computational study using the boundary element method, with a model flagellar beating pattern that has been identified from digital videomicroscopy. In particular a simple flagellar kinematics is observed and quantified using image processing and mode identification techniques, suggesting a simple mechanical driver for the Leishmania beat. Phase plane analysis and long-time simulation of a range of Leishmania swimming scenarios demonstrate an absence of stable boundary motility for an idealised model promastigote, with behaviours ranging from boundary capture to deflection into the bulk both with and without surface forces between the swimmer and the boundary. Indeed, the inclusion of a short-range repulsive surface force results in the deflection of all surface-bound promastigotes, suggesting that the documented surface detachment of infective metacyclic promastigotes may be the result of their particular morphology and simple hydrodynamics. Further, simulation elucidates a remarkable morphology-dependent hydrodynamic mechanism of boundary approach, hypothesised to be the cause of the well-established phenomenon of tip-first epithelial attachment of Leishmania promastigotes to the sandfly vector midgut.

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Acoustic bubbles have wide and important applications in ultrasonic cleaning, sonochemistry and medical ultrasonics. A two-microbubble system (TMS) under ultrasonic wave excitation is explored in the present study, by using the boundary element method (BEM) based on the potential flow theory. A parametric study of the behaviour of a TMS has been carried out in terms of the amplitude and direction of ultrasound as well as the sizes and separation distance of the two bubbles. Three regimes of the dynamic behaviour of the TMS have been identified in terms of the pressure amplitude of the ultrasonic wave. When subject to a strong wave with the pressure amplitude of 1 atm or larger, the two microbubbles become non-spherical during the first cycle of oscillation, with two counter liquid jets formed. When subject to a weak wave with the pressure amplitude of less than 0.5 atm, two microbubbles may be attracted, repelled, or translate along the wave direction with periodic stable separation distance, depending on their size ratio. However, for the TMS under moderate waves, bubbles undergo both non-spherical oscillation and translation as well as liquid jet rebounding.

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In this paper, both singular and hypersingular fundamental solutions of plane Cosserat elasticity are derived and given in a ready-to-use form. The hypersingular fundamental solutions allow to formulate the analogue of Somigliana stress identity, which can be used to obtain the stress and couple-stress fields inside the domain from the boundary values of the displacements, microrotation and stress and couple-stress tractions. Using these newly derived fundamental solutions, the boundary integral equations of both types are formulated and solved by the boundary element method. Simultaneous use of both types of equations (approach known as the dual boundary element method (BEM)) allows problems where parts of the boundary are overlapping, such as crack problems, to be treated and to do this for general geometry and loading conditions. The high accuracy of the boundary element method for both types of equations is demonstrated for a number of benchmark problems, including a Griffith crack problem and a plate with an edge crack. The detailed comparison of the BEM results and the analytical solution for a Griffith crack and an edge crack is given, particularly in terms of stress and couple-stress intensity factors, as well as the crack opening displacements and microrotations on the crack faces and the angular distributions of stresses and couple-stresses around the crack tip.

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Se propone un algoritmo para la simulación matemática del proceso remodelado óseo externo a nivel trabecular. Para ello se realizó el cálculo estructural con el método de los elementos de contorno y se integró con el modelo de remodelación ósea propuesto por Fridez9. Se incluyen varios ejemplos numéricos que muestran la validez y versatilidad del método propuesto. La velocidad en la obtención de la solución es una de las principales ventajas de este método.

An algorithm for the mathematical representation of external bone remodeling is proposed. The Boundary element method is used for the numerical analysis of trabecular bone, together whit the remodeling algorithm presented by Fridez9. The versatility and power of the algorithm discussed herein are shown by some numerical examples. As well, the method converges very fast to the solution, which is one of the main advantages of the proposed numerical scheme

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