Browsing by Author "Klotz, Thomas S"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Accurate Evaluation of Ellipsoidal Harmonics Using Tanh-Sinh Quadrature
    (2017-07-20) Klotz, Thomas S; Knepley, Matthew G
    Ellipsoidal coordinates are an orthogonal coordinate system under which the Laplace equation can be solved by separation of variables. While this has many benefits over spherical coordinates for a variety of potential problems, computation in ellipsoidal coordinates is difficult. Most notably, high-order harmonics can lack closed-form solutions and the associated normalization constants require approximating a singular integral. We provide a method for computing normalization constants to machine precision using tanh-sinh quadrature which exhibits exponential convergence for a large class of functions with singular endpoints. Combined with previous efforts to make ellipsoidal harmonics more accessible, the result is a library which makes computation in ellipsoidal coordinates as accessible as computation in spherical coordinates. Finally, we apply our implementation to the mixed-dielectric solvation problem and provide work-precision analysis for the results.
  • Thumbnail Image
    Item
    Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular Biology
    (2019-04-18) Klotz, Thomas S; Rivière, Béatrice M.; Knepley, Matthew G.
    The molecular electrostatics problem, which asks for the potential generated by a charged solute suspended in a dielectric solvent, is of great importance in computational biology. Poisson models, which treat the solvent as a dielectric continuum, have inherent inaccuracies which can ruin energy predictions. These inaccuracies are primarily due to the inability of continuum models to capture the structure of solvent molecules in close proximity to the solute. A common approach to overcome these inaccuracies is to adjust the dielectric boundary by changing atomic radii. This adjustment procedure can accurately reproduce the expected solvation free energy, but fails to predict thermodynamic behavior. The Solvation Layer Interface Method (SLIC) replaces the standard dielectric boundary condition in Poisson models with a nonlinear boundary condition which accounts for the small-scale arrangement of solvent molecules close to the dielectric interface. Remarkably, SLIC retains the accuracy of Poisson models and furthermore predicts solvation entropies and heat capacities, while removing the need to adjust atomic radii. In this thesis, we perform foundational numerical analysis for the SLIC model. The first major result is a proof that a solution exists for the nonlinear boundary integral equation arising in the SLIC model. We are able to do this by proving existence for an auxiliary equation whose solutions correspond to the SLIC model's equation. Next, we prove that solutions to the SLIC model are unique for spherical geometries, which are common in biological solutes. Finally, we have experimented with nonlinear solvers for the nonlinear BIE, such as Anderson Acceleration, as well as two discretization techniques, in order to provide scalable numerical methods which can be applied to a variety of problems in drug design and delivery.