Software for Exascale Computing - SPPEXA 2016-2019

This open access book summarizes the research done and results obtained in the second funding phase of the Priority Program 1648 "Software for Exascale Computing" (SPPEXA) of the German Research Foundation (DFG) presented at the SPPEXA Symposium in Dresden during October 21-23, 2019. In that respect, it both represents a continuation of Vol. 113 in Springer’s series Lecture Notes in Computational Science and Engineering, the corresponding report of SPPEXA’s first funding phase, and provides an overview of SPPEXA’s contributions towards exascale computing in today's sumpercomputer technology. The individual chapters address one or more of the research directions (1) computational algorithms, (2) system software, (3) application software, (4) data management and exploration, (5) programming, and (6) software tools. The book has an interdisciplinary appeal: scholars from computational sub-fields in computer science, mathematics, physics, or engineering will find it of particular interest

Biomolecular electrostatics with continuum models: a boundary integral implementation and applications to biosensors

The implicit-solvent model uses continuum electrostatic theory to represent the salt solution around dissolved biomolecules, leading to a coupled system of the Poisson-Boltzmann and Poisson equations. This thesis uses the implicit-solvent model to study solvation, binding and adsorption of proteins. We developed an implicit-solvent model solver that uses the boundary element method (BEM), called PyGBe. BEM numerically solves integral equations along the biomolecule-solvent interface only, therefore, it does not need to discretize the entire domain. PyGBe accelerates the BEM with a treecode algorithm and runs on graphic processing units. We performed extensive verification and validation of the code, comparing it with experimental observations, analytical solutions, and other numerical tools. Our results suggest that a BEM approach is more appropriate than volumetric based methods, like finite-difference or finite-element, for high accuracy calculations. We also discussed the effect of features like solvent-filled cavities and Stern layers in the implicit-solvent model, and realized that they become relevant in binding energy calculations. The application that drove this work was nano-scale biosensors-- devices designed to detect biomolecules. Biosensors are built with a functionalized layer of ligand molecules, to which the target molecule binds when it is detected. With our code, we performed a study of the orientation of proteins near charged surfaces, and investigated the ideal conditions for ligand molecule adsorption. Using immunoglobulin G as a test case, we found out that low salt concentration in the solvent and high positive surface charge density leads to favorable orientations of the ligand molecule for biosensing applications. We also studied the plasmonic response of localized surface plasmon resonance (LSPR) biosensors. LSPR biosensors monitor the plasmon resonance frequency of metallic nanoparticles, which shifts when a target molecule binds to a ligand molecule. Electrostatics is a valid approximation to the LSPR biosensor optical phenomenon in the long-wavelength limit, and BEM was able to reproduce the shift in the plasmon resonance frequency as proteins approach the nanoparticle

Spatio-temporal integral equation methods with applications

Electromagnetic interactions are vital in many applications including physics, chemistry, material sciences and so on. Thus, a central problem in physical modeling is the electromagnetic analysis of materials. Here, we consider the numerical solution of the Maxwell equation for the evolution of the electromagnetic field given the charges, and the Newton or Schr\\"odinger equation for the evolution of particles. By combining integral equation techniques with new spectral deferred correction algorithms in time and hierarchical methods in space, we develop fast solvers for the calculation of electromagnetism with relaxations of the model in different scenarios. The dissertation consists of two parts, aiming to resolve the challenges in the temporal and spatial direction, respectively. In the first part, we study a new class of time stepping methods for time-dependent differential equations. The core algorithm uses the pseudo-spectral collocation formulation to discretize the Picard type integral equation reformulation, producing a highly accurate and stable representation, which is then solved via the deferred correction technique. By exploiting the mathematical properties of the formulation and the convergence procedure, we develop some new preconditioning techniques from different perspectives that are accurate, robust, and can be much more efficient than existing methods. As is typical of spectral methods, the solution to the discretization is spectral accurate and the time step-size is optimal, though the cost of solving the system can be high. Thus, the solver is particularly suited to problems where very accurate solutions are sought or large time-step is required, e.g., chaotic systems or long-time simulation. In the second part, we study the hierarchical methods with emphasis on the spatial integral equations. In the first application, we implement a parallel version of the adaptive recursive solver for two-point boundary value problem by Cilk multithreaded runtime system based on the integral equation formulation. In the second application, we apply the hierarchical method to two-layered media Helmholtz equations in the acoustic and electromagnetic scattering problems. With the method of images and integral representations, the spatially heterogeneous translation operators are derived with rigorous error analysis, and the information is then compressed and spread in a fashion similar to fast multipole methods. The preliminary results suggest that our approach can be faster than existing algorithms with several orders of magnitude. We demonstrate our solver on a number of examples and discuss various useful extensions. Preliminary results are favorable and show the viability of our techniques for integral equations. Such integral equation methods could well have a broad impact on many areas of computational science and engineering. We describe further applications in biology, chemistry, and physics, and outline some directions for future work.Doctor of Philosoph

Efficient numerical algorithms for surface formulations of mathematical models for biomolecule analysis and design

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (p. 179-183).This thesis presents a set of numerical techniques that extend and improve computational modeling approaches for biomolecule analysis and design. The presented research focuses on surface formulations of modeling problems related to the estimation of the energetic cost to transfer a biomolecule from the gas phase to aqueous solution. The thesis discusses four contributions to modeling biomolecular interactions. First, the thesis presents an approach to allow accurate discretization of the most prevalent mathematical definitions of the biomolecule-solvent interface; also presented are a number of accurate techniques for numerically integrating possibly singular functions over the discretized surfaces. Such techniques are essential for solving surface formulations numerically. The second part of the thesis presents a fast multiscale numerical algorithm, FFTSVD, that efficiently solves large boundary-element method problems in biomolecule electrostatics. The algorithm synthesizes elements of other popular fast algorithms to achieve excellent efficiency and flexibility. The third thesis component describes an integral-equation formulation and boundary-element method implementation for biomolecule electrostatic analysis.(cont.) The formulation and implementation allow the solution of complicated molecular topologies and physical models. Furthermore, by applying the methods developed in the first half of the thesis, the implementation can deliver superior accuracy for competitive performance. Finally, the thesis describes a highly efficient numerical method for calculating a biomolecular charge distribution that minimizes the free energy' change of binding to another molecule. The approach, which represents a novel PDE-constrained methodology, builds on well-developed physical theory. Computational results illustrate not only the method's improved performance but also its application to realistic biomolecule problems.by Jaydeep Porter Bardhan.Ph.D