Algorithm development in computational chemistry

Thesis

This thesis presents algorithm development in computational chemistry, and applies new computer science concepts to voltammetric simulation. To begin, this thesis discusses why algorithm development is necessary, and inherent problems found in commercial simulation solvers. As a result of this discussion, this thesis describes the need for simulators to keep abreast of recent computational developments.

Algorithm development in this thesis is taken through stages.

Chapter 3 applies known theory relating to the stripping voltammetry at a macroelectrode to the diffusional model of a microdisk, using finite difference and alternating direction implicit simulation techniques.

Chapter 4 introduces the concept of parallel computing, and how computational hardware has developed recently to take advantage of out-of-order calculations, by processing them in parallel to reduce simulation time. The novel area of graphics card simulation for highly parallel algorithms is also explained in detail.

Chapter 5 discusses the adaptation of voltammetric finite difference algorithms to a purely parallel format for simulation by explicit solution. Through explicit solution, finite difference algorithms are applied to electrode geometries which necessitate a three-dimensional solution – elliptical electrodes; square, rectangular, and microband electrodes; and dual microdisk electrodes in collector-generator mode.

Chapter 6 introduces 'Random Walk' simulations, whereby individual particles in the simulation are modelled and their trajectories over time are calculated. The random walk technique in this thesis is improved for pure three-dimensional diffusion, and adapted to graphics cards, allowing up to a factor 4000 increase in speed over previous computational methods. This method is adapted to various systems of low concentration confined voltammetry (chapter 6.4) and single molecule detection, ultra low concentration cyclic voltammetry (chapter 6.5), and underpotential deposition of thallium on mobile silver nanoparticles (chapter 6.6).

Overall, this thesis presents, and applies, a series of algorithm development concepts in computational electrochemistry.

Authors: Cutress, I

• Publication date: 2011
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: Oxford University, UK
• Language: English
• Keywords: Algorithm Development; Algorithm; Theoretical Chemistry; GPGPU; Stochastic; Finite Difference; Electrochemistry; CUDA
• Subjects: Electrochemistry and electrolysis; Computational chemistry; Physical & theoretical chemistry; Theoretical chemistry