An Efficient Numerical Method for Simulating Electrochemically Driven Enzymatic Reactions

Honeychurch, Michael and Bernhardt, Paul (2006) An Efficient Numerical Method for Simulating Electrochemically Driven Enzymatic Reactions.

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Title An Efficient Numerical Method for Simulating Electrochemically Driven Enzymatic Reactions
Abstract/Summary We consider systems in which electroactive enzymes are immobilised on an electrode surface through physical adsorption or covalent attachment on an electrode surface and substrate(s), product(s) and inhibitor(s) are present in the bulk solution. We solve the governing equations numerically by fully implicit finite differences (FIFD). Our numerical method relies on the formation of a sparse matrix from matrix blocks, which we call the kinetic block, containing kinetic terms for the enzyme reactions, and mass transport block(s) which contain the terms for the mass transport of substrate(s), product(s) and inhibitor(s). The resultant non-linear sparse matrix equation is solved using the sparse matrix solver in the MATHEMATICA kernel which in turn uses UMFPACK multifrontal direct solver methods and Krylov iterative methods preconditioned by an incomplete LU factorization. Due to the non-linear nature of the problem the solution is iterated at each time step until the desired degree of precision is obtained. Adaptation to a variety of mechanisms is performed by changing the terms in the kinetic block and the boundary conditions in the mass transport blocks. Adaptation to a number of different voltammetric methods is achieved by changing one or two lines of code describing the how applied potential changes with time.
Keyword electrochemistry
Date 2006-02-01
Subjects 230116 Numerical Analysis
250699 Theoretical and Computational Chemistry not elsewhere classified
250107 Electrochemistry
Author Honeychurch, Michael
Bernhardt, Paul

Document type: Preprint
Collection: School of Chemistry and Molecular Biosciences
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Created: Tue, 14 Feb 2006, 10:00:00 EST by Michael Honeychurch