OXFORD UNIVERSITY COMPUTING LABORATORY

Computational Biology Group - Computational Modelling of Biosensors

Electrochemical sensors have a wide range of applications in a variety of fields including clinical medicine, environmental monitoring and pollution control. Mathematical modelling of such sensors is used to test new designs and modes of operation by simulation rather than the traditional yet costly "build and test" approach.

A chemical sensor is made up of two parts. The first is where the chemical reaction takes place when an excitation function is applied and this produces some kind of signal, e.g. a change in electrical potential, a flow of electrons or a colour change. The second part is the transducer which measures the magnitude of the signal. The aim is to obtain information about the system based on the excitation function and the measured response and also on appropriate models for the system. For example, the excitation function may be an applied potential at an electrode and the response function may be a flow of current there; the current is proportional to the concentration and can thus be translated into a measure of the amount of chemical present.

The governing equations for such problems model mass transfer and chemical reactions and hence these equations are typically (systems of) reaction-convection-diffusion equations. This research makes use of a variety of numerical and analytical techniques including finite difference and finite element methods, mesh refinement techniques and the use of locally valid series expansions. Our current research is focused in two main areas: frequency domain voltammetry and the simulation of processes. at microelectrodes.



Frequency domain voltammetry

Linear sweep voltammetry (DC voltammetry) involves sweeping the potential applied to an electrode over a range of interest and recording the current. A more powerful approach is to superimpose a periodic waveform onto the waveform used in linear sweep voltammetry; we consider the superimposition of both a sine wave and a square wave. The resulting signal (the current) may then be studied in the frequency domain so that the DC term and the harmonics due to the periodic waveform may be considered separately. It has been observed both experimentally and numerically that different system input parameters (double layer capacitance, uncompensated resistance etc.) affect different harmonics in different ways. Our aim is to use this information to enable us to solve the inverse problem, namely: given a current response, determine the system input parameters which produced that response.

References

  1. D.J. Gavaghan and A.M. Bond. A complete numerical simulation of the techniques of alternating current linear sweep and cyclic voltammetry: analysis of a reversible process by conventional and fast Fourier transform methods. J. Electroanal. Chem. 480 (2000) 133-149.
  2. D.J. Gavaghan, D. Elton, K.B. Oldham and A.M. Bond. Analysis of ramped square-wave voltammetry in the frequency domain. J. Electroanal. Chem. 512 (2001) 1-15.
  3. D.J. Gavaghan, D. Elton and A.M. Bond. A comparison of sinusoidal, square wave, sawtooth and staircase forms of transient voltammetry when a reversible process is analysed in the frequency domain. J. Electroanal. Chem. 513 (2001) 73-86.
  4. Anna A. Sher, Alan M. Bond, David J. Gavaghan, Kathryn Harriman, Stephen W. Feldberg, Noel W. Duffy, Si-Xuan Guo and Jie Zhang. Resistance, Capacitance and Electrode Kinetic Effects in Fourier Transformed Large Amplitude Sinusoidal Voltammetry: The Emergence of Powerful and Intuitively Obvious Tools for Recognition of Patterns of Behaviour. Anal. Chem. (submitted for publication)

Collaborators

The Bond Group at Monash University



Simulation of processes at microelectrodes

Microelectrodes have at least one dimension on the order of a few micrometers making them possible candidates for in vivo analysis. They can also be used to study fast chemical reactions since the rate of mass transport to and from the electrode surface is inversely proportional to the electrode size. In many experiments at microelectrodes the quantity of interest is the current flowing at the electrode surface: mathematically this is a linear functional of the solution to the governing equations. Microelectrodes are modelled using 2D equations and the difficulty when solving these equations numerically is that the solutions exhibit boundary singularities (i.e. there are points on the boundary at which the normal derivative of the solution is discontinuous). This means that on regular meshes the solution (and hence the functional) converge much more slowly than the optimal rate for smooth problems meaning that the accurate estimation of currents is very expensive. The aim of our research is to generate finite element meshes on which the current may be approximated to within a prescribed error tolerance using a minimum of computing resources. This entails the derivation of an a posteriori error bound for the functional - a computable upper bound on the error in the numerical approximation of the current - and using this bound to determine where the mesh should be refined to improve the accuracy. After each mesh refinement step the finite element solution and a posteriori error bound are recomputed until the error bound, and hence the actual error, are less than the prescribed tolerance.

References

  1. K. Harriman, D.J. Gavaghan, P. Houston, and E. Süli. Adaptive Finite Element Simulation of Currents at Microelectrodes to Guaranteed Accuracy. Application to a Simple Model Problem. Electrochem. Commun. 2 (2000) 150-156.
  2. K. Harriman, D.J. Gavaghan, P. Houston, and E. Süli. Adaptive Finite Element Simulation of Currents at Microelectrodes to Guaranteed Accuracy. Theory. Electrochem. Commun. 2 (2000) 157-162.
  3. K. Harriman, D.J. Gavaghan, P. Houston, and E. Süli. Adaptive Finite Element Simulation of Currents at Microelectrodes to Guaranteed Accuracy. First Order EC' Mechanism at Inlaid and Recessed Discs. Electrochem. Commun. 2 (2000) 163-170.
  4. K. Harriman, D.J. Gavaghan, P. Houston, and E. Süli. Adaptive Finite Element Simulation of Currents at Microelectrodes to Guaranteed Accuracy. An E Reaction at a Channel Microband Electrode. Electrochem. Commun. 2 (2000) 567-575.
  5. K. Harriman, D.J. Gavaghan, P. Houston, D. Kay, and E. Süli. Adaptive Finite Element Simulation of Currents at Microelectrodes to Guaranteed Accuracy. ECE and EC2E Mechanisms at Channel Microband Electrodes. Electrochem. Commun. 2 (2000) 576-585.
  6. K. Harriman, D.J. Gavaghan, and E. Süli. Adaptive Finite Element Simulation of Chronoamperometry at Microdisc Electrodes. Electrochem. Commun. 5 (2003) 519-529.
  7. K. Harriman, D.J. Gavaghan, and E. Süli. Time dependent EC', ECE and EC_2E mechanisms at microdisc electrodes: simulations using adaptive finite element methods. J. Electroanal. Chem. (In press)

Alternatively see the Technical Reports

  1. K. Harriman, D.J. Gavaghan, P. Houston, and E. Süli. Adaptive Finite Element Simulation of Steady State Currents at Microdisc Electrodes to a Guaranteed Accuracy. Technical report NA99/19.
  2. K. Harriman, D.J. Gavaghan, P. Houston, D. Kay and E. Süli. Adaptive Finite Element Simulation of Currents at Microelectrodes to a Guaranteed Accuracy. Application to Channel Microband Electrodes. Technical report NA00/09.

Collaborators

The Compton Group at the University of Oxford



People involved

Back to CBG homepage


[Oxford Spires]



Oxford University Computing Laboratory Courses Research People About us News