Dibdin G H
Medical Research Council Dental Group, University of Bristol Dental School, UK.
Comput Appl Biosci. 1992 Oct;8(5):489-500. doi: 10.1093/bioinformatics/8.5.489.
This finite-difference computer model is designed to simulate complex diffusion/reaction events in bacterial films. It is modular, each module mirroring closely a particular physical, chemical or biochemical factor. It is capable of handling > 20 diffusing/reacting species, but can be easily expanded or simplified to match particular systems. It was originally designed for modelling the events in dental plaque leading to tooth decay, but should find application in other fields. It allows for ion-exchange interactions with, for example, fixed charges on bacterial surfaces, which can act as pH and cation buffer sites. pH-dependent utilization of substrate is modelled implicitly, combining Michaelis-Menten kinetics with diffusion in a single iterative procedure. Advantages are given for computing diffusion of all other species explicitly using single-species diffusion coefficients, with charge-coupling by means of the algorithm Q-COUPLE. Activity corrections and enzyme pH-dependence are included. Chemical equilibria and mineral deposition/dissolution are computed iteratively node by node. The program is tested against some problems having analytical solutions, and an example is given of its application to demineralization of teeth as a result of bacterial action in dental plaque.
