Micro and macro-scale characterisation of an agarose-based physical and computational model for the testing and development of engineered responsive living systems

Abstract

The use of microbially-mediated processes to deal with geo-environmental problemshas raised the interest of geotechnical engineers over the last decade. Of particular interest to this study is the use of bacteria cells to catalyse chemical reactions that can potentially improve the properties of the ground. These bio-mediated methods are based on naturally-occurring processes and provideeffective, sustainable and economic engineering solutions. A frontier of this area of research is the development of the so-calledengineered responsiveliving systems. These systems normally involvethe use of bacteria cells that have been engineered to respond intelligently to inputs from theirenvironment, and they providebenefits that conventional bio-mediated processes are not able to offer.The work presented in this thesis contributes to the development of engineered responsive living systemsfor their use in geotechnical applications. One possible way of developing theseresponsive systems is to use agarose gels as a substitute for soils for the development of early stage physical and computational demonstrators. Agarose gels allow easier monitoring of the performance of the microbes, greater control of the chemical composition of the environment, a controlled simulation over the mechanical properties and a minimised risk of contamination, compared to soils. Thus, the ultimate aim of this research is to characterise at the micro and macro-scale an agarose-based system capable of testing engineered bacteria in a highly controllableenvironment and monitoring their response to external stimulus.The first part of this thesis involves a full-scale characterisation of Agarose Low Melt gel through a series of geotechnical testing techniques, including SEM, triaxial and oedometer testing;the second partfocuses onunderstandingthe growth and distribution of bacteria colonies within a volume of agarose geland exploring the factors that influence their behaviour; and the final partdescribes the development of a computational model that integrates geotechnical simulations with biological data and simulates the effect of a pressure-responsivegel-basedbiocementation system. The successful implementation of such gel-based model will help in the early development of a pressure-responsive bacteria-based systemand will assist in the validation of the proof of concept.