Computational Colloids Image For Web

Computational Colloids, Paper

Paper: Computational Colloids Project At SEED 2016

11 Jul , 2016  

The Computational Colloids project will feature in a Poster presented at SEED 2016 in Chicago (Synthetic Biology: Engineering, Evolution & Design).

The abstract for our poster is:

We report on a novel project to integrate a civil engineering application with Synthetic Biology through the development of a mechanical sensing bacteria system. The project integrates a team of molecular biologists, civil engineers and an architect. The aim of the project is to create a bio-based system to strengthen soils in response to mechanical forces. In this system, synthetic bacteria would act as a biological grout enabling, for example, self-constructing foundations. Aside from the geotechnical applications such a technology would push well beyond the current state of the art and challenge a new generation of engineering designers to think at multiple scales from molecular to the built environment and to anticipate civil engineering with living organisms.

Microbial activity is important to many geotechnical process and Bacteria can be responsible for cementing soils. Bacteria, such as Sporosarcina Pasteurii and Bacillus megatarium produce ammonia which, in turn, causes calcium carbonate to precipitate. micro-organisms also have a significant impact on the fertility of soils in the upper layers. Until recently it was thought that bacteria activity decreases substantially with depth. However, bacteria are known to move freely through many types of soils, and they can also attach to soil particles to form biofilm. This buildup of biofilms can, in turn, change the geotechnical characteristics of soils.

The growth, survivability and adaptation and associated genetic response of bacteria to pressure has been studied in in relation to low pressure (sub 0.1MPa) environments, and ocean bacteria in high pressure environments (from 10MPa to over 100MPa). However, little work has been done at moderate pressures associated with, for example, pore pressures in geotechnical processes (between 0.1 and 10MPa).

In our project, we have initially studied differential gene expression in response to moderate pressure using E. coli K12 as model organism. Selected gene promoters were cloned upstream of reporter genes to test sensitivity to pressure (at 0.1 to 1 MPa) and engineer mechanical sensing bacteria. In parallel experiments have been carried out to test that the promoters’ response was pressure-stress specific and not related to other biological stresses. We also developed a method to build a prototype system using hydrogels as a proxy for soil volumes and to visualize the response of the bacteria to pore pressure changes in three dimensions. In addition, we developed a computational model to link geotechnical modelling with gene expression data which integrates a finite element model of soils under load with diffusion models to calculate effective stress and pore pressure. The resulting visualisations give us an indication of how our proposed system may perform and support the process of model driven design.


Martyn Dade-Robertson

Aurelie Guyet

Javier Rodriguez Corral

Anil Wipat

Helen Mitrani

Meng Zhang


Image Credit:

Carolina Ramirez-Figueroa

Luis Henan


Leave a Reply

Your email address will not be published. Required fields are marked *