Computational Colloids: Engineered bacteria as computational agents in the design and manufacture of new materials and structures.

Lead Research Organisation: Newcastle University
Department Name: Architecture Planning and Landscape

Abstract

This project investigates how Civil Engineering may be integrated with the emerging field of Synthetic Biology. Combining these fields has potentially transformative implications for both and may generate a new field of Engineering Design.

Imagine a column of sand saturated with billions of engineered bacteria cells. As a force is applied to the top of the column, bacteria in the sand detect an increase in pressure. The bacteria respond by synthesising a new biological material to bind the grains together and resisting the load. The resulting structure would consist of a material where sand grains are only cemented where the forces through the material require.

We propose a proof of concept to show how we might design a manufacturing process where the material itself acts as manufacturer and designer, modelling and responding to its environment. 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.

Planned Impact

This project will a significant impact across both academia and industry with the potential to develop a new field of engineering design. Where digital technologies were transformative in the 20th century, the 21st century is likely to be transformed through biotechnologies and fields such as synthetic biology. This project proposes bridging the gap between the design of biological systems at the molecular scale and the design of material structures at the scale of the human built environment. It is likely to generate significant interest and potential controversy. In addition to academic publications and a dissemination strategy which includes media coverage, therefore, the project proposes to:

*Generate Data to add to open access repositories including the MIT run Registry of Standard Biological Parts and the Newcastle University run Registry of Standard Virtual parts. In addition the project will create a new web based resource to bring the work together.

*Disseminate the research through a high profile public exhibition to take place at the 'Centre for Life' in Newcastle. The exhibition will act as a catalyst to initiate public debate on the project and form the basis of our media dissemination strategy.

*Develop an international network of interested academic and industry partners including Henk Jonkers at Delft University (who specialises in Self Healing concrete using bacteria biomineralisation), Neri Oxman at MIT (pioneer of material based computation), the AutoDesks Bio, Nano, Programmable Matter group.
 
Title Catalytic Cell & Bacteria Sculpting. Exhibited at Global Community Biosummit. MIT Media Lab, Boston, USA. (October 11-13, 2019). 
Description Materials and a novel bioreactor produced from the Thinking Soils project developed into exhibitable material an exhibition at this Summit, The Summit included industry professionals as well as DIY Bio Community, Students and Academics. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2019 
Impact Invitation to enter teh Bio Design Challenge in 2020. Followup with a number of interested parties in the US. 
URL https://www.biosummit.org
 
Title Yggdrasil. Exhibited at the Biodesign: Here Now. London Design Festival 2019. OpenCell, London. (September 19-22, 2019) 
Description Exhibition of Materials and Novel Bioreactors produced as part of the London Design Festival in collaboration with Open Cell. The exhibition will have been seen by more than 1000 people across two days. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2019 
Impact Invitation to collaborate on a joint project on biomineralization with UCL. 
URL https://www.londondesignfestival.com/event/biodesign-here-now-2
 
Description We have developed a novel method using a purpose build pressure vessel to expose bacteria samples to pressures of 1MPa. Using a technique called RNA-Seq we found that one hundred genes were sensitive to pressure and that 26 of these genes displayed at least a 10-fold increased expression in response to our pressure condition.

We have engineered two strains of bacteria that carry a reporter system based on a GFP signaling gene integrated into the E. coli chromosome. GFP fluorescence was observed using light microscopy and was measured with a plate reader. We then successfully engineered a GFP tagged strain that displayed an increase of fluorescence in response to pressure and have chracterised the response from 0.1 - 1MPa.

We have developed a method in which bacteria can grow in a 3D volume of agar based hydrogels, then visualized and quantified cell distribution under a microscope for both E. coli and B. subtilise bacteria. The results from these tests allowed us to asses hydrogels as a soil substitute in WP2. We have ascertained that the hydrogels we are using have similar behavior to peat-type soils or soft clays.

We have built a finite element analysis model which integrates biological and geotechnical simulations to demonstrate variations in target gene expression for bacteria living in a body of soil, in response to pressure applied at the soil surface.
Exploitation Route The discovery pf the moderate pressure sensing gene is likely to be of most immediate value to the academic community - along with the work done to characterise hydrogels. The project itself is a pioneering collaboration with potential to influence research across a range of fields.
Sectors Construction,Digital/Communication/Information Technologies (including Software),Manufacturing, including Industrial Biotechology

URL http://www.synbio.construction/
 
Description The project has been covered extensively in the scientific media and popular press. The PI contributed an article to 'The Conversation' and further articles on the project have featured in AAAS Science, The Times (print and online editions) and The Daily Mail Online. A Bloomberg produced video has been distributed across multiple media outlets including Yahoo News and MSN. We are also tracking articles in more than a dozen international media outlets across Europe, America and East Asia. While most of these outlets do not give readership data we do know that the Times print edition has a distribution of approx. 400,000 and the Conversation article has also been accessed over 20,000 times. Our project website ( www.synbio.construction ) has also received over 800 unique visitors per month since the Bloomberg video was released in November. It should be noted that this was a pilot which lead to the EPSRC funded Thinking Soils Project (EP/R003629/1). Further reports on the ongoing finings and Impact can be found here.
First Year Of Impact 2016
Sector Construction,Manufacturing, including Industrial Biotechology
Impact Types Cultural

 
Description Design the Future 2: Thinking Soils: Engineered bacteria as computational agents in the design and manufacture of new materials and structures
Amount £598,309 (GBP)
Funding ID EP/R003629/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 10/2020
 
Description FLAIR Collaboration Grants
Amount £6,000 (GBP)
Funding ID FCG\R1\201040 
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2020 
End 12/2020
 
Description Biomineralization collaboration with Weismann Institute 
Organisation Weizmann Institute of Science
Country Israel 
Sector Academic/University 
PI Contribution We provided data and design concepts with utilised the research conducted by Dr. Kolodkin-Gal and colleagues on bacteria templating of mineral crystals.
Collaborator Contribution Following a conversation at the International Conference for Applied Microbiology we discussed the process of Biofilm templating of mineral crystals. This resulted in a joint paper: "Architects of nature: growing buildings with bacterial biofilms" and an application worth $100,000 to a joint Israel/UK finding scheme which is currently under consideration.
Impact Paper: Architects of nature: growing buildings with bacterial biofilms; Research Proposal: Genetic and Biochemical approach to grow building materials with bacterial biofilms and to sequester atmospheric carbon dioxide
Start Year 2017
 
Description Delft University Discussion and Presentation 
Organisation Delft University of Technology (TU Delft)
Country Netherlands 
Sector Academic/University 
PI Contribution Presented our early findings on pressure sensitive promoters in EColi and discussed the material potential in the context of the Henk Jonkers groups current work.
Collaborator Contribution Shared with us a methodological idea to use hydrogels as alternatives to soils in early prototypes.
Impact Methodological sharing - resulting in new ideas for the development of our key prototype. Cross disciplinary collaboration involving microbiologists, civil engineers and architectural designers.
Start Year 2015
 
Description Improving the strength of the World's first bio-brick grown from human urine by adaptation and isolation of microbial isolates 
Organisation University of Cape Town
Country South Africa 
Sector Academic/University 
PI Contribution This is an initial pilot research enabled by the work are have conducted on the metabolic pathways of Urease production and the application for biocementing. We are providing scientific expertise with a view to developing a collaborative grant.
Collaborator Contribution The partners have established a novel method and brick production technique. The partners are leading on this initial pilot stage.
Impact This is an early collaboration (initiated Feb 2020) so no firm outcomes have emerged yet.
Start Year 2020
 
Description Project Meeting with Henk Jonkers in Delft 
Organisation Delft University of Technology (TU Delft)
Department Civil Engineering and Geosciences
Country Netherlands 
Sector Academic/University 
PI Contribution Advised and presented our finding on the properties of Hydrogels and our early results on the presser sensor.
Collaborator Contribution Advised on approach to biomineralisation and provided support for the next phase of the Computational Colloids project
Impact As project partners on the Computational Colloids project Henk Jokers (DU Delft) and colleagues have provided advice on the experimental setups for testing or hydrogel materials and have begun to develop new research application with us on Biomineralization and Bio Cements.
Start Year 2015
 
Description Project Meeting with NASA 
Organisation National Aeronautics and Space Administration (NASA)
Department NASA Ames Exploration Center
Country United States 
Sector Public 
PI Contribution We communicated the key findings of our project with the Research Group at NASA and discussed overlaps with their current research priorities and mission.
Collaborator Contribution As part of a project visit we discussed possible applications for our technology and design proposal. This fed in to the development of the "Thinking Soils grant which is currently underway.
Impact Support Letter for successful EPSRC "Thinking Soils" Grant proposal.
Start Year 2017
 
Description ArcInTex Network Presentation in Paris EnsAD 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presentation as part of the EU Funded ARCInTex Network to a small (30-40) group of postgraduate students with a small number of academics and industry representatives from industry.
Year(s) Of Engagement Activity 2020
URL http://arcintex.hb.se/conferences-workshops/
 
Description Biological Architecture Lab - Edinburgh 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Workshop organised as part of Edinburgh University's Biological Architecture Lab. Gave a Keynote presentation on Computational Colloids and used the project as the basis for discussion on further collaborative research, possible postgraduate training and industry collaboration.
Year(s) Of Engagement Activity 2015
URL http://biological-architecture.bio.ed.ac.uk/
 
Description Interview for National Press: Daily Mail 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Media Report - published online for the Daily Mail entitled: Forget bricks, researchers say 'smart soil' will be used to grow the first homes on Mars"
Year(s) Of Engagement Activity 2017
URL http://www.dailymail.co.uk/sciencetech/article-3921894/
 
Description MBC (South Korean National TV) Documentary spot 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview as part of a South Korean Documentary on Bacteria and Technology.
Year(s) Of Engagement Activity 2017
 
Description Material Research Exchange 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Attended the congress with an information stall and posters presenting the outcomes of the Thinking Soils project alongside material samples. 3 Thinking Soils members attended with a view to developing industrial collaborations. The stall was approached by over 100 people during the event and we received over 50 contacts from organisation wanting to seek further collaboration including construction companies and private research companies involved in the development of new materials and IP.
Year(s) Of Engagement Activity 2020
URL http://www.materialresearchexchange.co.uk
 
Description National Press Article in Print and Online versions of "The Times" 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Press article in the times featuring our project entitled: "Bacteria in soil may stop homes collapsing" in both print and online editions of "The Times".
Year(s) Of Engagement Activity 2017
URL https://www.thetimes.co.uk/article/bacteria-in-soil-may-stop-homes-collapsing-w2bmpwb7p
 
Description Online Interview for AAAS Science 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Interview and atricle for AAAS popular science website entitled: Thinking Soils made of bacterial could keep buildings from collapsing
Year(s) Of Engagement Activity 2017
URL http://www.sciencemag.org/news/2016/10/thinking-soil-made-bacteria-could-keep-buildings-collapsing
 
Description Public Presentation at the Design Museum in London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact An invited presentation to a public Audience as part of the Design with the Living Symposium to an audience of members of the public, students, and other researchers. The Thinking soils project was presented as an exemplars of a new sort of design project. The speaker (Martyn Dade-Robertson) was approached by approx. a dozen students a with interest in pursuing similar research afterwards.
Year(s) Of Engagement Activity 2020
URL https://designmuseum.org/whats-on/talks-courses-and-workshops/design-with-the-living?utm_source=emai...
 
Description Radio Interview DRP1 (Danish National Radio) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interviews with Danish radio broadcaster on the implications of Computational Colloids and potential applications.
Year(s) Of Engagement Activity 2017
URL https://www.dr.dk/radio/p1/videnskabens-verden/videnskabens-verden-2016-10-19/#!
 
Description TV Interview for Reuters 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact TV Interview for Reuters which was distributed through a number of International Outlets including, for example, MSN News, Yahoo News and some national TV Broadcasts.
Year(s) Of Engagement Activity 2017
URL https://www.reuters.com/video/2016/12/05/future-buildings-could-grow-their-own-fo?videoId=370633607
 
Description Thinking Soils Presentation to NASA Ames 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact An invited presentation of Thinkings Soils to a team at NASA Ames to approx 20 research scientists and engineers interested in biotechnology for space missions.
Year(s) Of Engagement Activity 2018