Computational Colloids: Engineered bacteria as computational agents in the design and manufacture of new materials and structures.
Lead Research Organisation:
Newcastle University
Department Name: Sch of Architect, Planning & 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.
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.
*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.
Organisations
- Newcastle University (Lead Research Organisation)
- National Aeronautics and Space Administration (NASA) (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- Weizmann Institute of Science (Collaboration)
- University of Cape Town (Collaboration)
- Delft University of Technology (TU Delft) (Collaboration)
- Delft University of Technology (Project Partner)
- Autodesk (United States) (Project Partner)
Publications
Dade-Robertson M
(2017)
Architects of nature: growing buildings with bacterial biofilms.
in Microbial biotechnology
Dade-Robertson M
(2016)
Building Science: Synthetic Biology and emerging technologies in architectural research
in Architectural Research Quarterly
Dade-Robertson M
(2016)
Thinking Soils: A synthetic biology approach to material based design computation
Dade-Robertson M
(2018)
Design and modelling of an engineered bacteria-based, pressure-sensitive soil
in Bioinspiration & Biomimetics
Guyet A
(2018)
Mild hydrostatic pressure triggers oxidative responses in Escherichia coli.
in PloS one
Rodriguez Corral J
(2020)
Agarose gel as a soil analogue for development of advanced bio-mediated soil improvement methods
in Canadian Geotechnical Journal
Wang J
(2024)
A Numerical Bio-Geotechnical Model of Pressure-Responsive Microbially Induced Calcium Carbonate Precipitation
in Applied Sciences
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 | Water Kiln |
Description | A sculpture using biomioneralizaton to cement sand grains using a fabric holds and a passive soaking process. The resulting sculpture is a column with tiles suspended on an aluminium frame. |
Type Of Art | Artwork |
Year Produced | 2024 |
Impact | Exhibition opened with 50+ invited guests including industry p[artners from construction. This will be used to discuss further EPSRC grants - which are currently in process. |
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 | 10/2022 |
Description | Expanding Excellence in England (E3): The Hub for Biotechnology in the Built Environment |
Amount | £8,000,000 (GBP) |
Organisation | United Kingdom Research and Innovation |
Department | Research England |
Sector | Public |
Country | United Kingdom |
Start | 07/2019 |
End | 07/2022 |
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 | Initiated a collaboration on Algae Based biomineralization with Nottingham University |
Organisation | University of Nottingham |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Initial collaboration and development of prep-data for an EPSRC grant to be submitted this year. |
Collaborator Contribution | Developed some initial preparitory experiments. |
Impact | Non Yet - working on an EPSRC Grant |
Start Year | 2022 |
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 |