Case Study Algorithmic Living Matter
and Synthetic Biology

A synthetic biology network for modelling and programming cell-chell interactions

Prof Natalio Krasnogor and colleagues

"We are exploring a gap we call ‘The Logistics of Small Things’ probing the interface between operational research and nano-biological Sciences.” Prof Natalio Krasnogor, Principal Investigator. Next case study

How can insights from computer science be applied to optimize synthetic biology?

Nottingham’s leading-edge research at the interface of operational research and computer science concerns decision-support systems for the optimal handling of macroscopic objects, such as runway scheduling, examination timetabling problems, transport logistics, personnel rostering, and space allocation. Nano- and biosciences, in contrast, deal with zillions of micro/nano-scale objects. Little research has been done to bridge the gap between operational research and nanoscale physics, chemistry or bioscience technologies for which scale reductions bring about an explosion in objects’ quantities. To deliver practical applications soon, several logistics bottlenecks must be removed. We hope to lead the way doing precisely that.

"The most exciting aspect is when we give all the information we have to the computer scientists. They do their magic with their computers and they are able to make predictions on how our bacteria should behave and then we go back to test those predictions and they happen to be true.”

Dr Stephan Heeb, Molecular Medical Sciences

Highlights

This research has created an international network of collaborators, ‘SynBioNT: A Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions’ to generate new vigorous interactions between disciplines that impinge on (and contribute to) bottom-up and top-down synthetic biology – including computational, mathematical and operational research disciplines – by supporting a range of community building activities.

These activities, guided by and Principal Investigator Natalio Krasnogor, will be centred on the specific technical goal of achieving programmable interactions between biological and artificial cells and materials.

Prof Krasnogor’s computational research in tight collaboration with Prof Camara’s and Dr Heeb’s microbiology research should make it possible to develop coatings containing bacteria to paint on systems. Should a coated system come under attack from something, the system itself would change to a different colour or give off an odour for example.

Expertise

The SynBioNT group consists of researchers from cross-disciplinary backgrounds from a number of different universities. The principal investigator is Prof Natalio Krasnogor, whose research activities reside at the interface of computer science and the natural sciences, namely biology, physics and chemistry. In particular, his focus is on developing innovative and competitive search methodologies and intelligent decision support systems with an emphasis on transdisciplinary optimisation, modelling of complex systems and very-large datasets processing. Co-Investigator Prof Cameron Alexander from the School of Pharmacy has expertise in polymer therapeutics and leads the chemical aspects of this research.

Video

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Impact

Synthetic biology holds great promise for the design, construction and development of artificial (man-made) biological (sub)systems, offering viable new routes to genetically modified organisms, smart drugs as well as model systems to examine artificial genomes and proteomes.

The informed manipulation of such biological (sub)systems could have an enormous positive impact on our societies, with its effects being felt across a range of activities such as the provision of healthcare, and environmental protection and remediation.

Focusing on this specific technical challenge, the group hopes to contribute to bridging the gap between synthetic biology from the top down – knocking out or modifying functions of existing cells – and bottom-up synthetic biology, from first principles. Both approaches will have a role to play in the future of synthetic biology. The interaction between top-down systems (modified cells) and bottom-up systems (chells, protocells) provides the ideal background against which a new research community can be built and sustained.

Programmable artificial cells, either purely chemical or through a synthetic biology approach, will –we hope – pave the way for what we call “extreme everyware”. This technology offers exciting new challenges and opportunities for research at the leading edge of the Operations in a Digital World priority group.

Scale of research

SynBioNT: A Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions is one of only seven recent BBSRC/EPSRC networks in synthetic biology. SynBioNT groups together more than 120 UK and international leaders in this field. The Logistics of Small Things is a crossdisciplinary feasibility account.

Funding

As Principal Investigator, Prof Krasnogor attracted approximatedly £2.5M from the BBSRC, EPSRC, the European Union and ESF. In their areas, Prof M. Cámara, Prof P. Williams and Dr S. Heeb (School of Molecular Medical Sciences) have £5.5M in current funding mainly from the MRC, BBSRC, The Wellcome Trust, the European Union, the Royal Society and the British Council. Prof C. Alexander (School of Pharmacy) participates in grants in excess of £8M from EPSRC, BBSRC, EU and industry.

Contact

Professor Natalio Krasnogor, SynBioNT principal investigator

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Case Study Algorithmic Living Matter and Synthetic Biology