Software Control of Matter

The project outlines are now published, so that draws a line under the first phase of this Ideas Factory. The participants themselves have a bit more work to do, and are no doubt as we speak struggling with their universities’ administrations to define the costings. Then, when all the bureaucracy is done, the exciting and difficult bit starts - getting the work going and making a success of these ambitious and visionary proposals.

At the close of the week, I made some remarks to the effect that we could judge the success of the Ideas Factory by the degree to which the ideas that had been generated exceeded the resources put at its disposal. As David Bott commented a week ago, to fulfill all their ambitions in full, the three projects approved would probably have needed about double the money available. The £1.5 million assigned to them will enable them to get going and make considerable progress, and I’m confident that the ideas are so compelling, and the teams so strong that further funding will materialise from somewhere. But there were other good ideas that were discarded on the way, there are other scientists who I’m sure will want to get involved; there’s a much bigger potential program here than these initial resources can fund. We - that is the scientist participants, the mentors, and, I hope, our funders - will be working together over the coming months and years to keep this momentum going and to make that bigger program a reality.

For the moment, this probably marks the last of this series of regular posts on this blog. I’ll be returning to tending my own blog Soft Machines, but if there are more developments to report on the Software Control of Matter project we’ll report on them here. I think the blog experiment has been a great success; the 20 posts so far generated 171 comments and have been viewed more that 6,500 times in the two and a half weeks its been going. I’d like to thank everyone who has commented for their contributions; they’ve all been valuable, whether they have been detailed technical suggestions, encouraging words, or simply an appreciation of what we’ve been trying to do.

Richard Jones
Director

The final project to go forward from the Ideas Factory on the Software Control of Matter is based on theoretical chemistry/materials science and computer science, and we anticipate this linking strongly to the experimental activities funded from the Ideas Factory. As with the two experimental projects, a few administrative hurdles need to be jumped before EPSRC funding can be confirmed.

An ambition to assemble molecules and materials under atomically precise control demands a big leap forward in control engineering and computer science. Is it possible to anticipate the properties and needs of a ‘nano-assembler’? If so, there is a need for a high level instruction language and a computer compiler that translates commands in this language into instructions for the ‘nano-assembler’. This development will require a breakthrough in understanding of chemical synthesis that must embrace the radically new ‘pick and place’ assembly method which is now possible in scanning probe microscopy (SPM). The Matter Compiler project is thus both an exercise in foresight, to anticipate developments in this area, and a prototype implementation for the engineering control and computer science aspects of directed molecular assembly. It has as inputs data from SPM experiments of collaborators, energy landscapes for ‘pick and place’ reactions and the vast knowledge base of classical synthetic chemistry, including methodologies such as retrosynthesis. This will be supplemented by reaction schemes for ‘pick and place’ reactions deduced from first principles quantum chemistry calculations and the technology of object oriented databases and inference engines.

The team is led by Dr Harris Makatsoris (Engineering, Brunel University) and comprises Professor Malcolm Heggie (Chemistry, University of Sussex), Dr Nick Holliman (Computer Science, University of Durham), Dr Helen Wright (Computer Science, University of Hull) and Professor Jeremy Ramsden (Advanced Materials, Cranfield University).

Here’s a brief description of the second experimental project generated by the Ideas Factory. As before, this is not yet an officially announced and approved EPSRC project; various administrative steps remain to be completed, including a more formal costing. Again, we anticipate that this project will receive somewhat less than half of the £1.5 million available for the ideas factory.

We propose a scheme to revolutionise the synthesis of nanodevices, nanomachines, and, ultimately, functional materials via the positional assembly of molecules and nanoscale building blocks. Computer-directed actuators will be used to drive (with sub-nanometre to sub-Angstrom precision) the elements of a nanosystem along pre-defined and entirely deterministic trajectories, thereby achieving structures not accessible by mimicing natural assembly strategies alone. Linkages and bonding between the building blocks will also be initiated, modulated, and - in some cases - terminated by direct computer control. Our proposal rests on the parallel development of novel surface-bound, reconfigurable nanoscale building blocks (molecules, functionalised clusters, nanoparticles) and a prototype computer-controlled matter manipulator best described as a nanoscale conveyor belt. We focus on the generation of two major and immensely challenging functionalities for positionally-assembled nanomachines: switchable energy transduction and conformationally-driven motion. Our archetypal system comprises the following units: an energy harvester, a switchable/gateable link, and an optical or mechanical output. By arranging, configuring, and triggering these fundamental units our long-term goal is no less than the fabrication of an autonomous, abiotic nanomachine.

The project is a collaboration between Ras Raval (Chemistry, Liverpool), Lee Cronin (Chemistry, Glasgow), Philip Moriarty (Physics and Astronomy, Nottingham), Jeremy Baumberg (Physics, Southampton), Guenter Moebus (Materials, Sheffield), Robert G. Jones (Chemistry, Nottingham), Ashley Cadby (Physics, Sheffield), and Tom Grimsey (Fine Art and Sculpture, University of Brighton).

Here’s a brief description of the first experimental project generated by the Ideas Factory. This is not yet an officially announced and approved EPSRC project; various administrative steps remain to be completed, including a more formal costing. However, we anticipate that this project will receive slightly less than half of the £1.5 million available for the ideas factory.

We propose to create a molecular machine that will build new materials under software control. The output of the machine will be chains of building blocks linked by covalent bonds. The machine is modular and is designed to accept many different building blocks, from small molecules to nanoparticles, with a wide range of physical and chemical properties. In order to drive its development we will concentrate on using it to create two target products: a molecular wire, capable of transporting energy and electrical charge, and a catalyst. Software control starts with specification by the end-user of a sequence of building blocks. The target sequence is encoded in an instruction tape which can be read by the machine: the tape is itself a molecule, a synthetic DNA oligomer. The target sequence of building blocks is automatically converted into a control sequence of DNA bases, and the tape is produced by commercial solid-phase synthesis. The job of the machine is to read the instruction tape and to form the bonds between building blocks in the specified sequence. Every component of this molecular factory is itself a molecule: our ambition is to develop the system to the point where it could be distributed to end users as chemicals in plastic vials.

This project was developed by a team from Oxford, Southampton, Cambridge, Exeter Queen’s Belfast and York Universities. The project leader is Andrew Turberfield (Oxford), and the main collaborators are Rachel O’Reilly (Cambridge) and Eugen Stulz (Southampton), with additional contributions from Fred Currell (Queens Belfast), Andy Tyrell (York), and Nicola King (Exeter).

Richard Jones

Well, now the dust has settled and the Big Brother house has closed its doors it’s time to think of the future. As David suggested, we need to think carefully about how all this energy is taken forward, but not too carefully such that the momentum is lost!

Very shortly we wil be able release details of the outcomes of the sand pit and the work will be kicking off shortly after that.  In the mantime a huge thank you to Richard, the mentors and all the participants for entering in to the full spirit of the week and congratulations for surviving.

Oh, and if you’ve been reading all about this and would like to get involved then look out for a call for proposals for an IDEAS factory in the near future.

Paul

We’re all finally on our way home after a remarkable week. We hope to be able to release some details of the projects to be funded on Monday - you’ll read about them here first. In the meantime, I’m looking forward to a restful weekend.

Richard Jones

So, as Richard says, we have come to a decision on which projects go forward. We are now sworn to silence until the projects are announced. Meanwhile, the projects will now huddle to refine their resource requirements – which will magically come to use the money on offer - not a penny more, not a penny less. The projects are compelling in their vision, increasingly rigorous in their planning, but seem to me to be worryingly pragmatic in their requests!

As the resident industrialist I have had an interesting series of discussions during the week about the philosophies of research. From my point of view, the projects that have evolved have both “challenge” and “practicality”. I have seen them benefit enormously in their development from the “grounding” process, when the teams tried to see what they would make and how they would do it. The projects that are going forward will undoubtedly achieve great science. They have the potential t achieve great technology. What concerns me is what will happen next. If we get to the end of this work with a series of papers, some covers of prestigious journals, a high hit post on YouTube, then we will have done well – but wasted a significant fraction of what we have seen here this week. The EPSRC could do well to start planning what they will do next. How will they fulfil the next stage of the overall plan that has been hinted at several times this week as necessary? How could they work with the NIA, the evolving MNT Knowledge Transfer Network and so on. How can we maximise the chances of taking the ideas developed this week all the way?

David

Tonight the mentors and funders had to make the big decision - what projects go forward for funding, what doesn’t make the cut. It’s uncomfortable - all the more so because the process is so much more public than the usual anonymous peer review. But what’s important is that we’ve got tremendously exciting projects to look forward to, which we really don’t think would have been arrived at any other way. We were looking for a grand vision - real ambition, of a kind that scientists are sometimes reluctant to commit to. But we needed to be sure that, on the very first day of the project, it was clear exactly what the newly starting scientists on the project would do. And, while it’s obvious that for a sufficiently big vision, one can’t expect the route from here to there to be fully mapped out at the outset, we need to be sure that there are no obviously unbridgeable chasms in the way. We know, and the funders know too, that there is a significant risk of failure, but that’s as it has to be.

Now we’re in a tidying up phase; working on the details and doing the necessary, if less exciting, work of finalising the costings and tightening up the project management arrangements. Tomorrow I may be able to give some more details of what the outcome has been; for the moment I’ll say simply that, on the experimental side, we have two different approaches, each highly multidisciplinary, whose outcome is planned to be the software-directed deterministic synthesis of covalently bonded, functional nanoscale objects.

Richard Jones

And there’s a lot of talk about novelty. How novel are the proposals? How novel are the approaches? And how novel is what we’ve all been doing here all week? Is this really any different from a conference or a chat in a University common room.  Before we started, five days seemed like an age. Nearing the end, it feels pretty tight. There’s no denying that, as a way of funding science, this is pricey. As well as the cost of keeping everyone here, there are the opportunity costs of taking some of the country’s best scientists away from their desks.   For me, there are many reasons to do things like this, and many reasons why they make financial sense. But the important, intangible value is in bringing people together, bumping them into each other, sparking thoughts and challenging assumptions. Everyone talks about interdisciplinarity, multi-disciplinarity or whatever. Few are trying to make it work in practice.  

Our facilitators, Martin Taylor and Gudrun Friedrich, who run a company called ClearSpot Consulting, reminded me about ‘Forming, Storming, Norming and Performing.’ It’s something Bruce Tuckman talked about in the 60s and Wikipedia tells me that it informs Big Brother. At the end of a process, it’s difficult as a participant to look back and see the point of everything that happened. But I reckon that, as we come to performing stage, the storming part has been vital. My hope is that, in months to come, our scientists will look back and appreciate the new ideas and relationships that were seeded earlier in the week.

Jack 

At the end of today, after our first and only trip off-site, for a dinner in the nearby market town, we’re reflecting on what’s been very much the pivotal day in the Ideas Factory process. In the process we are following, four projects were developed and subjected to a kind of internal peer review. We did a lot of rethinking about the shape of the projects that were being developed and the boundaries between them, and the spread of skills needed for them. We finished the day with some concrete, yet rich and challenging, areas, to go forward. The task tomorrow is to make these into well-defined proposals, which the research council can feel comfortable about funding.

One consequence of the time it took to get through all this, was that the mysterious activities involving the theatre director had to be dropped for lack of time. We did, though, finish the day with another kind of lateral thought - sculptor Tom Grimsey, who’s been a full participant in the process, talked to us about his reflections and showed us some short films.

Some malleable sculptures by Tom Grimsey

Richard Jones