Taking the Pain out of Probes*

* I have unashamedly stolen this title from my friend and erstwhile colleague at Nottingham, Richard Woolley. Rich, I hope you’ll forgive the plagiarism.  

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Scanning probe microscopy is my first love when it comes to experimental science. Although I’ve spent quite a bit of time at synchrotrons over the years, I still turn to SPM first and foremost when it comes to probing the structure of matter. After all, what other technique allows us to not only see single atoms and molecules, but to interrogate them mercilessly, reaching down to the level of individual chemical bonds, and pick, prod, push, and/or pull them around a surface? What other technique enables us to capture not only the electronic structure (both filled and empty states in a single “shot”), but the vibrational “wobbles”, the potential energy landscape (of various forms), the probability density, and even the magnetic signature of a single atom or molecule (in parallel, and with energy resolutions that are in essence only thermally limited)?

And, as I suspect my fellow probe microscopists would heartily agree, what other technique is quite so damn irritating, fist-clenchingly frustrating, and hair-pullingly maddening at times?

Probe microscopists can spend hours, days, or sometimes even weeks trying to cajole the component at the very core of the microscope — the tip (or, more precisely, the atomistic structure at the very apex of the tip) — into behaving itself. We use a variety of recipes to modify the tip apex, ranging from rather gentle and delicate indentations (pushing the probe a few angstroms into the surface), picking up a molecule, or rather “tame” voltage pulses of a few volts… to plunging in, burying the probe, and ploughing a furrow across the substrate. And then we scan and hope to see atomic resolution. But even if we see atoms, it mightn’t be the right type of atomic resolution [1]. We might have a double tip (i.e. two atoms are involved in forming the image), or a triple tip, or, something else entirely

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Those images above are all of the atomic structure of the Si(100) surface (as described in this video, and as sketched in the top right corner of the slide, where we’re looking down on the surface. Large circles represent atoms that are “buckled” out of the surface, creating a zig-zag pattern — technically, a c(4×2) reconstruction — of non-planar pairs of atoms (dimers).) In each case, the surface has the same atomic structure — the variations from image to image are purely tip-related. And if we find the tip in a state that doesn’t give us the image we expect or need [2] then we crash, or hammer, or pulse, or bash, and swear repeatedly until we get what we want. Sometimes — usually around five minutes to lunchtime, or 5 pm on a Friday evening — the tip gets better. Other times it gets much, much worse. So we sit there for hours, trying to recover the tip. Or we change it for a new one. And then try to coerce that into showing us atoms, or more than atoms.

But we don’t need to suffer like this. There is a better way. And finding that lower — and hopefully minimum — frustration pathway to better probe microscopy was the subject of a meeting at the Institute of Physics on Friday. Organised by Martin Castell (Oxford) and myself, the theme of the meeting was machine learning for atomic resolution scanning tunnelling mcirscopy (STM) and atomic force microscopy (AFM.) In attendance were scientists from across the UK who each wanted to move our field forward so as to take the pain away (and, of course, consequently do rather more interesting experiments/theoretical calculations as well.) Oxford, Nottingham, King’s College London, Newcastle, Loughborough, University College London, Warwick, Liverpool Physics, St. Andrews, and Swansea were each represented on the day, with apologies from SPM researchers at Bath, Lancaster, Leeds, Liverpool Chemistry, and Cambridge (who were still keen to be involved but were unfortunately otherwise engaged.)

One striking statistic that was very evident when putting together a list of invitees for the meeting was that the ultrahigh vacuum/atomic resolution scanning probe community in the UK is rather skewed towards blokes of “a certain age” (and that most definitely includes me.) It’s been suggested — by Eugenie Hunsicker (Loughborough) — that one way to attempt to address this would be to consider a collaborative incubator project, a scheme funded by the University of Bath’s Inclusion Matters programme. (Nottingham is also an Inclusion Matters grant-holder.) That is definitely a funding strategy I, for one, would like to pursue, alongside other EPSRC networking opportunities.

My slides for the meeting are embedded below. I will add the PowerPoint/pdf files for the other presenters, if and when I get permission, at the foot of this post. (Giovanni Costantini (Warwick) has already given me permission so his slides are the first there.) The core motivation for the meeting was to bring as many probe microscopists as possible together — and perhaps choosing the last working day before the start of the new academic year for many was slightly ill-advised from that perspective — to discuss strategies for ensuring that we don’t spend a lot of time “reinventing the wheel” when it comes to developing machine learning protocols. And our main objective is therefore to put together a UK-wide network of groups working on the machine-learning-enabled probe microscopy theme.

Despite the prevailing ‘wisdom’ in some deluded corners, the UK of course can’t stand alone, isolated and insular, when it comes to scientific research (or anything else for that matter.) Science is inherently international in scope, and the vast majority of research in this fair and sceptred isle thrives on collaborative activities with our colleagues outside the UK.  When it comes to machine learning in scanning probe microscopy and nanoscience, in particular, we need to pay especially close attention to the exceptionally exciting and pioneering work being done by a number of groups across the world.

Some of those key groups are listed in the PowerPoint slides embedded above, including Bob Wolkow’s research team at the University of Alberta. Bob and his colleagues are very much setting the bar for the rest of us — particularly those of us who work extensively with silicon surfaces — when it comes to embedding machine learning in not just atomic resolution imaging but single atom manipulation. As Bob describes in this engaging TEDx video (uploaded just a few days ago), the STM (“See, Touch, Move”) is becoming ever more capable; one key advance that Bob’s group — in particular, PhD student researcher Taleana Huff and her colleagues — has made is the ability to repair/edit single atomic defects[3] :

Watch the video to get an insight into just how far the UoA team have pushed forward the state of the art in what is effectively 3D printing with atoms. Bob suggests that the latest advances from his group are potentially as disruptive as the transistor was to the vacuum tube. I’d cautiously agree with that statement, although moving from a UHV low temperature environment to the “big, bad world” outside the vacuum chamber is always going to be fraught with difficulty. I am looking forward immensely to spending a couple of weeks at UoA next year to learn more about the techniques pioneered there, thanks to funding from both UoA and Nottingham’s International Collaboration Fund.

I’ll provide updates on how the machine learning SPM network is progressing in future blog posts. For now, here are the slides from Giovanni, as promised above, and from Oli Gordon (Nottingham). (Oli is also pictured in the image that kicks off this post.)

Update 07:47 26/09/2019 It was hugely remiss of me not to highlight a very important upcoming (Jan 2020) conference in Kanazawa — The First International Conference on Big Data and Machine Learning in Microscopy. My sincere apologies to the organisers — sorry, Adam et al. — for not including this in the original post.


Presentations

Molecular-Scale Surface Analytics — Giovanni Costantini (Warwick)

Scanning Probe Tip State Recognition in Real-Time with Neural Networks — Oliver Gordon (Nottingham)

Machine Learning and (SI)STM — Peter Wahl (St. Andrews)

See also ““Nanoscale electronic inhomogeneity in FeSe0:4Te0:6 revealed through unsupervised machine learning”, P. Wahl et al. (submitted)

Multi-scale Computation in Nature: exploring the Interface between Computing, Synthetic Biology and Nanotechnology — Nat Krasnogor (Newcastle)


[1] …and how do we know what’s the right type of atomic resolution? That’s very much a moot point. Sometimes it’s whether the microscopist sees the same type of image as other groups have published previously. This is a slightly worrying way to do science.

[2] Note that we may not always want the highest possible spatial resolution. Different tip structures can have different densities of states, for one thing, and this can affect their ability to extract or move atoms (or molecules).

[3] Not that we’re bitter or anything, but an alumnus of the group, Peter Sharp, tried for very many months, years ago as part of his PhD, to get enough reproducibility to routinely “heal” single atom — more precisely, single dangling bond — defects in the manner that Taleana and her colleagues in Wolkow’s team have achieved. While Pete could definitely observe dangling bonds disappearing during a scan (see below — captured from Pete’s PhD thesis via my phone), which we interpreted as a transfer of a H atom from the tip, we could never quite get the transfer to happen reliably via chemomechanical force alone when we targetted a single dangling bond.

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The One That Got Away…

This is a guest post from Mo Beshr, an undergraduate student at TU Dublin who’ll soon be starting the final year of his Science with Nanotechnology degree. As part of his third year programme, Mo spent six months — from March until August — in our group. [Note to group: we really need to update our website.] Mo’s thoughts on his internship are below. The best of luck with your final year, Mo!


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I knew from before even starting university that I wanted to pursue a career in research as it’s been a long-time dream of mine to make a difference in the world — what better way is there than being on the forefront of science discovering something new every day! All students in my course were given the opportunity to carry out their placement in Ireland or abroad through the Erasmus programme. It was always a goal of mine to travel abroad and experience what it would be like to live independently. So once my supervisor at TU Dublin approached me about placement opportunities, I made it clear to him that I was keen to travel abroad.

I was offered countless research opportunities in various universities across Europe such as Germany, Switzerland and France. I’m not much of a languages guy, however, so I thought I’d give living in Nottingham in England a go; sure, they’re our neighbours from across the pond. But if we’re going to be serious, I immediately jumped at the idea of carrying out my placement in the University of Nottingham as I knew a lot about it through watching Sixty Symbols, Numberphile, and Periodic Videos on YouTube, which are channels that include videos on various topics in science explained by staff members of the university. As well as that, I had known of the great work carried out by the Nanoscience Group at the University and I was very excited to see how all that I had studied as a Nanoscience undergrad was applied. Thankfully I was accepted to carry out my work placement in the University of Nottingham working directly with the Nanoscience Group under the supervision of Professor Philip Moriarty between March and August 2019.

My work was focused on the use of ultrahigh vacuum, low temperature ( 5 K and 77 K) scanning tunnelling microscopy (STM) for atomic resolution imaging of metal and semiconductor surfaces, spectroscopy and manipulation of single atoms and molecules. As you can imagine, going from being a goofy student who attended a handful of lectures everyday to being thrown into the big bad world of research was quite daunting. However, with some time and excellent help and advice by the PhD researchers I worked with and my supervisor I got into the swing of things quickly.

Initially, the toughest tasks were understanding how the STM system I would be using operated and how to analyse STM images and spectra. During my initial time in Nottingham I worked with a PhD researcher named Alex Allen on his project, which involved taking scanning tunnelling spectra (STS) of a C60/ Ag(100) sample using the Createc low temperature STM system. When I had first arrived, a sample of C60/Ag(100) had already been inside the Createc STM chamber and only ever removed for annealing and deposition purposes. During one of our weekly meetings, Phil noticed there were porphyrin contaminants on our sample and in order to fix this we had to remove the sample first from the STM and then from the ultrahigh vacuum chamber. While doing this we were, of course, always observing the movements of the STM tip using the live video from the camera. We then replaced the sample.

Once cleaning of the sample had been completed (by sputtering with ions and subsequent annealing), we would bring the sample back into the STM chamber and scan it in order to make sure it was clean and had an atomically flat surface; on the final sputter-anneal cycle, we achieved atomic resolution. Deposition of the desired molecules would then take place. The deposition process involved placing the sample over a crucible of C60. The crucible was then heated up with a high current which in turn sublimes the buckminsterfullerene molecules, thus allowing for the molecules to impinge on the surface of the sample. Once deposition was complete, we collected liquid nitrogen — following my health and safety induction — and then pumped it through the manipulator arm. This was done in order to cool the sample and control just how the fullerene molecules crystallised on the surface.

Finally, the sample was returned to the STM and scanning commenced once again. The  cryostat surrounding the STM was regularly filled with liquid nitrogen, which keeps the sample cooled throughout the scans…

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In quite a few cases the scans were quite blurry or appeared smeared due to the STM tip being in a bad state. Sometimes the tip wasn’t atomically sharp and/or add more than one molecule on its apex, leading to multiple tunnelling current centres and thus “blurring” the image. In that case, a method known technically as, err, “crashing” was implemented — a clean area was found, and the tip was pushed into the surface to modify its apex. Once a tip had been “sharpened” and clear images were produced, we could carry out scanning tunnelling spectroscopy (STS) of the surface at any specific point. The tip would be positioned above a molecule. The bias was then varied, and the tunnelling current was recorded, giving a plot of the current-voltage characteristic for a single molecule. Differentiating the I(V) spectrum gives us information on the density of states of the molecules.

As well as gaining valuable experience in operating STM systems, I also obtained training in so-called “soft” skills. Literature review topics were assigned to me prior to carrying out any experimental work so I would have a better understanding of the topic of investigation. This involved me writing a report summarising the literature on that topic. The reviews were an excellent opportunity for me to improve my academic writing skills; with every review I could see improvement, and this prepared me very well for my end-of-placement report. After each literature review, I presented what I had found during group meetings, which was very intimidating as I had never given a presentation before! However, I improved with every presentation and the practice gave me great confidence when I returned to Ireland to present my work placement experience to my peers and lecturers.

Completing my work placement with the Nanoscience Group at Nottingham has let me  apply what I have learned in my three years as an undergraduate student and really opened my eyes to a future in research and academia. I now understand what it takes to be a researcher and I believe that I am now capable of pursuing my dream of becoming a researcher and hopefully to make a positive impact in the world of science. I hope this blog inspires other students like me to consider research as a future career path, as there is truly so much still out there to learn and find out. One tends to learn something new every day, and you realise that you are indeed on the frontline of science.

Molecules at Surfaces: What do we really know?

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MatsI’m writing this on the Liverpool Lime Street to Norwich train1, heading back after attending an inspiring and entertaining symposium at the University of Liverpool over the past couple of days. As the title of this post suggests, the symposium had molecules at surfaces as its theme. More than that, however, it was a celebration of the work – and often, the life and times — of Prof. Mats Persson (pictured right), a formidably talented, influential, and yet humble and unimposing theorist who has played a leading role in shaping and defining the research fields in which I work: surface science, nanoscience, and, in particular, scanning probe microscopy. The words “A true gentleman” were repeated regularly through the symposium by Mats’ former PhD students researchers, postdocs, and co-workers, for very good reason.

Organised by George Darling, Matthew Dyer, Jackie Parkinson, and Rasmita Raval, the symposium was one of the best meetings I’ve attended not just recently but throughout my career to date. Ras, a leading light in the UK surface science community who has worked closely with Mats since he arrived in Liverpool in 2006 (and with whom I had the pleasure of collaborating on the Giants Of The Infinitesimal project2), kicked off the symposium with an engaging overview of not just surface science at Liverpool but of the city itself, including, of course, mention of the age-old rivalry between the two primary religious factions: the Reds and the Blues3.

What I particularly enjoyed about the meeting was the blend of world-leading science – an accolade that is often thrown around with wild abandon regardless of the quality of the work, but in this case its usage is absolutely justified —  with personal anecdotes about Mats’ career and those of his (very many) collaborators. It brought home to me yet again just how important social dynamics are to the evolution of science, no matter what howls of outrage this suggestion might provoke in certain quarters. Yes, of course, we do our utmost to be as rigorous, objective, and systematic in our research as possible – well, most of us – but the direction of a field is influenced not just by the science but by the “many-body interactions” of those who do the science. (For those interested in finding out more about the extent to which developments in science are influenced by the sociology of scientists, I thoroughly recommend Harry CollinsGravity’s Kiss; it’s that rarity among science and technology studies (STS) books: a page-turner. Harry is going to be visiting Nottingham in a couple of months to give an invited seminar for The Politics, Perception, and Philosophy of Physics module and I’ll post a lot more about his work then (including this fascinating “Spot The Physicist” experiment.))

A great example of just why the “who” can be as important as the “what” was this morning’s thoroughly entertaining retrospective from Stephen Holloway, erstwhile Head of Chemistry at Liverpool. Stephen covered not just his memories of working with Mats but included fascinating anecdotes about the political landscape, the interpersonal conflicts, and the “Big Names” who influenced the evolution of surface science through his career from the seventies onwards. I’ll spare Stephen’s (and others’) blushes by not revealing the names he mentioned, but his stories of scientists not quite being able to put personal grudges behind them when reviewing or assessing the work of their rivals/nemeses is just one aspect of where the personal and the professional are blurred. (This post from the popular blogger Neuroskeptic emphasises just how entwined these dual aspects can be.)

A running gag throughout the symposium was that many of those presenting owed their tenure/academic positions, either directly or indirectly, to working with Mats. And, indeed, the line-up of presenters read like a “Who’s Who?” of the most respected and influential groups in experimental and theoretical surface science/nanoscience today. Highlights are too many to mention but in addition to Stephen Holloway’s opening act this morning, I particularly enjoyed Wilson Ho’s compelling overview of his pioneering inelastic tunnelling spectroscopy work4 which opened the scientific symposium yesterday afternoon; Leonhard Grill’s always-fascinating insights into the reactions, switching and dynamics of single molecules at surfaces (the “ask Mats” image that opens this post is taken from Leonhard’s presentation);  Richard Palmer’s characteristically absorbing overview of his group’s STM and STEM research; Takashi Kumagi’s next-generation nanoplasmonics using sculpted probes…

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…and Jascha Repp’s engrossing presentation of his group’s exceptionally impressive work on combining ultrafast optics with probe microscopy, enabling an unprecedented increase (by very, very many orders of magnitude) in the temporal resolution of the tunnelling microscope. This is Jascha presenting the working principle of the THz-STM:

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…and one of the stand-out moments of the symposium for me was a video of the internal vibrational dynamics of a single adsorbed molecule, captured with ~ 100 femtosecond temporal resolution using the THz-STM technique. There is no question that the exciting results Jascha presented represent a truly ground-breaking step forward in our ability to probe matter at not just the sub-molecular but the sub-Angstrom scale — perhaps not quite as seismic as the Nobel-winning gravitational wave discovery but, nonetheless, an achievement that will certainly cause considerable ripples across the surface science, nanoscience, and scanning probe communities for many years to come.

Two other talks particularly piqued my interest, due to both the fascinating insights into single molecule behaviour and the alignment with my particular research interests right now. Cyrus Hirjibehedin – formerly of UCL and now at Lincoln Lab, MIT (Cyrus’ move back to the other side of the pond is a major loss to the UK scanning probe/nano/surface/magnetism communities) — gave a typically energetic and compelling presentation on his work on probing and tuning magnetic behaviour in phthalocyanine molecules, while Nicolas Lorente, who manages to combine razor-sharp scientific insights with razor-sharp wit in his presentations, discussed fascinating work on the Jahn-Teller effect (I’ll discuss this in a future post), again in phthalocyanine molecules. We are eagerly awaiting delivery and installation of a Unisoku high magnetic field STM/AFM, kindly funded by EPSRC, and so spin will be a major focus of our group’s research at Nottingham in the coming years. We’ve got such a lot of catching up to do…

Finally, it would be remiss of me to close this overlong post without mentioning a prevailing and exceptionally important theme throughout the symposium: the very close interplay between experiment and theory. Almost every speaker highlighted the “feedback loop” between experimental and theoretical data, but it was David Bird of the University of Bath whose — once again, thoroughly engaging — perspective hammered this point home time and again…

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“Experiments Lead The Way”

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“You learn more when theory doesn’t agree with experiment than when it does”, and…

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“Simple models are best.”

This strong and very healthy experiment-theory interplay contrasts somewhat with other fields of physics, where sometimes experimental data seems to be almost an afterthought, at best, in the generation of new theories

A big thank-you to George, Matthew, Ras, and Jackie for organising such a great meeting. And, of course, enjoy your retirement, Mats!


A service that usually runs via Nottingham — cancellations, strikes, and acts of god/God/gods permitting — and with which I’m exceptionally familiar following very many fun, and occasionally somewhat gruelling, beamtime experiments at the now sadly defunct Daresbury Synchrotron Radiation Source. Daresbury is beside Warrington, which in turn is roughly midway between Liverpool and Manchester. I spent a lot of time (up to three months per year) at Daresbury in the late(-ish) nineties to early noughties, with very many hours whiled away sodden and/or freezing on the Warrington station platform, eyeing the announcement board and waiting for trains to collapse from a delayed-cancelled superposition into a more defined state…

2 Our friend and colleague Tom Grimsey, the powerhouse behind the Giants… project, sadly passed away almost five years ago. He was a wonderful man — full of enthusiasm for, and a hunger to learn about, all things nano, molecular, and atomic. I think that Ras would agree that Giants was such a fun project to work on because of the unique perspective Tom and Theo brought to our science. I couldn’t help but wonder a number of times during the symposium what Tom would have made of the incredible single molecule images presented during the talks.

3 Not being a football fan, I can’t comment further. (My dad was a lifelong Sunderland fanatic and my lack of interest in football may possibly not be entirely unrelated to this fact…)

4 …although I don’t quite yet share Wilson’s confidence in scanning probe microscopy’s ability to “see” intermolecular bonds.

Are the Nanobots Nigh?

The annual Pint Of Science festival, about which I’ve blogged previously and enthusiastically, is taking place this year from May 20 – 22 not only across the UK but in 24 countries worldwide. This, if I remember correctly, is the fourth consecutive year that I’ve done a Pint of Science talk, and I am looking forward immensely to speaking in the Scratching The Surface of Material Science session tonight in Parliament Bar in town, alongside my University of Nottingham colleagues Morgan Alexander and Nesma Aboulkhair. (Encouragingly, all of the Pint of Science events in Nottingham have sold out!)

The title of the talk I’ll give is “Artifical Intelligence at the Nanoscale (or Is The Nanopocalypse Nigh?“, and I’ll focus on recent developments in machine-learning-enabled scanning probe microscopy, of the type described in this Computerphile video put together by Sean Riley last year…

The PoS talk will, however, also roundly criticise the breathless enthusiasm of certain futurist pundits for a nano-enabled future. (OK, I’ll name names. I mean Ray Kurzweil.  We’re going to become immortal by 2045 according to Ray. Because nano.) I had a long, but ultimately exceptionally productive, exchange all the way back in 2004 about the considerable stumbling blocks that stand in the way of the molecular manufacturing nanotech that is a key enabling component of Kurzweil’s “vision”. At the time I didn’t have a blog but Richard Jones very kindly posted the exchange at his Soft Machines blog, and I was rather pleased to find that the debate is still available there.

Soft Machines is an exceptionally good read on everything from nanoscience to R&D policy to general economics and politics. Richard has also written an incisive and compelling critique of Kurzweil and others’ stance on transhumanism. You should give both the blog and the book, “Against Transhumanism: The Delusion of Technological Transcendence“, a read at the earliest opportunity. You won’t regret it.