What the success of the Rosetta mission means for our view of reality

Philae lander revised search area. Via the New York Times.

The European Space Agency’s epic Rosetta mission’s lost lander has woken up, as reported by the New York Times and many others.

Understanding fairly well the physical principles and the precision required for such accuracy over interplanetary distances, I find endeavors such as Rosetta to be a firm refutation of any radically subjective theories of reality.

No matter how illusory or confounded our picture of the world may be, logic and mathematics seem to grasp something objectively real, out there, uncaring and unaffected by our curiosity, yet reaffirming that science can form the basis of an accurate view of reality.

Just watched a related TED talk:

C&EN cover story on carbon nanotubes

Credit: Shutterstock, via C&EN.

About 15 years ago, the world was supposed to be witnessing the start of a revolution. Scientists said so in grant proposals and white papers. Public relations officers said so in press releases. Reporters said so in magazine articles. Carbon nanotubes were going to change the world.

They could power better televisions. They could replace the silicon in transistors and cutting-edge electronics. They could be used to build an elevator to space. But the nanotube revolution was not televised, silicon is still king of the semiconductors, and space elevators are not currently shuttling passengers to the moon.

So what happened? That’s what Ajayan, who has researched nanotubes for decades, is explaining to C&EN. The short answer, he says, is the same thing that happens with virtually every other exciting new material: hype.

The Chemical and Engineering news’ latest issue features a cover story on carbon nanotubes, the 1-dimensional nanosized cylinders of pure carbon that I did my PhD thesis on.

They interview many key players (and familiar names to anyone in the field), and also provide an excellent historical overview and statistics on current production and demand. A recommended, if somewhat US-centric, read. You can find the article here: Twists and Shouts: A Nanotube Story.

Edit: A couple of weeks later, Nature published a couple of news features that address very similar issues in graphene. You can read them here: Graphene booms in factories but lacks a killer app, and here:

Calculating the graphene C 1s core level binding energy

The methods described in the article use different ways to describe the carbon core electrons in order to calculate their binding energies. In this figure we compare the perturbation of the electronic structure caused by an atom with a core hole.

I have a new article just out, published as a Rapid Communication in Physical Review B. The work is a computational study co-authored with Duncan Mowbray and Mathias Ljungberg from San Sebastian, Spain, and Paola Ayala from Vienna.

As described in the post about my recent review article, X-ray photoelectron spectroscopy is an extremely useful tool for studying the composition of nanomaterials. However, to correlate measurements to actual atomic structures, we need to know their binding energies. In this work, we systematically calculate the core level binding  energy of graphene using two different methods, as described in the abstract:

X-ray photoelectron spectroscopy combined with first-principles modeling is a powerful tool for determining the chemical composition and electronic structure of novel materials. Of these, graphene is an especially important model system for understanding the properties of other carbon nanomaterials. Here, we calculate the carbon 1s core level binding energy of pristine graphene using two methods based on density functional theory total energy differences: a calculation with an explicit core-hole, and an all-electron extension of the delta self-consistent field (ΔSCF) method. We study systematically their convergence and computational workload, and the dependence of the energies on the chosen exchange-correlation functional. The ΔSCF method is computationally more expensive, but gives consistently higher C 1s energies. Although there is a significant functional dependence, the binding energy calculated using the PBE functional is found to be remarkably close to what has been measured for graphite.

You can find the article on the PRB website, or in manuscript form on arXiv.

My first review article (CC-BY)

In x-ray photoelectron spectroscopy, photons with high energies (thus, in the x-ray range) – denoted here by the wiggly line – interact with the core electrons of atoms in the material being measured, causing some of them to eject from the atom and escape the material into vacuum. The energies of the photoelectrons are then measured, and are characteristic not only of the element in question (here boron, carbon or nitrogen, with three, four and five valence electrons, respectively), but it’s chemical environment and bonding. In this way, the composition of the material can be elucidated, which is particularly useful for studying heteroatom doping.

The first review article that I have written (with Paola Ayala and Thomas Pichler) has just come out in the Beilstein Journal of Nanotechnology (CC-BY open access).

The purpose of review articles is to summarize – to the best of one’s abilities – the current best understanding of a topic. While previous experimental work by the author can be cited in the review, it doesn’t contain any original research. However, conclusions may (and should) be drawn from the literature, and directions for further research suggested.

The topic of the review was rather broad, namely x-ray photoelectron spectroscopy (a very widely used experimental technique for studying the composition and electronic structure of materials) of graphitic carbon nanomaterials (that is, graphite, graphene, carbon nanotubes and fullerenes) doped with heteroatoms (meaning that some of the carbon atoms have been intentionally replaced with other elements such as boron and nitrogen).

There are many hundreds of works published on this topic, so a systematic review was out of the question, and indeed would not had been so useful. Instead, we attempted to provide a useful reference to the technique, its theoretical background, and to highlight the works that we feel to be the most representative and most informative in the literature. That being said, despite citing 200 articles, we most certainly missed many deserving studies – so my sincere apologies to anyone who was left out!

The abstract of the review reads as follows:

X-ray photoelectron spectroscopy (XPS) is one of the best tools for studying the chemical modification of surfaces, and in particular the distribution and bonding of heteroatom dopants in carbon nanomaterials such as graphene and carbon nanotubes. Although these materials have superb intrinsic properties, these often need to be modified in a controlled way for specific applications. Towards this aim, the most studied dopants are neighbors to carbon in the periodic table, nitrogen and boron, with phosphorus starting to emerge as an interesting new alternative. Hundreds of studies have used XPS for analyzing the concentration and bonding of dopants in various materials. Although the majority of works has concentrated on nitrogen, important work is still ongoing to identify its precise atomic bonding configurations. In general, care should be taken in the preparation of a suitable sample, consideration of the intrinsic photoemission response of the material in question, and the appropriate spectral analysis. If this is not the case, incorrect conclusions can easily be drawn, especially in the assignment of measured binding energies into specific atomic configurations. Starting from the characteristics of pristine materials, this review provides a practical guide for interpreting X-ray photoelectron spectra of doped graphitic carbon nanomaterials, and a reference for their binding energies that are vital for compositional analysis via XPS.

The article is free to read on the website of the journal. Any feedback or tips about interesting studies we might have missed are most welcome!

2014 in review

The WordPress.com stats helper monkeys prepared a 2014 annual report for this blog.

“Only three posts in 2014… let’s see if I can do more in 2015.”

Here’s an excerpt:

A New York City subway train holds 1,200 people. This blog was viewed about 7,200 times in 2014. If it were a NYC subway train, it would take about 6 trips to carry that many people.

Click here to see the complete report.

Moving silicon atoms in graphene with atomic precision

aka The Story of an(other) Article

NOTE: This post is a greatly expanded adaptation of a press release I wrote to publicize our recent work appearing in Physical Review Letters (doi:10.1103/PhysRevLett.113.115501).

A video abstract where I briefly describe the research that is explained in more detail in this blog post (by Viktor Zdrachal from the Österreichische Zentralbibliothek für Physik).

This post explains the science behind the study for the general audience in as simple terms as I can manage.

The main part is followed by a description of getting the study published, intended more for working scientists
(jump to second part).

Two years ago I wrote a blog post titled “The Story of an Article” about the process of publishing a research article in ACS Nano. Now, I am again the lead author of a work appearing in Physical Review Letters, likewise the result of an international collaboration. Thanks to the open access policy of my funder, the Austrian Science Fund (FWF), we were able to pay a fee* to make the article free to read for everyone. My sincere thanks to the FWF!

Is it possible to see and control the movement of individual atoms in materials?

Legendary physicist Richard Feynman famously posed a question in his seminal 1959 talk “There is Plenty of Room at the Bottom“, which some consider to be a major inspiration for the field of nanoscience – research into the structure and properties of matter in the nanometer scale (10-9 m, or one billionth of a meter). His question was: is it possible to see and control the movement of individual atoms in materials? For a time this vision seemed more science fiction than science, but starting with groundbreaking scanning tunneling microscopy experiments in the late 1980s it has become scientific reality.

Three visual examples of the size and the scale of nanotechnology from Nano.gov.

In recent years, it has become possible to directly see individual atoms also using electron microscopy. This is naturally extremely valuable for us trying to study matter at these scales. Electron microscopes work in similar way as normal optical microscopes: light that scatters from an object makes it visible to the eye or a camera. However, the wavelength of visible light is so large compared to atoms, molecules or nanostructures that it is not possible to see these using light. Electrons, on the other hand, interact readily with nano-objects, and thus using them instead of visible light allows scientists to image and visualize things like carbon nanomaterials – nanosized materials composed of carbon – or even single atoms. Lenses to focus the electron beams need to use electric and magnetic fields instead of being made of glass, and a fluorescent screen is needed to make the electrons visible. These days these are invariably combined with so-called charge-coupled device (CCD) cameras to record the images. Nonetheless, the basic principle is quite similar, as shown below.

Comparison of light and transmission electron microscopes by McGraw-Hill Higher Education.

One further detail is worth mentioning: instead of standard transmission electron microscopy (TEM) where a parallel beam of electrons pass through the sample, an alternative is to focus the beam into a very small spot (these days around 1 Ångström, or 1/10 of a nanometer, in diameter), scan the beam over the sample, and measure the electrons that are scattered from each position of the probe. This is called scanning transmission electron microscopy (STEM) and it has certain advantages over TEM, most of which are too technical to get into here. But one thing is important for our purposes: since STEM images are usually formed by collecting electrons that have scattered to certain angles by the sample, heavier atoms that have more positively charged protons in their nucleus cause greater scattering of the electrons, and thus show up bright in the images (so called Z-contrast, Z being the atomic number).

A visualisation of single-layer graphene created by Jani Kotakoski.
A visualization of single-layer graphene created by Jani Kotakoski.

Unlike light, electrons have mass and carry enough energy that they can cause damage by hitting the nuclei of the material under study.

Electron microscopy is especially useful for studying graphene, which is a one-atom-thick sheet of pure carbon that was discovered in 2004 and received a Nobel Prize in Physics a few years later. This is because electrons passing through such a thin material only interact with a single plane of atoms, making interpretation of the images very straightforward. However, there is a crucial difference in using electrons instead of light to image materials: electrons have mass, and they need to be accelerated to rather high energies for good imaging. This means that the electrons carry enough energy that they can cause damage by hitting the nuclei of the material under study, knocking out atoms in a billiard-ball fashion. For this and other reasons, electron microscopy experiments in graphene have typically involved imperfect structures, or resulted in damage during observation.

With this preliminary information in mind, let’s turn to our latest study. For the 6 months or so before the recent publication, I had been leading an international collaboration that grew between two groups here at the University of Vienna — the Tailored Hybrid Structures group of Paola Ayala where I work, and the electron microscopy team of Jannik Meyer — along with two research teams in the UK: a microscopy team at the SuperSTEM laboratory in Daresbury led by Quentin Ramasse, and materials scientists at the University of Manchester led by Ursel Bangert (now at the University of Limerick in Ireland).

The collaboration (minus me).

In modern nanoscience, computer simulations based on quantum mechanics are a crucial tool for understanding and interpreting experiments.

The study started when myself and my good friend and colleague Jani Kotakoski were looking at the electron beam stability of a related but slightly different system using computer simulations. We were surprised by our predictions, but had no direct means to test whether the findings would bear out in reality. Luckily, I spotted a fresh-off-the-presses article whose authors included Ursel, Quentin, Demie Kapaptsoglou and Recep Zan, again on a similar but related system. We got with touch with them via email, and it soon turned out that Quentin and Demie had been working on a material that was a perfect test case for our findings.

Finally, researchers from the Nion Company headed by Ondrej Krivanek from the US joined the collaboration to help in the analysis and interpretation of the data. Nion is the developer and manufacturer of the cutting-edge electron microscopes used by both our teams. Due to their advanced electron optics (correcting aberrations, or imperfections, unavoidably present in electromagnetic lenses), the Nion microscopes only need to accelerate electrons to energies of 60 kiloelectronvolts (keV, thousands of electron volts) and still be able to see individual atoms. This is lower than most microscopes, which require energies of 80-200 keV for a similar resolution.

A silicon dopant (large yellow ball, carbon atoms in black) in graphene, buckling out of the plane. Visualisation by Toma Susi (CC-BY).

The study now published in Physical Review Letters focused on single-layer graphene with silicon atoms embedded into the lattice (such atoms are often called dopants), previously synthesized and characterized by our UK collaborators. Due to the larger size of silicon compared to carbon, these dopant atoms protrude – stick out – from the plane (as shown above), which makes for interesting dynamics under electron irradiation. The detailed computer simulations that I performed in Vienna showed that 60 keV electrons are not energetic enough to likely cause the outright ejection of atoms, in line with what had been observed.

Experimental electron microscopy observation of the (bright) silicon atom jumping from one lattice site to the next.
Electron microscopy observation of the (bright) silicon atom “jumping” from one lattice site (b) to the next (c). Panels (d) and (e) show the corresponding simulated structures. By Toma Susi (CC-BY, doi:10.1103/PhysRevLett.113.115501)

Due to the interplay of the moving atoms, the silicon–carbon bond is inverted.

Crucially, however, carbon atoms next to a silicon dopant are slightly less strongly bound than other atoms in the structure. Because of this, they can receive just enough of a kick even from 60 keV electrons so that they almost escape from the lattice, but are recaptured due to an attractive interaction with the silicon atom (basically, the carbon atom would rather be bonded with the silicon and other carbon atoms than by itself). Meanwhile, the silicon relaxes (moves into an energetically more preferred place) into to the lattice position left empty by the impacted carbon atom, which thus lands back into the lattice on the opposite side from where it started. In effect, the silicon–carbon bond is inverted, which was directly seen by the microscopy teams, an example of which is shown below. The video shown at the top of this post also illustrates this process based on the computer simulations.

Visualisation of the silicon-carbon bond inversion by Toma Susi (CC-BY, doi:10.1103/PhysRevLett.113.115501)

We found very good correspondence between the simulations and the experiments.

In total, the SuperSTEM microscopy team observed 38 such jumps, 19 of them in a single unbroken time series (basically, a movie of the silicon atom jumping around), schematically shown in the figure below. We were able to analyze the jumps as a stochastic process (something that happens due to a random influence, which in this case is the impact of a electron to the nucleus of the carbon atom). This gave us an estimate for the probability of the bond inversion, which in turn could be directly compared to the simulations, and a remarkable agreement was obtained. The close correspondence between the simulations (which describe the motion of atoms) and the imaging (which is too slow to see the motion, but gives a solid reason to believe the process really happens) was one of the main reasons our study was accepted for publication in Physical Review Letters.

An illustration of a time series of 19 consecutive "jumps" of the silicon atom in the graphene lattice. By Toma Susi, from the PRL article.
An illustration of a time series of 19 consecutive “jumps” of the silicon atom in the graphene lattice. Panel (a) shows the times of each jump from the start of the experiment, with the colors denoting jumps in each of the three lattice directions. (b) The path of the silicon atom in the lattice, showing 19 jumps. (c) Analysis of the doses required for each jump as a Poisson process. By Toma Susi (CC-BY, doi:10.1103/PhysRevLett.113.115501).

Besides being beautiful physics, the findings open promising possibilities for atomic-scale engineering. What makes our results truly intriguing is that the bond flip is directional – the silicon moves to take the place of the carbon atom that was hit by a probe electron. This means that it should be possible to control the movement of one or more silicon atoms in the lattice with atomic precision. So perhaps we’ll see a new kind of quantum corral or a university logo made of atoms of silicon in graphene in the near future 🙂

That concludes my explanation! I hope you got something out of it, though I’m painfully aware of how difficult it is to talk about research in simple terms. I’ve added a poll below you can answer to let me know how understandable the post was.

Continue reading Moving silicon atoms in graphene with atomic precision

The personal webpage of Dr. Toma Susi, with a blog about physics… mostly.