A new type of supernova has been defined by researchers from the US. Designated type Iax, this new class is seen to be less energetic and fainter than previously defined and similar type Ia events – and may even leave behind part of its originating star.
Previously, only two classes of supernovae were recognized – core-collapse events, the explosion of stars 10–100 times as massive as our Sun, and type Ia supernovae, which involve the complete destruction of a white dwarf. Now, a team led by Ryan Foley at the Harvard-Smithsonian Center for Astrophysics has identified 25 members of the new type Iax class based on optical spectroscopic and photometric studies. Its work has shown these stars to be less energetic and with a lower absolute magnitude than would be expected with their type Ia cousin. The team believes that the supernovae of this new class originate from a binary star system comprised of a white dwarf that gathers helium from a companion star, which has lost its outer hydrogen.
Runt of the litter?
“A type Iax supernova is essentially a mini supernova…it’s the runt of the supernova litter,” says Foley. “It turns out that type Iax supernovae are relatively common, but we only recently discovered them because they’re very faint, some only 1% as bright as type Ia supernovae.”
As a result of their absence from elliptical galaxies – which are populated by older stars – it is believed that type Iax supernovae come from young star systems. This observed distribution may be related to the relatively short lifetimes of helium-burning stars, which do not last long enough to be found in elliptical galaxies. The team is uncertain what causes the white dwarf to become a supernova. One theory suggests that the overlying helium shell ignites first, transmitting a shockwave into the white dwarf within, with the opposing hypothesis proposing that the dwarf core might go first, in response to the influence of the surrounding helium.
Chances of survival
In some cases, the researchers believe that the supernovae events might be so weak that the white dwarf may even survive the explosion. “It’s a little uncertain exactly what will happen to the white dwarf,” Foley told physicsworld.com, explaining that such a partial deflagration might be expected to leave the star with a lower mass, but with added energy received from the supernova. “Both of these changes should make the star bigger and hotter,” Foley concludes, “so I expect some sort of puffed up white dwarf.”
Unlike other supernovae, members of the type Iax are too varied and faint to be used as standard candles – objects with a known luminosity and observed brightness that can be used to reveal their distance from Earth. However, the researchers believe that the new class could offer insights into supernovae in general. Not only do these events showcase a previously unknown way for a star to explode – with a slower moving ejecta that is easier to analyse – but their physical similarities to, and differences from, type Ia supernovae enable us to focus our models of this existing class of event.
Careful consideration
“From an observational point of view, the substantial sample of events that resemble SN 2002cx [the prototypical member of the new class] and the estimate that these sort of events happen [a third] as often as classical type Ia supernovae is compelling,” comments Craig Wheeler of the University of Texas at Austin, US, who was not involved in the research. He adds that while the proposed model – of a fully or partial deflagrating white dwarf with a companion helium star – fits well with the observed properties, such models warrant careful consideration before any firm conclusions are reached.
“If this is the appropriate interpretation, then these events come with a promise to teach us more about the nature of thermonuclear explosions,” Wheeler adds. “Elucidating the nature of these events also holds great promise to aid us in better understanding stellar evolution in binary star systems in all its great variety.”
Next, Foley and colleagues are hoping to address the possibility that the white dwarves might, in some cases, survive going supernova. In order to work on this theory, the team simply needs to observe more supernovae, Foley explains, adding the caveat that this kind of observation will only be possible for the closest supernovae. “The current sample is relatively small,” he says, adding that “with a larger sample, we can hopefully unlock additional mysteries about the frequency, energy, asymmetry and other properties of these supernovae.”
The work is to be published in The Astrophysical Journal. A pre-print of the research is available on arXiv.
Burst of particles created when a muon interacts with the NOvA Far Detector. (Courtesy: NOvA collaboration)
By Hamish Johnston
Deep in the North Woods in Minnesota the snow is starting to melt, and the giant NOvA Far Detector is coming to life. Designed to register the arrival of neutrinos that will be created 810 km away at Fermilab near Chicago, the detector has recorded its first 3D images. These are not of neutrinos, but of the trajectories of fast-moving particles that are created in a process that begins with a cosmic ray colliding with Earth’s atmosphere.
Knots are very much a part of everyday life. In some cases, they are extremely useful: sailors and climbers, for example, need them for their own safety or to secure boats and equipment. But in other cases, knots are a nuisance. You may have found this yourself the last time you tried to reel in a long extension cable after, say, vacuuming your attic or mowing the lawn. Invariably, there is a knot in the cable when you want to store it away, and in order to un-knot it, you need to repeatedly pull one of its ends through the entangled region – a rather dull and lengthy procedure, as anyone who has ever tried to untangle headphone wires or Christmas tree lights can confirm.
The theory of how knots form, and how different knots can be distinguished, began as a rather abstract mathematical discipline. Developed by a trio of Scottish physicists – Peter Guthrie Tait, James Clerk Maxwell and William Thomson (later Lord Kelvin) – in the late 19th century (see September 2010 pp35–40), it was originally intended to support the now-abandoned idea that atoms might consist of knotted tubes of aether. Since then, however, physicists have also found practical applications for knot theory. One important example concerns the possible configurations of DNA molecules. Like extension cables, the filaments that make up DNA can become knotted in all sorts of ways, and research into the kinds of knots formed by DNA is telling us some interesting things about the molecule’s properties.
For example, one might imagine that DNA knots will make it difficult for proteins to read, transcribe and replicate the knotted portion of the molecule. Excessive DNA knotting can even prevent cell division and lead to cell death. Moreover, the DNA inside bacteria and human cells is so long (millimetres and metres, respectively) that one would expect to observe knots very frequently. However, certain enzymes, known as topoisomerases, have evolved to solve this problem by cutting DNA and gluing it back together. On the other hand, within some very small viruses, where there is space only for the DNA itself, knots are inevitable because of the tight confinement – yet the knots that form do not stop the virus from infecting its host. A better understanding of DNA knots may therefore give us some insights into these important cellular processes.
Loose ends
Before going into more detail about DNA knots, we first need some basic information about knot theory. Knots are grouped according to the minimum number of crossings they contain, and each knot in a group is given a number. For example, the simplest non-trivial knot, the trefoil knot, is known as 31: it has three crossings, and it bears the subscript 1 because it is the first and only possible knot with three crossings. Figure 1 shows representations of the trefoil knot along with several other simple knots. Note that in diagrams like these, it is crucial to retain information about which segment is on top at a crossing. For instance, if you flip the top and bottom segments in just one crossing of the trefoil knot, the resulting curve no longer contains any knots at all: it has become an unknot (0).
1 Families of knots This knot table shows “simple’’ knots with up to six crossings, including the trefoil with three crossings and the “unknot” with zero. These knots are simple in the sense that they have a single knotted component, whereas “composite” knots are formed by gluing together two or more simple knots. (Courtesy: IOP Publishing/Davide Marenduzzo, Cristian Micheletti and Enzo Orlandini)
Now imagine trying to draw a knot as a closed curve on a surface. If the surface is a sphere, such as a balloon, the only knot that can be drawn without any self-intersections is the unknot. However, if the surface has the topology of a torus, such as a doughnut or a bagel, an infinite number of knots can be drawn on it (figure 2). These are called torus knots, and examples include the trefoil and 51 (cinquefoil) knots.
A second important family of knots is twist knots. To create one such knot, take a rope and hold it fixed at its two extremities. Then take the middle of the rope and twist the whole loop an integer number of times. Soon, the rope should start to look like a heavily used office telephone cord, a phenomenon known as “supercoiling”. Finally, take one of the ends, pass it through the top loop of the rope, and then link the ends so that the rope is now knotted. By increasing the number of twists, you can create a trefoil (which, notably, is a twist knot as well as a torus knot), a figure of eight (41), a three-twist (52) or a Stevedore’s knot (61).
Of these two families, twist knots are more commonly found in nature. This is because when unravelling a twisted cord, it is easy to inadvertently pass one end of the cord through a loop – and the same is true if some natural process rather than a human is doing the unravelling. A more rigorous way of saying that twist knots are easy to produce is to note that their “unknotting number” is 1. The unknotting number is the minimum number of times that a knot must be passed through itself in order to untie it. Equivalently, it is equal to the minimum number of crossings that must be flipped to obtain the unknot. With just a bit more drawing and thinking (and perhaps the aid of your headphone wires), it is fairly easy to show that the unknotting number of a 51 torus knot is 2. This knot is more difficult to form by mistake, as the cord has to pass through itself twice, rather than once.
A new twist
Based on these arguments, it seems logical to suspect that DNA molecules will frequently form twist knots, and that 52 twist knots will appear much more frequently than 51 torus knots. But how can this hypothesis be tested? After all, a DNA molecule is only about 2 nm (2 × 10–9 m) wide. When it is inside a cell or in solution, it occupies a space measured in microns; within viruses, it is even more compact. Given the tiny size of such a molecule, how can we determine which knots have formed in it?
2 Knots for breakfast A trefoil knot is both a twist knot and a torus knot. Here, the trefoil knot is drawn on a bagel. (Courtesy: George Hart)
Of course, it is possible to obtain images of a particular knotted DNA molecule directly, using electron microscopes. But if we want to know the probabilities of forming different types of knots – the “knot spectrum” – we need information about an entire population of molecules. One way to obtain this knot spectrum is through simulations. DNA molecules in solution can be made to form loops (by making their loose ends attractive to one another), so we can model them as fluctuating looped elastic rods, the bending rigidity of which matches that of DNA.
However, it is also possible to determine the knot spectrum experimentally thanks to a rather clever trick. DNA molecules are negatively charged, so one can use a weak electric field to drive them through a dilute substance called agarose gel, which is a jelly-like material filled with microscopic holes (a bit like a squishy bath sponge). As one might expect, small DNA molecules will pass through these holes more quickly than large and cumbersome ones, since bigger molecules become tangled up with the polymers that make up the agarose gel. In a simple model, one can treat the velocity of the DNA molecule in the gel as being inversely proportional to the size of the sphere that best approximates the molecule’s average shape. If the DNA under consideration is highly knotted, it will be crumpled up and smaller in size, so it will move more quickly through the gel than it would if it were unknotted. Remarkably, it is possible to separate knots with up to roughly 10 crossing numbers by looking at how fast they move in agarose gel – the first group of molecules to pass through the agarose will have 10 crossings, the next nine and so on.
This measurement technique enabled researchers to confirm in the 1990s that in solution, looped DNA molecules a few microns in length do indeed form twist knots, and that “simpler” knots with lower unknotting numbers are more probable (see, for instance, V V Rybenkov et al. 1993 PNAS90 5307). Indeed, the statistics of the knots formed in the simulations and in the experiments are pleasingly very similar, which suggests that DNA loops could potentially be used as a test bed for probing ideas on knot theory.
However, a new twist in the field of DNA knots arrived in 2005 when Javier Arsuaga and collaborators studied DNA knots in a type of virus called a bacteriophage. Also known as phages, bacteriophages (literally “bacteria eaters”) are viruses that infect bacteria. They work in a remarkably simple fashion. Using a molecular motor, phages tightly pack DNA in their interior so that it reaches almost crystalline density. The phage then exploits the high pressure that results from this tight packing to fire the DNA into the cytoplasm of its bacterial host as soon as the protein shell containing the phage DNA (the capsid) is “untapped”.
One might naively expect that knots would be a bad thing
The only difference between phage DNA and the previously studied DNA in solution is the degree of confinement, which is much more dramatic in phages since they are so small: about 40–70 nm across. But does this confinement affect the knots that can form within the capsid?
The research of Arsuaga et al. suggests that it very much does: they found that knots occurred far more frequently in the phage DNA than in “unconstrained” DNA in a solution. More specifically, in natural or “wild-type” infective phages, about half the DNA molecules were found to be knotted. The researchers also discovered that the viral DNA often contained torus knots, while twist knots were virtually absent – quite unlike the pattern observed for DNA in solution.
Do these results tell us something more about DNA structure, at least within phages? To find out, it was necessary to extend existing models of fluctuating elastic loops to the case in which the loops are confined within a sphere of radius R – which, to be relevant for the case of phage DNA, must be much smaller than the contour length of the DNA molecule itself. These simulations did reproduce the intuitive result that confinement increases the likelihood of forming knots: the DNA molecule in the narrow space of the phage has more opportunities to cross itself several times, so knots can readily form. However, the simulations were unable to reproduce any bias in favour of torus over twist knots and, unlike in experiments, the number of 52 twist knots observed was always larger than the number of 51 torus knots. Moreover, when R was set to a realistic value of 25 nm, the DNA configurations found by simulations were very disordered and the knots formed very complicated, with far more crossings than found experimentally.
Was the disagreement between simulation and experiment the result of an incomplete understanding of DNA–DNA interactions within the bacteriophage? Or was the bias in favour of torus knots a result of some other effect – such as the “molecular motor” inside the phage, which may rotate the DNA while it is packaged, thereby potentially affecting its conformation?
Our group, as part of an interdisciplinary collaboration, found a possible answer to this question in 2009, when we simulated the packaging and ejection of DNA molecules inside a modified type of phage called a P4 cosmid (PNAS106 22269). Though still infective, cosmids are mutants that contain only half the genome of the natural, wild-type phage. This makes them more treatable computationally, and experiments have shown that the knot spectra of P4 and P4 cosmids are qualitatively similar. To create our simulated DNA segments, we began with the fluctuating elastic rod models described earlier, but added an extra ingredient: the new simulations contained an “orienting” interaction between model DNA segments that kicked in whenever two segments got close to each other. This orienting interaction was designed to favour a small twist angle between the contacting segments. You can think of it as like the interaction that occurs when two chiral, corkscrew objects, such as pieces of fusilli, lock at an angle when forced into close contact (figure 3a).
3 DNA rigidity (a) Two chiral objects such as fusilli lock at an angle when pushed into contact with each other. We think that a similar process takes place with two double helical DNA filaments within a phage. (b) Structure of DNA inside a phage, with the orienting interaction switched on, from computer simulations. (Courtesy: Shutterstock/nulinukas; Marenduzzo et al.)
For the fusilli, the origin of the orienting interaction is geometric. For DNA, it may be mainly electrostatic, but whatever its ultimate origins, the effects of adding this interaction to our models were dramatic. When we used realistic values of parameters such as DNA rigidity (inferred from studies of DNA liquid-crystalline phases in solution), the simulations showed that, to begin with, the DNA inside the phage capsid is now ordered into a spool-like structure (figure 3b). This agrees with previous models for DNA packing and with electron microscopy pictures of phage DNA. Importantly, the twist knots are now strongly suppressed, and the knot spectrum is much more compatible with the experimental one.
Another knotty problem
While the puzzle of the twist knot absence was perhaps solved, another big question remained. One might naively expect that knots would be a bad thing for phages, because in order to be infective, they need to eject DNA from their interior into a bacterium, and the presence of knots might cause the DNA to get stuck. So how could the P4 phage have highly knotted DNA and still be infective?
A final answer to this question is still pending, but simulations suggest that the explanation may have to do with the concept of “knot localization”. If you tie a knot in a string and pull it tight, the knot will eventually localize such that it occupies a certain small region. But for DNA confined within a phage, our simulations suggest that the opposite happens: the knot delocalizes, spreading out over the whole DNA filament. In other words, the knottedness becomes a global property of the curve, one that cannot be captured by looking at a small fraction of the molecule.
This is crucial, because during the DNA ejection process, it is exactly the dynamics of such a small fraction (specifically, the bit that is close to the opening in the phage capsid) that dictates the physics of the process. If the knot is delocalized, this fragment will look no different for a torus knot than it will for an unknot, so simulations show that DNA ejection should proceed at approximately the same speed as it would if the molecule contained no knots at all. One can imagine further that torus knots may provide another advantage during ejection, as their toroidal (spool-like) geometry means that they may be readily unrolled, avoiding the formation or accumulation of self-entanglement – much as a spool helps prevent fishing lines from becoming tangled.
In bacteria, by contrast, knot localization seems to have beneficial effects. DNA molecules in bacteria are usually negatively supercoiled: in other words, the DNA helix is twisted less than it would be in a “normal” or undeformed strand, where the helical pattern repeats every 10 base pairs. Negative supercoiling is advantageous for the bacterial cell because it weakens the DNA helix, making it easier to break the hydrogen bonds keeping the helix together – something the cell must do whenever it “unzips” the DNA helix in order to transcribe and replicate it. But negative supercoiling may also help the bacterial cell remove problematic DNA knots. This is because if a knot happens to develop in a supercoiled strand, it normally becomes tight and localized, as shown in recent research by Guillaume Witz and collaborators from various institutions in Lausanne, Switzerland. This presumably makes it easier for the knot-removing topoisomerase enzyme to find, since the enzyme is attracted to regions of high DNA curvature.
The general picture we are developing is that in bacterial and human cells, DNA knots create many more problems than they do in viruses. Hence, control of these knots is very important, and we have discussed how topoisomerase enzymes have evolved to remove them. Usually, the removal of knots is a good thing, but in some circumstances we might actually prefer the DNA to remain knotted. For example, drugs that inhibit the functioning of topoisomerase enzymes have been used to treat cancer, because they prevent cells from dividing. So while topology and knot theory have already provided us with important insights into the physics of phage DNA, if we can uncover even more of the mysteries of DNA knots, it might open up new perspectives in biotechnology or even medicine. But before we get there, a lot more work has to be done.
If you’re a member of the Institute of Physics, the April 2013 issue of Physics World is now ready to view online or through our apps.
This month marks the 60th anniversary of the discovery of the structure of DNA by James Watson and Francis Crick and – to celebrate that milestone – we have a great feature on an unusual aspect of the famous double helix: namely, how knot theory can help us to understand how and why DNA tangles up.
Elsewhere in the issue, we continue the biophysics theme by looking at the damage caused to the human brain by blows from sports injuries or by the shock waves from exploding bombs. This is not traditional physics territory by any means, but surely there is no harm in physicists bringing a fresh perspective to such matters?
Our final feature this month looks at the history of Maxwell’s demon – the tiny being originally devised by James Clerk Maxwell as a thought experiment to evade the second law of thermodynamics. But, as Philip Ball explains, some of the physicist’s contemporaries actually believed it was an intelligent being that could bridge hidden worlds and provide a scientific route to immortality of the human soul.
Novel history: In Stuart Clark’s fictional story, physicist and priest Georges Lemaître is a key character. (Courtesy: Catholic University of Leuven)
Einstein and Lemaître
The first two books in Stuart Clark‘s trilogy of scientific novels (see May 2012) offered up a heady mix of history, physics and intrigue, concentrating on periods when political upheaval coincided with scientific revolution. In the first instalment, The Sky’s Dark Labyrinth, the main characters are Galileo and Kepler; in The Sensorium of God Halley, Hooke and Newton take centre stage. This pattern continues in the trilogy’s concluding novel, The Day Without Yesterday, which begins in 1914 with Albert Einstein fretting over relativity in Berlin while the cosmologist Georges Lemaître dodges bullets in the trenches of his native Belgium. Einstein is the obvious choice for a central character and, initially, Lemaître makes a highly effective foil. A devout Catholic who was decorated for his wartime service and later became a priest, he could hardly be more different from Einstein, a non-observant Jew whose Swiss citizenship kept him out of the fighting. The wartime setting also gives Clark a chance to explore the rise of antisemitism in Germany and the roles that Einstein’s (mostly Jewish) colleagues played in the war effort. The postwar period presents Clark with a problem, however. By the 1920s Einstein’s resolute opposition to quantum theory was starting to nudge him out of the scientific mainstream. Lemaître, for his part, did not make his seminal contribution to cosmology until 1927, when he published a (largely overlooked) paper suggesting that the universe was expanding. That leaves a gap of several years in which the pairing of Einstein and Lemaître seems forced, and the book loses its way somewhat. Another problem is that the minor characters in The Day Without Yesterday – Arthur Stanley Eddington, Edwin Hubble and Niels Bohr among them – are largely one-dimensional, and prone to disappearing from the narrative as quickly as they are introduced. The exceptions are Einstein’s first and second wives, Mileva and Elsa; as in the trilogy’s first two books, the central character’s family life is described, warts and all, in a way that is both detailed and believable. One might have wished for a stronger conclusion to this generally excellent trilogy, but overall, the strengths of The Day Without Yesterday outweigh its weaknesses.
2013 Polygon £12.99hb 252pp
Elementary misgivings
“When you have eliminated the impossible, whatever remains, however improbable, must be the truth.” As a scientific motto, Sherlock Holmes’ famous aphorism takes some beating. Indeed, there are plenty of scientists out there (your reviewer among them) who trace their interest in the subject back to a childhood spent reading and re-reading the adventures of Arthur Conan Doyle’s great detective. Couple this reservoir of scientific interest with the recent resurgence of Holmesian characters in popular culture, and a book that explains Sherlock’s scientific side with wit and flair ought to find a ready audience. Unfortunately, The Scientific Sherlock Holmes is not that book. For starters, author James O’Brien takes quite a long time to get on to his actual subject. Instead of beginning with the science, he devotes the first 47 pages (nearly a third of the book’s main text) to a largely irrelevant analysis of how the 60 stories in the Holmes “canon” differ from previous works of detective fiction, followed by a flabbily repetitive summary of the main characters. The latter might be useful for readers less familiar with the canon, but O’Brien’s copious references to past works of Sherlockian scholarship will put many newcomers off long before they get there. Likewise, anyone unversed in Holmesian abbreviations such as BOSC (short for The BOSCombe Valley Mystery) or CROO (The Adventure of the CROOked Man) will quickly tire of flipping back to the table in which they are defined. Hard-core enthusiasts won’t mind either of these things, of course – but if they are O’Brien’s real audience, then why frustrate them with such a laboured introduction? Once the book gets going, it is possible to see glimpses of how good it could have been. For example, the chapter on chemistry includes a superb explanation of how Holmes deduced that a character in The Musgrave Ritual had been dead “some days” before being discovered in a tiny sealed chamber. By estimating the volume of the chamber and using the ideal gas law to estimate the quantity of oxygen present, O’Brien, an emeritus professor of chemistry at Missouri State University, is able to show that the man must have expired at least three days before Holmes finds his body. There are several such passages, but not enough to sustain a whole book.
2013 Oxford University Press £18.99/$29.95hb 200pp
Researchers in the US have made a graphene loudspeaker that has an excellent frequency response across the entire audio frequency range (20 Hz–20 kHz). While the speaker has no specific design, it is already as good as, or even better than, certain commercial speakers and earphones in terms of both frequency response and power consumption.
Loudspeakers work by vibrating a thin diaphragm. These vibrations then create pressure waves in surrounding air that produce different sounds depending on their frequency. The human ear can detect frequencies of between 20 Hz (very low pitch) and 20 KHz (very high pitch), and the quality of a loudspeaker depends on how flat its frequency response is – that is, the consistency of the sound it produces over the entire 20 Hz–20 KHz range.
“Thanks to its ultralow mass, our new graphene loudspeaker fulfils this important requirement because it has a fairly flat frequency response in the human audible region,” says team leader Alex Zettl of the University of California, Berkeley. He told physicsworld.com that the fact that “graphene is also an exceptionally strong material means that it can be used to make very large, extremely thin film membranes that efficiently generate sound”.
Because the graphene diaphragm is so thin, the speaker does not need to be artificially damped (unlike commercial devices) to prevent unwanted frequency responses, but is simply damped by surrounding air. This means that the device can operate at just a few nano-amps and so uses much less power than conventional speakers – a substantial advantage if it were to be employed in portable devices, such as smartphones, notebooks and tablets.
High-fidelity sound
The Berkeley researchers made their loudspeaker from a 30 nm thick, 7 mm wide sheet of graphene that they had grown by chemical vapour deposition (CVD). They then sandwiched this diaphragm between two actuating perforated silicon electrodes coated with silicon dioxide to prevent the graphene from accidentally shorting to the electrodes at very large drive amplitudes. When power is applied to the electrodes, an electrostatic force is created that makes the graphene sheet vibrate, so creating sound. By changing the level of power applied, different sounds can be produced. “These sounds can easily be heard by the human ear and also have high fidelity, making them excellent for listening to music, for example,” says Zettl.
The researchers have already tested their device against high-quality commercial earphones of a similar size (Sennheiser® MX-400) and found that its frequency response over the 20 Hz to 20 kHz range is comparable, if not better.
The Berkeley team says that its CVD technique for fabricating the speaker is very straightforward and could easily be scaled up to produce even larger-area diaphragms and thus bigger speakers. “The configuration we describe could also serve as a microphone,” adds Zettl.
A preprint of the research is available on the arXiv server.
Whether you love giving them or loathe the entire experience, everyone has to deliver a presentation at some point during an academic career – be they student or professional researcher. It might be the presentation of your results to supervisors and peers. Or it might be an outreach talk to explain your research to people who have probably never heard of you or your very interesting academic niche. There is no magic formula to giving a successful presentation, but instinctively I think we all know when it’s gone well. Likewise, I think we all know when we could have spent a bit more time whipping those slides into shape, or when we perhaps should have put a bit more thought into the appropriateness of that risqué joke.
In an interesting article that appeared in the March issue of Physics World, writer and broadcaster Sharon Ann Holgate examines how lessons from sports psychology can help academics win over their audiences when it matters. She writes about the need to “build up” to the event of giving a talk, in the same way that an athlete would prepare for a competition. Holgate writes about the need to make manageable changes to a talk, and of practicing in front of relatives and peers. She also emphasizes the importance of imagining the delivery of a successful talk. She lays out a framework called PETTLEP, developed by the sports psychologist David Smith. PETTLEP includes elements such as imagining your physical sensations as you give the talk, the environment in which you are giving the talk, the tasks required, etc. You can read the full article here.
In this week’s Facebook poll, we want you to respond to the following question:
What is the most common problem with academic presentations?
Too long
Dodgy slides
Pitched at the wrong level
Failure to engage the audience
Use of Comic Sans typeface
Please cast your vote by visiting our Facebook page. If you want to select something else as a choice, please can you post a comment on the poll to let us know what you have in mind.
In last week’s poll we asked you whether you think more leading scientists should engage in public service. The question was inspired by a new docudrama aired on UK television last week about the role Richard Feynman played in the investigation into the causes of the Challenger disaster. Depicting the events of the real investigation, Feynman’s analytical approach helps the inquiry get to the bottom of the technical and bureaucratic errors in this dark chapter in NASA’s history.
Perhaps enthused by Feynman’s brilliance, 93% of respondents voted that “yes”, more leading should get involved with public service. While the remaining 7% believe that “no” they should not.
The poll also led to an interesting discussion on our Facebook page. For instance, one follower, Antoine de Saint-Exupéry, wrote “I admire those that have the skills and motivation to do so and they should certainly be supported. I do not, however, feel that there is necessarily a need for more leading scientists to do so.” Meanwhile, another participant, Jonathan Shimwell, was more cautious. “I really like engagement, but when it is done badly, it can have negative effects. Pressuring people to do outreach, particularly those who don’t want to be included, probably increases the likelihood of bad outreach,” he wrote.
Thanks for all your participation and we hope to hear from you again this week.
Hidden in plain sight? The experimental set-up with the cylindrical rod being cloaked seen. (Courtesy: Andrea Alù)
The first “mantle” invisibility cloak – in which a very thin “metascreen” cancels light scattering off an object, making it invisible – has been built by a team of researchers in the US. The cloak is just microns thick and can hide 3D objects from microwaves in their natural environment, in all directions and from all of the observers’ positions. The team claims that its device should be easier to produce than traditional cloaks that are based on the bulk properties of the metamaterial being used.
Traditional invisibility cloaks surround the object to be cloaked with a layer of bulk metamaterial, the refractive index of which is specifically tailored to guide electromagnetic waves around the outside of the cloaked object, thus making it appear to an observer that they are looking at empty space. While in theory these cloaks are amazing, they are problematic in practice. The permittivity and permeability of the metamaterials need to be highly anisotropic to allow the refractive index to vary in the required manner. To accommodate the anisotropy required, the cloak needs to be of comparable thickness to the object being cloaked. This restricts the movement of the object inside. The cloaks will often only work for a narrow range of wavelengths. Manufacturing tolerances are usually very low, so producing such cloaks is difficult. Alternative designs have been proposed to get round some of these problems, but these too have their own limitations.
Mantle cloaking
The mantle cloak, which was first proposed by electrical engineer Andrea Alù of the University of Texas at Austin in 2009, relies not on a bulk metamaterial but on an extremely thin “metascreen” that, when struck by incident electromagnetic radiation, produces an electromagnetic field in antiphase to the radiation scattered from the incident object, so making the object invisible – that is, the phase difference between the scattered fields from the cloak and the object being cloaked interfere and cancel each other out. The cloak, Alù claims, would be able to work over a broader range of wavelengths than many of the traditional cloaks using bulk metamaterials. In fact, the thinner the cloak could be made, the broader the bandwidth of radiation over which it would work.
The latest work from Alù and colleagues is an experimental realization of that original proposal. The researchers have used a 66 μm-thick flexible polycarbonate film covered with a fishnet design of 20 μm-thick copper strips to produce the required antiphase scattering to render an 18 cm cylindrical rod invisible to microwaves, provided the illuminated object is in a uniform electric and magnetic field. The cloak showed optimal functionality when the microwaves were at a frequency of 3.6 GHz and over a moderately broad bandwidth. Since the scattering of both the electric and magnetic fields is cancelled, there is no requirement for the object not to interact with one field or for the waves to be polarized in a particular direction. In principle, Alù suggests, the surface could be atomically thin.
Complex object
John Pendry of Imperial College London finds the research interesting. However, he cautions that the researchers have only cancelled the scattering of the electric and magnetic fields to the first order, and higher-order coefficients will become important in certain situations, such as when the light source is very close to the object and the illuminating wavefronts are radial rather than planar, or if the object is much larger than the wavelength of the incident light. Nevertheless, Pendry says that “Whereas a full cloak is a complex object, if you’re trying to cancel the scattering in just two dipole channels, it’s a much simpler design process, and this enables them to do the cloaking with a much thinner object than you could do otherwise.”
The researchers are now hoping to extend the cloak to try to find one that works at visible frequencies, and they also want to look at applications of the technology. “We have proposed using this technology for the next generation of optical nanodevices, for optical computing, switching, biomarkers and energy absorbers,” explains Alù. “For sensing, we suggest that we may be able to realize optimal sensors that receive signals without perturbing the measurements, by cancelling any interference between the sensor and the set-up that is being sensed.”
The mantra for popular-science books is to minimize the use of equations. In The Theoretical Minimum: What You Need to Know to Start Doing Physics, authors Leonard Susskind and George Hrabovsky have taken the opposite approach by producing a physics book for the educated general public that emphasizes the mathematics needed to solve physics problems.
When I first heard about the premise of the book, I was intrigued. Is there a group of people who want to solve physics and mathematics problems, and not simply read about the gee-whiz physics that is the standard fare of most popular-science books? To my surprise, apparently there is. The Theoretical Minimum is the product of a series of lectures that Susskind presented for the general public in the Stanford area – all of which can be found video-recorded on the Web – and these lectures attracted a large following of people who were, in Susskind’s words “hungry to learn physics”. Indeed, Hrabovsky himself was one of those people. Now president of the Madison Area Science and Technology organization, which is devoted to research and education, Hrabovsky has no formal scientific training but taught himself physics and mathematics – presumably through courses and books similar to The Theoretical Minimum.
This thirst for academic learning outside of a conventional university degree reminded me of the recent and rapid growth of so-called massive open online courses, or MOOCs: open-access (i.e. free) university courses that give people of any age or background the chance to learn about a subject that interests them, at their own pace (see p9 of the print edition). Like MOOCs, The Theoretical Minimum allows knowledge-lovers to get their teeth into the kind of physics and mathematics problems that one would normally face during a university degree. As Susskind puts it, it is intended for “people who once wanted to study physics, but life got in the way”.
The book is written in the form of 11 short lectures that cover classical mechanics, plus a final chapter on electromagnetism. Though replete with equations, it remains very readable. Abstract concepts are well explained, usually in a couple of different ways to give the reader a good conceptual overview of the principle at hand. For example, one does not need to understand every detail of a given equation in order to comprehend its power and its use, since these are explained in the text. In addition, each lecture includes several exercises, allowing readers to put their problem-solving skills into practice. (Solutions to the exercises are posted on the Web.) The first three chapters include mathematical interludes on trigonometry, vector notation, differentiation and integration. These discussions are complete, and would serve as a good reminder for someone who is already familiar with calculus; however, they are also rather terse, and would likely be too advanced for someone who wishes to learn it for the first time.
I found it satisfying to finally gain a basic understanding of Lagrangian and Hamiltonian mechanics
Is this really just the minimum you need to know to start doing physics? To me, the answer is an emphatic “no”: this book covers far more than the minimum. The first five chapters cover the core classical mechanics principles of motion and dynamics, including conservation of energy and momentum, while the material covered in the second half of the book (chapters 6–12) is usually considered “advanced classical mechanics”. This material – which includes Lagrangian and Hamiltonian mechanics and their applications to electric and magnetic forces – is often not taught at undergraduate level in the UK since it is not part of the Core of Physics syllabus issued by the Institute of Physics. Indeed, I did not cover these subjects during my undergraduate physics degree at the University of Oxford. As such, I can attest to the readability of the book: I was able to understand what an equation that I had never seen before represents, without having to pick apart and understand every term that makes it up. In fact, I found it satisfying to finally gain a basic understanding of Lagrangian and Hamiltonian mechanics, since I had sometimes wished we had covered these subjects in my degree. I even felt like I had been partially duped during my degree after reading Susskind’s comment that the Euler–Lagrange equations comprise “all of classical physics in a nutshell”!
There is, however, a flip side to my satisfaction at filling in some holes left by my undergraduate degree: I found myself wondering how much someone who has not had formal mathematics or physics training would really get out of The Theoretical Minimum. The concepts presented in it are not only advanced, but also abstract and unintuitive, and I would imagine they would be quite daunting to someone new to the subject. At the very least, they would leave newcomers scratching their heads. The book is really about explaining mathematics and abstract physics and does very little to relate these concepts back to everyday life. In addition, in many instances I thought that the explanation would benefit from a diagram or two. Susskind is one of the fathers of string theory, arguably one of the most abstract and theoretical areas of physics. However, the rest of us are not: we need a more tangible way to learn.
In summary, although this book probably offers more than many readers will have bargained for, it does provide a clear description of advanced classical physics concepts, and gives readers who want a challenge the opportunity to exercise their brain in new ways. Thanks to the breadth of accompanying information (for example, exercises and video-recorded lectures on the Web), it also enables them to learn at their own pace, and hopefully most will get some fun and satisfaction from it. If members of the general public really are pulling for these types of courses, ones that offer rigour and a challenge, I enthusiastically encourage them.
A team of researchers in the US claims to have found clear evidence of a microbe that conducts electricity along protein filaments, just like a metal. By showing that aromatic amino acids are critical to both the electrical and respiratory activities of Geobacter sulfurreducens, the group claims to have unequivocal proof that the bacteria funnel electrons up and down “microbial nanowires” using the exact the same principles as the synthetic organic materials used in electronics.
Geobacter is found in anaerobic soils and sediments the world over. Since its discovery in 1987, it has attracted special attention because of its handy ability to “breathe” pollutants such as iron oxide in mud and wastewater in the way that we breathe oxygen, purifying the source in the process.
Electron transfer is at the heart of all respiration. In order to survive in oxygen-starved environments, Geobacter expels electrons along the fine hair-like filaments it secretes, called pili. “This is unusual because it is using something outside the cell, whereas all other electron acceptors that life uses are typically brought inside the cell,” explains the new study’s lead author, microbiologist Derek Lovley of the University of Massachusetts Amherst in the US.
Biological bombshell
Discovered by Lovley and colleagues in 2005, the pili are only about 5 nm wide but can be up to 20,000 nm in length – many times longer than the bacterial cell itself. In 2011 Lovley’s team went on to show that the pili exhibit metallic-like conductivity, whereby they transport electrons along continuous structures over centimetre distances thousands of times the length of the cell, earning them the nickname “nanowires”.
Physicists tended to take this news in their stride, says Lovley, but the same cannot be said for biologists. “For [us], Geobacter‘s behaviour represented a paradigm shift. It goes against all that we are taught about biological electron transfer, which usually involves electrons hopping [or tunnelling] from one molecule to another,” he explains. It did not help that precisely how the pili were achieving this remarkable feat remained a mystery.
Genetic tweaks
To better understand how this metallic-like conductivity worked, the team looked for inspiration from synthetic organic polymers, the conductivity of which is derived from the overlapping pi–pi orbitals of aromatic compound structures. These ringed structures share electrons suspended in a cloud, which allows the overlapping electrons to flow – a concept that led Lovley to hypothesize that perhaps the aromatic amino acids present in the pili had something to do with their unique properties.
Using genetic-manipulation techniques, the researchers switched the suspect aromatic amino acids in key regions of the Geobacter‘s genome with a non-aromatic amino acid – alanine. The new strain of Geobacter looked identical to the old one under a microscope, but its pili were pitifully poor when it came to electrical conductivity. “It was like pulling the copper out of an extension cord – it still looks the same but it cannot conduct electricity anymore,” Lovley explains.
Critically, the cells were also severely hampered in their ability to dump electrons onto iron oxide in the standard respiration process, implying that conductive pili are central to the biological functioning of the cell. “From my perspective, this is huge,” says Lovley, adding that it “really takes away any conjecture that this might not be important in the biological process”.
Nanowires versus biofilms
And yet, resistance to the idea remains. In 2012 Moh El-Naggar, a physicist from the University of Southern California, and colleagues published results outlining why the Amherst group’s basic hypothesis is physically impossible. Others within the field query the experimental methods used to draw the initial conclusions about the pili’s metallic-like conductivity – including US Naval Research Laboratory researcher Leonard Tender, who published a list of reasons, also in 2012, on why he believes the experiments were flawed. Another researcher, who wishes to remain anonymous, says “Trying to be as objective as possible, I cannot think of anybody in the field who accepts the Lovley group’s hypothesis.”
A particular point of contention is whether the electron-shifting properties of pili can be localized to them alone, or whether the greater “biofilm” that their linked networks form part of – along with the bacterial cells themselves and other extracellular secreted materials such as proteins and polysaccharides – is really responsible.
Compelling evidence
With this latest paper, the tide of opinion might finally be turning in Lovley’s favour though. Christian Pfeffer, from Aarhus University in Denmark – part of a Danish–American team that recently discovered conductive cable-like multicellular bacterial filaments in marine sediments – thinks the study “adds a vital component” to current understanding of Geobacter‘s conductive properties. “I am excited to see whether the ongoing structural studies will soon lead to a model of the actual electron transport, which would also greatly inspire research on other microbial long-distance electron-transport systems,” he says.
Harry Gray of the California Institute of Technology – one of the world’s premier experts on how electrons move in biological systems – says he is “fascinated” by the Geobacter system. “It is clear that electron transport over these very long distances cannot be explained by single-step tunnelling,” he says.
Clearly, the idea that bacteria might conduct electricity like a metal is deeply divisive, but the Amherst group is undeterred. “In biology, it has been a controversial idea ever since we proposed it, which is why we are just keeping after it and trying to learn more,” says Lovley. Next on the researchers’ agenda is an attempt to elucidate the physical structure of the pili, in the hope that this might eventually allow scientists to synthesize similar materials instead of having to grow Geobacter, which is used in bioremediation and microbial fuel cells among other things, in the lab.
The study is published in the open access journal mBio.
