David J. Wineland: trapping ions for clocks and computers

Simon Thwaite recently completed a D.Phil. in Atomic & Laser Physics at the University of Oxford, and is currently a postdoctoral researcher at the Ludwig Maximilian University in Munich. The first part of his post series commenting on the 2012 Nobel Prize in Physics can be found here.

In this post he gives an overview of the field of trapped ions, describes two of its most important applications, and describes what goes on behind the scenes when a trapped ion interacts with a laser beam.

David J. Wineland – probing trapped atoms with light

David Wineland, an experimental physicist at the National Institute for Standards and Technology (NIST) in Boulder, Colorado, is one of the leading researchers in the field of trapped ions: that is, the study of how positively-charged ions (i.e. atoms stripped of one or more electrons) may be trapped, cooled, and manipulated.  This field shares many similarities with experiments on neutral atoms (laser cooling, for example, is just as useful for ions as it is for neutral atoms), but also has a number of significant differences. The most important difference that distinguishes ions from atoms is, obviously enough, the fact that ions have a non-zero net electrical charge. This has two very important consequences.

Trapped ions: trapping and interactions

A string of trapped ions (red dots) lined up in a Paul trap
can be imaged with a tightly-focused laser beam and CCD camera.

Image credit: Rainer Blatt experimental group, University of Innsbruck.

Applying an electric field to an ion produces a force on the ion: positive ions are drawn in the direction of the field. [In contrast, applying an electric field to a neutral atom changes the ‘shape’ of the atom slightly, since the positively-charged nucleus and negatively-charged electron cloud are drawn in opposite directions, but produces no net force.] Consequently, whereas traps for neutral atoms must rely on combinations of laser light and magnetic fields, ions can be trapped just by electric fields. Most of the recent trapped-ion experiments use some variation on the Paul trap (a.k.a. the quadrupole ion trap) which uses a combination of static (DC) and oscillating (AC) electric fields to trap ions along a 1-dimensional line.

The “ISW mystery” deepens considerably (II)

[... continued from yesterday]

[Note added April 29: Through correspondence with some of the authors from what I label as the "French group" below I have learned that the density threshold was actually applied in their work as well. This makes things rather confusing as it means that their methods and the methods of "the DHB" are much more similar. However, they have also updated their paper to reflect new knowledge about the void catalogues and see a slightly more significant signal, similar to what Planck find (see note below). Everything is rather confusing right now. Again, once the dust has settled, I will write a post clearing everything up.]

[Note added March 21: Wow, sometimes science moves quickly. Today Planck released its data. They appear to confirm the anomalous spots in the original "Granett" (Hawaiian) result. They also appear to confirm the new anomalous result that was present in the paper that is now retracted (see the note below from March 19), albeit with a slightly reduced significance. It is unclear exactly what is going on, but it is clear that it is something interesting. I will keep you informed as things progress.]

[Noted added March 19: The paper described in the second half of this post (I called its authors the DHB) has been withdrawn from the journal it was submitted to (see the new abstract at this link: http://arxiv.org/abs/1301.6136). It is unclear whether the problems that the authors found in their analysis will affect their conclusions. However, I suggest you are cautious regarding how you interpret the conclusions I have drawn below based on this paper. I will keep you informed as/when things progress.]

A really neat figure from arXiv:1301.5849 showing the locations and sizes of the various catalogues of voids being examined. A larger redshift means the void is further away from us and one Megaparsec (Mpc) corresponds to three million light years. The purple "Granett et al." box is the original catalogue used by the Hawaiian group back in 2008. 

Isn't this just "a posteriori" statistics?

There is another possible explanation for the mystery. The probability of ZOBOV picking out these lines of sight at random is exceedingly small (less than 0.003), but it isn't zero. Might this have just been a crazy fluke?

Suppose 100 different groups of physicists look for unexpected, but interesting, signals in cosmological data. Then, even if each group is very careful you still expect one of them to find something that would seem to them to be unlikely. Unfortunately, they would be the only ones to publish their results. So we wouldn't see one “detection” paper and ninety-nine papers consistent with no detection. We would just see the one “detection” paper.

The best way to determine whether this is what happened is to look for the signal in other surveys.  If the original measurement was a fluke, it won't show up anywhere else. But, if it does show up again, then the chances that it was a fluke will significantly diminish.

The Friday before last a paper appeared that did exactly this. A French group took two catalogues of voids (so no over-densities), which have been produced by applying ZOBOV to a new catalogue of galaxies (these ones are closer to us). The French group then did more or less the same thing as the Hawaiians did. They examined images of the CMB along the lines of sight of these voids, averaged the temperature in all the images and checked whether the resulting signal could have happened at random.

They found no significant result.

This was quite sobering to read on the day. The paper did verify the significance of the original measurement, but not finding it in the new catalogues was highly suggestive that the story I painted above of a sort of community wide “look elsewhere effect” was true.

Hold on though!

Things at this date in time did look bad for the anomaly, but there was one important piece missing from the French group's analysis. The Hawaiians only used the most extreme over and under-dense regions in their analysis. ZOBOV found many more than 50 regions for them and if they had used all of them, they also wouldn't have obtained a statistically significant signal. This was always a crucial part of their analysis because we already knew from other observations that the observed ISW effect from most of the universe is as small as the predicted signal.

What would the French group have seen if they had only examined the most extreme voids?

A new observation

Apparently it is a rule of thumb for observers, that the more interesting your observation is, the more boring you are meant to make your title. These guys probably deserve a promotion. The paper is here.

Three days later (last Monday) a mixture of physicists from Durham, Hawaii and Baltimore (the DHB) released a paper. It answered the question posed above. For anybody interested in finding new physics, the answer is very exciting.

The “ISW mystery” deepens considerably

Other than my initials, what secrets does the CMB hide that are waiting to be seen only when the CMB is examined in just the right way?

This time last year I wrote a few posts describing what I called the “ISW mystery” (Part I, II, III and IV). A year has passed, it is time for an update on the mystery.

The very short summary is that things are starting to get more than a little bit exciting. All of the plausible ways in which the calculation of the expected ISW signal could have been wrong have been checked and eliminated as possibilities; if the measured signal is real, it is too large for the standard cosmological model. Much, much more excitingly, the observation that generated the mystery has now been repeated in another region of the universe and a very similar and equally anomalous signal was found; the apparent anomaly was not a statistical fluke.

The preprint of the paper describing this new observation was released just a week ago.

What is the “ISW mystery”?

The image that began the mystery. Why is that spot so hot, and how did it get that cold ring around it?

A quick recap will probably be useful. The integrated Sachs-Wolfe (ISW) effect describes the heating and cooling of light as it passes through gravitational peaks and valleys late in the evolution of the universe. In the standard cosmological model, these peaks and valleys decay with time, so a light ray gains (or loses) more energy entering an over-dense (or under-dense) region of the universe than it loses (or gains) leaving it. The effect is very, very small. Almost every source of light in the universe is not known well enough to be used to detect it. Only the cosmic microwave background (CMB) is uniform enough that these tiny fluctuations could ever be detected.

However, even then, the primary fluctuations in the the temperature of the CMB are bigger than the secondary ones created by the ISW effect. We can measure these fluctuations but we could never know how much is due to the ISW effect and how much is primordial. The only thing we can do is look at the structures in the universe nearby and see if on average the CMB is slightly hotter (colder) along lines of sight where the nearby universe is over-dense (under-dense). The bigger, primordial fluctuations in the CMB should have nothing to do with local structures (the CMB has come from much further away). Therefore, if this signal were to be found in the CMB, the most plausible explanation would be an ISW effect.

A group in Hawaii decided to look for this signal in a slightly unusual way. Firstly, they made a catalogue of significant over and under-dense regions in a particular survey of galaxies. Then, they only examined patches of the CMB that existed along the line of sight of each of these regions. They then found that the patches aligned with over-densities were hotter on average than a randomly selected patch and those aligned with under-densities were colder (with more than “\(4\sigma\)” significance). This is what one would expect from an ISW effect. The “ISW mystery” is that these patches were too hot and too cold. The ISW effect simply shouldn't be that big.

The importance of checking the anomaly from every angle

The human machine: decommissioned components

The previous post in this series can be found here. 

Happy 2013 from all of us here in the Trenches! We successfully made it one more time around the sun, and if that's not a good excuse for a party I don't know what is! Sadly, however, not all of your cells have been having such a swimmingly good time since the calendar ticked over to January the first - in fact nearly one trillion of them have died in the past fortnight alone, at a rate of roughly 70 billion a day, or 800,000 per second. Don't be alarmed, however, as this has been going on for your whole life and is a vitally important part of being a multicellular organism such as yourself. A human without cell death would be like society without human death - overcrowded, unpleasant, and rife with infirmity. Your body needs a system by which damaged, old, or infected cells can be removed in a controlled manner; this process is known as apoptosis.

In this post I will be discussing what we know about how apoptosis works and how it is a key player in the development of cancer and the fighting of infectious disease. I'll also show how our understanding of how this process works has allowed us to devise targeted therapeutics against a number of debilitating conditions.

Cellular suicide - picking the moment

Your cells are team players - they're willing to do anything to serve you, including laying down their lives. Apoptosis depends on this loyalty because it is actually a form of suicide that your cells perform on themselves. Arguably the most important aspect of this is timing - if your cells are in the habit of committing suicide before it is necessary then you'll waste a lot of energy and resources building replacements that shouldn't be needed. On the other hand, if the cell leaves it too late to kill itself then it may find itself incapable of doing so.

So, how does a cell know when to die? Well the most obvious markers for cell death are simply the various forms of damage that can occur to the components of the cell itself. If a cell's membrane becomes damaged, for example, this can cause excess calcium to leak into the cell and so be sensed by a number of calcium-binding proteins, such as calpain, which in turn signal that apoptosis should begin. Similarly, damage to DNA is sensed by the complex machinery of the DNA repair pathway. For example, PARP is a protein that binds to single-strand breaks in DNA caused by DNA damaging agents such as radiation (think sunburn!) or chemical mutagens like free radicals. PARP and other DNA damage sensors relay their information to a number of signalling proteins, most importantly p53. If p53 is activated in response to DNA damage it signals to stop the usual processes of cell division and begin DNA repair, but if the damage is just too bad it makes the call to start apoptosis and destroy the cell.

A three dimensional fractal in 3D

The video below is a fractal. It is also three dimensional. It has also been rendered from two different locations very close to each other. Therefore, you can also see it in three dimensions.

If you're not used to using YouTube's 3d capabilities then don't worry, this guy has a tutorial video explaining how to see the full three-dimensionality of the video without the need for glasses. It's just like magic eye in reverse, basically (though I'm not sure how good it is for your eye muscles).

If you liked that you should read the description of how the Mandelbulb was discovered. The Mandelbulb was made by people looking for a three dimensional analogue of the well known Mandelbrot set. If you don't know what the Mandelbrot set is, first watch this video, then read about what you just saw at Wikipedia.

None of the Mandelbulb, or the Mandelbrot set or the 3d fractal (a Mandelbox) shown above were designed by a human mind. All of the complexity found in the images comes about from defining structures in two or three dimensional space as the set of points that are or are not solutions to relatively simple mathematical algorithms. For example, the algorithm describing the Mandelbrot set can be described in just one line:

"... the Mandelbrot set is the set of values of c in the complex plane for which the orbit of 0 under iteration of the complex quadratic polynomial \(z_{n+1} = z_n^2 + c\) remains bounded".

All of the complexity you can see in the entire ten minutes of the Mandelbrot set video I linked to above is defined in that one simple sentence.

Twitter: @just_shaun

Cinema verité - biology style

Animations of scientific principles are becoming more and more popular as a way of condensing complex data into an easily accessible format, particularly in the field of biology. Nonetheless, a recent article in Nature has raised a number of interesting points about how the visualisation of biological processes should not be taken lightly. Biology is unnervingly complex and there is still much that we don't understand - how are we to know how much of an animation is based on actual data and how much is just 'filling in the gaps'? This is not limited to the layperson - humans are very visual creatures and we are more easily swayed by pictures than words, experts are no exception. This is not new, journals have included idealised representations of biological processes for decades, but the advancement in computer animation has opened the door for more sophisticated animations that may imply a more thorough understanding where one does not exist. 

That said, I don't believe that researchers actively seek to mislead when presenting their findings in animated form, rather that they have to take the necessary steps to complete the movie - inherently requiring some artistic licence. And, for the most part, the bits being filled in are done so with reasonable scientific assumptions in mind and are not wild fantasy. The medium is an exciting one, and one that will hopefully play a significant role in not only disseminating scientific understanding, but also help to further research by highlighting gaps in our understanding. We must, however, always be vigilant when interpreting these animations as they are exactly that - animations - and not actual footage of molecular biology.

An excellent example of biological animation is the 'Inner Life of a Cell' video by a group in Harvard. I love this video, which depicts the events that occur upon the activation of T cell, and is pretty accurate in that almost everything show is backed up by real evidence. The 'motor protein' kinesin at 3:40 is particularly impressive because its mechanism of 'walking' along microtubules is backed up by extensive structural and biochemical studies, yet it just looks so much like a drunk guy who's been pulled over by the police and is trying to walk in a straight line! If you get the chance, I really recommend watching the video and reading the article mentioned above. Enjoy!

The human machine: circuits and wires

The previous post in this series can be found: here.

In the first post of this 'human machine' series, I explained how 'energy' (that abstract entity) is processed and used by our bodies in order to converted the chemical energy in our food into the work energy required to keep us ticking over nicely. I discussed in this how we are all actually powered by electrical circuits that buzz along in the internal membranes of our cell's power stations, the mitochondria. Better yet, not only are we powered by currents of electrons, familiar to us as standard electricity, but also by currents of protons, and so are actually working off energy being extracted from two forms of electrochemical potential. We're pretty sophisticated machines!

The work energy generated by these processes is used in myriad ways, but one very important one is the creation of another electrical current that is the foundation of everything you've ever done and every thought you've ever had: the neuronal action potential. This is the electrical signals that run along the neurons in your brain and body in general, constantly relaying information back and forth throughout the whole complex machine. Without it we would be like plants, with one part of our bodies completely unaware of what's happening to the rest of it, and animal life as it is familiar to us would be entirely impossible. Most people have, I expect, heard of the notion of electrical signals running throughout our bodies (it's why the machines built the Matrix, right?), but few will actually know what that means. In today's post I'm going to be talking about what neuronal signals actually are, and so explain why being hit by lightning is a bad thing but being defibrillated (like in ER) can be a good thing.