Archive for June, 2008

First X-ray diffraction image of a single virus

Friday, June 20th, 2008

Virus x-ray

X-ray crystallography has been a workhorse technique for chemists since the 1940s and 50s. For many years, it was the only way to determine the 3D structure of complex biological molecules such haemoglobin, DNA and insulin. Many a Nobel prize has been won poring over diffraction images with a magnifying glass.

But x-ray crystallography has a severe limitation: it only works with molecules that form into crystals and that turns out to be a tiny fraction of the proteins that make up living things.

So for many years scientists have searched in vain for a technique that can image single molecules in 3D with the resolution, utility and cost-effectiveness of x-ray diffraction.

That search might now be over. Today, John Miao at the University of California, Los Angeles, makes the claim that he and his team have taken the first picture of a single unstained virus using a technique called x-ray diffraction microscopy. Until now this kind of imaging has only been done with micrometre-sized objects.

Miao’s improvement comes from taking a diffraction pattern of the virus and then subtracting the diffraction pattern of its surroundings. The resolution of his images is a mere 22 nanometres, that’s an improvement of three orders of magnitude.

If confirmed, that’s an extraordinary breakthrough. With brighter x-ray sources, the team says higher resolution images will be possible and that it’s just a matter of time before they start teasing apart the 3D structures of the many proteins that have eluded biologists to date.

But best of all, x-ray diffraction gear is so cheap that this kind of technique should be within reach of almost any university lab in the world.

Ref: Quantitative Imaging of Single, Unstained Viruses with Coherent X-rays

Why gamma ray bursts are not standard candles

Thursday, June 19th, 2008

GRB noncandles

A revolution is currently underway in our knowledge of gamma ray bursts thanks to NASA’s Swift telescope which has been looking out for them from its perch in orbit since 2004.

But in the wild enthusiasm to embrace the firehose of data that Swift is sending back, it looks as if astronomers have made a basic mistake in their analysis, says Li-Xin Li, a theorist at the Max-Plank Institute for Astrophysics in Garching, Germany.

Gamma ray bursts emit a huge amount of energy in a very short period of time. One of the peculiar discoveries in the Swift data is that the total energy emitted in a burst has a very narrow distribution of around 10^44 Joules.

A number of astrophysicists say this is evidence that GRBs are standard candles. In other words, that GRBs all emit the same amount of energy so measuring their brightness gives you a good idea of their distance.

Cosmological distances are notoriously tricky to measure so finding a new standard candle is a major discovery for astronomers.

Sadly, there is a mistake in this reasoning, say Li. He reckons that astronomers have failed to account for a serious problem in the GRB data known as Malmquist-type selection bias that is well known in other types of astronomical surveys.

The bias comes about because observers see only the brightest GRBs from the most distant parts of the universe because dimmer ones are undetectable at present. So the number of faint GRBs is significantly underestimated.

Re-examine the data with this in mind and the notion of GRBs as standard candles rapidly begins to look untenable.

Still, it was a nice idea while it lasted.

Ref: Are Gamma-Ray Bursts a Standard Energy Reservoir?

The embarrassing lightness of photons

Wednesday, June 18th, 2008

Photon force

Here’s a conundrum for you. What is the momentum of light in a transparent dielectric medium?

If the answer doesn’t trip off your tongue, that might be because nobody else knows either. Amazingly, there are two lines of thought:
In 1908, the German mathematician Hermann Minkowski guessed that the momentum was equal to nE/c (where n is the refractive index, and E and c are the energy and speed of light in a vacuum).

A year later,  his contemporary Max Abraham suggested that the momentum is equal to E/nc.

A century since then and we’re none the wiser. An embarrassing state of affairs for theoretical physics, wouldn’t you agree?

Today Weilong She and pals from Sun Yat-Sen University in Guangzhou, China, announce that they have the answer. And they got it by measuring the recoil on the end face of a nanometre-sized fibre exerted by outgoing light. (This isn’t the well known pressure caused by specular reflection but something  a little more subtle.)

The experiment is impressive because it is designed in such a way that if Minkowski were correct the fibre should be pushed in one direction and in the other if Abraham were correct.

So the result is the first to unambiguously favour one theorist over the other.

And the winner is…drum roll…Abraham.

It’s about time.
Ref: Observation of a Push Force on the End Face of a nm Fiber Taper Exerted by Outgoing Light

How to bury an ion (and find it again later)

Tuesday, June 17th, 2008

Buried ions

The future of computing depends on our ability to bury single ions within the crystal structure of silicon and diamond in a way that allows us to find them again, quickly and repeatably.

The burying part of all this isn’t difficult: simply aim a beam of ions at a substrate and you can be pretty sure one or two of them will end up buried inside the crystal structure. The trick is to know where they’re buried so you can find them again later.

That’s a trick that Thomas Schenkel and pals at the Lawrence Berkeley National Laboratory overlooking San Francisco, seem to have perfected for the first time. Their technique is to fire the ion beam through a hole in the tip of a scanning force microscope. The hole defines the position of the burial while the scanning force microscope can easily find the location again later.

Schenkel has used the technique to bury nitrogen atoms in diamond and antimony in silicon, which is impressive. (The team even says it has discovered that antimony doesn’t migrate when the substrate is later heated, which is an important result in itself. Ions that move after you bury them are difficult to find later!)

But the bigger picture is that ion burial is one of the enabling technologies that will make quantum computing possible. So it’s just possible that Schenkel and co have created the first facility in which quantum computers will be forged.

Ref: Single-atom Doping for Quantum Device Development in Diamond and Silicon

Extraterrestrial nucleobases found in meteorite

Monday, June 16th, 2008

ET nucleobases

In 1969, a large meteorite fell near the town of Murchison in Victoria, Australia. Scientists collected more than 100 kilograms of rock, making it the largest sample of carbonaceous chondrite ever recovered.

Since then numerous groups have found evidence that the Murchison meteorite contains common amino acids, the building blocks of proteins, as well as nucleobases, the subunits from which nuclei acids such as DNA are formed.

But critics point out that its hardly surprising that a rock which has slammed into the Earth at warp drive velocity should end up covered in muck. If you’re going to make the claim that the these building blocks of life came from space, you’ve got to prove it, they say.

Today, Zita Martins from Imperial College, London and a few pals say they’ve found the first unambiguous evidence that this gloop really is extraterrestrial.

What they did was collect samples of one and two ring nucleobases called pyramidines and purines respectively and analyse the percentage of the carbon-13 isotope they contain.

On Earth, carbon-13 makes up about 1 per cent of naturally occuring carbon. The compunds in the Murchison meteorite on the other hand contained as much as 44 per cent carbon-13. That’s about as good a signature of extraterrestrial origin as you can get.

The discovery has important implications for our understanding of how life must have evolved on Earth. The best evidence is that pre-biotic compounds such as nucleobases could not have formed easily in the conditions that existed on the early Earth. So where could it have come from?

Hmmm…at that time (about 4 billion years ago), the Earth was bombarded by about a billion tonnes of carbonaceous chondrite meteorite. Does that look like a smoking gun or what?

Ref: Extraterrestrial nucleobases in the Murchison meteorite

In case ya missed ‘em…

Sunday, June 15th, 2008

This week’s sweetmeats from the physics arXiv blog:

Testing “spooky action-at-a-distance” on the International Space Station

Oil prices: a classic bubble economy?

Cellphone records reveal the basic pattern of human mobility

Let the SPIT wars begin

How to build a quantum eavesdropper

Adam ‘n’ Eve

Saturday, June 14th, 2008

Other highlights from the physics arXiv this week…

Planetesimal Formation around the Snow Line in MRI-driven Turbulent Protoplanetary Disks

On Career Longevity Distributions in Professional Sports

Dark Entropy

Landau’s Last Paper and its Impact on Developments in Mathematics, Physics and Other Disciplines in New Millennium

Whispering-gallery Modes and Light Emission from a Si-nanocrystal-based Single Microdisk Resonator

Metaferroelectrics: Artificial Ferroelectricity in Metamaterials

Quantum Theory of Radical-Ion-Pair Recombination

How to build a quantum eavesdropper

Friday, June 13th, 2008

Quantum eavesdropping

In the cat and mouse game of preparing and eavesdropping on secret messages, quantum encryption trumps all. At least, that’s what we’ve been told.

The truth is a little more complex. Quantum key distribution, the quantum technique by which a classical encryption key can be transferred, is perfectly secure in theory. In practice, there are a number of loopholes that can give an eavesdropper a grandstand view of the conversation.

Here’s one loophole. The security of quantum encryption schemes depends on our inability to make a copy of a quantum state. If that were possible, Eve could make a copy of the message and pass on the original without anybody being the wiser. But in the quantum world, copying anything destroys the original, so the sender and receiver can always tell if they’ve been overheard by examining the error rates in their message. If it rises above a certain limit, the line is not secure.

That would be pretty convincing were it not for our ability to make imperfect copies of quantum states without destroying the original. That’s a loophole that an eavesdropper can exploit to extract information from a quantum message without the sender or receiver knowing. It should work as long as Eve is careful to keep the error rate below the critical limit.

Today, Yuta Okubo from the University of Tskuba in Japan and a few mates outline the design of a quantum eavesdropper that works on just this principle. They’ve yet to build their device but the publication of its plans should raise the blood pressure in a few government agencies and more than one hi-tech start up that has been selling quantum encryption as a new generation of perfectly secure communication.

Ref: Proposal of an Eavesdropping Experiment for BB84 QKD Protocol with 1→3 Phase-covariant Quantum Cloner

Let the SPIT wars begin

Thursday, June 12th, 2008


If SPAM arrives in your inbox at 4am, the chances are your antispam software will catch it. But even if it doesn’t, you won’t lose much sleep over its arrival.

But it’ll be a different story with SPIT (spam over internet telephony). Junk phone calls at 4am are going to drive you mad because the chances are that antispit software won’t be able to intercept the call.

Today, Andreas Schmidt and pals from the Fraunhofer-Insitute for Secure Information Technology in Darmstadt Germany explain why intercepting SPIT is so much harder than spotting SPAM.  The main difference between junk calls and junk email is that the email arrives at your mail server before you access it. This gives the server time to analyse its content and filter out the junk before it gets to you.

Internet telephony, on the other hand, goes straight through to you in (more or less) real time, giving your server little or no time to analyse its content.

There are still a number of strategies that could be employed to filter out SPIT. For example, white lists that allow only calls from predetermined callers, Turing tests such as audio CAPTCHAs that make a caller prove he or she is human and payment-at-risk services where the caller makes a small payment in advance and is refunded immediately if the receiver acknowledges the call as legitimate.

But Schmidt and pals don’t seem confident that these techniques will work. They happily point out the disadvantages of each strategy, showing how most are either impractical or easily  circumvented by a determined spitter.

They have even created a program that implements all of these attacks. Their idea is to use the program as a benchmarking tool against which people can test antispitting strategies.

Spitting is a problem that is likely to get worse. Much worse, if the estimates are correct that as much as 90 per cent of email traffic is SPAM .

So to all you computer security guys out there: hustle, hustle, hustle. I need my sleep.

Ref: Spam over Internet Telephony and How to Deal With It

Cellphone records reveal the basic pattern of human mobility

Wednesday, June 11th, 2008

Mobile phone movement

A few months back, we saw what happens when researchers get their paws on anonymixed mobile phone records. Albert-Laszlo Baribasi at the University of Notre Dame in Indiana and some buddies used them to discover entirely new patterns of human behaviour.

Now Baribasi has dug deeper into the data and discovered a single basic pattern of human mobility.  It’s nothing special: lots of smallish journeys interspersed with occasional long ones (the length of the journey actually follows a power law).

That’s more or less what you’d expect but experimental confirmation is important.

Human mobility is one of the crucial factors in understanding the spread of epidemics. Until now, the models that predict how disease spreads have had to rely on educated guesses about the way human travel patterns might affect this process.

Baribasi’s work will take just little of the guesswork out of future efforts and that can’t be bad.

Ref: Understanding Individual Human Mobility Patterns