Researchers at the Lawrence Berkeley National Laboratory have used advanced imaging techniques to solve the structure of one of nature's most important molecular machines. A clearer picture of this motor-like protein, which spins along strands of bacterial messenger RNA to read and translate it into proteins, may help pharmaceutical researchers develop new antibiotics. The researchers studied a version of the protein called Rho from E. coli bacteria. This type of protein, called a transcription factor, is also important in human development and disease.

In the video below, Rho, which is shaped like a hexagon with a hole in the center, is shown in cross section as it walks along the RNA strand, shown in orange. Rho spirals in such a way that it can only move in one direction along the RNA strand, which is crucial to making proteins properly.

In order to get a better picture of Rho, the Berkeley researchers used the lab's Advanced Light Source, which accelerates electrons to very high energies in order to create some of the brightest x-rays in the world. Using these x-rays, they were able to see a part of Rho's structure that was previously not very well understood.

The European Center for Nuclear Research announced today that when the Large Hadron Collider (LHC) goes online this November, it will be running experiments at half the energy it was designed for. This is in part because it is warming up, but it's also a sign of bigger problems, according to the New York Times. At $9 billion, the LHC is the most expensive physics machine in the world and has been under development for 15 years. It was switched on nearly a year ago but has yet to collide any particles due to failed electrical connections. But a far bigger problem will remain after those connections are fixed--one that will prevent researchers at the accelerator from pursuing some of the big questions the machine was built to address, at least for a few years.

The LHC was designed to accelerate particles for extremely high-energy collisions, creating particles never before seen. These include the predicted Higgs boson--which, according to some physicists, gives other particles mass--and whatever it is that makes up dark matter, an unknown substance that constitutes 25 percent of the universe. But many of the LHC's powerful magnets, which accelerate particles for these collisions, cannot operate at the energies for which they were designed and tested. Magnets have to be trained, pumped with higher and higher currents until they can handle tremendous energies. When the LHC's magnets sat outside for some time between training and installation, a scientist told the Times, they might have lost this training. Until this is fixed, the accelerator cannot operate at its planned capacity of seven trillion electron volts.

The European Center announced today that the LHC will go online this November at 3.5 trillion electron volts until its operators gain experience, when it will be revved up to five trillion. At the end of 2010, it will be shut down to bring it up to the full seven trillion. However, even at 3.5 trillion, the LHC will be more powerful than today's highest-energy particle accelerator, Fermilab's Tevatron, which creates collisions at one trillion electron volts.

As Dennis Overbye reported in the Times, the decision to run the LHC at lower energies instead of first retraining the magnets was a tough one--and the decision illustrates how eager physicists are to tackle the really big questions. Overbye writes:

[S]ome physicists admit to being impatient. "I've waited 15 years," said Nima Arkani-Hamed, a leading particle theorist at the Institute for Advanced Study in Princeton. "I want it to get up running. We can't tolerate another disaster. It has to run smoothly from now."

The delays are hardest on younger scientists, who may need data to complete a thesis or work toward tenure. Slowing a recent physics brain drain from the United States to Europe, some have gone to work at Fermilab, where the rival Tevatron accelerator has been smashing together protons and antiprotons for the last decade.

Credit: CERN

Physicists and science enthusiasts were excited last month when the Large Hadron Collider, the most ambitious particle accelerator ever built, went online. Nine days later, the accelerator was shut down because of a helium leak. (The superconducting magnets that steer particles on their 27-kilometer collision course are cooled with large volumes of liquid helium.)

Yesterday, CERN, the European Organization for Nuclear Research, released a report detailing what went wrong. Steven Nahn, an MIT physics professor currently working from CERN, says that the analysis took some time because the area had to be warmed up from near absolute zero before it could be accessed for investigation. The problem, the report concludes, arose because of a faulty electrical connection between two magnets, which led to mechanical problems.

"The fact that this happened surprised no one in this business," says Nahn. "You're just starting up a machine that's taken you 20 years to build, you're gonna run into some problems--you can't possibly foresee everything." Over the next several years, Nahn and his thousands of collaborators hope to use the accelerator to solve long-standing physics problems, such as why fundamental particles have mass.

The collider is slated to go online again in early 2009.