Fall 2012



Credit: Jen Sloan (design), George Shulin/ (mouse), Claire L. Evans/ (sunglasses)

Blind Mice See

by Sebastien Lounis

The results of a new UC Berkeley study may offer some hope for the nearly 40 million people who suffer from blindness worldwide. In a recent paper published in the journal Neuron, researchers led by Professor Richard Kramer of the department of Molecular and Cell Biology have shown that a simple chemical, known as AAQ, can restore light sensitivity to the retina for prolonged periods of time. AAQ—or acrylamide-azobenzene-quaternary ammonium when spelled out in its full, tongue-twisting form—is a small molecule that acts as a “photoswitch,” responding to light by making neurons in the retina more or less excitable and likely to fire. This switching can replace the action of dead, degenerated or missing (due to genetic mutation) rods and cones, the normally photoactive cells in the vertebrate eye. By injecting AAQ directly into the eyes of blind mice with fully degenerated rods and cones, Kramer’s group showed its ability to restore both the electrical firing of neurons in the retina, as well as light-induced behavioral responses. In particular, the treated mice showed pupils that contract in response to light and also avoided bright light, much like fully seeing animals. “The first time we observed them responding to light, it blew us away,” says Kramer.

Perhaps most exciting about the efficacy of AAQ as a retinal photoswitch is the simplicity and reversibility of treatment. Other current remedies for the loss of visual acuity, while also promising, require highly invasive or permanent procedures to restore sight, and typically target only a fraction of the retina. “AAQ is able to render nearly every cell in the retina light sensitive,” says Alexandra Polosukhina, the lead author of the study. Requiring only a minor injection and fully reversible, treatment with AAQ is also much less risky for the prospective patient. Eventually, an even less invasive slow release pill could be viable. Despite its promise, however, Polosukhina is careful to stress the early stage of this research. “It’s still a little too soon to guess exactly what type of vision AAQ and related compounds could restore,” she cautions. “Nevertheless, they could someday allow for contrast sensitivity, object recognition, and a better standard of living for individuals suffering from blindness.”

Credit: Jen Sloan (design), Fernandobrasilien/ (periodic table)

Elemental Christening

by Christopher Smallwood

Elements 114 and 116, known previously by the temporary monikers ununquadium and ununhexium, have officially been recognized as flerovium (Fl) and livermorium (Lv). The names honor the collaborative efforts of research teams at the Flerov Laboratory of Nuclear Reactions in Russia and Lawrence Livermore National Laboratory (LLNL), and were formalized last May by the International Union of Pure and Applied Chemistry (IUPAC). The new elements were synthesized by using a cyclotron to blast plutonium or curium targets with calcium ions, then waiting and hoping for instances of fusion. “It’s actually a very rare process,” says chemist Ken Moody of LLNL, a U.S. Department of Energy National Laboratory that is operated in part by UC Berkeley. “It can be frustrating waiting for weeks at a time while the cyclotron runs. You have to be stubborn.” Stubbornness has paid off this year. Flerovium joins group 14 of the periodic table, taking a seat beneath lead and tin. Livermorium shares a column with smelly tellurium, and radioactive polonium. At present, however, the defining characteristic of both elements seems to be brevity of existence: livermorium isotopes decay within milliseconds to flerovium, and Fl-289, flerovium’s most stable isotope, has a half-life of a minute or less. The announcement is part of an ongoing effort by researchers to manufacture “superheavy” elements, which inhabit the bottom of the periodic table. Progress has been steady, and an IUPAC Joint Working Party has already been established to weigh the relative merits of discovery claims for elements 113, 115, 117, and 118. With enough evidence, flerovium and livermorium may soon have named company. BSRium, anyone?

Molecules of carbon dioxide (blue and green) are captured within the pores of a zeolite mineral (red and tan). Credit: Michael Deem, Rice University

From Air to Zeolites

by Rachel Hood

Two-thirds of the electricity generated in the United States comes from power plants that burn fossil fuels and emit vast quantities of carbon dioxide (CO2). If this greenhouse gas could be captured before it escapes into the air, its effect on the global climate could be mitigated. One popular strategy, known as carbon capture and sequestration (CCS), involves capturing CO2 before it is released and storing it underground. The downside of this method is that CCS requires energy input of its own, known as parasitic energy. This makes it difficult to limit CO2 release without simultaneously increasing the amount of fossil fuel that must be burned, undermining the benefits of capturing carbon in the first place and driving up energy costs. However, recent UC Berkeley research might tip the scales toward a brighter future for carbon capture.

Led by Professor Berend Smit of the Departments of Chemical and Biomolecular Engineering and Chemistry at UC Berkeley, a team of scientists at Cal, Lawrence Berkeley National Laboratory, Rice University and the Electric Power Research Institute have developed a computational method to identify molecules that bind and sequester CO2 more effectively than current technologies, decreasing the amount of parasitic energy required for CCS. This method estimates the ability of specific compounds to capture CO2 and evaluates databases of millions of candidate compounds much more quickly than was previously possible. “Since we can do these calculations so efficiently,” Smit explains, “we can compute the lowest parasitic energy among all possible structures within a class of materials.” Smit’s group identified a number of minerals called zeolites (commonly used in industrial processes) that could reduce the energy diverted to CCS from a power plant’s overall output. Having this ability to predict a particular molecule’s effectiveness at sequestering CO2 will be a powerful tool for making our energy industry cleaner. Ultimately, Smit says, “our biggest hope is for the community to know that we are working on solutions.”

Credit: LBNL, Roy Kaltschmidt

So Long, Franklin

by Keith Cheveralls

Just as each iteration of the iPhone dethrones its predecessor from the pinnacle of consumer electronics to a quaint reminder of product cycles past, so too do supercomputers fall victim to the march of progress. After five years and over one billion computational hours, Franklin the supercomputer was retired in early May of this year.

Maintained by the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory (LBL), Franklin was a Cray XT4 supercomputer, formerly the seventh most powerful computer in the world, and a scientific workhorse used by thousands of researchers to simulate everything from ocean currents to atomic nuclei to novel rechargeable batteries. “The Franklin machine enabled discoveries that improved our fundamental understanding of biology, chemistry and physics,” says Kathy Yelick, the Associate Laboratory Director for Computing Sciences at LBL and a professor of Electrical Engineering and Computer Science at UC Berkeley.

Over its lifetime, Franklin was as prolific as it was powerful. “I would estimate about 5000 scientific papers were produced using computations run on Franklin,” Yelick says. The burden of continuing this impressive scientific output now rests with Franklin’s replacement, a Cray XE6 supercomputer that is already up and crunching. With around 150,000 processor cores, it is the eighth most powerful computer in the world—for now.