Volume 5, Issue 34 January 2008
Souping Up Superconductors
Alessandra Lanzara is a Berkeley professor of physics and a member of Lawrence Berkeley National Laboratory's Materials Sciences Division. Photo credit: courtesy Alessandra Lanzara
Imagine a world where electricity was virtually free and the means to store it limitless. Alessandra Lanzara, a Berkeley professor of physics, sees a way to reach this goal: by restringing the power grid with high temperature superconductors.
"There is a lot of waste getting electricity from its production site to your home. This is because materials that carry a current have resistivity; their conduction isn't perfect," Lanzara says.
Superconductors, on the other hand, can transmit a current without loss when chilled below a critical temperature. Power lines made of superconductors, Lanzara argues, could retain the energy now lost to waste, drastically increasing the amount available for use and decreasing its cost. Superconductors can also hold a current indefinitely without any loss of power, making them ideal for storing intermittent energy from sources like the sun.
There is a catch, however-the expense of keeping power lines cold largely offsets any gains in energy efficiency. The first superconductor, discovered in 1911, operated at a phenomenally cold -269 degrees Celsius. Since then, scientists have hit upon so-called high temperature superconductors. Made of ceramics mixed with other elements such as copper and oxygen, these materials must still be chilled to below -140 degrees Celsius to conduct electricity freely.
Lanzara uses a method called photoemissions spectroscopy to measure electron behavior within superconductors. Here, a photon of light hits a sample of graphene. The released electron reveals how it was traveling in the sample. Image credit: Alessandra Lanzara
"We are trying to understand, when you cool them down, what the driving force is behind superconductivity. If you identify the mechanism here, maybe you can use this information to engineer a new material that superconducts at a higher temperature," Lanzara says.
A superconductor's remarkable properties derive from the flow of electrons within it. Lanzara observes this movement in superconductors using a technique called photoemission spectroscopy. Using light, she excites electrons to emerge from her sample. By mapping the angles and velocities of exiting electrons, Lanzara can deduce how they were moving inside each material.
Under normal conditions, electrons are negatively charged and should repel one another. But when a metallic superconductor drops below a critical temperature, its electrons suddenly begin traveling in pairs. The movement of these particles is akin to two bowling balls rolling across a mattress. The first electron deforms the energetic space through which electrons travel. This makes a second electron following close behind likely to follow the same path. In traditional superconductors, the mattress effect can be identified by the atomic vibrations, or phonons, it triggers.
"The big question is whether this mattress effect is still at work in the new ceramic superconductors," Lanzara says.
To find out, Lanzara has developed a new twist on photoemissions spectroscopy. She measures not only the speed and trajectory of emerging electrons, but also their spin dynamics as well. This additional piece of data allows Lanzara to describe in unprecedented detail how electrons behave within a sample.
Lanzara has developed a way to improve graphene's superconductivity. Growing graphene on silicon carbide disrupts the symmetry of its atoms, and opens a gap in its electron bands crucial for its use in electronic devices. Image credit: Alessandra Lanzara
Lanzara also studies another material with unusual properties: graphene. Essentially made of carbon atoms interlocked in open rings, graphene's airy structure lets electrons travel long distances through it at ballistic speeds without hitting any obstructions. This simple lattice also allows graphene to be molded into shapes just one atom thick. Meanwhile, its high carbon content can withstand very high temperatures. For these reasons, graphene is a leading candidate to replace silicon in a new generation of tiny, superfast computer chips.
But before this can happen, scientists must learn to modulate graphene's electrical properties. Silicon functions as a transistor because there is a gap between its tightly bound valence band electrons and its more loosely bound conduction electrons.
Graphene normally lacks this gap. But Lanzara has been able to induce a gap by growing a thin layer of graphene on semiconducting substrates. Her approach could lead to methods of mass manufacturing graphene for electronic devices.
"I like basic research, but when I chose which type of physics to go into, for me it was really important to have a potential application," Lanzara says. "If I figure out what is going on with this material, maybe I can make a big change in the way we live and contribute to something really special."
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Truth in Data
Professor of Biostatistics and Statistics Mark van der Laan. Photo credit: courtesy Mark van der Laan
Scientific findings influence everything from our eating habits-are bananas healthier than blueberries?-to cancer treatments that can spell the difference between life and death. But when it comes to scientific studies, results can be deceiving. According to a 2005 literature review, published research claims are more likely to be false than true.
The problem, says Mark van der Laan, lies neither with science nor data. A Berkeley professor of biostatistics and statistics, van der Laan develops data analysis methods that promise to make studies more accurate and reliable.
One major aspect of his research involves clinical trials. Often, these trials enroll hundreds or thousands of subjects, may last for many years, and cost hundreds of millions of dollars to administer. But, on average, roughly one in four subjects drops out before a study's official endpoint.
What to do with this incomplete, or censored, data constitutes a major dilemma. At present, most studies simply discard censored data, but van der Laan says ignoring this information is not only wasteful, it also can introduce a dangerous bias to study results.
Roughly a quarter of all patients tend to drop out of clinical trials evaluating drugs and other medical treatments. Photo credit: David Richfield
In drug trials, for example, dropouts often develop side effects or fail to respond to the treatment. "Maybe the people you're tossing out are very different kinds of people than the rest of the trial participants. So the sample you've used isn't representative of the group you were originally looking at," says van der Laan. "By ignoring them, you're tossing away all of the bad outcomes. Your treatment will look better than it really is."
He is developing statistical methods that allow censored data to be incorporated in study results. His methods first try to understand why subjects drop out. Medical files frequently indicate why someone switched to a different treatment. Once the reasons behind a patient's noncompliance are understood, it's possible to account for the bias incurred by omitting this data. Similarly, van der Laan's methods can help predict the outcomes for these patients if they had participated in the trial to its end.
Currently, says van der Laan, censored data in clinical trials is handled with naïve and often biased methods. To help change that, he has begun collaborating with the Food and Drug Administration to demonstrate that techniques to incorporate censored data are robust, efficient, and reliable enough for medical studies.
He is also studying how to estimate the proportionate effect of a particular intervention. He uses a technique called causal inference to address such questions as the effect of smoking on lung disease or the impact of hormone replacement therapy on heart disease.
One of van der Laan's research areas is causal inference, an area of statistics that resolve questions such as whether cigarette smoking causes lung disease. Photo credit: Tomasz Sienicki
The problem is that data often come from subjects who have elected a certain treatment, and they might not be a statistically representative pool. "Perhaps the women who took hormone replacement therapy were wealthier, or more educated, or more compliant than other women," says van der Laan. "Maybe we're seeing the effect of these confounding factors rather than the effects of the intervention."
Often, van der Laan says, disentangling such factors is impossible. But many scientists will continue to massage their data until they find a correlation to ensure the study appears in a journal. He hopes to overcome this "pressure to publish" by convincing journals to publish negative results and require scientists to declare their analysis methods before a study begins.
"It's why I often say statistics is a brutal field if you do it right," says van der Laan. As rough as getting to the truth might be, the result should be more informed decisions and better health for all.
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The Copy Machine of the Cell
Michael Botchan is a professor of biochemistry and molecular biology and a faculty affiliate of QB3. photo credit: Ed Ralston
There comes a time in many a cell's life when it feels the need to reproduce. But before it can split into two, it must fashion a second set of genetic instructions to pass on to the new cell.
When Berkeley professor of biochemistry and molecular biology Mike Botchan first began studying chromosome copying, basic questions about the process remained unknown. He wanted to understand how and where DNA replication began. Over the past three decades, Botchan has been instrumental in piecing together the story of what he calls "the elaborate dance of replication."
Botchan began by studying viruses, the simplest of all life forms. These microbes contain relatively few genes in their chromosome, borrowing much of the machinery needed to duplicate their own DNA from host cells. Because the viral chromosome constitutes a tiny fraction of the DNA in a host cell, its chances of encountering the necessary copying proteins are low. To compensate, Botchan found, viruses use a DNA sequence that binds strongly to these replication proteins.
To decipher the string of events required to start replication, Botchan mapped the initiation site-a place on a chromosome where replication begins-in a virus. He found that a certain DNA sequence attracts a virus protein involved in replication initiation. Only then can the virus helicase, which unwinds and separates the strands of DNA, bind to the chromosome and start unraveling DNA. The unwinding process attracts cellular proteins needed to copy the virus chromosome.
Botchan found a protein complex that higher animals use to locate where DNA replication should begin. In a fruit fly egg, this complex (red) can be seen where there is both DNA (blue) and new strands of DNA are being replicated from component nucleotides (green). Image credit: courtesy Michael Botchan
But do more complex organisms, such as insects and humans, copy their DNA in a similar fashion? To find out, Botchan studied a case of unchecked DNA replication in fruit fly embryos. The cells that go on to form the fly's eggshell duplicate certain sections of their DNA with astonishing rapidity, initiating replication at many sites at once. In these cells, Botchan found and characterized a complex of proteins that finds the initiation site and prepares the chromosome so that a core replication machine can be assembled there. The core replication machine includes a six-protein complex used at all DNA replication sites. Several of these proteins form a pinwheel structure that encircles DNA, while another links to the polymerase enzyme that "reads" the sequence. In cells actively copying their DNA, all of these proteins are located right on top of one another.
Botchan found that this core DNA replication protein complex has no preference for particular stretches of DNA. This explains why DNA duplication can occur at many sites simultaneously in fly embryos. Early on in development, a fly's chromosomes resemble long necklaces of DNA. But as the embryo matures, its chromosomes curl into spirals resembling a coiled telephone cord. Now replication can begin only at well-defined initiation sites. This is because the core replication complex can only bind to open regions of the chromosome where other cell-specific protein complexes help it to attach.
A chromosome's three-dimensional coils also help determine which genes are turned on and shut off. "The process of getting the chromosome prepared for gene expression and replication go hand in glove," Botchan says. "The same factors that recognize certain DNA sequences for initiation also make the region of the chromosome available for protein transcription."
Botchan's work, along with research by Berkeley biologists Eva Nogales and James Berger, helps prove that DNA replication has changed very little across evolution. "All three kingdoms of life share a basic core machinery that assembles on DNA and prepares it for unwinding," Botchan says. Organisms ranging from E. coli to fruit flies, they find, have nearly identical chromosome copying methods, cementing the relationship of all life forms back to that first ancestral cell.
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