Volume 3, Issue 22 August/September 2006
Simulating the Stars
Richard Klein uses supercomputers around the country to run his simulations.
There are one hundred billion stars in our own galaxy alone, yet we know very little about how they got there. Star formation has been one of the richest problems in astrophysics for decades. Recently though, UC Berkeley astronomer Richard Klein and his colleagues have learned a great deal about this mystery by watching the mathematics behind them unfold on a computer screen.
"You can gain insight into some of these problems with analytical approximation and solving equations with pencil and paper, but the types of systems we're dealing with now are so complicated that you can't fully describe the phenomena unless you do large scale numerical simulations," says Klein, an adjunct professor of astronomy at Berkeley who is also a staff scientist at Lawrence Livermore National Laboratory.
A slice through a 3-D simulation of a turbulent clump of molecular hydrogen, with the densest areas shown in red. The zoom-in shows a protostar accreting gas and creating a dense wake behind it. The simulation shows that a protostar, once formed, cannot accrete much more gas from the surrounding clump, contradicting the competitive accretion theory. (Credit: Mark Krumholz)
For the last ten years, Klein and his collaborators have developed high-resolution computer simulations that enable them to model their theories of star formation in three dimensions. Last year, Klein, former grad student Mark Krumholz, and physics and astronomy professor Chris McKee used their supercomputer simulations to knock down a commonly-held theory about star formation inside cold clouds of molecular hydrogen. In previous years, Klein and colleague Jonathan Arons of the Department of Astronomy not only proposed and modeled a novel theory about the formation of photon bubbles on the surface of neutron stars, but made headlines when they used an orbiting telescope to confirm their theory.
"Fifteen years ago, simulations like these would have taken 50,000 years to run on a single processor machine of the time," Klein says. "But with today's supercomputers, they might take a month running on a machine with several hundred processors working in parallel."
While the exponential increase in computing power has been a boon for Klein's research, the real secrets to his success are the computer programs he and his team develop, and the analytical work that accompanies the code. The simulations, he explains, are so complicated that they'd be meaningless unless you had an idea of what you were looking for.
"It's like mining in the side of a mountain," he says. "You really need to know the kind of jewel you're after before you start digging."
An image from NASA's Hubble Space Telescope of 30 Doradus, a vast region of gas and dust where stars are born.
Since the 1980s, researchers have attempted to use simulations to follow the birth of stars from their likely birthplace in dynamical turbulent clouds. The problem was that then state-of-the-art computers, and the code written for them, could only model the phenomena in two dimensions, an inherent discrepancy between the simulation and the real world. In the 1990s though, Klein noticed that applied mathematicians had developed extremely economical methods to solve similar equations having to do with fluid dynamics in three dimensions. Klein and his collaborators were the first to apply the method, called Adaptive Mesh Refinement, to problems in astrophysics.
"We now had the capability of solving equations that could go over many order of magnitudes of spatial scales all in one computer simulation," he says. "And we had a field day with that."
Klein and McKee founded the Berkeley Astrophysical Fluid Dynamics Group as a hub to bring this new breed of mathematical models to problems throughout the cosmos. Along the way, the group has advanced the understanding of how winds are generated from the hot accreting disks surrounding black holes and theories about the interactions of shock waves from supernovae with clumps of gas in the galaxy. Those collisions compress the clouds and may lead to the formation of new stars.
An image from a simulation of high mass star formation.
(courtesy the researchers)
These days, the group is focused on the development and modeling of a comprehensive theory of star formation, accounting for radiation, hydrodynamics, gravity, magnetic fields, and all other physical phenomena as they relate to the birth of stars. On one hand is the question of how low mass stars, like our own sun, form. Another very different problem surrounds the formation of stars that may be a hundred times the mass of the sun. These massive stars play an important role in the evolution of the galaxy as they explode into supernovae and spew forth the heavy elements that surround us and are part of us.
"It's amazing that out of pure thought you can sometimes write down a set of equations and use those to model the way that nature actually works," Klein says.
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Life 2.0
Jay Keasling (center) with graduate students Doug Pitera (right) and Sydnor Withers (left). "My dream is to see my laboratory's technology producing inexpensive drugs for the Third World," says Keasling. (Bart Nagel photo)
For 3.6 billion years, evolution has governed the biology of this planet. Molecular biologists can now shift bits of DNA from one organism to another, but the parts they play with are limited to what Mother Nature provides. Recently, Mother Nature teamed up with a handful of researchers whose aim is nothing short of reengineering life. UC Berkeley chemical engineer Jay Keasling is leading a new center funded by the National Science Foundation to create the future of synthetic biology, where genes, proteins, and cells are snapped together to build living systems.
"The idea of synthetic biology is to do for biology what electrical engineers have done for circuit design and chemists have done for the synthesis of chemicals," says Jay Keasling, professor in the Departments of Chemical Engineering and Bioengineering. "We're turning biology into an engineering field."
Already, Keasling--who also heads the Lawrence Berkeley National Laboratory's Synthetic Biology Department and QB3's Berkeley Center for Synthetic Biology--has made strides in converting bacteria into chemical factories that produce the anti-malaria treatment artemisinin for pennies instead of dollars. Similar microbial factories could crank out the costly anti-cancer drug Taxol, synthesized naturally by the Pacific yew tree, or produce a promising anti-AIDS drug derived from the Samoan mamala tree.
Under the umbrella of the new Synthetic Biology Engineering Research Center (SynBERC), funded with a $16 million, five-year NSF grant, Keasling and his colleagues are beginning to engineer organisms that produce hydrogen, octane, or molecules for alternative energy applications. The Synthetic Biology researchers are also prototyping a bacterium that eats toxic waste, such as heavy metals. Keasling is leading the charge to engineer a single-cell soil microorganism, Pseudomonas putida, that would swim into a pool of pesticides or nerve agents and degrade the chemicals. Another project's goal is to develop the next-generation of tumor-fighting drug delivery systems in the form of a novel microbe.
Sweet wormwood, or Artemisia annua, used by Chinese herbalists since A.D. 150 to treat fevers, today holds promise of a cure for malaria, a disease that kills one African child every 30 seconds. (Bart Nagel photo)
SynBERC is a collaborative effort among UC Berkeley, Harvard, the University of California, San Francisco, and the Massachusetts Institute of Technology. Together, the researchers will create a "parts store" of interchangeable components that can be combined together to make devices, for instance a microorganism that "eats" heavy metals or nerve agents for bioremediation of hazardous waste sites.
"We'd want to build devices that can be put inside a chassis, a cell," says Keasling. "Energy will be one of the greatest applications of this."
Recently, the group began designing an organism that can ferment cellulose as a raw source of renewable energy. While ethanol is often touted as an ideal alternative fuel whose production could be boosted with synthetic biology, Keasling points out that it can't be piped easily and has relatively low energy content. Instead, he'd like to engineer a benign organism to degrade waste paper or biomass and convert it into octane. However, inserting cellulose-converting proteins into a bacterium and scaling the process up to be practical is no easy task.
"You've got a relatively complicated and dirty system," Keasling says. So you've got to engineer a microbe to actually go in, find the cellulose, turn it into sugar, and then through its metabolism turn that into fuel."
UC Berkeley's Jay Keasling (left) and ethnobotanist Paul Alan Cox (right) sign agreement with village elders in Samoa, agreeing to share with them any royalties from sales of an anti-AIDS drug derived from the native mamala tree. (Photo courtesy Steven King)
Along with energy, Keasling envisions a revolution in medicine driven in part by advances in synthetic biology. Someday, he hopes to engineer stem cells that can be programmed to build replacement organs for transplant into patients without rejection. Closer to reality, though, are microbes that hone in on tumors in the body and release drugs to attack the cancer cells.
"It's the ultimate in detection, deployment, and tumor killing in a single apparatus," Keasling says.
While progress is rapidly accelerating, synthetic biology is still in its infancy. In many ways, it's where genetic engineering was before the launch of the Human Genome Project. And the public fear surrounding genetic engineering is not lost on Keasling. Ideally, synthetic biology will be self-regulated, he says, without the need for government intervention. But before scientists can convince the public that the field is safe, they themselves have to be sure that it is safe. To that end, the SynBERC researchers will also be exploring the societal implications of their work, from how intellectual property laws may need to be reconsidered to the ethics of reinventing biology from the bottom up.
"It's getting easier to engineer life, and synthetic biology will make it simpler still," Keasling says. If the public doesn't realize you can use it to make new drugs or renewable energy, it will look like we're tinkering with life. As scientists, it's our responsibility to prove that synthetic biology has tremendous potential to save lives."
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Mapping the Future of Field Geology
George Brimhall also teaches a groundbreaking undergraduate course titled, "Crossroads of Earth Resources and Society: Iconic Events in American History and Their Influence Today."
In 1818, William "Strata" Smith ushered in the modern practice of field geology with his publication of the first hand-painted, color geological map of England and Wales. Two centuries later, the tools haven't changed much. Recently though, UC Berkeley geologist George Brimhall and his colleagues have developed mapping software that they hope will bring field geology kicking and screaming into the digital age.
Today's field scientists use paper topographic maps and a box of colored pencils," says Brimhall, professor of geology in the Department of Earth and Planetary Science. "They're using technology from the second grade to map complex problems in geology of great importance to society."
Brimhall's software application GeoMapper leverages two developments in information technology. Geographical Information Systems (GIS) are tools for the creation, access, and analysis of high-resolution spatial data. The GIS digital maps enable the easy correlation of data from different sources. For example, aerial photography of a region might be overlaid with rainfall information and land use maps or geophysical maps of earthquake epicenters and magnitudes. Google Earth is one example of a GIS. However, the systems available to geologists provide much higher resolution of features on the ground. Indeed, GIS has been a common laboratory research tool for geologists for some time, but in the field, paper still reigns supreme.
Using GeoMapper, Brimhall and his colleagues created a map of mine waste dumps in Spenceville, California. The team flew in a helicopter over the site to take infrared spectra samples of the ground below that provided insight into the surface mineralogy. (courtesy the researchers)
Currently, a geologist might walk across a piece of land with a paper map in hand. As she recognizes various kinds of rocks, she colors those on the map. For example, a red band might indicate shale while blue pencil denotes granite. Back in the lab, that data from the field must then be entered manually into the computer so the new information can be overlaid on top of GIS maps. Brimhall's approach is to eliminate that middle step through inexpensive portable computers, GPS technology that pinpoints your exact location on the planet, and innovative software. The software provides a scientifically intuitive user interface of pictorial "buttons" to map and label rock types, faults, structures, and earth resources. Using a portable PC equipped with a stylus interface, the geologist an click directly on the pictorial buttons and "write" directly on the screen. A small GPS system plugged into the tablet keeps track of the user's location in the field.
A map with a legend showing a portion of the interpreted surface mineralogy at Spenceville. (courtesy the researchers)
"The result is that the field geologist can do that visual translation, writing observations about the rocks and structures, directly into the GIS system right then while their location is automatically recorded," Brimhall says.
GeoMapper is used to create these maps in the field. Of course, data capture is just one of the benefits of the portable mapping system. The technology isn't just for making digital maps, but accessing them as well.
"You can load satellite images, detailed topographic maps, and field data onto the tablet PC so you can view a huge amount of 3D geospatial information while you're outside," Brimhall says. "This brings information to the geologists when they need it, out in the natural environment, not just when you're sitting at your computer back in the office."
In one experiment, the researchers tested the system's value in screening abandoned mines to identify those most in need of environmental remediation. The team employed a chemical spectrometer to identify areas with the most
In one early demonstration, the researchers used GeoMapper to create a raised-relief scale model of the University of California, Berkeley campus 3 by 6 feet in size for use by blind and disabled students to learn their way around the campus. (courtesy the researchers)
"Instead of having to walk every square inch of ground, you can spend your time much more judiciously just by virtue of having this information on your computer with you," Brimhall says. "This is really about making science portable."
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Berkeley's Scientific Legacy
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