The method, published in the May 4 issue of Nature Nanotechnology, enables more precise shaping of microchip components than what is possible with current technology. More precise component shapes could help manufacturers build smaller and better microchips, the key to more powerful computers and other devices.

“We are able to achieve a precision and improvement far beyond what was previously thought achievable,” said electrical engineer Stephen Chou, the Joseph C. Elgin Professor of Engineering, who developed the method along with graduate student Qiangfei Xia. Chou’s lab has previously pioneered a number of innovative chip making techniques, including a revolutionary method for making nanometer-scale patterns using imprinting.

Microchips work best when the structures fabricated on them are straight, thin and tall. Rough edges and other defects can degrade or even ruin chip performance in most applications. In integrated circuits, for instance, such flaws could cause current to leak and voltage to fluctuate. In optic devices, they could interfere with the transmission of light. In biological devices, they could impede the flow of DNA and other biomaterials.

“These chip defects pose serious roadblocks to future advances in many industries,” Chou said.

To deal with this problem, researchers try to improve the process used to make the microchips. However, Chou said such an approach works only to a point; eventually chip makers will run up against fundamental physical limits of current manufacturing techniques. In particular, the electrons and photons that are used like chisels to carve out the microscopic features on a chip always have some random behavior. This effect becomes pronounced at very small scales and limits the accuracy of component shapes.

“What we propose instead is a paradigm shift: Rather than struggle to improve fabrication methods, we could simply fix the defects after fabrication,” said Chou. ???And fixing the defects could be automatic — a process of self-perfection.???

Chou’s method, termed Self-Perfection by Liquefaction (SPEL), achieves this by melting the structures on a chip momentarily, and guiding the resulting flow of liquid so that it re-solidifies into the desired shapes. This is possible because natural forces acting on the molten structures, such as surface tension — the force that allows some insects to walk on water — smooth the structures into geometrically more accurate shapes. Lines, for instance, become straighter, and dots become rounder.

Simple melting by direct heating has previously been shown to smooth out the defects in plastic structures. This process can’t be applied to a microchip, for two reasons. First, the key structures on a chip are not made of plastic, which melts at temperatures close to the boiling point of water, but from semiconductors and metals, which have much higher melting points. Heating the chip to such temperatures would melt not just the structures, but nearly everything else on the chip. Secondly, the melting process would widen the structures and round off their top and side surfaces, all of which would be detrimental to the chip.

Chou’s team overcame the first obstacle by using a light pulse from so-called excimer laser, similar to those used in laser eye surgery, because it heats only a very thin surface layer of a material and causes no damage to the structures underneath. The researchers carefully designed the pulse so that it would melt only semiconductor and metal structures, and not damage other parts of the chip. The structures need to be melted for only a fraction of a millionth of a second, because molten metal and semiconductors can flow as easily as water and have high surface tension, which allows them to change shapes very quickly.

To overcome the second obstacle, Chou’s team placed a plate on top of the melting structures to guide the flow of liquid. The plate prevents a molten structure from widening, and keeps its top flat and sides vertical, Chou said. In one experiment, it made the edges of 70 nanometer-wide chromium lines more than five times smoother. The resulting line smoothness was far more precise than what semiconductor researchers believe to be attainable with existing technology.

The conventional approach to fixing chip defects is to measure the exact shape of each defect, and provide a correction precisely tailored to it — a slow and expensive process, Chou said. In contrast, Chou’s guided melting process fixes all defects on a chip in a single quick and inexpensive step. “Regardless of the shape of each defect, it always gets fixed precisely and with no need for individual shape measurement or tailored correction,” Chou said.

One of the big surprises from this work is observed when the guiding plate is placed not in direct contact with the molten structures, but at a distance above it. In this situation, the liquid material from the structures rises up and reaches the plate by itself, causing line structures to become taller and narrower — both highly desirable outcomes from a chip design perspective.

“The authors demonstrate improved edge roughness and dramatically altered aspect ratios in nanoscale features,” said Donald Tennant, director of operations at the NanoScale Science and Technology Facility at Cornell University. The techniques “may be a way forward when nanofabricators bump up against the limits of lithography and pattern transfer,” he said.

Next, Chou’s group plans to demonstrate this technique on large (8-inch) wafers. Several leading semiconductor manufacturers have expressed keen interest in the technique, Chou said.

[Steven Schultz @ Princeton University Engineering School]

Among the most important and complex molecules in the human body, sugars control not just metabolism but also how cells communicate with one another. Graduating senior Jeffery Martin has put his basic knowledge of sugars to exceptional use by creating a lab-on-a-chip device that builds complex, highly specialized sugar molecules, mimicking one of the most important cellular structures in the human body — the Golgi Apparatus.

“Almost completely independently he has been able to come closer than researchers with decades more experience to creating an artificial Golgi,” said Robert Linhardt, the Ann and John H. Broadbent Jr. ‘59 Senior Constellation Professor of Biocatalysis and Metabolic Engineering at Rensselaer and Martin’s adviser. “He saw a problem in the drug discovery process and almost instantly devised a way to solve it.”

Cells build sugars in a cellular organelle known as the Golgi Apparatus. Under a microscope, the Golgi looks similar to a stack of pancakes. The strange-looking organelle finishes the process of protein synthesis by decorating the proteins with highly specialized arrangements of sugars. The final sugar-coated molecule is then sent out into the cell to aid in cell communication and to help determine the cell’s function in the body.

Martin’s artificial Golgi functions in a surprisingly similar way to the natural Golgi, but he gives the ancient organelle a very high-tech makeover. His chip looks similar to a miniature checker board where sugars, enzymes, and other basic cell materials are suspended in water and can be transported and mixed by applying electric currents to the destination squares on the checker board. Through this process sugars can be built in an automated fashion where they are exposed to a variety of enzymes found in the natural Golgi. The resulting sugars can then be tested on living cells either on the chip or in the lab to determine their effects. With the chip’s ability to process many combinations of sugars and enzymes, it could help researchers quickly uncover new sugar-based drugs, according to Martin.

Scientists have known for years that certain sugars can serve as extremely beneficial therapeutics for humans. One well-known example is heparin, which is among the most widely used drugs in the world. Heparin is formed naturally in the Golgi organelle in cells of the human body as well as in other animals like pigs. Heparin acts as an anticoagulant preventing blood clots, which makes it a good therapeutic for heart, stroke, and dialysis patients.

The main source of heparin is currently the intestines of foreign livestock and, as recent news reports highlight, the risk of contamination from such sources is high. So researchers are working around the clock to develop a safer, man-made alternative to the drug that will prevent outside contamination. A synthetic alternative would build the sugar from scratch, helping eliminate the possibility of contamination he explained.

“I am very grateful to have the privilege of working with Dr. Linhardt who has discovered the recipe to make fully synthetic heparin,” Martin said. “Because we know the recipe, I am going to use it as a model to test the device. If our artificial Golgi can build fully functional heparin, we can then use the artificial organelle to produce many different sugar variants by altering the combination of enzymes used to synthesize them. Another great thing about these devices is that they are of microscale size, so that if needed we could fill an entire room with them to increase throughput for drug discovery.”

There are millions of possible sugar combinations that can be formed and scientists currently only know the function of very few of them like heparin. “Since it is known that these types of sugars play a part in many important biological processes such as cell growth, cell differentiation, blood coagulation, and viral defense mechanisms, we feel that that this artificial Golgi will help our team to develop a next generation of sugar-based drugs, known as glycotheraputics,” Martin said. “We are going to start making new combinations and we simply don’t know what we are going to find. We could find a sugar whose signal blocks the spread of cancer cells or initiates the differentiation of stem cells. We just don’t know.”

Martin, a Barry M. Goldwater Scholar and native of the small town of Boylston, Mass., is graduating from Rensselaer on May 17, 2008 with a nearly perfect GPA. He plans to continue on at Rensselaer as a graduate student, working with Linhardt to test and further develop his artificial Golgi.

[Gabrielle DeMarco @ Rensselaer Polytechnic Institute]

In a paper published today in Nature Biotechnology, researchers led by Los Alamos National Laboratory and the U.S. Department of Energy Joint Genome Institute announced that the genetic sequence of the fungus Tricoderma reesei has uncovered important clues about how the organism breaks down plant fibers into simple sugars. The finding could unlock possibilities for industrial processes that can more efficiently and cost effectively convert corn, switchgrass and even cellulose-based municipal waste into ethanol. Ethanol from waste products is a more-carbon-neutral alternative to gasoline.

The fungus T. reesei rose to dubious fame during World War II when military leaders discovered it was responsible for rapid deterioration of clothing and tents in the South Pacific. Named after Dr. Elwyn T. Reese, who, with colleagues, originally isolated the hungry fungus, T. reesei was later identified as a source of industrial enzymes and a role model for the conversion of cellulose and hemicellulose — plant fibers — into simple sugars.

The organism uses enzymes it creates to break down human-indigestible fibers of plants into the simplest form of sugar, known as a monosaccharide. The fungus then digests the sugars as food.

Researchers decoded the genetic sequence of T. reesei in an attempt to discover why the deep green fungus was so darned good at digesting plant cells. The sequence results were somewhat surprising. Contrary to what one might predict about the gene content of a fungus that can eat holes in tents, T. reesei had fewer genes dedicated to the production of cellulose-eating enzymes than its counterparts.

“We were aware of T. reesei’s reputation as producer of massive quantities of degrading enzymes, however we were surprised by how few enzyme types it produces, which suggested to us that its protein secretion system is exceptionally efficient,” said Los Alamos bioscientist Diego Martinez (also at the University of New Mexico), the study’s lead author. The researchers believe that T. reesei’s genome includes “clusters” of enzyme-producing genes, a strategy that may account for the organism’s efficiency at breaking down cellulose.

On an industrial scale, T. reesei could be employed to secrete enzymes that can be purified and added into an aqueous mixture of cellulose pulp and other materials to produce sugar. The sugar can then be fermented by yeast to produce ethanol.

“The sequencing of the Trichoderma reesei genome is a major step towards using renewable feedstocks for the production of fuels and chemicals,” said Joel Cherry, director of research activities in second-generation biofuels for Novozymes, a collaborating institution in the study. “The information contained in its genome will allow us to better understand how this organism degrades cellulose so efficiently and to understand how it produces the required enzymes so prodigiously. Using this information, it may be possible to improve both of these properties, decreasing the cost of converting cellulosic biomass to fuels and chemicals.”

[James E. Rickman @ DOE/Los Alamos National Laboratory]