Revolutionary computer chips in development at the University of Wisconsin-Madison could make future computers much more efficient and powerful.
With funding from a Defense Advanced Research Projects Agency (DARPA) young investigator award, Jing Li, an assistant professor of electrical and computer engineering at UW-Madison, is creating fully morphable computer chips that can be configured to perform complex calculations, store massive amounts of information within the same integrated unit and perform efficient communication across units.
She has named the new chips “Liquid Silicon.” “Liquid means software and silicon means hardware. It is a collaborative software/hardware technique,” says Li. “You can have a supercomputer in a box if you want. We want to target a lot of very interesting and data-intensive applications, including facial or voice recognition, natural language processing, and graph analytics.”
The chips will pack a powerful computational punch, while being able to store significant amounts of data—tasks that require two entirely different types of hardware in modern computers.
That separation makes our machines less efficient.
“There’s a huge bottleneck when classical computers need to move data between memory and processor,” says Li. “We’re building a unified hardware that can bridge the gap between computation and storage.”
Right now, processor and memory chips are separately produced by different manufacturing foundries owned by different industries. Then, they are assembled together by system engineers on printed circuit boards to make computers and smartphones. The wide separation between computation and storage means that even simple operations, like searches, require multiple steps to accomplish: first fetching data from the memory, then sending that data all the way through the deep storage hierarchy to the processor core.
The chips that Li is developing, by contrast, incorporate memory, computation and communication into the same device using monolithic 3D integration: silicon CMOS circuitry on the bottom connected with solid-state memory arrays on the top using dense metal-to-metal links.
End users will be able to configure the devices to allocate more or fewer resources to memory or computation, depending on what types of applications a system needs to run.
“It can be dynamic and flexible,” says Li. “We originally worried it might be too hard to use because there are too many options. But with proper optimization, anyone can take advantage of the rich flexibility offered by our hardware.”
To help people harness the new chip’s potential, Li’s group also is developing software that translates popular programming languages into the chip’s machine code, a process called compilation.
“If I just handed you something and said, ‘This is a supercomputer in a box,’ you might not be able to use it if the programming interface is too difficult,” says Li. “You cannot imagine people programming in terms of binary zeroes and ones. It would be too painful.”
Thanks to her compilation software, programmers will be able to port their applications directly onto this new type of hardware without changing their coding habits.
To evaluate the performance of prototype liquid silicon chips, Li and her students established an automated testing system they built from scratch. The platform is so versatile that it can reveal reliability problems that even the most advanced industry testing setup typically cannot observe. That’s also why multiple companies recently have sent chips to Li for evaluation.
Given that testing accounts for more than half the consumer cost of computer chips, having such advanced infrastructure at UW-Madison will not only help make liquid silicon chips a reality, but also facilitate future research.
“We can do all types of device-level, circuit-level and system-level testing with our platform,” says Li. “Our industry partners told us that our testing system does the entire job of a test engineer automatically.”
Li is the first computational researcher at UW-Madison ever to receive a DARPA Young Faculty Award. In 2016, she joins 25 other young faculty award recipients nationwide whose research topics range from gene therapy to machine learning. The grant guarantees $500,000 of support for two years.
Scientists have identified a new “multicomponent” virus — one containing different segments of genetic material in separate particles — that can infect animals, according to research published today in the journal Cell Host & Microbe.
This new pathogen, called Guaico Culex virus (GCXV), was isolated from several species of mosquitoes in Central and South America. GCXV does not appear to infect mammals, according to first author Jason Ladner, Ph.D., of the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID). However, the team also isolated a related virus — called Jingmen tick virus, or JMTV — from a nonhuman primate. Further analysis demonstrates that both GCXV and JMTV belong to a highly diverse and newly discovered group of viruses called the Jingmenvirus group.
Taken together, the research suggests that the host range of this virus group is quite diverse–and highlights the potential relevance of these viruses to animal and human health.
“Animal viruses typically have all genome segments packaged together into a single viral particle, so only one of those particles is needed to infect a host cell,” Ladner explained. “But in a multicomponent virus, the genome is divided into multiple pieces, with each one packaged separately into a viral particle. At least one particle of each type is required for cell infection.”
Several plant pathogens have this type of organization, but the study published today is the first to describe a multicomponent virus that infects animals.
Working with collaborators including the University of Texas Medical Branch and the New York State Department of Health, the USAMRIID team extracted and sequenced virus from mosquitoes collected around the world. The newly discovered virus is named for the Guaico region of Trinidad, where the mosquitoes that contained it were first found.
In collaboration with a group at the University of Wisconsin-Madison, the USAMRIID investigators also found the first evidence of a Jingmenvirus in the blood of a nonhuman primate, in this case a red colobus monkey living in Kibale National Park, Uganda. The animal showed no signs of disease when the sample was taken, so it is not known whether the virus had a pathogenic effect.
Jingmenviruses were first described in 2014 and are related to flaviviruses — a large family of viruses that includes human pathogens such as yellow fever, West Nile and Japanese encephalitis viruses.
“One area we are focused on is the identification and characterization of novel viruses,” said the paper’s senior author Gustavo Palacios, Ph.D., who directs USAMRIID’s Center for Genome Sciences. “This study allowed us to utilize all our tools–and even though this virus does not appear to affect mammals, we are continuing to refine those tools so we can be better prepared for the next outbreak of disease that could have an impact on human health.”
While it is difficult to predict, experts believe that the infectious viruses most likely to emerge next in humans are those already affecting other mammals, particularly nonhuman primates.
See NPR.org for a more detailed explanation . . .
Researchers at the University of Wisconsin–Madison have confirmed that a benign bacterium called Wolbachia pipientis can completely block transmission of Zika virus in Aedes aegypti, the mosquito species responsible for passing the virus to humans.
Matthew Aliota, a scientist at the UW–Madison School of Veterinary Medicine(SVM) and first author of the paper — published today (July 1, 2016) in the journal Scientific Reports — says the bacteria could present a “novel biological control mechanism,” aiding efforts to stop the spread of Zika virus.
Thirty-nine countries and territories in the Americas have been affected by the Zika epidemic, and it is expected that at least 4 million people will be infected by the end of the year. Scientists believe the virus is responsible for a host of brain defects in developing fetuses, including microcephaly, and has contributed to an uptick in cases of a neurological disorder called Guillain-Barre syndrome. There are not yet any approved Zika virus vaccines or antiviral medications, and ongoing mosquito control strategies have not been adequate to contain the spread of the virus.
Researchers led by Jorge Osorio, a UW–Madison professor of pathobiological sciences, and Scott O’Neill of the the Eliminate Dengue Program (EDP) and Monash University in Melbourne, Australia, are already releasing mosquitoes harboring the Wolbachia bacterium in pilot studies in Colombia, Brazil, Australia, Vietnam and Indonesia to help control the spread of dengue virus. Their work is supported by the Bill and Melinda Gates Foundation.
An important feature of Wolbachia is that it is self-sustainable, making it a very low-cost approach for controlling mosquito-borne viral diseases that are affecting many tropical countries around the world.
A novel, inexpensive method for detecting the Zika virus could help slow spread of outbreak, and potentially other future pandemic diseases
An international, multi-institutional team of researchers led by synthetic biologist James Collins, Ph.D., at the Wyss Institute for Biologically Inspired Engineering at Harvard University, has developed a low-cost, rapid paper-based diagnostic system for strain-specific detection of the Zika virus, with the goal that it could soon be used in the field to screen blood, urine, or saliva samples.
“The growing global health crisis caused by the Zika virus propelled us to leverage novel technologies we have developed in the lab and use them to create a workflow that could diagnose a patient with Zika, in the field, within 2-3 hours,” said Collins, who is a Wyss Core Faculty member, and Termeer Professor of Medical Engineering & Science and Professor of Biological Engineering at the Massachusetts Institute of Technology (MIT)’s Department of Biological Engineering.
Building off previous work done at Harvard’s Wyss Institute by Collins and his team, along with collaborators from Massachusetts Institute of Technology (MIT), the Broad Institute of Harvard and MIT, Harvard Medical School (HMS), University of Toronto, Arizona State University (ASU), University of Wisconsin-Madison (UW-Madison), Boston University (BU), Cornell University, and Addgene, joined their efforts to quickly prototype the rapid diagnostic test and describe their methods in a study published online May 6 in the journal Cell, all within a matter of six weeks. Collins is the paper’s corresponding author.
Emerging innovation during the Ebola health crisis
In October 2014, Collins’ team developed a breakthrough method for embedding synthetic gene networks — which could be used as programmable diagnostics and sensors – on portable, small discs of ordinary paper.