Research on Blue Waters Points to Cheaper DNA Sequencing with Graphene

February 19, 2018

Feb. 19 — Since its discovery in 2004, graphene has captured imaginations and sparked innovation in the scientific community. Perhaps rightly so as it is 200 times stronger than the strongest steel but still flexible, incredibly light but extremely tough, and conducts heat and electricity more efficiently than copper. Professor Jerry Bernholc of North Carolina State University is utilizing the National Center for Supercomputing Applications’ Blue Waters supercomputer at the University of Illinois at Urbana-Champaign to explore graphene’s applications, including its use in nanoscale electronics and electrical DNA sequencing.

Graphene and Nanoscale Electronics

Currently, the trend toward smaller silicon semiconductors seems to be slowing down as it reaches limits of small scale. The world is moving past Moore’s Law, the idea that every two years computer processing speed will double and costs will decrease. Transistor density is still increasing but speed increases have slowed dramatically. In addition to that, systems are no longer shrinking like they did in the past as transistors reach physical limits.

This is bad news for those trying to use very fast computers, or any electronics for that matter, that have been getting thinner and thinner.

However, graphene may be a new way forward.

“We’re looking at what’s beyond Moore’s law, whether one can devise very small transistors based on only one atomic layer, using new methods of making materials,” Bernholc says. “We are looking at potential transistor structures consisting of a single layer of graphene, etched into lines of nanoribbons, where the carbon atoms are arranged like a chicken wire pattern. We are looking at which structures will function well, at a few atoms of width.”

Trying to do computations like this on normal computers is impossible, so Bernholc and his team utilized the Blue Waters supercomputer.

“We are doing quantum mechanical computations with thousands of atoms, and several thousands of electrons, and that requires very fast, very powerful systems, and we need to do calculations in parallel,” Bernholc says. “The computer chips are not fast enough—one computer chip in a desktop machine cannot do such calculations. On Blue Waters, we use thousands of nodes in parallel, so we can complete quantum mechanical calculations in a time that’s practical and receive results in a timely fashion.”

GRAPHENE AND DNA SEQUENCING

Bernholc is among the researchers who think that graphene may also play a major role in the push to decrease prices for gene sequencing. With 19 companies offering personal, direct-to-consumer genetics tests, it is easier than ever to sequence DNA, learning your family history and identifying genetic risks.

Some forms of sequencing DNA include electrophoresis, which involves running a current through gel with DNA segments in it, causing DNA strands of varying lengths to move to different locations (shorter strands move faster). This allows comparison between known DNA strands and unknown ones.

As graphene is an excellent conductor of electricity, it is not surprising its use in gene sequencing is being explored. Recently, a group of researchers in California explored the possibility of using nanotubes (a tubular cousin of graphene) to electrically detect a single nucleotide addition during DNA replication. If the nucleotides can also be distinguished electrically, one would be able to sequence DNA and other genetic materials more cheaply and accurately. Currently, DNA sequencing involves complex labeling and readout schemes, which are quite costly and time-consuming. But nanotubes could lead to a simple nanocircuit that could operate faster and be much cheaper.

Bernholc and his team ran calculations to reproduce the California experiment, but changed the electrical conditions. This enabled them to perform calculations that allowed for some DNA base pairs to be distinguished, but not others. There are four chemical bases that are used to store information in DNA: adenine (A), guanine (G), cytosine (C) and thymine (T). The sequence of the DNA tells the cells in your body what proteins and chemicals to make. The bases pair up with each other (A with T and C with G) to form base pairs.

“That allows us to distinguish A from T. G and T are very clear, we can tell G and T from C and A, but we cannot distinguish C and A at the moment using graphene,” Bernholc says. “That’s where more work is needed, but we are moving towards being able to have a new way to sequence DNA.”

For Bernholc’s team and other researchers, the possibilities for graphene’s applications—nanoscale electronics, DNA sequencing and beyond—seem endless.

About NCSA

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign provides supercomputing and advanced digital resources for the nation’s science enterprise. At NCSA, University of Illinois faculty, staff, students, and collaborators from around the globe use advanced digital resources to address research grand challenges for the benefit of science and society. NCSA has been advancing one third of the Fortune 50® for more than 30 years by bringing industry, researchers, and students together to solve grand challenges at rapid speed and scale.

About the Blue Waters Project

The Blue Waters petascale supercomputer is one of the most powerful supercomputers in the world, and is the fastest sustained supercomputer on a university campus. Blue Waters uses hundreds of thousands of computational cores to achieve peak performance of more than 13 quadrillion calculations per second. Blue Waters has more memory and faster data storage than any other open system in the world. Scientists and engineers across the country use the computing and data power of Blue Waters to tackle a wide range of challenges. Recent advances that were not possible without these resources include computationally designing the first set of antibody prototypes to detect the Ebola virus, simulating the HIV capsid, visualizing the formation of the first galaxies and exploding stars, and understanding how the layout of a city can impact supercell thunderstorms.


Source: Susan Szuch, NCSA

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

AI Chip Start-up Groq to Detail Technology Progress in Fall

August 13, 2020

AI chip startup Groq announced yesterday it had closed its most recent funding round, saying the new investments will help it double in size by the end of this year and double again by the end of next year as it transiti Read more…

By John Russell

Intel Speeds NAMD by 1.8x: Saves Xeon Processor Users Millions of Compute Hours

August 12, 2020

Potentially saving datacenters millions of CPU node hours, Intel and the University of Illinois at Urbana–Champaign (UIUC) have collaborated to develop AVX-512 optimizations for the NAMD scalable molecular dynamics cod Read more…

By Rob Farber

Intel’s Optane/DAOS Solution Tops Latest IO500

August 11, 2020

Intel’s persistent memory technology, Optane, and its DAOS (Distributed Asynchronous Object Storage) stack continue to impress and gain market traction. Yesterday, Intel reported an Optane and DAOS-based system finishe Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows users to virtually “walk” around the massive supercomputer Read more…

By Oliver Peckham

Supercomputer Simulations Examine Changes in Chesapeake Bay

August 8, 2020

The Chesapeake Bay, the largest estuary in the continental United States, weaves its way south from Maryland, collecting waters from West Virginia, Delaware, DC, Pennsylvania and New York along the way. Like many major e Read more…

By Oliver Peckham

AWS Solution Channel

University of Adelaide Provides Seamless Bioinformatics Training Using AWS

The University of Adelaide, established in South Australia in 1874, maintains a rich history of scientific innovation. For more than 140 years, the institution and its researchers have had an impact all over the world—making vital contributions to the invention of X-ray crystallography, insulin, penicillin, and the Olympic torch. Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

Student Success from ‘Scratch’: CHPC’s Proof is in the Pudding

August 7, 2020

Happy Sithole, who directs the South African Centre for High Performance Computing (SA-CHPC), called the 13th annual CHPC National conference to order on December 1, 2019, at the Birchwood Conference Centre in Kempton Pa Read more…

By Elizabeth Leake

AI Chip Start-up Groq to Detail Technology Progress in Fall

August 13, 2020

AI chip startup Groq announced yesterday it had closed its most recent funding round, saying the new investments will help it double in size by the end of this Read more…

By John Russell

Intel Speeds NAMD by 1.8x: Saves Xeon Processor Users Millions of Compute Hours

August 12, 2020

Potentially saving datacenters millions of CPU node hours, Intel and the University of Illinois at Urbana–Champaign (UIUC) have collaborated to develop AVX-51 Read more…

By Rob Farber

Intel’s Optane/DAOS Solution Tops Latest IO500

August 11, 2020

Intel’s persistent memory technology, Optane, and its DAOS (Distributed Asynchronous Object Storage) stack continue to impress and gain market traction. Yeste Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows use Read more…

By Oliver Peckham

Research: A Survey of Numerical Methods Utilizing Mixed Precision Arithmetic

August 5, 2020

Within the past years, hardware vendors have started designing low precision special function units in response to the demand of the machine learning community Read more…

By Hartwig Anzt and Jack Dongarra

Implement Photonic Tensor Cores for Machine Learning?

August 5, 2020

Researchers from George Washington University have reported an approach for building photonic tensor cores that leverages phase change photonic memory to implem Read more…

By John Russell

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

Machines, Connections, Data, and Especially People: OAC Acting Director Amy Friedlander Charts Office’s Blueprint for Innovation

August 3, 2020

The path to innovation in cyberinfrastructure (CI) will require continued focus on building HPC systems and secure connections between them, in addition to the Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

Leading Solution Providers

Contributors

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and in Read more…

By Oliver Peckham

John Martinis Reportedly Leaves Google Quantum Effort

April 21, 2020

John Martinis, who led Google’s quantum computing effort since establishing its quantum hardware group in 2014, has left Google after being moved into an advi Read more…

By John Russell

$100B Plan Submitted for Massive Remake and Expansion of NSF

May 27, 2020

Legislation to reshape, expand - and rename - the National Science Foundation has been submitted in both the U.S. House and Senate. The proposal, which seems to Read more…

By John Russell

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This