Supercomputer Simulations Show New Phenomenon with Nanopore Data Sequencing

September 28, 2018

Sept. 28, 2018 — Any truck operator knows that hydraulics do the heavy lifting. Water does the work because it’s nearly incompressible at normal scales. But things behave strangely in nanotechnology, the control of materials at the scale of atoms and molecules. Using supercomputers, scientists found a surprising amount of water compression at the nanoscale. These findings could help advance medical diagnostics through creation of nanoscale systems that detect, identify, and sort biomolecules.

Molecular dynamics simulation of DNA capture and translocation through a graphene nanopore. Supercomputer simulations helped reveal a new phenomenon of water compression at the nanoscale. (Aleksei Aksimentiev)

The unexpected effect comes from the action of an electric field on water in very narrow pores and in very thin materials. That’s according to research by Aleksei Aksimentiev and James Wilson of the Department of Physics at the University of Illinois at Urbana–Champaign. They published their findings in Physical Review Letters, June of 2018.

“We found that an electric field can compress water locally, and that water compression would prevent molecules from being transported through small pores,” Aksimentiev said. “This is a very counterintuitive effect, because usually it is assumed that a higher electric field would propel molecules faster through the pore. But because the electric field also compresses water, the outcome would be the opposite. That is, the higher electric field would not allow molecules to pass through.” In effect, the water compression generated by the higher electric field pushed DNA molecules away from the nanopore channels.

Aksimentiev and Wilson worked with a one-atom-thick graphene membrane. They poked a hole in it 3.5 nanometers wide, just wide enough to let a strand of DNA through. An external electric field pulled the DNA through the hole, like threading a needle. The nucleotide letters A-C-T-G that make the rungs of the double stranded DNA produce signals as they go through the pore, analogous to playing a tape in a tape recorder. This method being developed, called nanopore sequencing, is an alternative to conventional sequencing. It doesn’t depend on polymerase chain reaction enzymes to amplify DNA and in theory allows for much longer reads.

“We’ve been working in the study of nanopore sequencing for some time already, and the goal of the field is to use nanotechnology to read the sequence of DNA, RNA, and proteins directly, without using any kind of enzymes.”

Aksimentiev and Wilson were trying initially in the study to quantify how frequently DNA gets captured by graphene pores. Their goal is to increase the capture and in turn the yield of DNA sequenced through the nanopore.

“Surprisingly, we found that as we were increasing this field to increase the rate of DNA capture, we found that it actually doesn’t go through after a certain threshold voltage, which was a bit shocking,” Aksimentiev said.

“We started looking for all possible things that could go wrong with our simulations,” Aksimentiev explained. “We checked everything, and we convinced ourselves that this was indeed a real thing. It’s physics speaking to us through all-atom simulations.”

They measured the force from the electric field on the DNA molecules, using different DNA constructs and varying the concentration of electrolye solution and the size of the pores and of the membrane. “From these measurements, we came up with this idea that it is water compression that prevents DNA from going through,” Aksimentiev said.

Size is everything when it came to the computational challenges of simulating the nanopores. “The problem is that we have to take into account the motion of every atom in our system,” Aksimentiev said. “The systems typically are comprised of 100,000 atoms. That was critically important for the discovery of the phenomenon that we have done.”

Supercomputer time was awarded through XSEDE, the Extreme Science and Engineering Discover Environment, funded by the National Science. Foundation. XSEDE allocations allowed the researchers use of the Stampede1 and Stampede2 systems at the Texas Advanced Computing Center; and Blue Waters at the National Center for Supercomputing Applications.

Aksimentiev credited XSEDE with a lion’s share of the nanoscale study. “I would say that without XSEDE we would not be where we are in our project. Without XSEDE, I don’t see how we would be able to accomplish the work that we do. It’s not just this project. It’s not just this system, but there are so many different systems that our group and other groups are investigating. What I like about XSEDE is that it gives access to diverse systems. The XSEDE portal itself is another benefit, because in one portal I can see everything that happens on all the machines. That makes it very easy to manage allocations and jobs,” Aksimentiev said.

“Specifically to Stampede2,” Aksimentiev continued, “we were able to run many simulations in parallel. It’s not only that our individual simulation uses many cores of Stampede2. At the same time, we also had to run multi copy simulations, where many simulations run at the same time. That allowed us to measure the forces with the precision that allowed us to conclude about the nature of the physical phenomenon. It’s been amazing how fast and how accurate the Stampede2 machine works.”

James Wilson, a postdoctoral researcher working with Aksimentiev, added that ” by running the simulations on Stampede2, I was able to finish twenty simulations in a couple of days, cutting down my time to solution immensely.” He explained that just one NAMD molecular dynamics simulation would take about two weeks on local workstations.

“The most important thing,” Aksimentiev said, “is that highly accurate, precise simulations on big computers is a discovery tool. This work truly attributes to it, because we set out to do something else. We discovered a new phenomenon in nanopores. And we explain it through simulations. There’s so many discoveries to be made with computers. That’s why supercomputer research is worth funding.”

The next step in this work, furthered Aksimentiev, is to see if the effect also occurs in biological channels and not just with the graphene membrane. They’re also exploring the degree of sorting and separation possible for proteins, the cellular machinery of life. “Already in this paper we show that for one protein, we were able to differentiate variants. We’d like to apply it to more complex systems and also find conditions where the effect manifests at lower fields, which would expand its application to detection of biomarkers,” Aksimentiev said.

The study, “Water-Compression Gating of Nanopore Transport,” (doi: 10.1103/PhysRevLett.120.268101) was published June of 2018 in Physical Review Letters. The authors are Aleksei Aksimentiev and James Wilson of the University of Illinois at Urbana–Champaign. This work was supported by grants from the National Institutes of Health (Grants No. R01-GM114204 and No. R01 HG007406), and through a cooperative research agreement with the Oxford Nanopore Technologies. The authors gladly acknowledge supercomputer time provided through XSEDE Allocation Grant No. MCA05S028 and the Blue Waters petascale supercomputer system (UIUC).


Source: Jorge Salazar, TACC

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!

NOAA Announces Major Upgrade to Ensemble Forecast Model, Extends Range to 35 Days

September 23, 2020

A bit over a year ago, the United States’ Global Forecast System (GFS) received a major upgrade: a new dynamical core – its first in 40 years – called the finite-volume cubed-sphere, or FV3. Now, the National Oceanic and Atmospheric Administration (NOAA) is bringing the FV3 dynamical core to... Read more…

By Oliver Peckham

AI Silicon Startup Graphcore Launches Channel Partner Program

September 23, 2020

AI compute platform vendor Graphcore has launched its first formal global channel partner program to promote and boost the sales of its AI processors and blade computing products. The formalized, all-new Graphcore Elite Partner Program follows the company’s past history of working with several... Read more…

By Todd R. Weiss

Arm Targets HPC with New Neoverse Platforms

September 22, 2020

UK-based semiconductor design company Arm today teased details of its Neoverse roadmap, introducing V1 (codenamed Zeus) and N2 (codenamed Perseus), Arm’s second generation N-series platform. The chip IP vendor said the new platforms will deliver 50 percent and 40 percent more... Read more…

By Tiffany Trader

Microsoft’s Azure Quantum Platform Now Offers Toshiba’s ‘Simulated Bifurcation Machine’

September 22, 2020

While pure-play quantum computing (QC) gets most of the QC-related attention, there’s also been steady progress adapting quantum methods for select use on classical computers. Today, Microsoft announced that Toshiba’ Read more…

By John Russell

Oracle Cloud Deepens HPC Embrace with Launch of A100 Instances, Plans for Arm, More 

September 22, 2020

Oracle Cloud Infrastructure (OCI) continued its steady ramp-up of HPC capabilities today with a flurry of announcements. Topping the list is general availability of instances with Nvidia’s newest GPU, the A100. OCI als Read more…

By John Russell

AWS Solution Channel

The Water Institute of the Gulf runs compute-heavy storm surge and wave simulations on AWS

The Water Institute of the Gulf (Water Institute) runs its storm surge and wave analysis models on Amazon Web Services (AWS)—a task that sometimes requires large bursts of compute power. Read more…

Intel® HPC + AI Pavilion

Berlin Institute of Health: Putting HPC to Work for the World

Researchers from the Center for Digital Health at the Berlin Institute of Health (BIH) are using science to understand the pathophysiology of COVID-19, which can help to inform the development of targeted treatments. Read more…

IBM, CQC Enable Cloud-based Quantum Random Number Generation

September 21, 2020

IBM and Cambridge Quantum Computing (CQC) have partnered to achieve progress on one of the major business aspirations for quantum computing – the goal of generating verified, truly random numbers that can be used for a Read more…

By Todd R. Weiss

NOAA Announces Major Upgrade to Ensemble Forecast Model, Extends Range to 35 Days

September 23, 2020

A bit over a year ago, the United States’ Global Forecast System (GFS) received a major upgrade: a new dynamical core – its first in 40 years – called the finite-volume cubed-sphere, or FV3. Now, the National Oceanic and Atmospheric Administration (NOAA) is bringing the FV3 dynamical core to... Read more…

By Oliver Peckham

Arm Targets HPC with New Neoverse Platforms

September 22, 2020

UK-based semiconductor design company Arm today teased details of its Neoverse roadmap, introducing V1 (codenamed Zeus) and N2 (codenamed Perseus), Arm’s second generation N-series platform. The chip IP vendor said the new platforms will deliver 50 percent and 40 percent more... Read more…

By Tiffany Trader

Oracle Cloud Deepens HPC Embrace with Launch of A100 Instances, Plans for Arm, More 

September 22, 2020

Oracle Cloud Infrastructure (OCI) continued its steady ramp-up of HPC capabilities today with a flurry of announcements. Topping the list is general availabilit Read more…

By John Russell

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

Future of Fintech on Display at HPC + AI Wall Street

September 17, 2020

Those who tuned in for Tuesday's HPC + AI Wall Street event got a peak at the future of fintech and lively discussion of topics like blockchain, AI for risk man Read more…

By Alex Woodie, Tiffany Trader and Todd R. Weiss

IBM’s Quantum Race to One Million Qubits

September 15, 2020

IBM today outlined its ambitious quantum computing technology roadmap at its virtual Quantum Summit. The eye-popping million qubit number is still far out, agrees IBM, but perhaps not that far out. Just as eye-popping is IBM’s nearer-term plan for a 1,000-plus qubit system named Condor... Read more…

By John Russell

Nvidia Commits to Buy Arm for $40B

September 14, 2020

Nvidia is acquiring semiconductor design company Arm Ltd. for $40 billion from SoftBank in a blockbuster deal that catapults the GPU chipmaker to a dominant position in the datacenter while helping troubled SoftBank reverse its financial woes. The deal, which has been rumored for... Read more…

By Todd R. Weiss and George Leopold

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

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

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

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

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

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Leading Solution Providers

Contributors

Oracle Cloud Infrastructure Powers Fugaku’s Storage, Scores IO500 Win

August 28, 2020

In June, RIKEN shook the supercomputing world with its Arm-based, Fujitsu-built juggernaut: Fugaku. The system, which weighs in at 415.5 Linpack petaflops, topp Read more…

By Oliver Peckham

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

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

DOD Orders Two AI-Focused Supercomputers from Liqid

August 24, 2020

The U.S. Department of Defense is making a big investment in data analytics and AI computing with the procurement of two HPC systems that will provide the High Read more…

By Tiffany Trader

Microsoft Azure Adds A100 GPU Instances for ‘Supercomputer-Class AI’ in the Cloud

August 19, 2020

Microsoft Azure continues to infuse its cloud platform with HPC- and AI-directed technologies. Today the cloud services purveyor announced a new virtual machine Read more…

By Tiffany Trader

Japan’s Fugaku Tops Global Supercomputing Rankings

June 22, 2020

A new Top500 champ was unveiled today. Supercomputer Fugaku, the pride of Japan and the namesake of Mount Fuji, vaulted to the top of the 55th edition of the To Read more…

By Tiffany Trader

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

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 code. These optimizations will be incorporated into release 2.15 with patches available for earlier versions. Read more…

By Rob Farber

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