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Primeur weekly 2019-08-12

Focus

The quest for European HPC research and innovation funding ...

Quantum computing

Unique electrical properties in quantum materials can be controlled using light ...

Light for the nanoworld ...

Middleware

Ohio Supercomputer Center to host seventh meeting of the MVAPICH Users Group ...

Hardware

Cray reports second quarter 2019 financial results ...

Mellanox Ethernet and InfiniBand solutions deliver breakthrough performance for AMD EPYC 7002 processor-based data centres ...

Phison at the forefront of PCIe Gen4 storage market with a portfolio of products ...

Researchers embrace imperfection to improve biomolecule transport ...

2nd Gen AMD EPYC processors set new standard for the modern data centre with record-breaking performance and significant TCO savings ...

HPE ProLiant shatters 37 world records ...

Cray awarded contracts with the U.S. Army Research Laboratory and the Army Engineering and Research Development Center ...

Cray Shasta supercomputer to power weather forecasting for the U.S. Air Force ...

GRC partners with Prasa to bring liquid immersion cooling to data centres in India ...

Excelero debuts Excelero NVEdge, software for creating NVMe All Flash Arrays (NAFA) from high-availability (HA) servers ...

Excelero honoured with Flash Memory Summit 2019 Best of Show Award for third year in a row ...

Simulation technique can predict microstructures of alloy materials used in jet engines - before they are made ...

Supermicro now offering AMD EPYC 7002 series processor-based systems to customers who want to transform their data centres ...

Boston now offers AMD EPYC 7002 series processor-based systems to customers ...

Lenovo and Intel announce multiyear global collaboration to extend HPC and AI leadership ...

Xilinx expands Alveo portfolio with industry's first adaptable compute, network and storage accelerator card built for any server and any Cloud ...

Penguin Computing expands Altus product family with AMD EPYC 7002 series processor-based systems, reaching new levels of data centre performance ...

Applications

Stanford researcher develops data standards for brain imaging and applies rigorous computational methods to work ...

HPE advances its intelligent data platform with acquisition of MapR business assets ...

Turbulence meets a shock ...

The Cloud

UC San Diego, UC Berkeley, and University of Washington announce 'CloudBank' Award ...

Researchers embrace imperfection to improve biomolecule transport


Laboratory-engineered membrane defects with edges that spiral downward would give biomolecules like DNA, RNA and proteins no other option than to sink into a nanopore for delivery, sorting and analysis. Graphic courtesy: Manish Shankla.
5 Aug 2019 Urbana-Champaign - While watching the production of porous membranes used for DNA sorting and sequencing, University of Illinois researchers wondered how tiny steplike defects formed during fabrication could be used to improve molecule transport. They found that the defects - formed by overlapping layers of membrane - make a big difference in how molecules move along a membrane surface. Instead of trying to fix these flaws, the team set out to use them to help direct molecules into the membrane pores.
Physics professor Aleksei Aksimentiev, left, and graduate student Manish Shankla. Photo by L. Brian Stauffer.

Their findings are published in the journal Nature Nanotechnology .

Nanopore membranes have generated interest in biomedical research because they help researchers investigate individual molecules - atom by atom - by pulling them through pores for physical and chemical characterization. This technology could ultimately lead to devices that can quickly sequence DNA, RNA or proteins for personalized medicine.

In 2014, University of Illinois physics professor Aleksei Aksimentiev and graduate student Manish Shankla demonstrated a graphene membrane that controlled a molecule's movement through a nanopore by means of electrical charge. They discovered that once the molecules are on the surface of the membrane, it is very difficult to get them to shuffle into the membrane's pores because molecules like to stick to the surface.

While on sabbatical at Delft University of Technology in the Netherlands, Aleksei Aksimentiev found that DNA tends to accumulate and stick along the edges of fabrication-formed defects that occur as linear steps spanning across the membrane's surface. The Illinois team's goal was to find a way to use these flaws to direct the stuck molecules into the nanopores, as a principle that can also apply to the delivery, sorting and analysis of biomolecules.

To refine and confirm their observations, the researchers used the Blue Waters supercomputer at the National Center for Supercomputing Applications at Illinois and the XSEDE supercomputer to model the system and molecule movement scenarios at the atomic level.

"Molecular dynamics simulations let us watch what is happening while simultaneously measuring how much force is required to get the molecule to clear a step", Aleksei Aksimentiev stated. "We were surprised to find that it takes less force to move a molecule down a step than up. Although it may seem intuitive that gravity would make stepping down easier, it is not the case here because gravity is negligible at the nanoscale, and the force required to move up or down should be the same."

Aleksei Aksimentiev said team members originally thought they could use concentric defect patterns that form around the pores to force the molecules down, but their simulations showed the molecules congregating along the edges of the steps. That is when it dawned on them: A defect with edges that spiral into a pore, combined with an applied directional force, would give the molecule no other option than to go into the pore - kind of like a drain.

"This way, we can drop molecules anywhere on the membrane covered with these spiral structures and then pull the molecules into a pore", he stated.

The researchers have not yet produced a membrane with spiral defects in the laboratory, but that task may be easier than trying to rid a graphene membrane of the current molecule-immobilizing step defects, they said.

"When manufactured at scale, defect-guided capture may potentially increase the DNA capture throughput by several orders of magnitude, compared with current technology", Manish Shankla stated.

"After a long development process, we are excited to see this principle used in a variety of other materials and applications such as delivery of individual molecules to reaction chambers for experiments", the researchers stated.

The National Institutes of Health, National Science Foundation and the Dutch Research Council supported this research.

In this supercomputer simulation, a DNA molecule, directed by a force, moves down a fabrication-formed step defect along the surface of a graphene membrane. Video courtesy: Manish Shankla.
Source: University of Illinois at Urbana-Champaign

Back to Table of contents

Primeur weekly 2019-08-12

Focus

The quest for European HPC research and innovation funding ...

Quantum computing

Unique electrical properties in quantum materials can be controlled using light ...

Light for the nanoworld ...

Middleware

Ohio Supercomputer Center to host seventh meeting of the MVAPICH Users Group ...

Hardware

Cray reports second quarter 2019 financial results ...

Mellanox Ethernet and InfiniBand solutions deliver breakthrough performance for AMD EPYC 7002 processor-based data centres ...

Phison at the forefront of PCIe Gen4 storage market with a portfolio of products ...

Researchers embrace imperfection to improve biomolecule transport ...

2nd Gen AMD EPYC processors set new standard for the modern data centre with record-breaking performance and significant TCO savings ...

HPE ProLiant shatters 37 world records ...

Cray awarded contracts with the U.S. Army Research Laboratory and the Army Engineering and Research Development Center ...

Cray Shasta supercomputer to power weather forecasting for the U.S. Air Force ...

GRC partners with Prasa to bring liquid immersion cooling to data centres in India ...

Excelero debuts Excelero NVEdge, software for creating NVMe All Flash Arrays (NAFA) from high-availability (HA) servers ...

Excelero honoured with Flash Memory Summit 2019 Best of Show Award for third year in a row ...

Simulation technique can predict microstructures of alloy materials used in jet engines - before they are made ...

Supermicro now offering AMD EPYC 7002 series processor-based systems to customers who want to transform their data centres ...

Boston now offers AMD EPYC 7002 series processor-based systems to customers ...

Lenovo and Intel announce multiyear global collaboration to extend HPC and AI leadership ...

Xilinx expands Alveo portfolio with industry's first adaptable compute, network and storage accelerator card built for any server and any Cloud ...

Penguin Computing expands Altus product family with AMD EPYC 7002 series processor-based systems, reaching new levels of data centre performance ...

Applications

Stanford researcher develops data standards for brain imaging and applies rigorous computational methods to work ...

HPE advances its intelligent data platform with acquisition of MapR business assets ...

Turbulence meets a shock ...

The Cloud

UC San Diego, UC Berkeley, and University of Washington announce 'CloudBank' Award ...