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Primeur weekly 2016-11-14

Exascale supercomputing

Berkeley Lab to lead AMR co-design centre for DOE's Exascale Computing Project ...

Exascale Computing Project announces $48 million to establish Exascale co-design centres ...

US Exascale Computing Project awards $34 million for software development ...

Quantum computing

Breakthrough in the quantum transfer of information between matter and light ...

Focus on Europe

European Commission reveals its forthcoming call for energy efficient, high performance processors ...

World-leading HPC centres partner to form accelerated computing institute ...

Atos Bull to boost Dutch research at SURFsara with first Bull sequana supercomputer installed ...

Middleware

Allinea tools yield a 50% speed up for genome applications at the Earlham Institute ...

NERSC's 'Shifter' scales up to more than 9,000 Cori KNL processors ...

DDN's Big Data storage provides Aalto University ample capacity and fast access to vital research data ...

DDN unveils industry's fastest multi-level security Lustre solution ...

DDN delivers new burst buffer appliance and updates block and file appliances, completing total product line refresh ...

Atos Bull tackles storage bottlenecks for High Performance Computing ...

Cycle Computing debuts the newest version of its groundbreaking CycleCloud ...

Hardware

University of Toronto selects CoolIT Systems to liquid cool signal processor for CHIME project ...

CoolIT Systems optimizes Trade and Match solution with custom closed-loop liquid cooling ...

SDSC to host high-speed, large data transfer experiment at SC16 Show ...

Cray XC40 "Theta" supercomputer accepted at Argonne National Laboratory ...

Cray launches next-generation supercomputer: the Cray XC50 ...

Cray reports third quarter 2016 financial results ...

Mellanox drives Virtual Reality to new levels with breakthrough performance ...

Mellanox announces 200Gb/s HDR InfiniBand solutions enabling record levels of performance and scalability ...

Computers made of genetic material? ...

CoolIT Systems to showcase best-in-class HPC liquid cooling offering at SC16 ...

Applications

BoschDoc, AHCODA-DB and OpenML winners of the Data Prize 2016 ...

Blue Waters simulates largest membrane channel made of DNA origami ...

Cray joins iEnergy, the oil and gas industry's foremost community for exploration and production ...

Large-scale computer simulations reveal biological growth processes ...

NASA science and technology advancements demonstrated at Supercomputing Conference ...

Unlocking big genetic datasets ...

Accelerating cancer research with deep learning ...

System opens up high-performance programming to non-experts ...

Studying structure to understand function within 'material families' ...

Chury is much younger than previously thought ...

TOP500

Global supercomputing capacity creeps up as Petascale systems blanket Top 100 ...

InfiniBand chosen by nearly 4x more end-users versus proprietary offerings in 2016 as shown on the TOP500 supercomputers list ...

The Cloud

SURFnet selects eight Cloud providers for Dutch education and research ...

Blue Waters simulates largest membrane channel made of DNA origami


University of Illinois at Urbana-Champaign researcher Aleksei Aksimentiev used Blue Waters supercomputer and DNA origami to create the largest synthetic membrane channel.
7 Nov 2016 Urbana-Champaign - What do you get when you cross an art form with something found in all living organisms? It may sound unusual, but DNA origami is something that has been explored in the scientific community for the last 10 years. DNA is a string of four nucleotide bases (A, T, G and C), each of which pairs only with one other base (A with T and G with C). In DNA origami, researchers take a long single strand of DNA - picture a ladder sawed in half vertically, and fold it into a shape using staple strands that have the corresponding bases. Everything from smiley faces to robots has been made using this method. While those are 2D, 3D shapes can also be made.

Aleksei Aksimentiev's group at the University of Illinois at Urbana-Champaign has been using this method to simulate membrane channels using the Blue Waters supercomputer at the National Center for Supercomputing Applications (NCSA) on the University of Illinois campus. In their most recent paper, published in ACS Nano , members of Aleksei Aksimentiev's group, Chen-Yu Li, a graduate student at the University of Illinois and Jejoong Yoo, a postdoctoral fellow with the Center for the Physics of Living Cells, were able to create the largest synthetic membrane channel yet.

"The largest membrane channel ever made is as big as the largest pores that are found in biology, so in a sense we span all of the range of the biological channels in nature but mimic them in DNA", Aleksei Aksimentiev stated, "which offers interesting possibilities - how do we make them selective, how do we add gates that open and close, stuff like that."

To understand why this is such a big deal, first you have to understand cells. Encapsulating each of our cells is a membrane made of lipids and proteins. We also have pores in the membrane of certain cells. Some membranes allow ions to pass through and some allow water to pass through.

To build a synthetic channel that has the same functionality as a biological channel or that does something similar, the traditional approach is to try to take what already exists and introduce small modifications. However, it's difficult if engineers want to completely redesign the channel since it's still unknown how to solve problems that involve folding the membrane protein.

Aleksei Aksimentiev's collaborator in England, Ulrich Keyser at the University of Cambridge, came up with the idea to use DNA instead of modifying the protein; the DNA structures would be modified so they could be compatible with the membrane. They were able to put the modified DNA structures in the membrane but they still had a problem - they didn't know how to make the channels work.

"That's where we came in with Blue Waters, we decided to simulate these channels", Aleksei Aksimentiev stated. "One of the things we've discovered is that water can also flow around the DNA helix threaded through a biological membrane, which led us to a single DNA helix design. This smallest ever synthetic DNA channel passes ions as biological ion channels do."

There are a few possible applications. When the technology is perfected, researchers could explore utilizing it for drug delivery by modifying the channels to recognize selective tissues and open up the membrane. It could also be used in artificial tissues to give the cells a way to communicate.

Aleksei Aksimentiev's work is supported by NSF under awards DMR-1507985 and PHY-1430124.
Source: National Center for Supercomputing Applications - NCSA

Back to Table of contents

Primeur weekly 2016-11-14

Exascale supercomputing

Berkeley Lab to lead AMR co-design centre for DOE's Exascale Computing Project ...

Exascale Computing Project announces $48 million to establish Exascale co-design centres ...

US Exascale Computing Project awards $34 million for software development ...

Quantum computing

Breakthrough in the quantum transfer of information between matter and light ...

Focus on Europe

European Commission reveals its forthcoming call for energy efficient, high performance processors ...

World-leading HPC centres partner to form accelerated computing institute ...

Atos Bull to boost Dutch research at SURFsara with first Bull sequana supercomputer installed ...

Middleware

Allinea tools yield a 50% speed up for genome applications at the Earlham Institute ...

NERSC's 'Shifter' scales up to more than 9,000 Cori KNL processors ...

DDN's Big Data storage provides Aalto University ample capacity and fast access to vital research data ...

DDN unveils industry's fastest multi-level security Lustre solution ...

DDN delivers new burst buffer appliance and updates block and file appliances, completing total product line refresh ...

Atos Bull tackles storage bottlenecks for High Performance Computing ...

Cycle Computing debuts the newest version of its groundbreaking CycleCloud ...

Hardware

University of Toronto selects CoolIT Systems to liquid cool signal processor for CHIME project ...

CoolIT Systems optimizes Trade and Match solution with custom closed-loop liquid cooling ...

SDSC to host high-speed, large data transfer experiment at SC16 Show ...

Cray XC40 "Theta" supercomputer accepted at Argonne National Laboratory ...

Cray launches next-generation supercomputer: the Cray XC50 ...

Cray reports third quarter 2016 financial results ...

Mellanox drives Virtual Reality to new levels with breakthrough performance ...

Mellanox announces 200Gb/s HDR InfiniBand solutions enabling record levels of performance and scalability ...

Computers made of genetic material? ...

CoolIT Systems to showcase best-in-class HPC liquid cooling offering at SC16 ...

Applications

BoschDoc, AHCODA-DB and OpenML winners of the Data Prize 2016 ...

Blue Waters simulates largest membrane channel made of DNA origami ...

Cray joins iEnergy, the oil and gas industry's foremost community for exploration and production ...

Large-scale computer simulations reveal biological growth processes ...

NASA science and technology advancements demonstrated at Supercomputing Conference ...

Unlocking big genetic datasets ...

Accelerating cancer research with deep learning ...

System opens up high-performance programming to non-experts ...

Studying structure to understand function within 'material families' ...

Chury is much younger than previously thought ...

TOP500

Global supercomputing capacity creeps up as Petascale systems blanket Top 100 ...

InfiniBand chosen by nearly 4x more end-users versus proprietary offerings in 2016 as shown on the TOP500 supercomputers list ...

The Cloud

SURFnet selects eight Cloud providers for Dutch education and research ...